diff --git a/.gitignore b/.gitignore index dc7ed9cd..ae2f3ea1 100644 --- a/.gitignore +++ b/.gitignore @@ -150,6 +150,8 @@ fabric.properties *.nar *.ear *.zip +# but track the test fixture crates +!core/src/test/resources/crates/**/*.zip *.tar.gz *.rar diff --git a/MIGRATION.md b/MIGRATION.md new file mode 100644 index 00000000..a7f77a3e --- /dev/null +++ b/MIGRATION.md @@ -0,0 +1,239 @@ +# Migrating to the Jackson-free core + +Starting with version 3, ro-crate-java is split into a Jackson-free core and +pluggable JSON backends. This guide explains what changes for your code when +you upgrade from the previous, Jackson-based 2.x API. + +**Summary** + +- The artifact coordinates for the Jackson 2 backend are unchanged + (`edu.kit.datamanager:ro-crate-java`), so your dependency declaration keeps + working. +- The high-level API (the `RoCrate` builder and the entity builders) is + source-compatible. Most code needs no changes at all. +- Code that used Jackson types from the library (`ObjectNode`, `JsonNode`, + `ArrayNode`, …) must switch to the neutral JSON model of the core. The + method names and semantics deliberately mirror Jackson, so this is mostly a + type rename. +- A few internal Jackson classes were removed (see + [Removed classes](#removed-classes)). + +## Modules + +| Module | Artifact | Purpose | +| ---------- | ------------------------------------------------------------ | ------------------------------------------------------------------------------------------- | +| `core` | (internal, pulled in transitively) | Crate model, reader/writer, validation API, neutral JSON model — no JSON library dependency | +| `jackson2` | `edu.kit.datamanager:ro-crate-java` (historical coordinates) | Jackson 2 backend, for existing consumers | +| `jackson3` | `edu.kit.datamanager:ro-crate-java-jackson3` | Jackson 3 (`tools.jackson`) backend | + +The core contains no JSON code itself. The backend module provides it, and the +core selects the backend at runtime with Java's `ServiceLoader`: the backend +jar carries a `META-INF/services` file that names its implementation classes, +and the core loads whatever is listed there. Exactly one backend must be on +the classpath. Depending on `edu.kit.datamanager:ro-crate-java` puts the +Jackson 2 backend there; `edu.kit.datamanager:ro-crate-java-jackson3` puts the +Jackson 3 backend there. The two core entry points that use it are `Json` +(JSON input and output) and `Validation` (schema validation). + +## Type mapping + +The Jackson types that used to leak into the public API are replaced by the +neutral JSON model from the **`core`** module, package +`edu.kit.datamanager.ro_crate.json`: + +| Before (`com.fasterxml.jackson.databind…`) | After (`edu.kit.datamanager.ro_crate.json…`) | +| ------------------------------------------ | -------------------------------------------- | +| `JsonNode` | `JsonValue` | +| `ObjectNode` | `JsonObject` | +| `ArrayNode` | `JsonArray` | +| `TextNode` | `JsonString` | +| `IntNode` / `LongNode` / `DoubleNode` | `JsonNumber` | +| `BooleanNode` | `JsonBoolean` | +| `NullNode` | `JsonNull` | +| `MissingNode` | `JsonMissing` | + +The neutral model is not a general-purpose JSON library: it implements exactly +the subset of Jackson's API the library needs, with the same method names and +semantics (`path()`, `get()`, `has()`, `asText()`, `fields()`, `size()`, +iteration, …). + +## Changing the imports + +Before (Jackson types came from `com.fasterxml.jackson.databind…`): + +```java +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.node.ObjectNode; + +ObjectNode properties = entity.getProperties(); +JsonNode name = properties.path("name"); +``` + +After (the neutral model lives in the `core` module, +`edu.kit.datamanager.ro_crate.json`): + +```java +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; + +JsonObject properties = entity.getProperties(); +JsonValue name = properties.path("name"); +``` + +## Common changes + +### Properties + +The method names are unchanged. Only the types in the signatures are now neutral. +Scalar `addProperty` overloads (`String`, `int`, `double`, `boolean`) exist on +the builders, so most property code needs no JSON types at all. The +`addProperty(String, JsonValue)` overload replaces the old +`addProperty(String, JsonNode)`: + +```java +import edu.kit.datamanager.ro_crate.json.JsonString; +import edu.kit.datamanager.ro_crate.entities.data.FileEntity; + +// was: builder.addProperty("description", new TextNode("long description")) +builder.addProperty("description", new JsonString("long description")); +``` + +### Building JSON trees + +Before, you would have used Jackson's `ObjectMapper` or `JsonNodeFactory`. +Now use the factory methods of `edu.kit.datamanager.ro_crate.json.Json` +(**`core`** module): + +```java +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; + +JsonObject obj = Json.objectNode() + .put("name", "Result table") + .put("contentSize", 26452); +JsonArray tags = Json.arrayNode().add("science").add("survey"); + +builder.setAllIfValid(obj); // was: setAll(ObjectNode); setAll is deprecated +``` + +### Parsing JSON + +The `edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper` class was +removed. Parse with the core's `Json` entry point instead, which delegates to +the active backend: + +```java +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; + +JsonValue parsed = Json.parse(new java.io.File("ro-crate-metadata.json")); +``` + +## Converting between Jackson and the neutral model + +If your code works with its own JSON trees, for example parsed with your own +`ObjectMapper`, convert them at the boundary to the neutral model. Both +backend modules provide the same helpers on their adapter class. With the +Jackson 2 backend (`edu.kit.datamanager:ro-crate-java`, package +`edu.kit.datamanager.ro_crate.json.jackson2`): + +```java +import com.fasterxml.jackson.databind.JsonNode; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson2.Jackson2JsonAdapter; + +JsonNode jacksonNode = yourObjectMapper.readTree(json); +JsonValue neutral = Jackson2JsonAdapter.toNeutral(jacksonNode); +// and back, if needed: +JsonNode again = Jackson2JsonAdapter.toJackson(neutral); +``` + +With the Jackson 3 backend (`edu.kit.datamanager:ro-crate-java-jackson3`, +package `edu.kit.datamanager.ro_crate.json.jackson3`), the same methods exist +for Jackson 3 node types: + +```java +import tools.jackson.databind.JsonNode; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson3.Jackson3JsonAdapter; + +JsonNode jacksonNode = yourJsonMapper.readTree(json); +JsonValue neutral = Jackson3JsonAdapter.toNeutral(jacksonNode); +// and back, if needed: +JsonNode again = Jackson3JsonAdapter.toJackson(neutral); +``` + +If your application uses Jackson 3, depend on the Jackson 3 artifact; the +classpath then contains only one Jackson version. The neutral model covers +only the subset of the JSON API the library needs, so do advanced tree +manipulation on your own nodes before converting. + +## Validation + +The core defines two validation interfaces: + +- Crate-level: `edu.kit.datamanager.ro_crate.validation.ValidatorStrategy`, + implemented by the JSON-schema class of the backend module: + `edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation` in the + `jackson2` module (historical fully qualified name, now with neutral JSON + types in its signatures), `edu.kit.datamanager.ro_crate.validation.jackson3.JsonSchemaValidation` + in the `jackson3` module. +- Entity-level: `edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy`, + which the entity builders use to check that properties follow the RO-Crate + rules (for example, that they are flat). + +Like the JSON backends, the implementations are listed in `META-INF/services` +files and loaded with `ServiceLoader`. The core requires exactly one +implementation of each interface on the classpath; this is why a backend +module must be present. + +### When validation runs + +The crate-level validation runs automatically at three places, always with +the discovered backend implementation: + +- when an `RoCrate` is created from a builder, +- when a crate is read from a folder or zip file, +- when a crate is saved with `CrateWriter`. + +Validation problems are printed to the standard error stream; the operation +itself continues, because `validate()` only returns a boolean, which these +places ignore. + +### Running validation explicitly + +```java +import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; +import edu.kit.datamanager.ro_crate.validation.Validator; + +Validator validator = new Validator( + new JsonSchemaValidation("my-profile-schema.json")); +boolean valid = validator.validate(crate); +``` + +With the `jackson2` backend, import +`edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation`; with the +`jackson3` backend, `edu.kit.datamanager.ro_crate.validation.jackson3.JsonSchemaValidation`. + +### Providing your own validator + +Implement the interface and pass it to the `Validator`: + +```java +Validator validator = new Validator(crate -> { + // your checks; return false and report problems if the crate is invalid + return true; +}); +validator.validate(crate); +``` + +## Removed classes + +Internal classes without a replacement: + +- `edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper` — use + `edu.kit.datamanager.ro_crate.json.Json.parse` / `Json.write` (see above). +- `edu.kit.datamanager.ro_crate.entities.serializers.HasPartSerializer` and + `edu.kit.datamanager.ro_crate.entities.serializers.ObjectNodeSerializer` — + serialization is handled by the backend's `JsonAdapter`. diff --git a/README.md b/README.md index 6d896722..4b3aa09b 100644 --- a/README.md +++ b/README.md @@ -13,28 +13,79 @@ and avoiding crates which do not fully comply to the specification, at the same - [Instructions for your build manager (e.g., Gradle, Maven, etc.)](https://central.sonatype.com/artifact/edu.kit.datamanager/ro-crate-java) - [Quick-Start](#quick-start) +- [Migration guide: from the Jackson-based 2.x API to the Jackson-free core](MIGRATION.md) - [JavaDoc Documentation](https://javadoc.io/doc/edu.kit.datamanager/ro-crate-java) - [Related Publications](https://publikationen.bibliothek.kit.edu/publikationslisten/get.php?referencing=all&external_publications=kit&lang=de&format=html&style=kit-3lines-title_b-authors-other&consider_suborganizations=true&order=desc%20year&contributors=%5B%5B%5B%5D%2C%5B%22p20751.105%22%5D%5D%5D&title_contains=crate) +## Modules + +The library is split into a Jackson-free core plus two JSON backend modules: + +- **`core`** — the crate model, reader/writer and validation API, working on a + neutral JSON tree model (`edu.kit.datamanager.ro_crate.json`). It has no + dependency on any JSON library. JSON (de-)serialization and JSON-schema + validation are plugged in via the `JsonAdapter` and `ValidatorStrategy` + service-provider interfaces, discovered with Java's `ServiceLoader`: + exactly one backend must be on the classpath. +- **`jackson2`** — the Jackson 2 backend. It publishes under the historical + coordinates `edu.kit.datamanager:ro-crate-java`, so existing consumers keep + resolving the same artifact; it transitively pulls in the core. +- **`jackson3`** — the Jackson 3 backend (`tools.jackson`), published as + `edu.kit.datamanager:ro-crate-java-jackson3`. + +To use the Jackson 3 backend, depend on the Jackson 3 artifact instead of the +historical one, e.g. in Gradle: + +```groovy +implementation "edu.kit.datamanager:ro-crate-java-jackson3:" +``` + +No further configuration is needed: the backend registers itself via +`META-INF/services`. At runtime, the core's JSON and validation entry points +(the `edu.kit.datamanager.ro_crate.json.Json` and +`edu.kit.datamanager.ro_crate.validation.Validation` classes) discover it with +`ServiceLoader`, so they use whichever backend is on the classpath. If you do +not care about the JSON backend, do nothing: keep depending on +`edu.kit.datamanager:ro-crate-java` as before — the backend comes with it. + ## Build the library / documentation - Building (with tests): `./gradlew clean build` - Building (without tests): `./gradlew clean build -x test` - Building with release profile: `./gradlew -Dprofile=release clean build` - Doing a release: `./gradlew -Dprofile=release clean build release` - - Will prompt you about version number to use and next version number - - Will make a git tag which can later be used in a GitHub release - - A GitHub release will trigger the CI for publication. See also `.github/workflows/publishRelease.yml`. + - Will prompt you about version number to use and next version number + - Will make a git tag which can later be used in a GitHub release + - A GitHub release will trigger the CI for publication. See also `.github/workflows/publishRelease.yml`. - Build documentation: `./gradlew javadoc` On Windows, replace `./gradlew` with `gradlew.bat`. +## Examples + +The `examples` module contains small, self-contained example programs. Each +example exists twice: once written against the current API (run with either +backend) and once against the released 2.1.2 artifact (`examples/src/legacy`). +A parity test compares the outputs byte-for-byte, so the examples double as a +behavior-comparison suite between the released version and the current +development state. + +- Run every variant and compare: `./gradlew :examples:test` +- Run a single variant: `./gradlew :examples:runLegacyCreateMinimalCrate`, + `./gradlew :examples:runCurrent-jackson2CreateMinimalCrate`, + `./gradlew :examples:runCurrent-jackson3CreateMinimalCrate` +- Outputs are written to `examples/build/examples//.txt` +- List available example tasks: `./gradlew :examples:tasks --group examples` + +Each variant runs in its own JVM instance, since the JSON backends register via +`META-INF/services` and must not share a classpath. + ## RO-Crate Specification Compatibility -- ✅ [Version 1.1](https://www.researchobject.org/ro-crate/1.1/) ([Extracted examples as well-described unit tests/guide](src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java)) +- ✅ [Version 1.1](https://www.researchobject.org/ro-crate/1.1/) ([Extracted examples as well-described unit tests/guide](core/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java)) - 🛠️ Version 1.2-DRAFT - - ✅ Reading and writing crates with additional profiles or specifications ([examples for reading](src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java), [examples for writing](src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java)) - - ✅ Adding profiles or other specifications to a crate ([examples](src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java)) + - ✅ Reading and writing crates with additional profiles or specifications ([examples for reading](core/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java), [examples for writing](core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java)) + - ✅ Adding profiles or other specifications to a crate ([examples](core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java)) ## Quick-start @@ -58,7 +109,7 @@ RoCrate myFirstCrate = STARTER_CRATE A built or imported crate can of course also be modified afterwards. Take a look at our further documentation: -- **There is a well-documented example-driven guide in [LearnByExampleTest.java](src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java) to help you get started.** -- You may also be interested in the examples we extracted from the [specification in version 1.1](https://www.researchobject.org/ro-crate/1.1/), which are available in [ExamplesOfSpecificationV1p1Test.java](src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java). -- There is a [module with all well-described guiding tests](src/test/java/edu/kit/datamanager/ro_crate/examples/) available. +- **There is a well-documented example-driven guide in [LearnByExampleTest.java](core/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java) to help you get started.** +- You may also be interested in the examples we extracted from the [specification in version 1.1](https://www.researchobject.org/ro-crate/1.1/), which are available in [ExamplesOfSpecificationV1p1Test.java](core/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java). +- There is a [module with all well-described guiding tests](core/src/test/java/edu/kit/datamanager/ro_crate/examples/) available. - The [JavaDoc Documentation](https://javadoc.io/doc/edu.kit.datamanager/ro-crate-java) is also available online. diff --git a/build.gradle b/build.gradle index 708e8fe9..b81db06a 100644 --- a/build.gradle +++ b/build.gradle @@ -1,203 +1,39 @@ plugins { - id 'java' - id 'jvm-test-suite' - id 'application' - id 'jacoco' - // Instructions: https://github.com/researchgate/gradle-release // Available versions: https://plugins.gradle.org/plugin/net.researchgate.release id 'net.researchgate.release' version '3.2.0' - id "maven-publish" // Publishing of JAR to Nexus instances (e.g., OSSRH) // https://github.com/gradle-nexus/publish-plugin id "io.github.gradle-nexus.publish-plugin" version "2.0.0" - id "io.freefair.maven-publish-java" version "9.8.2" } group = 'edu.kit.datamanager' -description = "A library for easy creation and modification of valid RO-Crates." println "Running gradle version: $gradle.gradleVersion" println "Building ${name} version: ${version}" println "JDK version: ${JavaVersion.current()}" -println "Profile (system property): ${System.getProperty('profile')}" - -java { - sourceCompatibility = JavaVersion.VERSION_17 - targetCompatibility = JavaVersion.VERSION_17 -} - -if (JavaVersion.current() == JavaVersion.VERSION_17) { - println "Setting encoding to UTF-8 manually" - compileJava.options.encoding = "UTF-8" - compileTestJava.options.encoding = "UTF-8" -} - -repositories { - mavenCentral() -} - -ext { - jacksonVersion = '2.22.4' -} - -dependencies { - // JUnit setup for testing - testImplementation(platform("org.junit:junit-bom:6.1.3")) - testImplementation('org.junit.jupiter:junit-jupiter') - testRuntimeOnly('org.junit.platform:junit-platform-launcher') - // JSON object mapping / (de-)serialization - implementation "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}" - implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${jacksonVersion}" - // http client - implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.14' - // common file system operations - implementation group: 'commons-io', name: 'commons-io', version: '2.22.0' - // read from and write to zip files - implementation group: 'net.lingala.zip4j', name: 'zip4j', version: '2.11.6' - // compare json documents in tests - implementation 'com.github.fslev:json-compare:8.4' - // url validator - implementation group: 'commons-validator', name: 'commons-validator', version: '1.11.0' - // logging - implementation group: 'org.slf4j', name: 'slf4j-jdk14', version: '2.0.20' - // JSON-LD, Zenodo mapping - implementation group: 'com.apicatalog', name: 'titanium-json-ld', version: '1.7.0' - // metadata validation, profiles based on JSON schema - implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.9" - implementation 'org.glassfish:jakarta.json:2.0.1' - //JTE for template processing - implementation('gg.jte:jte:3.2.4') - implementation("org.freemarker:freemarker:2.3.35") -} - -// enable -Xlint:deprecation -tasks.withType(JavaCompile).configureEach { - options.compilerArgs << "-Xlint:deprecation" -} - -logging.captureStandardOutput LogLevel.INFO -def signingTasks = tasks.withType(Sign) -tasks.withType(AbstractPublishToMaven).configureEach{ - mustRunAfter(signingTasks) - } - -sourceSets { - main { - java { - srcDirs = ['src/main/java'] - } - } - - test { - java { - // compileClasspath += sourceSets.main.output - //runtimeClasspath += sourceSets.main.output - srcDirs = ['src/test/java'] - } - } - - performanceTest { - java { - compileClasspath += sourceSets.main.output - runtimeClasspath += sourceSets.main.output - srcDirs = ['src/performanceTest/java'] +// for plugin net.researchgate.release +// see https://github.com/researchgate/gradle-release +release { + //define template for tagging, e.g. v1.0.0 + tagTemplate = 'v${version}' +} + +// for plugin io.github.gradle-nexus.publish-plugin +// see https://github.com/gradle-nexus/publish-plugin +nexusPublishing { + repositories { + //select sonatype repository as publication destination + sonatype { + nexusUrl.set(uri("https://ossrh-staging-api.central.sonatype.com/service/local/")) + snapshotRepositoryUrl.set(uri("https://central.sonatype.com/repository/maven-snapshots/")) } } } -configurations { - performanceTestImplementation.extendsFrom implementation -} - -// Task for creating a resource file with the version info -tasks.register("generateVersionProps", WriteProperties) { t -> - def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "main"].join(File.separator)) - def outputFile = generatedResourcesDir.map { it.file("version.properties") } - - t.destinationFile = outputFile.get().asFile - t.property("version", version) -} - -tasks.register("generateVersionPropsTest", WriteProperties) { t -> - def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "test"].join(File.separator)) - def outputFile = generatedResourcesDir.map { it.file("version.properties") } - - t.destinationFile = outputFile.get().asFile - t.property("version", version) -} - -tasks.register('performanceContextEntitiesBenchmark', JavaExec) { - description = "Run the context entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.ContextualEntitiesPerformance' -} - -tasks.register('performanceLocalDataEntitiesBenchmark', JavaExec) { - description = "Run the local data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.LocalDataEntitiesPerformance' -} - -tasks.register('performanceRemoteDataEntitiesBenchmark', JavaExec) { - description = "Run the remote data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.RemoteDataEntitiesPerformance' -} - -tasks.register('performanceMixEntitiesBenchmark', JavaExec) { - description = "Run the remote data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.MixtureOfEntitiesPerformance' -} - -tasks.register('performanceDeletionEntitiesBenchmark', JavaExec) { - description = "Run the remote data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.DeletionEntitiesPerformance' -} - -tasks.register('performanceMultipleCratesBenchmark', JavaExec) { - description = "Run the remote data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.multiplecrates.MultipleCratesBenchmark' -} - -tasks.register('performanceReadWriteMultipleCratesBenchmark', JavaExec) { - description = "Run the remote data entities benchmarks." - classpath = sourceSets.performanceTest.runtimeClasspath - mainClass = 'edu.kit.datamanager.ro_crate.multiplecrates.MultipleCratesWriteAndRead' -} - -compileJava { - dependsOn generateVersionProps -} - -test { - useJUnitPlatform() - dependsOn generateVersionPropsTest - finalizedBy jacocoTestReport -} - -jacocoTestReport { - dependsOn test - reports { - csv.required = true - xml.required = true // codecov plugin may depend on xml format report - } -} - -jacoco { - toolVersion = "0.8.15" -} - -// maxParallelForks(2) -// failFast = true - -if (System.getProperty('profile') == "release") { - println 'Using release profile for building ' + project.getName() - apply from: 'gradle/profile-release.gradle' +subprojects { + apply from: rootProject.file('gradle/module-common.gradle') } apply from: 'gradle/updateCff.gradle' diff --git a/core/build.gradle b/core/build.gradle new file mode 100644 index 00000000..5a0034fa --- /dev/null +++ b/core/build.gradle @@ -0,0 +1,142 @@ +/* + * The Jackson-free core of ro-crate-java. + * + * This module must not have any dependency on a concrete JSON library: the + * neutral JSON tree model talks to a backend (jackson2 or jackson3 module) + * through the JsonAdapter and validation SPIs, discovered via ServiceLoader. + */ + +plugins { + id 'application' + id 'jacoco' +} + +description = "A library for easy creation and modification of valid RO-Crates (Jackson-free core)." + +repositories { + mavenCentral() +} + +dependencies { + // JUnit setup for testing + testImplementation(platform("org.junit:junit-bom:6.1.3")) + testImplementation('org.junit.jupiter:junit-jupiter') + testRuntimeOnly('org.junit.platform:junit-platform-launcher') + // the JSON backend is required to run the tests (provides the JsonAdapter) + testImplementation project(':jackson2') + // compare json documents in tests (test scope only; works on JSON strings) + testImplementation 'com.github.fslev:json-compare:8.4' + // http client + implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.14' + // common file system operations + implementation group: 'commons-io', name: 'commons-io', version: '2.22.0' + // read from and write to zip files + implementation group: 'net.lingala.zip4j', name: 'zip4j', version: '2.11.6' + // url validator + implementation group: 'commons-validator', name: 'commons-validator', version: '1.11.0' + // logging + implementation group: 'org.slf4j', name: 'slf4j-jdk14', version: '2.0.20' + // JSON-LD, Zenodo mapping + implementation group: 'com.apicatalog', name: 'titanium-json-ld', version: '1.7.0' + implementation 'org.glassfish:jakarta.json:2.0.1' + // template processing for the preview + implementation("org.freemarker:freemarker:2.3.35") + implementation('gg.jte:jte:3.2.4') +} + +jacocoTestReport { + dependsOn test + reports { + csv.required = true + xml.required = true // codecov plugin may depend on xml format report + } +} + +jacoco { + toolVersion = "0.8.15" +} + +// maxParallelForks(2) +// failFast = true + +// Task for creating a resource file with the version info +tasks.register("generateVersionProps", WriteProperties) { t -> + def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "main"].join(File.separator)) + def outputFile = generatedResourcesDir.map { it.file("version.properties") } + + t.destinationFile = outputFile.get().asFile + t.property("version", version) +} + +tasks.register("generateVersionPropsTest", WriteProperties) { t -> + def generatedResourcesDir = project.layout.buildDirectory.dir(["resources", "test"].join(File.separator)) + def outputFile = generatedResourcesDir.map { it.file("version.properties") } + + t.destinationFile = outputFile.get().asFile + t.property("version", version) +} + +tasks.register('performanceContextEntitiesBenchmark', JavaExec) { + description = "Run the contextual entities benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.ContextualEntitiesPerformance' +} + +tasks.register('performanceLocalDataEntitiesBenchmark', JavaExec) { + description = "Run the local data entities benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.LocalDataEntitiesPerformance' +} + +tasks.register('performanceRemoteDataEntitiesBenchmark', JavaExec) { + description = "Run the remote data entities benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.RemoteDataEntitiesPerformance' +} + +tasks.register('performanceMixEntitiesBenchmark', JavaExec) { + description = "Run the mixture of entities benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.MixtureOfEntitiesPerformance' +} + +tasks.register('performanceDeletionEntitiesBenchmark', JavaExec) { + description = "Run the deletion entities benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.singlecratebenchmarks.DeletionEntitiesPerformance' +} + +tasks.register('performanceMultipleCratesBenchmark', JavaExec) { + description = "Run the multiple crates benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.multiplecrates.MultipleCratesBenchmark' +} + +tasks.register('performanceReadWriteMultipleCratesBenchmark', JavaExec) { + description = "Run the multiple crates write and read benchmarks." + classpath = sourceSets.performanceTest.runtimeClasspath + mainClass = 'edu.kit.datamanager.ro_crate.multiplecrates.MultipleCratesWriteAndRead' +} + +compileJava { + dependsOn generateVersionProps +} + +test { + dependsOn generateVersionPropsTest + finalizedBy jacocoTestReport +} + +sourceSets { + performanceTest { + java { + compileClasspath += sourceSets.main.output + runtimeClasspath += sourceSets.main.output + srcDirs = ['src/performanceTest/java'] + } + } +} + +configurations { + performanceTestImplementation.extendsFrom implementation +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/Crate.java b/core/src/main/java/edu/kit/datamanager/ro_crate/Crate.java similarity index 95% rename from src/main/java/edu/kit/datamanager/ro_crate/Crate.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/Crate.java index 652ccdcc..9e90b5ef 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/Crate.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/Crate.java @@ -1,21 +1,20 @@ package edu.kit.datamanager.ro_crate; -import java.io.File; -import java.util.Collection; -import java.util.Map; -import java.util.Optional; -import java.util.Set; - import edu.kit.datamanager.ro_crate.context.CrateMetadataContext; -import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionConfig; -import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionResult; import edu.kit.datamanager.ro_crate.entities.AbstractEntity; import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; import edu.kit.datamanager.ro_crate.entities.data.DataEntity; import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; +import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionConfig; +import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionResult; import edu.kit.datamanager.ro_crate.preview.CratePreview; import edu.kit.datamanager.ro_crate.special.CrateVersion; +import java.io.File; +import java.util.Collection; +import java.util.Map; +import java.util.Optional; +import java.util.Set; /** * An interface describing an ROCrate. @@ -24,7 +23,6 @@ * @version 1 */ public interface Crate { - /** * Mark the crate as imported, i.e. it has been read from a file * or is for other reasons not considered a new crate. @@ -53,7 +51,7 @@ public interface Crate { *

* NOTE: If there is no version in the crate, it does not comply with the * specification. - * + * * @return the class representation indication the version of this crate, if * available. */ @@ -67,7 +65,7 @@ public interface Crate { *

* This corresponds technically to all conformsTo values, excluding the RO crate * version / specification. - * + * * @return a collection of the profiles or specifications this crate conforms * to. */ @@ -143,7 +141,8 @@ public interface Crate { * @param parentId the ID of the parent entity. Must not be null. * @throws IllegalArgumentException if parentId is null or not found, or not a DataEntity. */ - void addDataEntity(DataEntity entity, String parentId) throws IllegalArgumentException; + void addDataEntity(DataEntity entity, String parentId) + throws IllegalArgumentException; void addContextualEntity(ContextualEntity entity); @@ -179,7 +178,9 @@ public interface Crate { * @param addInverseRelationships if true, also adds isPartOf relationships from child to parent * @return result object containing information about what was processed, as well as potential errors. */ - HierarchyRecognitionResult createDataEntityFileStructure(boolean addInverseRelationships); + HierarchyRecognitionResult createDataEntityFileStructure( + boolean addInverseRelationships + ); /** * Automatically recognizes hierarchical file structure from DataEntity IDs @@ -190,5 +191,7 @@ public interface Crate { * @param config configuration object specifying how the recognition should behave * @return result object containing information about what was processed, as well as potential errors. */ - HierarchyRecognitionResult createDataEntityFileStructure(HierarchyRecognitionConfig config); + HierarchyRecognitionResult createDataEntityFileStructure( + HierarchyRecognitionConfig config + ); } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java b/core/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java new file mode 100644 index 00000000..f68e86a0 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java @@ -0,0 +1,674 @@ +package edu.kit.datamanager.ro_crate; + +import edu.kit.datamanager.ro_crate.context.CrateMetadataContext; +import edu.kit.datamanager.ro_crate.context.RoCrateMetadataContext; +import edu.kit.datamanager.ro_crate.entities.AbstractEntity; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; +import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; +import edu.kit.datamanager.ro_crate.externalproviders.dataentities.ImportFromDataCite; +import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognition; +import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionConfig; +import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionResult; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.payload.CratePayload; +import edu.kit.datamanager.ro_crate.payload.RoCratePayload; +import edu.kit.datamanager.ro_crate.preview.CratePreview; +import edu.kit.datamanager.ro_crate.preview.CustomPreview; +import edu.kit.datamanager.ro_crate.special.CrateVersion; +import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; +import edu.kit.datamanager.ro_crate.validation.Validation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.io.File; +import java.net.URI; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.StreamSupport; + +/** + * The class that represents a single ROCrate. + *

+ * To build or modify it, use a instance of {@link RoCrateBuilder}. In the case + * features of RO-Crate DRAFT specifications are needed, refer to + * {@link BuilderWithDraftFeatures} and its documentation. + * + * @author Nikola Tzotchev on 6.2.2022 г. + * @version 1 + */ +public class RoCrate implements Crate { + + protected final CratePayload roCratePayload; + protected CrateMetadataContext metadataContext; + protected CratePreview roCratePreview; + protected RootDataEntity rootDataEntity; + protected ContextualEntity jsonDescriptor; + + protected Collection untrackedFiles; + + /** + * Indicates whether this crate has been imported from an external source. + * This is used to determine if ro-crate-java should add a CreateAction + * or an UpdateAction in the provenance on export. + */ + protected boolean isImported = false; + + @Override + public RoCrate markAsImported() { + this.isImported = true; + return this; + } + + @Override + public boolean isImported() { + return this.isImported; + } + + @Override + public CratePreview getPreview() { + return this.roCratePreview; + } + + public void setRoCratePreview(CratePreview preview) { + this.roCratePreview = preview; + } + + @Override + public void setMetadataContext(CrateMetadataContext metadataContext) { + this.metadataContext = metadataContext; + } + + @Override + public String getMetadataContextValueOf(String key) { + return this.metadataContext.getValueOf(key); + } + + @Override + public Set getMetadataContextKeys() { + return this.metadataContext.getKeys(); + } + + @Override + public Map getMetadataContextPairs() { + return this.metadataContext.getPairs(); + } + + public ContextualEntity getJsonDescriptor() { + return jsonDescriptor; + } + + @Override + public void setJsonDescriptor(ContextualEntity jsonDescriptor) { + this.jsonDescriptor = jsonDescriptor; + } + + @Override + public RootDataEntity getRootDataEntity() { + return rootDataEntity; + } + + @Override + public void setRootDataEntity(RootDataEntity rootDataEntity) { + this.rootDataEntity = rootDataEntity; + } + + /** + * Default constructor for creation of an empty crate. + */ + public RoCrate() { + this.roCratePayload = new RoCratePayload(); + this.untrackedFiles = new HashSet<>(); + this.metadataContext = new RoCrateMetadataContext(); + rootDataEntity = new RootDataEntity.RootDataEntityBuilder().build(); + jsonDescriptor = new JsonDescriptor(); + } + + /** + * A constructor for creating the crate using a Crate builder for easier + * creation. + * + * @param roCrateBuilder the builder to use. + */ + public RoCrate(RoCrateBuilder roCrateBuilder) { + this.roCratePayload = roCrateBuilder.payload; + this.metadataContext = roCrateBuilder.metadataContext; + this.roCratePreview = roCrateBuilder.preview; + this.rootDataEntity = roCrateBuilder.rootDataEntity; + this.jsonDescriptor = roCrateBuilder.descriptorBuilder.build(); + this.untrackedFiles = roCrateBuilder.untrackedFiles; + Validator defaultValidation = new Validator(Validation.crateStrategy()); + defaultValidation.validate(this); + } + + @Override + public Optional getVersion() { + JsonValue conformsTo = this.jsonDescriptor.getProperty("conformsTo"); + if (conformsTo.isArray()) { + return StreamSupport.stream(conformsTo.spliterator(), false) + .filter(JsonValue::isObject) + .map(obj -> obj.path("@id").asText()) + .map(CrateVersion::fromSpecUri) + .filter(Optional::isPresent) + .map(Optional::get) + .findFirst(); + } else if (conformsTo.isObject()) { + return CrateVersion.fromSpecUri(conformsTo.get("@id").asText()); + } else { + return Optional.empty(); + } + } + + @Override + public Collection getProfiles() { + JsonValue conformsTo = this.jsonDescriptor.getProperty("conformsTo"); + if (conformsTo.isArray()) { + return StreamSupport.stream(conformsTo.spliterator(), false) + .filter(JsonValue::isObject) + .map(obj -> obj.path("@id").asText()) + .collect(Collectors.toSet()); + } else { + return Collections.emptySet(); + } + } + + @Override + public String getJsonMetadata() { + JsonObject node = Json.objectNode(); + + node.setAll(this.metadataContext.getContextJsonEntity()); + + var graph = Json.arrayNode(); + graph.add(this.rootDataEntity.toJson()); + + graph.add(this.jsonDescriptor.toJson()); + if ( + this.roCratePayload != null && + this.roCratePayload.getEntitiesMetadata() != null + ) { + graph.addAll(this.roCratePayload.getEntitiesMetadata()); + } + node.set("@graph", graph); + return node.toString(); + } + + @Override + public DataEntity getDataEntityById(String id) { + return this.roCratePayload.getDataEntityById(id); + } + + @Override + public Optional getDataSetById(String id) { + DataEntity data = this.roCratePayload.getDataEntityById(id); + if (data instanceof DataSetEntity) { + return Optional.of((DataSetEntity) data); + } + return Optional.empty(); + } + + @Override + public Set getAllDataEntities() { + return new HashSet<>(this.roCratePayload.getAllDataEntities()); + } + + @Override + public ContextualEntity getContextualEntityById(String id) { + return this.roCratePayload.getContextualEntityById(id); + } + + @Override + public Set getAllContextualEntities() { + return new HashSet<>(this.roCratePayload.getAllContextualEntities()); + } + + @Override + public AbstractEntity getEntityById(String id) { + return this.roCratePayload.getEntityById(id); + } + + /** + * {@inheritDoc} + *

+ * Note: This will also link the DataEntity to the root node using the root + * nodes hasPart property. + * + * @param entity the DataEntity to add to this crate. + */ + @Override + public void addDataEntity(DataEntity entity) { + this.metadataContext.checkEntity(entity); + this.roCratePayload.addDataEntity(entity); + this.rootDataEntity.addToHasPart(entity.getId()); + } + + @Override + public void addDataEntity(DataEntity entity, String parentId) + throws IllegalArgumentException { + if (parentId == null) { + throw new IllegalArgumentException("Parent ID is null."); + } + + DataEntity parentEntity = parentId.equals("./") + ? this.getRootDataEntity() + : this.getDataEntityById(parentId); + + if (parentEntity == null) { + throw new IllegalArgumentException("Parent ID not found in the crate."); + } + + if (parentEntity.getTypes().contains("File")) { + throw new IllegalArgumentException("Parent entity cannot be a File."); + } + + if (!parentEntity.getTypes().contains("Dataset")) { + throw new IllegalArgumentException( + "Parent entity must be a Dataset in order to contain another DataEntity as a part." + ); + } + + this.metadataContext.checkEntity(entity); + + if (parentEntity instanceof DataSetEntity) { + ((DataSetEntity) parentEntity).addToHasPart(entity.getId()); + } else { + parentEntity.addProperty("hasPart", entity.getId()); + } + this.roCratePayload.addDataEntity(entity); + } + + @Override + public void addContextualEntity(ContextualEntity entity) { + this.metadataContext.checkEntity(entity); + this.roCratePayload.addContextualEntity(entity); + } + + @Override + public void deleteEntityById(String entityId) { + // delete the entity firstly + this.roCratePayload.removeEntityById(entityId); + // remove from the root data entity hasPart + this.rootDataEntity.removeFromHasPart(entityId); + // remove from the root entity and the file descriptor + JsonUtilFunctions.removeFieldsWith( + entityId, + this.rootDataEntity.getProperties() + ); + JsonUtilFunctions.removeFieldsWith( + entityId, + this.jsonDescriptor.getProperties() + ); + } + + @Override + public void setUntrackedFiles(Collection files) { + this.untrackedFiles = files; + } + + @Override + public void deleteValuePairFromContext(String key) { + this.metadataContext.deleteValuePairFromContext(key); + } + + @Override + public void deleteUrlFromContext(String key) { + this.metadataContext.deleteUrlFromContext(key); + } + + @Override + public void addFromCollection(Collection entities) { + this.roCratePayload.addEntities(entities); + } + + @Override + public void addItemFromDataCite(String locationUrl) { + ImportFromDataCite.addDataCiteToCrate(locationUrl, this); + } + + @Override + public Collection getUntrackedFiles() { + return this.untrackedFiles; + } + + @Override + public HierarchyRecognitionResult createDataEntityFileStructure( + boolean addInverseRelationships + ) { + HierarchyRecognitionConfig config = + new HierarchyRecognitionConfig().withSetInverseRelationships( + addInverseRelationships + ); + return this.createDataEntityFileStructure(config); + } + + @Override + public HierarchyRecognitionResult createDataEntityFileStructure( + HierarchyRecognitionConfig config + ) { + return new HierarchyRecognition(this, config).buildHierarchy(); + } + + /** + * The inner class builder for the easier creation of a ROCrate. + */ + public static class RoCrateBuilder { + + private static final String PROPERTY_DESCRIPTION = "description"; + + CratePayload payload; + CratePreview preview = new CustomPreview(); + CrateMetadataContext metadataContext; + ContextualEntity license; + RootDataEntity rootDataEntity; + Collection untrackedFiles = new HashSet<>(); + + JsonDescriptor.Builder descriptorBuilder = new JsonDescriptor.Builder(); + + /** + * The default constructor of a builder. + * + * @param name the name of the crate. + * @param description the description of the crate. + * @param datePublished the published date of the crate. + * @param licenseId the license identifier of the crate. + */ + public RoCrateBuilder( + String name, + String description, + String datePublished, + String licenseId + ) { + this.payload = new RoCratePayload(); + this.metadataContext = new RoCrateMetadataContext(); + this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder() + .addProperty("name", name) + .addProperty(PROPERTY_DESCRIPTION, description) + .build(); + this.setLicense(licenseId); + this.addDatePublishedWithExceptions(datePublished); + } + + /** + * The default constructor of a builder. + * + * @param name the name of the crate. + * @param description the description of the crate. + * @param datePublished the published date of the crate. + * @param license the license entity of the crate. + */ + public RoCrateBuilder( + String name, + String description, + String datePublished, + ContextualEntity license + ) { + this.payload = new RoCratePayload(); + this.metadataContext = new RoCrateMetadataContext(); + this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder() + .addProperty("name", name) + .addProperty(PROPERTY_DESCRIPTION, description) + .build(); + this.setLicense(license); + this.addDatePublishedWithExceptions(datePublished); + } + + /** + * A default constructor without any params where the root data entity + * will be plain. + */ + public RoCrateBuilder() { + this.payload = new RoCratePayload(); + this.metadataContext = new RoCrateMetadataContext(); + rootDataEntity = new RootDataEntity.RootDataEntityBuilder().build(); + } + + /** + * A constructor with a crate as template. + * + * @param crate the crate to copy. + */ + public RoCrateBuilder(RoCrate crate) { + this.payload = crate.roCratePayload; + this.preview = crate.roCratePreview; + this.metadataContext = crate.metadataContext; + this.rootDataEntity = crate.rootDataEntity; + this.untrackedFiles = crate.untrackedFiles; + this.descriptorBuilder = new JsonDescriptor.Builder(crate); + } + + public RoCrateBuilder addName(String name) { + this.rootDataEntity.addProperty("name", name); + return this; + } + + /** + * Adds an "identifier" property to the root data entity. + *

+ * This is useful e.g. to assign e.g. a DOI to this crate. + * @param identifier the identifier to add. + * @return this builder. + */ + public RoCrateBuilder addIdentifier(String identifier) { + this.rootDataEntity.addProperty("identifier", identifier.strip()); + return this; + } + + public RoCrateBuilder addDescription(String description) { + this.rootDataEntity.addProperty(PROPERTY_DESCRIPTION, description); + return this; + } + + /** + * Adds a data entity to the crate. + *

+ * Note: This will also link the DataEntity to the root node using the + * root nodes hasPart property. + * + * @param dataEntity the DataEntity to add to this crate. + * @return returns the builder for further usage. + */ + public RoCrateBuilder addDataEntity(DataEntity dataEntity) { + this.metadataContext.checkEntity(dataEntity); + this.payload.addDataEntity(dataEntity); + this.rootDataEntity.addToHasPart(dataEntity.getId()); + return this; + } + + public void addDataEntity(DataEntity entity, String parentId) + throws IllegalArgumentException { + if (parentId == null) { + throw new IllegalArgumentException("Parent ID is null."); + } + + DataEntity parentEntity = parentId.equals("./") + ? this.rootDataEntity + : this.payload.getDataEntityById(parentId); + + if (parentEntity == null) { + throw new IllegalArgumentException("Parent ID not found in the crate."); + } + + if (parentEntity.getTypes().contains("File")) { + throw new IllegalArgumentException("Parent entity cannot be a File."); + } + + if (!parentEntity.getTypes().contains("Dataset")) { + throw new IllegalArgumentException( + "Parent entity must be a Dataset in order to contain another DataEntity as a part." + ); + } + + this.metadataContext.checkEntity(entity); + + if (parentEntity instanceof DataSetEntity) { + ((DataSetEntity) parentEntity).addToHasPart(entity.getId()); + } else { + parentEntity.addProperty("hasPart", entity.getId()); + } + this.payload.addDataEntity(entity); + } + + public RoCrateBuilder addContextualEntity( + ContextualEntity contextualEntity + ) { + this.metadataContext.checkEntity(contextualEntity); + this.payload.addContextualEntity(contextualEntity); + return this; + } + + /** + * Setting the license of the crate. + * + * @param license the license to set. + * @return this builder. + */ + public RoCrateBuilder setLicense(ContextualEntity license) { + this.license = license; + // From our tests, it seems like if we only have the ID for our license, we do + // not need to add an extra entity. + if (license.getProperties().size() > 1) { + this.addContextualEntity(license); + } + this.rootDataEntity.addIdProperty("license", license.getId()); + return this; + } + + /** + * Setting the license of the crate using only a license identifier. + * + * @param licenseId the licenses identifier. Should be a resolveable + * URI. + * @return the builder + */ + public RoCrateBuilder setLicense(String licenseId) { + ContextualEntity licenseEntity = + new ContextualEntity.ContextualEntityBuilder().setId(licenseId).build(); + this.setLicense(licenseEntity); + return this; + } + + /** + * Adds a property with date time format. The property should match the + * ISO 8601 date format. + * + * @param dateValue time string in ISO 8601 format + * @return this builder + * @throws IllegalArgumentException if format is not ISO 8601 + */ + public RoCrateBuilder addDatePublishedWithExceptions(String dateValue) + throws IllegalArgumentException { + this.rootDataEntity.addDateTimePropertyWithExceptions( + "datePublished", + dateValue + ); + return this; + } + + public RoCrateBuilder setContext(CrateMetadataContext context) { + this.metadataContext = context; + return this; + } + + public RoCrateBuilder addUrlToContext(String url) { + this.metadataContext.addToContextFromUrl(url); + return this; + } + + public RoCrateBuilder addValuePairToContext(String key, String value) { + this.metadataContext.addToContext(key, value); + return this; + } + + public RoCrateBuilder setPreview(CratePreview preview) { + this.preview = preview; + return this; + } + + public RoCrateBuilder addUntrackedFile(File file) { + this.untrackedFiles.add(file); + return this; + } + + /** + * @return a crate with the information from this builder. + */ + public RoCrate build() { + return new RoCrate(this); + } + } + + /** + * Builder for Crates, supporting features which are not in a final + * specification yet. + *

+ * NOTE: This will change the specification version of your crate. + *

+ * We only add features we expect to be in the new specification in the end. + * In case a feature will not make it into the specification, we will mark + * it as deprecated and remove it in new major versions. If a feature is + * finalized, it will be added to the stable {@link RoCrateBuilder} and + * marked as deprecated in this class. + */ + public static class BuilderWithDraftFeatures extends RoCrateBuilder { + + /** + * @see RoCrateBuilder#RoCrateBuilder() + */ + public BuilderWithDraftFeatures() { + super(); + } + + /** + * @see RoCrateBuilder#RoCrateBuilder(String, String, String, String) + */ + public BuilderWithDraftFeatures( + String name, + String description, + String datePublished, + String licenseId + ) { + super(name, description, datePublished, licenseId); + } + + /** + * @see RoCrateBuilder#RoCrateBuilder(String, String, String, + * ContextualEntity) + */ + public BuilderWithDraftFeatures( + String name, + String description, + String datePublished, + ContextualEntity licenseId + ) { + super(name, description, datePublished, licenseId); + } + + /** + * @see RoCrateBuilder#RoCrateBuilder(RoCrate) + */ + public BuilderWithDraftFeatures(RoCrate crate) { + super(crate); + this.descriptorBuilder = new JsonDescriptor.Builder(crate); + } + + /** + * Indicate this crate also conforms to the given specification, in + * addition to the version this builder adds. + *

+ * This is helpful for profiles or other specifications the crate + * conforms to. Can be called multiple times to add more specifications. + * + * @param specification a specification or profile this crate conforms + * to. + * @return the builder + */ + public BuilderWithDraftFeatures alsoConformsTo(URI specification) { + descriptorBuilder + .addConformsTo(specification) + // usage of a draft feature results in draft version numbers of the crate + .setVersion(CrateVersion.LATEST_UNSTABLE); + return this; + } + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java b/core/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java similarity index 82% rename from src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java index dfe6548e..658db7ca 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/context/CrateMetadataContext.java @@ -1,9 +1,7 @@ package edu.kit.datamanager.ro_crate.context; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.entities.AbstractEntity; - +import edu.kit.datamanager.ro_crate.json.JsonObject; import java.util.Map; import java.util.Set; @@ -16,8 +14,7 @@ * @version 1 */ public interface CrateMetadataContext { - - ObjectNode getContextJsonEntity(); + JsonObject getContextJsonEntity(); boolean checkEntity(AbstractEntity entity); @@ -39,9 +36,9 @@ public interface CrateMetadataContext { Set getKeys(); /** - * Get an immutable map of the context. - * @return an immutable map containing the context key-value pairs - */ + * Get an immutable map of the context. + * @return an immutable map containing the context key-value pairs + */ Map getPairs(); void deleteValuePairFromContext(String key); diff --git a/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java b/core/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java similarity index 68% rename from src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java index d76cf86b..884a2f41 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java @@ -1,20 +1,15 @@ package edu.kit.datamanager.ro_crate.context; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.entities.AbstractEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.special.IdentifierUtils; import java.io.IOException; import java.util.*; import java.util.function.Consumer; import java.util.function.Function; - -import edu.kit.datamanager.ro_crate.special.IdentifierUtils; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; @@ -28,9 +23,11 @@ */ public class RoCrateMetadataContext implements CrateMetadataContext { - public static final String DEFAULT_CONTEXT = "https://w3id.org/ro/crate/1.1/context"; - protected static final String DEFAULT_CONTEXT_LOCATION = "default_context/version1.1.json"; - protected static JsonNode defaultContext = null; + public static final String DEFAULT_CONTEXT = + "https://w3id.org/ro/crate/1.1/context"; + protected static final String DEFAULT_CONTEXT_LOCATION = + "default_context/version1.1.json"; + protected static JsonValue defaultContext = null; protected final Set urls = new HashSet<>(); protected final HashMap contextMap = new HashMap<>(); @@ -63,9 +60,8 @@ public RoCrateMetadataContext(Collection urls) { * * @param context the Json object of the context. */ - public RoCrateMetadataContext(JsonNode context) { - - Consumer addPairs = x -> { + public RoCrateMetadataContext(JsonValue context) { + Consumer addPairs = x -> { var iterate = x.fields(); while (iterate.hasNext()) { var next = iterate.next(); @@ -74,7 +70,7 @@ public RoCrateMetadataContext(JsonNode context) { } }; if (context.isArray()) { - for (JsonNode jsonNode : context) { + for (JsonValue jsonNode : context) { if (jsonNode.isTextual()) { this.addToContextFromUrl(jsonNode.asText()); } else if (jsonNode.isObject()) { @@ -108,14 +104,13 @@ public RoCrateMetadataContext(JsonNode context) { * } * * - * @return an ObjectNode containing the JSON-LD context representation + * @return an JsonObject containing the JSON-LD context representation */ @Override - public ObjectNode getContextJsonEntity() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ArrayNode array = objectMapper.createArrayNode(); - ObjectNode jsonNode = objectMapper.createObjectNode(); - ObjectNode finalNode = objectMapper.createObjectNode(); + public JsonObject getContextJsonEntity() { + JsonArray array = Json.arrayNode(); + JsonObject jsonNode = Json.objectNode(); + JsonObject finalNode = Json.objectNode(); for (String e : urls) { array.add(e); } @@ -150,19 +145,20 @@ public ObjectNode getContextJsonEntity() { */ @Override public boolean checkEntity(AbstractEntity entity) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode node = entity.getProperties().deepCopy(); + JsonObject node = (JsonObject) entity.getProperties().deepCopy(); node.remove("@id"); node.remove("@type"); - Set types = objectMapper.convertValue( - entity.getProperties().path("@type"), - new TypeReference<>() {} + Set types = extractStringValues( + entity.getProperties().path("@type") ); - final Function isFail = checkMeStr -> this.contextMap.get(checkMeStr) == null - && this.contextMap.keySet().stream() - .noneMatch(key -> checkMeStr.startsWith(key + ":")); + final Function isFail = checkMeStr -> + this.contextMap.get(checkMeStr) == null && + this.contextMap + .keySet() + .stream() + .noneMatch(key -> checkMeStr.startsWith(key + ":")); // check if the items in the array of types are present in the context for (String s : types) { @@ -188,7 +184,7 @@ public boolean checkEntity(AbstractEntity entity) { } // check if the fields of the entity are present in the context - for (var names = node.fieldNames(); names.hasNext();) { + for (var names = node.fieldNames(); names.hasNext(); ) { String s = names.next(); if (IdentifierUtils.isUrl(s)) { // full URLs are considered fine @@ -213,16 +209,17 @@ public boolean checkEntity(AbstractEntity entity) { public void addToContextFromUrl(String url) { this.urls.add(url); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - - JsonNode jsonNode = null; + JsonValue jsonNode = null; if (url.equals(DEFAULT_CONTEXT)) { if (defaultContext != null) { jsonNode = defaultContext; } else { - try { - jsonNode = objectMapper.readTree( - getClass().getClassLoader().getResource(DEFAULT_CONTEXT_LOCATION)); + try ( + var contextStream = getClass() + .getClassLoader() + .getResourceAsStream(DEFAULT_CONTEXT_LOCATION) + ) { + jsonNode = Json.parse(contextStream); } catch (IOException e) { e.printStackTrace(); } @@ -233,8 +230,7 @@ public void addToContextFromUrl(String url) { CloseableHttpResponse response; try (CloseableHttpClient httpclient = HttpClients.createDefault()) { response = httpclient.execute(httpGet); - jsonNode = objectMapper.readValue(response.getEntity().getContent(), - JsonNode.class); + jsonNode = Json.parse(response.getEntity().getContent()); } catch (IOException e) { System.err.printf("Cannot get context from url %s%n", url); return; @@ -243,17 +239,66 @@ public void addToContextFromUrl(String url) { defaultContext = jsonNode; } } - this.contextMap.putAll(objectMapper.convertValue(jsonNode.get("@context"), - new TypeReference<>() { - })); + this.contextMap.putAll(extractStringPairs(jsonNode.get("@context"))); + } + + /** + * Mirrors the former {@code convertValue(..., TypeReference>)}: + * collects the text values of a JSON value (a single string or an array of + * strings) into a set. + */ + private static Set extractStringValues(JsonValue value) { + Set result = new HashSet<>(); + if (value == null || value.isNull()) { + return result; + } + if (value.isArray()) { + for (JsonValue element : value) { + if (element.isTextual()) { + result.add(element.asText()); + } + } + } else if (value.isTextual()) { + result.add(value.asText()); + } + return result; } - /** - * Adds a key-value pair to the context. - * - * @param key the key to add. It may be a prefix or a term. - * @param value the value to add - */ + /** + * Mirrors the former {@code convertValue(..., TypeReference>)}: + * collects the string pairs of a context object. Non-object values mirror + * the former Jackson conversion failure (an IllegalArgumentException). + */ + private static Map extractStringPairs(JsonValue value) { + Map result = new HashMap<>(); + if (value == null || value.isNull()) { + return result; + } + if (!value.isObject()) { + throw new IllegalArgumentException( + "Cannot read context pairs from a non-object JSON value" + ); + } + for ( + Iterator names = ((JsonObject) value).fieldNames(); + names.hasNext(); + + ) { + String name = names.next(); + JsonValue entryValue = ((JsonObject) value).get(name); + if (entryValue.isTextual()) { + result.put(name, entryValue.asText()); + } + } + return result; + } + + /** + * Adds a key-value pair to the context. + * + * @param key the key to add. It may be a prefix or a term. + * @param value the value to add + */ @Override public void addToContext(String key, String value) { this.contextMap.put(key, value); @@ -266,8 +311,9 @@ public void addToContext(String key, String value) { */ @Override public String getValueOf(String key) { - return Optional.ofNullable(this.contextMap.get(key)) - .orElseGet(() -> this.other.get(key)); + return Optional.ofNullable(this.contextMap.get(key)).orElseGet(() -> + this.other.get(key) + ); } /** @@ -310,5 +356,4 @@ public void deleteValuePairFromContext(String key) { public void deleteUrlFromContext(String url) { this.urls.remove(url); } - } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java new file mode 100644 index 00000000..36a40dfc --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java @@ -0,0 +1,729 @@ +package edu.kit.datamanager.ro_crate.entities; + +import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; +import edu.kit.datamanager.ro_crate.entities.validation.EntityValidation; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.payload.Observer; +import edu.kit.datamanager.ro_crate.special.IdentifierUtils; +import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; +import edu.kit.datamanager.ro_crate.validation.Validation; +import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +/** + * Abstract Entity parent class of every singe item in the json metadata file. + * + * @author Nikola Tzotchev on 3.2.2022 г. + * @version 1 + */ +public class AbstractEntity { + + /** + * This set contains the types of an entity (ex. File, Dataset, ect.) It is + * a set because it does not make sense to have duplicates + */ + private Set types; + + /** + * Contains the whole list of properties of the entity It uses a custom + * serializer because of cases where a single array element should be + * displayed as a single value. ex: "key" : ["value"] + * <=> "key" : "value" + */ + private JsonObject properties; + + private static final EntityValidation entityValidation = new EntityValidation( + Validation.entityStrategy() + ); + + /** + * This set contains all the ids of the entities that are linked by + * this entity. This information is provided to crate payloads to make + * the removal of entities faster. + */ + private final Set linkedTo; + + private final Set observers; + + public void addObserver(Observer observer) { + this.observers.add(observer); + } + + private void notifyObservers() { + this.observers.forEach(observer -> observer.update(this.getId())); + } + + /** + * Constructor that takes a builder and instantiates all the fields from it. + * + * @param entityBuilder the entity builder passed to the constructor. + */ + public AbstractEntity(AbstractEntityBuilder entityBuilder) { + this.types = entityBuilder.types; + this.properties = entityBuilder.properties; + this.linkedTo = entityBuilder.relatedItems; + this.observers = new HashSet<>(); + if (this.properties.get("@id") == null) { + if (entityBuilder.id == null) { + this.properties.put("@id", UUID.randomUUID().toString()); + } else { + this.properties.put("@id", entityBuilder.id); + } + } + } + + public Set getLinkedTo() { + return linkedTo; + } + + /** + * Returns the types of this entity. + * + * @return a set of type strings. + */ + public Set getTypes() { + return types; + } + + /** + * Returns a Json object containing the properties of the entity. + * + * @return JsonObject representing the properties. + */ + public JsonObject getProperties() { + if (this.types != null) { + this.properties.set("@type", typesNode()); + } + return properties; + } + + /** + * The types as a JSON value, mirroring the former + * {@code MyObjectMapper.valueToTree(types)}: the shared mapper had + * {@code WRITE_SINGLE_ELEM_ARRAYS_UNWRAPPED} enabled, so a single type + * serialized to a plain string and multiple types to a string array + * (in the iteration order of the underlying set). + */ + private JsonValue typesNode() { + JsonArray typeArray = Json.arrayNode(); + for (String type : this.types) { + typeArray.add(type); + } + return this.types.size() == 1 ? typeArray.get(0) : typeArray; + } + + public JsonValue getProperty(String propertyKey) { + return this.properties.get(propertyKey); + } + + /** + * Returns the value of the property with the given key as a String. + * If the property is not found, it returns null. + * + * @param propertyKey the key of the property. + * @return the value of the property as a String or null if not found. + */ + public String getIdProperty(String propertyKey) { + return Optional.ofNullable(this.properties.get(propertyKey)) + .map(jsonNode -> jsonNode.path("@id").asText(null)) + .orElse(null); + } + + public String getId() { + JsonValue id = this.properties.get("@id"); + return id == null ? null : id.asText(); + } + + /** + * Set all the properties from a Json object to the Entity. The entities are + * first validated to filter any invalid entity properties. + * + * @param obj the object that contains all the json properties that should + * be added. + */ + public void setProperties(JsonValue obj) { + // validate whole entity + if (entityValidation.entityValidation(obj)) { + this.properties = ((JsonObject) obj).deepCopy(); + this.notifyObservers(); + } + } + + /** + * Serializes this entity into its JSON-LD representation. + * + *

This replaces the former Jackson bean serialization of entities + * (annotations plus custom serializers): properties are unwrapped with + * the same filtering the former {@code ObjectNodeSerializer} applied + * (empty objects, nulls and empty arrays skipped; empty objects removed + * from arrays; single-element arrays unwrapped), and data set entities + * append their {@code hasPart} references at the end, mirroring the + * former {@code HasPartSerializer}. + * + * @return the neutral JSON object representing this entity + */ + public JsonObject toJson() { + JsonObject output = Json.objectNode(); + // getProperties() intentionally refreshes the @type property first + JsonObject source = (JsonObject) JsonUtilFunctions.unwrapSingleArray( + getProperties() + ); + for (var field : source.entries()) { + String name = field.getKey(); + JsonValue value = field.getValue(); + if (value.isObject() && value.size() == 0) { + continue; + } + if (value.isNull()) { + continue; + } + if (value.isArray()) { + JsonArray array = (JsonArray) value; + // mirrors the former serializer: drop empty object elements + for (int i = array.size() - 1; i >= 0; i--) { + JsonValue element = array.get(i); + if (element.isObject() && element.size() == 0) { + array.remove(i); + } + } + if (array.isEmpty()) { + continue; + } + } + output.set(name, value); + } + appendAdditionalJsonProperties(output); + return output; + } + + /** + * Hook for subclasses that carry additional JSON properties beyond their + * stored tree; appends nothing by default. + */ + protected void appendAdditionalJsonProperties(JsonObject output) {} + + protected void setId(String id) { + this.properties.put("@id", id); + } + + /** + * removes one property from an entity. + * + * @param key the key of the entity, which will be removed. + */ + public void removeProperty(String key) { + this.getProperties().remove(key); + this.notifyObservers(); + } + + /** + * Removes a collection of properties from an entity. + * + * @param keys collection of keys, which will be removed. + */ + public void removeProperties(Collection keys) { + this.getProperties().remove(keys); + this.notifyObservers(); + } + + /** + * Adds a property to the entity. + *

+ * It may override values, if the key already exists. + * + * @param key the key of the property. + * @param value value of the property. + */ + public void addProperty(String key, String value) { + if (key != null && value != null) { + this.properties.put(key, value); + this.notifyObservers(); + } + } + + /** + * Adds a property to the entity. + *

+ * It may override values, if the key already exists. + * + * @param key the key of the property. + * @param value value of the property. + */ + public void addProperty(String key, long value) { + if (key != null) { + this.properties.put(key, value); + this.notifyObservers(); + } + } + + /** + * Adds a property to the entity. + *

+ * It may override values, if the key already exists. + * + * @param key the key of the property. + * @param value value of the property. + */ + public void addProperty(String key, double value) { + if (key != null) { + this.properties.put(key, value); + this.notifyObservers(); + } + } + + /** + * Adds a generic property to the entity. + *

+ * It may fail with an error message on stdout, in which case the + * value is not added. + * It may override values, if the key already exists. + * This is the most generic way to add a property. The value is a + * JsonValue that could contain anything possible. It is limited to + * objects allowed to flattened documents, which means any literal, + * an array of literals, or an object with an @id property. + * + * @param key String key of the property. + * @param value The JsonValue representing the value. + */ + public void addProperty(String key, JsonValue value) { + if (addProperty(this.properties, key, value)) { + notifyObservers(); + } + } + + private static boolean addProperty( + JsonObject whereToAdd, + String key, + JsonValue value + ) { + boolean validInput = key != null && value != null; + if (validInput && entityValidation.fieldValidation(value)) { + whereToAdd.set(key, value); + return true; + } + return false; + } + + /** + * Add a property that looks like this: "name" : {"@id" : "id"} If the + * name property already exists add a second @id to it. + * + * @param name the "key" of the property. + * @param id the "id" of the property. + */ + public void addIdProperty(String name, String id) { + if (id == null || id.isBlank()) { + return; + } + mergeIdIntoValue(id, this.properties.get(name)).ifPresent(newValue -> + this.properties.set(name, newValue) + ); + this.linkedTo.add(id); + this.notifyObservers(); + } + + /** + * Merges the given id into the current value, + * using this representation: {"@id" : "id"}. + *

+ * The current value can be null without errors. + * Only the id will be considered in this case. + *

+ * If the id is null-ish, it will not be added, similar to a null-ish value. + * If the id is already present, nothing will be done. + * If it is not an array and the id is not present, an array will be applied. + * + * @param id the id to add. + * @param currentValue the current value of the property. + * @return The updated value of the property. + * Empty if value does not change! + */ + protected static Optional mergeIdIntoValue( + String id, + JsonValue currentValue + ) { + if (id == null || id.isBlank()) { + return Optional.empty(); + } + + JsonObject newIdObject = Json.objectNode().put("@id", id); + if ( + currentValue == null || currentValue.isNull() || currentValue.isMissing() + ) { + return Optional.ofNullable(newIdObject); + } + + boolean isIdAlready = currentValue.asText().equals(id); + boolean isIdObjectAlready = currentValue.path("@id").asText().equals(id); + boolean isArrayWithIdPresent = currentValue + .valueStream() + .anyMatch(node -> node.path("@id").asText().equals(id)); + if (isIdAlready || isIdObjectAlready || isArrayWithIdPresent) { + return Optional.empty(); + } + + if ( + currentValue.isArray() && + currentValue instanceof JsonArray currentValueAsArray + ) { + currentValueAsArray.add(newIdObject); + return Optional.of(currentValueAsArray); + } else { + // property is not an array, so we make it an array + JsonArray newNodes = Json.arrayNode(); + newNodes.add(currentValue); + newNodes.add(newIdObject); + return Optional.of(newNodes); + } + } + + /** + * Adds everything from the properties to the property "name" as id. + * + * @param name the key of the property. + * @param properties a collection containing all the id as String. + */ + public void addIdListProperties(String name, Collection properties) { + JsonArray node = Json.arrayNode(); + if (this.properties.get(name) == null) { + node = Json.arrayNode(); + } else { + if (!this.properties.get(name).isArray()) { + node.add(this.properties.get(name)); + } + } + for (String s : properties) { + this.linkedTo.add(s); + node.add(Json.objectNode().put("@id", s)); + } + if (node.size() == 1) { + this.properties.set(name, node.get(0)); + } else { + this.properties.set(name, node); + } + notifyObservers(); + } + + /** + * Adding new type to the property (which may have multiple such ones). + * + * @param type the String representing the type. + */ + public void addType(String type) { + if (this.types == null) { + this.types = new HashSet<>(); + } + this.types.add(type); + this.properties.set("@type", typesNode()); + } + + /** + * Checks if the date matches the ISO 8601 date format. + * + * @param date the date as a string + * @throws IllegalArgumentException if format does not match + */ + private static void checkFormatISO8601(String date) + throws IllegalArgumentException { + String regex = + "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$"; + Pattern pattern = Pattern.compile(regex); + Matcher matcher = pattern.matcher(date); + if (!matcher.matches()) { + throw new IllegalArgumentException( + "Date MUST be a string in ISO 8601 format" + ); + } + } + + /** + * Adds a property with date time format. The property should match the ISO 8601 + * date format. + *

+ * Same as {@link #addProperty(String, String)} but with internal check. + * + * @param key key of the property (e.g. datePublished) + * @param value time string in ISO 8601 format + * @throws IllegalArgumentException if format is not ISO 8601 + */ + public void addDateTimePropertyWithExceptions(String key, String value) + throws IllegalArgumentException { + if (value != null) { + checkFormatISO8601(value); + this.properties.put(key, value); + this.notifyObservers(); + } + } + + /** + * This a builder inner class that should allow for an easier creating of + * entities. + * + * @param The type of the child builders so that they to can use the + * methods provided here. + */ + public abstract static class AbstractEntityBuilder> { + + private Set types; + protected Set relatedItems; + private JsonObject properties; + private String id; + + protected AbstractEntityBuilder() { + this.properties = Json.objectNode(); + this.relatedItems = new HashSet<>(); + } + + protected String getId() { + return this.id; + } + + /** + * Setting the id property of the entity, if the given value is not + * null. If the id is not encoded, the encoding will be done. + *

+ * NOTE: IDs are not just names! The ID may have effects + * on parts of your crate! For example: If the entity represents a + * file which will be copied into the crate, writers must use the + * ID as filename. + * + * @param id the String representing the id. + * @return the generic builder. + */ + public T setId(String id) { + if (id != null && !id.equals(RootDataEntity.ID)) { + if (IdentifierUtils.isValidUri(id)) { + this.id = id; + } else { + this.id = IdentifierUtils.encode(id).orElse(this.id); + } + } + return self(); + } + + /** + * Adding a type to the builder types. + * + * @param type the type to add. + * @return the generic builder. + */ + public T addType(String type) { + if (this.types == null) { + this.types = new HashSet<>(); + } + if (type != null && !type.isEmpty()) { + this.types.add(type); + } + return self(); + } + + /** + * Adds multiple types in one call. + * + * @param types the types to add. + * @return the generic builder. + */ + public T addTypes(Collection types) { + if (this.types == null) { + this.types = new HashSet<>(); + } + this.types.addAll(types); + return self(); + } + + /** + * Adds a property with date time format. The property should match the ISO 8601 + * date format. + *

+ * Same as {@link #addProperty(String, String)} but with internal check. + * + * @param key key of the property (e.g. datePublished) + * @param value time string in ISO 8601 format + * @return this builder + * @throws IllegalArgumentException if format is not ISO 8601 + */ + public T addDateTimePropertyWithExceptions(String key, String value) + throws IllegalArgumentException { + if (value != null) { + checkFormatISO8601(value); + this.properties.put(key, value); + } + return self(); + } + + /** + * Adding a property to the builder. + * + * @param key the key of the property in a string. + * @param value the JsonValue value of te property. + * @return the generic builder. + */ + public T addProperty(String key, JsonValue value) { + if (AbstractEntity.addProperty(this.properties, key, value)) { + this.relatedItems.addAll( + JsonUtilFunctions.getIdPropertiesFromProperty(value) + ); + } + return self(); + } + + /** + * Adding a property to the builder. + * + * @param key the key of the property as a string. + * @param value the value of the property as a string. + * @return the generic builder. + */ + public T addProperty(String key, String value) { + this.properties.put(key, value); + return self(); + } + + public T addProperty(String key, int value) { + this.properties.put(key, value); + return self(); + } + + public T addProperty(String key, double value) { + this.properties.put(key, value); + return self(); + } + + public T addProperty(String key, boolean value) { + this.properties.put(key, value); + return self(); + } + + /** + * ID properties are often used when referencing other entities within + * the ROCrate. This method adds automatically such one. + *

+ * Instead of {@code "name": "id" } + * this will add {@code "name" : {"@id": "id"} } + * + * Does nothing if name or id are null. + * + * @param name the name of the ID property. + * @param id the ID. + * @return the generic builder + */ + public T addIdProperty(String name, String id) { + AbstractEntity.mergeIdIntoValue(id, this.properties.get(name)).ifPresent( + newValue -> { + this.properties.set(name, newValue); + this.relatedItems.add(id); + } + ); + return self(); + } + + /** + * This is another way of adding the ID property, this time the whole + * other Entity is provided. + * + * @param name the name of the property. + * @param entity the other entity that is referenced. + * @return the generic builder. + */ + public T addIdProperty(String name, AbstractEntity entity) { + if (entity != null) { + return addIdProperty(name, entity.getId()); + } + return self(); + } + + /** + * This adds multiple id entities to a single key. + * + * @param name the name of the property. + * @param entities the Collection containing the multiple entities. + * @return the generic builder. + */ + public T addIdFromCollectionOfEntities( + String name, + Collection entities + ) { + if (entities != null) { + for (var e : entities) { + addIdProperty(name, e); + } + } + return self(); + } + + /** + * Deprecated. Equivalent to {@link #setAllIfValid(JsonObject)}. + * + * @param properties the Json representing all the properties. + * @return the generic builder, either including all given properties + * * or unchanged. + * + * @deprecated To enforce the user know what this method does, + * we want the user to use one of the more explicitly named + * methods {@link #setAllIfValid(JsonObject)} or + * {@link #setAllIfValid(JsonObject)}. + * @see #setAllIfValid(JsonObject) + */ + @Deprecated(since = "2.1.0", forRemoval = true) + public T setAll(JsonObject properties) { + return setAllIfValid(properties); + } + + /** + * This sets everything from a json object to the property, + * if the result is valid. Otherwise, it will do nothing. + *

+ * Valid means here that the json object needs to be flat as specified + * in the RO-Crate specification. In principle, this means that + * primitives and objects referencing an ID are allowed, + * as well as arrays of these. + * + * @param properties the Json representing all the properties. + * @return the generic builder, either including all given properties + * or unchanged. + */ + public T setAllIfValid(JsonObject properties) { + if (AbstractEntity.entityValidation.entityValidation(properties)) { + this.properties = properties; + this.relatedItems.addAll( + JsonUtilFunctions.getIdPropertiesFromJsonNode(properties) + ); + } + return self(); + } + + /** + * This sets everything from a json object to the property. Can be + * useful when the entity is already available somewhere. + *

+ * Errors on validation are printed, but everything will be added. + * For more about validation, see {@link #setAllIfValid(JsonObject)}. + * + * @param properties the Json representing all the properties. + * @return the generic builder with all properties added. + */ + public T setAllUnsafe(JsonObject properties) { + // This will currently only print errors. + AbstractEntity.entityValidation.entityValidation(properties); + this.properties = properties; + JsonValue typeProps = properties.path("@type"); + if (typeProps.isArray()) { + typeProps.valueStream().forEach(value -> this.addType(value.asText())); + } else if (typeProps.isTextual()) { + this.addType(typeProps.asText()); + } + this.relatedItems.addAll( + JsonUtilFunctions.getIdPropertiesFromJsonNode(properties) + ); + return self(); + } + + public abstract T self(); + + public abstract AbstractEntity build(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java new file mode 100644 index 00000000..c803b14a --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java @@ -0,0 +1,196 @@ +package edu.kit.datamanager.ro_crate.entities.contextual; + +import java.util.Collection; +import java.util.HashSet; +import java.util.Optional; + +/** + * This class represents a detailing provenance of entities. + * + * Relevant specification link: Provenance + * of entities + * + * @author sabrinechelbi + */ +public class ActionEntity extends ContextualEntity { + + public ActionEntity(AbstractActionEntityBuilder entityBuilder) { + super(entityBuilder); + this.addType(entityBuilder.type.getName()); + this.addProperty("name", entityBuilder.name); + this.addProperty("description", entityBuilder.description); + + this.addDateTimePropertyWithExceptions( + "startTime", + entityBuilder.startTime + ); + this.addDateTimePropertyWithExceptions("endTime", entityBuilder.endTime); + + entityBuilder.status.ifPresent(status -> + this.addIdProperty("actionStatus", status.getId()) + ); + this.addIdProperty("agent", entityBuilder.agent); + this.addIdListProperties("instrument", entityBuilder.instruments); + this.addIdListProperties("result", entityBuilder.results); + this.addIdListProperties("object", entityBuilder.objects); + } + + abstract static class AbstractActionEntityBuilder> extends AbstractContextualEntityBuilder { + + protected ActionType type; + protected String description; + protected String name; + protected String startTime; + protected String endTime; + protected String agent; + protected Optional status = Optional.empty(); + + protected Collection objects = new HashSet<>(); + protected Collection results = new HashSet<>(); + protected Collection instruments = new HashSet<>(); + + protected AbstractActionEntityBuilder(ActionType type) { + this.type = type; + } + + public T setDescription(String description) { + this.description = description; + return self(); + } + + public T setName(String name) { + this.name = name; + return self(); + } + + public T setStartTime(String startTime) { + this.startTime = startTime; + return self(); + } + + public T setEndTime(String endTime) { + this.endTime = endTime; + return self(); + } + + public T setAgent(String agent) { + this.agent = agent; + return self(); + } + + public T setStatus(ActionStatus status) { + this.status = Optional.ofNullable(status); + return self(); + } + + /** + * Same as calling {@link #addObject(String)} with each element of the + * collection. + * + * From the specification: "A curation Action MUST have at least one object + * which associates it with either the root data entity Dataset or one of its + * components." + * + * @param objects see {@link #addObject(String)} + * @return this builder + */ + public T addObjects(Collection objects) { + this.objects.addAll(objects); + return self(); + } + + /** + * Adds a object to the collection of objects of this ActionEntity. + * + * From the specification: "A curation Action MUST have at least one object + * which associates it with either the root data entity Dataset or one of its + * components." + * + * @param object the object to add to this ActionEntity. Duplicates will be + * ignored/removed. "The object upon which the action is carried + * out, whose state is kept intact or changed. Also known as the + * semantic roles patient, affected or undergoer (which change + * their state) or theme (which doesn't). E.g. John read a book." + * (Schema.org definition) + * @return this builder + */ + public T addObject(String object) { + this.objects.add(object); + return self(); + } + + /** + * Same as calling {@link #addResult(String)} with each element of the + * collection. + * + * @param results see {@link #addResult(String)} + * @return this builder + */ + public T addResults(Collection results) { + this.results.addAll(results); + return self(); + } + + /** + * Adds a result to the collection of results of this ActionEntity. + * + * @param result the result to add to this ActionEntity. Duplicates will be + * ignored/removed. "The result produced in the action. E.g. John + * wrote a book." (Schema.org definition) + * @return this builder + */ + public T addResult(String result) { + this.results.add(result); + return self(); + } + + /** + * Same as calling {@link #addInstrument(String)} with each element of the + * collection. + * + * @param instruments see {@link #addInstrument(String)} + * @return this builder + */ + public T addInstruments(Collection instruments) { + this.instruments.addAll(instruments); + return self(); + } + + /** + * Adds a instrument to the collection of instruments of this ActionEntity. + * + * @param instrument the instrument to add to this ActionEntity. Duplicates will + * be ignored/removed. "The object that helped the agent + * perform the action. E.g. John wrote a book with a pen." + * (Schema.org definition) + * @return this builder + */ + public T addInstrument(String instrument) { + this.instruments.add(instrument); + return self(); + } + + @Override + public abstract ActionEntity build(); + } + + public static final class ActionEntityBuilder + extends AbstractActionEntityBuilder + { + + public ActionEntityBuilder(ActionType type) { + super(type); + } + + @Override + public ActionEntityBuilder self() { + return this; + } + + @Override + public ActionEntity build() { + return new ActionEntity(this); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java new file mode 100644 index 00000000..73cb5e7e --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java @@ -0,0 +1,18 @@ +package edu.kit.datamanager.ro_crate.entities.contextual; + +public enum ActionStatus { + ACTIVE_ACTION_STATUS("http://schema.org/ActiveActionStatus"), + COMPLETED_ACTION_STATUS("http://schema.org/CompletedActionStatus"), + FAILED_ACTION_STATUS("http://schema.org/FailedActionStatus"), + POTENTIAL_ACTION_STATUS("http://schema.org/PotentialActionStatus"); + + private final String id; + + ActionStatus(String id) { + this.id = id; + } + + public String getId() { + return id; + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java new file mode 100644 index 00000000..45ed2aa8 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java @@ -0,0 +1,20 @@ +package edu.kit.datamanager.ro_crate.entities.contextual; + +/** + * Enumeration class representing action types. + * @author sabrinechelbi + */ +public enum ActionType { + CREATE("CreateAction"), + UPDATE("UpdateAction"); + + private final String name; + + ActionType(String name) { + this.name = name; + } + + public String getName() { + return name; + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java similarity index 74% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java index 1897b6df..c0d699d7 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntity.java @@ -14,8 +14,7 @@ public ContextualEntity(AbstractContextualEntityBuilder entityBuilder) { super(entityBuilder); } - abstract static class AbstractContextualEntityBuilder - > extends AbstractEntityBuilder { + abstract static class AbstractContextualEntityBuilder> extends AbstractEntityBuilder { @Override public abstract ContextualEntity build(); @@ -25,8 +24,9 @@ abstract static class AbstractContextualEntityBuilder * This is the Contextual entity builder base class, * as of right now it does not contain any methods. */ - public static final class ContextualEntityBuilder extends - AbstractContextualEntityBuilder { + public static final class ContextualEntityBuilder + extends AbstractContextualEntityBuilder + { @Override public ContextualEntityBuilder self() { diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java new file mode 100644 index 00000000..fec0b4e7 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java @@ -0,0 +1,96 @@ +package edu.kit.datamanager.ro_crate.entities.contextual; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.special.CrateVersion; +import java.net.URI; +import java.util.HashSet; +import java.util.Set; + +public class JsonDescriptor extends ContextualEntity { + + protected static final String CONFORMS_TO = "conformsTo"; + public static final String ID = "ro-crate-metadata.json"; + + /** + * Returns a JsonDescriptor with the conformsTo value set to the latest stable + * version. + */ + public JsonDescriptor() { + super( + staticPropertiesPrefilledBuilder().addIdProperty( + CONFORMS_TO, + CrateVersion.LATEST_STABLE.conformsTo + ) + ); + } + + protected static ContextualEntityBuilder staticPropertiesPrefilledBuilder() { + return new ContextualEntity.ContextualEntityBuilder() + .setId(ID) + .addType("CreativeWork") + .addIdProperty("about", "./"); + } + + private JsonDescriptor(ContextualEntityBuilder builder) { + super(builder); + } + + /** + * Builder for the JsonDescriptor. + *

+ * Defaults to the latest stable crate version and no other conformsTo values. + */ + public static final class Builder { + + CrateVersion version = CrateVersion.LATEST_STABLE; + Set otherConformsToValues = new HashSet<>(); + + public Builder() { + // default + } + + public Builder(Crate crate) { + crate.getVersion().ifPresent(v -> this.version = v); + this.otherConformsToValues.addAll(crate.getProfiles()); + } + + public Builder setVersion(CrateVersion version) { + this.version = version; + return this; + } + + public Builder addConformsTo(String uri) { + this.otherConformsToValues.add(uri); + return this; + } + + public Builder addConformsTo(URI uri) { + this.otherConformsToValues.add(uri.toString()); + return this; + } + + public JsonDescriptor build() { + if (this.otherConformsToValues.isEmpty()) { + // in this case we do not need an array + ContextualEntityBuilder entityBuilder = + staticPropertiesPrefilledBuilder().addIdProperty( + CONFORMS_TO, + this.version.conformsTo + ); + return new JsonDescriptor(entityBuilder); + } else { + // use an array to collect all values into an array of simple @id objects. + JsonArray array = Json.arrayNode(); + array.add(Json.objectNode().put("@id", this.version.conformsTo)); + for (String other : this.otherConformsToValues) { + array.add(Json.objectNode().put("@id", other)); + } + ContextualEntityBuilder entityBuilder = + staticPropertiesPrefilledBuilder().addProperty(CONFORMS_TO, array); + return new JsonDescriptor(entityBuilder); + } + } + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java similarity index 80% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java index 71f90618..42a36e02 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntity.java @@ -15,7 +15,9 @@ public class OrganizationEntity extends ContextualEntity { * * @param entityBuilder the builder from which to create the entity. */ - public OrganizationEntity(AbstractOrganizationEntityBuilder entityBuilder) { + public OrganizationEntity( + AbstractOrganizationEntityBuilder entityBuilder + ) { super(entityBuilder); this.addProperty("address", entityBuilder.address); this.addProperty("email", entityBuilder.email); @@ -24,9 +26,7 @@ public OrganizationEntity(AbstractOrganizationEntityBuilder entityBuilder) { this.addType(TYPE); } - abstract static class AbstractOrganizationEntityBuilder> - extends AbstractContextualEntityBuilder { + abstract static class AbstractOrganizationEntityBuilder> extends AbstractContextualEntityBuilder { String address; String email; @@ -60,8 +60,9 @@ public T setLocationId(String placeId) { /** * A builder for the organization entity. */ - public static final class OrganizationEntityBuilder extends - AbstractOrganizationEntityBuilder { + public static final class OrganizationEntityBuilder + extends AbstractOrganizationEntityBuilder + { @Override public OrganizationEntityBuilder self() { diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java similarity index 89% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java index 84cb8731..e211e57b 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntity.java @@ -25,9 +25,7 @@ public PersonEntity(AbstractPersonEntityBuilder entityBuilder) { this.addType(TYPE); } - abstract static class AbstractPersonEntityBuilder - > - extends AbstractContextualEntityBuilder { + abstract static class AbstractPersonEntityBuilder> extends AbstractContextualEntityBuilder { String affiliation; String contactPoint; @@ -68,7 +66,8 @@ public T setFamilyName(String familyName) { * Person Entity builder for easier creation of Person entities. */ public static final class PersonEntityBuilder - extends AbstractPersonEntityBuilder { + extends AbstractPersonEntityBuilder + { @Override public PersonEntityBuilder self() { diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java similarity index 89% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java index bf5dd3e3..fc02ccd4 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntity.java @@ -21,8 +21,7 @@ public PlaceEntity(AbstractPlaceEntityBuilder entityBuilder) { this.addType(TYPE); } - abstract static class AbstractPlaceEntityBuilder> extends - AbstractContextualEntityBuilder { + abstract static class AbstractPlaceEntityBuilder> extends AbstractContextualEntityBuilder { String geo; @@ -44,7 +43,8 @@ public T setGeo(ContextualEntity geo) { * A builder class for the easier Place entity construction. */ public static final class PlaceEntityBuilder - extends AbstractPlaceEntityBuilder { + extends AbstractPlaceEntityBuilder + { @Override public PlaceEntityBuilder self() { diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java new file mode 100644 index 00000000..520fd982 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java @@ -0,0 +1,190 @@ +package edu.kit.datamanager.ro_crate.entities.data; + +import static edu.kit.datamanager.ro_crate.special.IdentifierUtils.isUrl; + +import edu.kit.datamanager.ro_crate.entities.AbstractEntity; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import java.net.URI; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.List; + +/** + * The base class of every data entity. + * + * @author Nikola Tzotchev on 4.2.2022 г. + * @version 1 + */ +public class DataEntity extends AbstractEntity { + + private Path path; + + /** + * The constructor that takes an DataEntity builder and instantiates the + * entity. + * + * @param entityBuilder the builder passed as argument. + */ + public DataEntity(AbstractDataEntityBuilder entityBuilder) { + super(entityBuilder); + if (!entityBuilder.authors.isEmpty()) { + this.addIdListProperties("author", entityBuilder.authors); + } + this.path = entityBuilder.location; + } + + /** + * Adds an author ID to the entity. + *

+ * Calling this multiple times will add multiple author IDs. + * + * @param id the identifier of the author. + */ + @SuppressWarnings("unused") + public void addAuthorId(String id) { + this.addIdProperty("author", id); + } + + /** + * Gets the path of this entity. + *

+ * When reading a crate, this will point to the entity's file within the crate. + * When creating a new entity or crate, it might point to a file outside the crate, + * as set by {@link DataEntityBuilder#setLocation(Path)}. + * Such a file will be copied into the crate when writing. + * + * @return the path to the file this entity represents. + */ + public Path getPath() { + return path; + } + + abstract static class AbstractDataEntityBuilder> extends AbstractEntityBuilder { + + private Path location; + private List authors = new ArrayList<>(); + + /** + * Sets the location of the data entity to make a copy from when writing the crate. + *

+ * Use this if you want to copy the associated file to the crate. + * Do not use it if the file should already be considered (e.g. + * as part of a DataSetEntity). + *

+ * If the ID has not been set manually in beforehand, it will be derived + * from the path. Use {@link #setId(String)} to override it or set it in + * beforehand. Note that another call of this method will + * not override the ID as it has been set by the previous call! + * + * @param path the location of the data. May be null, in which case + * nothing happens. + * @return this builder + */ + public T setLocation(Path path) { + if (path != null) { + if (this.getId() == null) { + this.setId(path.getFileName().toString()); + } + this.location = path; + } + return self(); + } + + /** + * A variant of {@link #setLocation(Path)} which may throw exceptions. + * + * @param path the location of the data + * @return this builder + * @throws IllegalArgumentException if path is null + */ + public T setLocationWithExceptions(Path path) + throws IllegalArgumentException { + if (path == null) { + throw new IllegalArgumentException( + "The given path should not be null." + ); + } + return setLocation(path); + } + + /** + * Same as {@link #setLocation(Path)} but instead of associating this + * entity with a file, it will point to some place on the internet. + *

+ * Via the specification, this means the uri will be set as the ID. This + * call is therefore equivalent to {@link #setId(String)}. + * + * @param uri the URI, should point at the data reachable on the + * internet. + * @return this builder + */ + public T setLocation(URI uri) { + if (uri != null && this.getId() == null) { + this.setId(uri.toString()); + } + return self(); + } + + /** + * A variant of {@link #setLocation(URI)} which may throw exceptions. + * + * @param uri the given uri + * @return this builder + * @throws IllegalArgumentException if uri is null or not a valid URL + */ + public T setLocationWithExceptions(URI uri) + throws IllegalArgumentException { + if (!isUrl(uri.toString())) { + throw new IllegalArgumentException( + "This Data Entity remote ID does not resolve to a valid URL." + ); + } + return setLocation(uri); + } + + public T setLicense(String id) { + this.addIdProperty("license", id); + return self(); + } + + public T setLicense(ContextualEntity license) { + this.addIdProperty("license", license.getId()); + return self(); + } + + public T addAuthor(String id) { + this.authors.add(id); + return self(); + } + + public T setContentLocation(String id) { + this.addIdProperty("contentLocation", id); + return self(); + } + + @Override + public abstract DataEntity build(); + } + + /** + * Data Entity builder class that allows for easier data entity creation. + *

+ * If not explicitly mentioned, all methods avoid Exceptions and will + * silently ignore null-parameters, in which case nothing will happen. Use + * the available *WithExceptions-methods in case you need them. + */ + public static final class DataEntityBuilder + extends AbstractDataEntityBuilder + { + + @Override + public DataEntityBuilder self() { + return this; + } + + @Override + public DataEntity build() { + return new DataEntity(this); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java new file mode 100644 index 00000000..51f701ba --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java @@ -0,0 +1,159 @@ +package edu.kit.datamanager.ro_crate.entities.data; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.util.HashSet; +import java.util.Set; +import java.util.stream.Collectors; + +/** + * A helping class for the creating of Data entities of type Dataset. + * + * @author Nikola Tzotchev on 5.2.2022 г. + * @version 1 + */ +public class DataSetEntity extends DataEntity { + + public static final String TYPE = "Dataset"; + + /** + * Points to the parts of this dataset. + *

+ * This will be serialized to and deserialized from the "hasPart" property + * and exists for convenience to represent the additional capabilities of + * a DataSetEntity over a normal DataEntity. + */ + public Set hasPart; + + /** + * Constructor for instantiating a Dataset entity from the builder. + * + * @param entityBuilder the builder passed as argument. + */ + public DataSetEntity(AbstractDataSetBuilder entityBuilder) { + super(entityBuilder); + this.hasPart = entityBuilder.hasPart + .stream() + .filter(s -> !s.isBlank()) + .collect(Collectors.toSet()); + this.addType(TYPE); + } + + public void removeFromHasPart(String str) { + this.hasPart.remove(str); + } + + public void addToHasPart(String id) { + if (id != null && !id.isEmpty()) { + this.hasPart.add(id); + } + } + + /** + * Check if the hasPart property contains a specific id. + * + * @deprecated use {@link #hasPart(String)} instead. + * + * @param id the id to check for + * @return true if the id is present, false otherwise + */ + @Deprecated(forRemoval = true) + public boolean hasInHasPart(String id) { + return this.hasPart.contains(id); + } + + /** + * Check if the hasPart property contains a specific id. + * @param id the id to check for + * @return true if the id is present, false otherwise + */ + public boolean hasPart(String id) { + return this.hasPart.contains(id); + } + + /** + * Appends the hasPart references, mirroring the former + * {@code HasPartSerializer}: a single {@code {"@id": ...}} object for one + * element, an array of such objects otherwise, in set iteration order. + */ + @Override + protected void appendAdditionalJsonProperties(JsonObject output) { + if (this.hasPart.isEmpty()) { + return; + } + JsonArray array = Json.arrayNode(); + for (String id : this.hasPart) { + array.add(Json.objectNode().put("@id", id)); + } + output.set("hasPart", this.hasPart.size() == 1 ? array.get(0) : array); + } + + abstract static class AbstractDataSetBuilder> extends AbstractDataEntityBuilder { + + Set hasPart; + + public AbstractDataSetBuilder() { + this.hasPart = new HashSet<>(); + } + + public T setHasPart(Set hasPart) { + this.hasPart = hasPart; + return self(); + } + + public T addToHasPart(DataEntity dataEntity) { + if (dataEntity != null) { + this.hasPart.add(dataEntity.getId()); + this.relatedItems.add(dataEntity.getId()); + } + return self(); + } + + public T addToHasPart(String dataEntity) { + if (dataEntity != null) { + this.hasPart.add(dataEntity); + this.relatedItems.add(dataEntity); + } + return self(); + } + + @Override + public T setAllUnsafe(JsonObject properties) { + super.setAllUnsafe(properties); + JsonValue hasPart = properties.path("hasPart"); + String txt = hasPart.asText(); + if (!txt.isBlank()) { + this.hasPart.add(txt); + } + hasPart + .valueStream() + .map(JsonValue::asText) + .filter(value -> !value.isBlank()) + .forEach(value -> this.hasPart.add(value)); + return self(); + } + + @Override + public abstract DataSetEntity build(); + } + + /** + * Builder for the helping class DataSetEntity. + */ + public static final class DataSetBuilder + extends AbstractDataSetBuilder + { + + @Override + public DataSetBuilder self() { + return this; + } + + @Override + public DataSetEntity build() { + return new DataSetEntity(this); + } + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java similarity index 83% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java index 44a2a4e1..d5eda533 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/FileEntity.java @@ -15,8 +15,7 @@ public FileEntity(AbstractFileEntityBuilder entityBuilder) { this.addType(TYPE); } - abstract static class AbstractFileEntityBuilder> extends - AbstractDataEntityBuilder { + abstract static class AbstractFileEntityBuilder> extends AbstractDataEntityBuilder { public T setEncodingFormat(String encodingFormat) { this.addProperty("encodingFormat", encodingFormat); @@ -30,7 +29,9 @@ public T setEncodingFormat(String encodingFormat) { /** * Builder class for the easier creation of the File entities. */ - public static final class FileEntityBuilder extends AbstractFileEntityBuilder { + public static final class FileEntityBuilder + extends AbstractFileEntityBuilder + { @Override public FileEntityBuilder self() { diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java similarity index 86% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java index 01133112..cc2e75e2 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntity.java @@ -20,7 +20,8 @@ public RootDataEntity(AbstractDataSetBuilder entityBuilder) { * Builder class for easier creation of root data entities. */ public static final class RootDataEntityBuilder - extends AbstractDataSetBuilder { + extends AbstractDataSetBuilder + { @Override public RootDataEntityBuilder self() { @@ -30,9 +31,8 @@ public RootDataEntityBuilder self() { @Override public RootDataEntity build() { // small hack not to get the command line message - this.setLocation(Paths.get("./")) - .setId("./"); + this.setLocation(Paths.get("./")).setId("./"); return new RootDataEntity(this); } } -} \ No newline at end of file +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java similarity index 77% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java index 27f86e32..1d3f9a3b 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntity.java @@ -9,7 +9,10 @@ */ public class WorkflowEntity extends FileEntity { - private static final Set TYPES = Set.of("SoftwareSourceCode", "ComputationalWorkflow"); + private static final Set TYPES = Set.of( + "SoftwareSourceCode", + "ComputationalWorkflow" + ); /** * Constructor for creating the workflow entity from a builder. @@ -23,8 +26,7 @@ private WorkflowEntity(AbstractWorkflowEntityBuilder entityBuilder) { this.addIdListProperties("output", entityBuilder.output); } - abstract static class AbstractWorkflowEntityBuilder> extends AbstractFileEntityBuilder { + abstract static class AbstractWorkflowEntityBuilder> extends AbstractFileEntityBuilder { List input = new ArrayList<>(); List output = new ArrayList<>(); @@ -46,8 +48,9 @@ public T addOutput(String output) { /** * A builder for easier creation of workflow entities. */ - public static final class WorkflowEntityBuilder extends - AbstractWorkflowEntityBuilder { + public static final class WorkflowEntityBuilder + extends AbstractWorkflowEntityBuilder + { @Override public WorkflowEntityBuilder self() { diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java similarity index 72% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java index aa54c3ca..c966fb04 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidation.java @@ -1,7 +1,6 @@ package edu.kit.datamanager.ro_crate.entities.validation; - -import com.fasterxml.jackson.databind.JsonNode; +import edu.kit.datamanager.ro_crate.json.JsonValue; /** * Class used for validation of entities before their creation. @@ -14,11 +13,11 @@ public EntityValidation(EntityValidationStrategy strategy) { this.strategy = strategy; } - public boolean entityValidation(JsonNode entity) { + public boolean entityValidation(JsonValue entity) { return strategy.validateEntity(entity); } - public boolean fieldValidation(JsonNode entity) { + public boolean fieldValidation(JsonValue entity) { return strategy.validateFieldOfEntity(entity); } } diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java similarity index 53% rename from src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java index 644b49e7..fd7dce9a 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/EntityValidationStrategy.java @@ -1,13 +1,12 @@ package edu.kit.datamanager.ro_crate.entities.validation; -import com.fasterxml.jackson.databind.JsonNode; +import edu.kit.datamanager.ro_crate.json.JsonValue; /** * Interface for the strategy of the entity validation. */ public interface EntityValidationStrategy { + boolean validateEntity(JsonValue entity); - boolean validateEntity(JsonNode entity); - - boolean validateFieldOfEntity(JsonNode field); + boolean validateFieldOfEntity(JsonValue field); } diff --git a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java similarity index 69% rename from src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java index 6a76ec02..26b99559 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromDataCite.java @@ -1,10 +1,5 @@ package edu.kit.datamanager.ro_crate.externalproviders.dataentities; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.Crate; import edu.kit.datamanager.ro_crate.RoCrate; import edu.kit.datamanager.ro_crate.RoCrate.RoCrateBuilder; @@ -15,8 +10,10 @@ import edu.kit.datamanager.ro_crate.entities.data.DataEntity; import edu.kit.datamanager.ro_crate.externalproviders.organizationprovider.RorProvider; import edu.kit.datamanager.ro_crate.externalproviders.personprovider.OrcidProvider; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; import java.io.IOException; import java.time.LocalDateTime; import java.util.ArrayList; @@ -52,7 +49,7 @@ private ImportFromDataCite() {} /** * This will take a DataCite entry and create a crate from it. - * + * * Except of the url, all parameters are optional. If present, they will be * added to the crate. * @@ -65,12 +62,12 @@ private ImportFromDataCite() {} * @return the created crate. */ public static Crate createCrateFromDataCiteResource( - String url, - Optional name, - Optional description, - Optional datePublished, - Optional licenseId) { - + String url, + Optional name, + Optional description, + Optional datePublished, + Optional licenseId + ) { RoCrateBuilder builder = new RoCrate.RoCrateBuilder(); name.ifPresent(builder::addName); description.ifPresent(builder::addDescription); @@ -90,8 +87,9 @@ public static Crate createCrateFromDataCiteResource( * @param crate the existing crate. */ public static void addDataCiteToCrate(String url, Crate crate) { - var entities = - getEntitiesFromDataCiteResource(Objects.requireNonNull(getJsonNodeFromDataCite(url))); + var entities = getEntitiesFromDataCiteResource( + Objects.requireNonNull(getJsonNodeFromDataCite(url)) + ); crate.addFromCollection(entities); } @@ -106,12 +104,12 @@ public static void addDataCiteToCrate(String url, Crate crate) { * @return the created crate. */ public static Crate createCrateFromDataCiteJson( - JsonNode json, - Optional name, - Optional description, - Optional datePublished, - Optional licenseId) { - + JsonValue json, + Optional name, + Optional description, + Optional datePublished, + Optional licenseId + ) { RoCrateBuilder builder = new RoCrate.RoCrateBuilder(); name.ifPresent(builder::addName); description.ifPresent(builder::addDescription); @@ -123,20 +121,18 @@ public static Crate createCrateFromDataCiteJson( return crate; } - public static void addDataCiteToCrateFromJson(JsonNode json, Crate crate) { + public static void addDataCiteToCrateFromJson(JsonValue json, Crate crate) { var entities = getEntitiesFromDataCiteResource(json); crate.addFromCollection(entities); } - private static JsonNode getJsonNodeFromDataCite(String url) { + private static JsonValue getJsonNodeFromDataCite(String url) { CloseableHttpClient httpClient = HttpClients.createDefault(); HttpGet request = new HttpGet(url); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode jsonNode; + JsonObject jsonNode; try { CloseableHttpResponse response = httpClient.execute(request); - jsonNode = objectMapper.readValue(response.getEntity().getContent(), - ObjectNode.class); + jsonNode = (JsonObject) Json.parse(response.getEntity().getContent()); } catch (IOException e) { e.printStackTrace(); return null; @@ -144,48 +140,51 @@ private static JsonNode getJsonNodeFromDataCite(String url) { return jsonNode; } - private static List getEntitiesFromDataCiteResource(JsonNode jsonNode) { - + private static List getEntitiesFromDataCiteResource( + JsonValue jsonNode + ) { List entityList = new ArrayList<>(); - final ObjectMapper objectMapper = MyObjectMapper.getMapper(); - final Map relationType = Stream.of(new String[][]{ - {"IsCitedBy", "isPartOf"}, - {"Cites", "citation"}, - {"IsSupplementTo", "isPartOf"}, - {"IsSupplementedBy", "isPartOf"}, - {"IsContinuedBy", "isPartOf"}, - {"Continues", "isBasedOn"}, - {"IsDescribedBy", "hasPart"}, - {"Describes", "isPartOf"}, - {"HasMetadata", "hasPart"}, - {"IsMetadataFor", "isPartOf"}, - {"HasVersion", "hasPart"}, - {"IsVersionOf", "isPartOf"}, - {"IsNewVersionOf", "isBasedOn"}, - {"IsPreviousVersionOf", "PredecessorOf"}, - {"IsPartOf", "isPartOf"}, - {"HasPart", "hasPart"}, - {"IsPublishedIn", "isPartOf"}, - {"IsReferencedBy", "isPartOf"}, - {"References", "citation"}, - {"IsDocumentedBy", "hasPart"}, - {"Documents", "isPartOf"}, - {"IsCompiledBy", "hasPart"}, - {"Compiles", "isPartOf"}, - {"IsVariantFormOf", "isBasedOn"}, - {"IsOriginalFormOf", "sameAs"}, - {"IsIdenticalTo", "sameAs"}, - {"IsReviewedBy", "hasPart"}, - {"Reviews", "isPartOf"}, - {"IsDerivedFrom", "isBasedOn"}, - {"IsSourceOf", "isBasedOn"}, - {"IsRequiredBy", "isPartOf"}, - {"Requires", "hasPart"}, - {"IsObsoletedBy", "hasPart"}, - {"Obsoletes", "isBasedOn"} - }).collect(Collectors.collectingAndThen( + final Map relationType = Stream.of(new String[][] { + { "IsCitedBy", "isPartOf" }, + { "Cites", "citation" }, + { "IsSupplementTo", "isPartOf" }, + { "IsSupplementedBy", "isPartOf" }, + { "IsContinuedBy", "isPartOf" }, + { "Continues", "isBasedOn" }, + { "IsDescribedBy", "hasPart" }, + { "Describes", "isPartOf" }, + { "HasMetadata", "hasPart" }, + { "IsMetadataFor", "isPartOf" }, + { "HasVersion", "hasPart" }, + { "IsVersionOf", "isPartOf" }, + { "IsNewVersionOf", "isBasedOn" }, + { "IsPreviousVersionOf", "PredecessorOf" }, + { "IsPartOf", "isPartOf" }, + { "HasPart", "hasPart" }, + { "IsPublishedIn", "isPartOf" }, + { "IsReferencedBy", "isPartOf" }, + { "References", "citation" }, + { "IsDocumentedBy", "hasPart" }, + { "Documents", "isPartOf" }, + { "IsCompiledBy", "hasPart" }, + { "Compiles", "isPartOf" }, + { "IsVariantFormOf", "isBasedOn" }, + { "IsOriginalFormOf", "sameAs" }, + { "IsIdenticalTo", "sameAs" }, + { "IsReviewedBy", "hasPart" }, + { "Reviews", "isPartOf" }, + { "IsDerivedFrom", "isBasedOn" }, + { "IsSourceOf", "isBasedOn" }, + { "IsRequiredBy", "isPartOf" }, + { "Requires", "hasPart" }, + { "IsObsoletedBy", "hasPart" }, + { "Obsoletes", "isBasedOn" }, + }).collect( + Collectors.collectingAndThen( Collectors.toMap(data -> data[0], data -> data[1]), - Collections::unmodifiableMap)); + Collections::unmodifiableMap + ) + ); final Collection citation = new HashSet<>(); final Collection hasPart = new HashSet<>(); @@ -193,7 +192,6 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso final Collection IsPartOf = new HashSet<>(); final Collection sameAs = new HashSet<>(); - // the id of the main entity String id = null; var identifiers = jsonNode.get("identifiers"); @@ -207,7 +205,7 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso // main entity type String type = "CreativeWork"; - JsonNode types = jsonNode.get("types"); + JsonValue types = jsonNode.get("types"); var schemaType = types.get("schemaOrg"); if (schemaType != null) { type = schemaType.asText(); @@ -215,7 +213,7 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso // the title String title; - JsonNode titles = jsonNode.get("titles"); + JsonValue titles = jsonNode.get("titles"); if (titles == null || titles.isEmpty()) { // no title title = null; @@ -225,11 +223,11 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso // publicationYear String publicationYear; - JsonNode pubYear = jsonNode.get("publicationYear"); + JsonValue pubYear = jsonNode.get("publicationYear"); publicationYear = pubYear != null ? pubYear.asText() : null; // the creators + their affiliations - JsonNode creators = jsonNode.get("creators"); + JsonValue creators = jsonNode.get("creators"); List creatorsList = new ArrayList<>(); if (creators != null) { for (var e : creators) { @@ -240,15 +238,16 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso // the publisher OrganizationEntity publisher = null; - JsonNode publisherNode = jsonNode.get("publisher"); + JsonValue publisherNode = jsonNode.get("publisher"); if (publisherNode != null && publisherNode.isTextual()) { publisher = new OrganizationEntity.OrganizationEntityBuilder() - .addProperty("name", publisherNode.asText()).build(); + .addProperty("name", publisherNode.asText()) + .build(); entityList.add(publisher); } // contributors - JsonNode contributors = jsonNode.get("contributors"); + JsonValue contributors = jsonNode.get("contributors"); List contributorsList = new ArrayList<>(); if (contributors != null) { for (var e : contributors) { @@ -258,8 +257,8 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso } // description - ArrayNode descriptionArray = objectMapper.createArrayNode(); - JsonNode descriptionNode = jsonNode.get("descriptions"); + JsonArray descriptionArray = Json.arrayNode(); + JsonValue descriptionNode = jsonNode.get("descriptions"); if (descriptionNode != null) { for (var e : descriptionNode) { var desc = e.get("description"); @@ -271,7 +270,7 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso String dateCreated = null; String dateModified = null; String datePublished = null; - JsonNode dates = jsonNode.get("dates"); + JsonValue dates = jsonNode.get("dates"); if (dates != null) { for (var el : dates) { String dataType = el.get("dateType").asText(); @@ -298,15 +297,15 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso } // subjects which are mapped to keywords - JsonNode subjects = jsonNode.get("subjects"); - ArrayNode keyWordsArray = objectMapper.createArrayNode(); + JsonValue subjects = jsonNode.get("subjects"); + JsonArray keyWordsArray = Json.arrayNode(); if (subjects != null) { for (var sub : subjects) { keyWordsArray.add(sub.get("subject").asText()); } } - Consumer addRelatedEntity = (entity) -> { + Consumer addRelatedEntity = entity -> { var mapEntry = relationType.get(entity.getProperty("keywords").asText()); if (mapEntry != null) { switch (mapEntry) { @@ -330,32 +329,32 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso }; // relatedIdentifiers - JsonNode related = jsonNode.get("relatedIdentifiers"); + JsonValue related = jsonNode.get("relatedIdentifiers"); if (related != null) { for (var element : related) { String relatedId = element.get("relatedIdentifier").asText(); String relatedIdType = element.get("relatedIdentifierType").asText(); String relationTypeString = element.get("relationType").asText(); DataEntity relatedItem = new DataEntity.DataEntityBuilder() - .addType("CreativeWork") - .setId(relatedId) - .addProperty("description", relatedIdType) - .addProperty("keywords", relationTypeString) - .build(); + .addType("CreativeWork") + .setId(relatedId) + .addProperty("description", relatedIdType) + .addProperty("keywords", relationTypeString) + .build(); entityList.add(relatedItem); addRelatedEntity.accept(relatedItem); } } - // geolocations - JsonNode geo = jsonNode.get("geoLocations"); + JsonValue geo = jsonNode.get("geoLocations"); Collection geoSet = new HashSet<>(); if (geo != null) { for (var geoThing : geo) { // geo point - ContextualEntity geoEntity = new ContextualEntity.ContextualEntityBuilder() + ContextualEntity geoEntity = + new ContextualEntity.ContextualEntityBuilder() .addType("Place") .build(); @@ -367,10 +366,10 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso if (geoThing.get("geoLocationPoint") != null) { var point = geoThing.get("geoLocationPoint"); var geoCoordinate = new ContextualEntity.ContextualEntityBuilder() - .addType("GeoCoordinates") - .addProperty("latitude", point.get("pointLatitude")) - .addProperty("longitude", point.get("pointLongitude")) - .build(); + .addType("GeoCoordinates") + .addProperty("latitude", point.get("pointLatitude")) + .addProperty("longitude", point.get("pointLongitude")) + .build(); entityList.add(geoCoordinate); geoEntity.addIdProperty("geo", geoCoordinate.getId()); } @@ -384,9 +383,14 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso String topRightLongitude = box.get("eastBoundLongitude").asText(); String topRightLatitude = box.get("northBoundLatitude").asText(); - boxString = bottomLeftLongitude + "," + bottomLeftLatitude + " " - + topRightLongitude + "," + topRightLatitude; - + boxString = + bottomLeftLongitude + + "," + + bottomLeftLatitude + + " " + + topRightLongitude + + "," + + topRightLatitude; } if (geoThing.get("geoLocationPolygon") != null) { StringBuilder stringBuilder = new StringBuilder(); @@ -394,13 +398,18 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso var point = polygonEl.get("polygonPoint"); String longitude = point.get("pointLongitude").asText(); String latitude = point.get("pointLatitude").asText(); - stringBuilder.append(longitude).append(",").append(latitude).append(" "); + stringBuilder + .append(longitude) + .append(",") + .append(latitude) + .append(" "); } polygonString = stringBuilder.toString(); } if (boxString != null || polygonString != null) { - ContextualEntity shapeEntity = new ContextualEntity.ContextualEntityBuilder() + ContextualEntity shapeEntity = + new ContextualEntity.ContextualEntityBuilder() .addType("GeoShape") .addProperty("box", boxString) .addProperty("box", polygonString) @@ -420,7 +429,7 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso } // alternateIdentifier - ArrayNode alternate = objectMapper.createArrayNode(); + JsonArray alternate = Json.arrayNode(); if (jsonNode.get("alternateIdentifiers") != null) { for (var el : jsonNode) { alternate.add(el.get("alternateIdentifier").asText()); @@ -428,15 +437,15 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso } // size - ArrayNode sizes = null; + JsonArray sizes = null; if (jsonNode.get("sizes") != null) { - sizes = (ArrayNode) jsonNode.get("sizes"); + sizes = (JsonArray) jsonNode.get("sizes"); } // format - ArrayNode formats = null; + JsonArray formats = null; if (jsonNode.get("formats") != null) { - formats = (ArrayNode) jsonNode.get("formats"); + formats = (JsonArray) jsonNode.get("formats"); } // rights @@ -458,7 +467,8 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso rightsIdentifier = element.get("rightsIdentifier").asText(); } - ContextualEntity license = new ContextualEntity.ContextualEntityBuilder() + ContextualEntity license = + new ContextualEntity.ContextualEntityBuilder() .addType("CreativeWork") .addProperty("name", licenseName) .setId(rightsUri) @@ -475,7 +485,6 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso Set funderSet = new HashSet<>(); Set grandSet = new HashSet<>(); if (jsonNode.get(fundingNameString) != null) { - for (var el : jsonNode.get(fundingNameString)) { var funderId = el.get("funderIdentifierType"); PersonEntity funder; @@ -483,10 +492,13 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso funder = OrcidProvider.getPerson(funderId.asText()); } else { funder = new PersonEntity.PersonEntityBuilder() - .addProperty("name", el.get("funderName")) - .setId(el.get("funderIdentifier") == null - ? null : el.get("funderIdentifier").asText()) - .build(); + .addProperty("name", el.get("funderName")) + .setId( + el.get("funderIdentifier") == null + ? null + : el.get("funderIdentifier").asText() + ) + .build(); } funderSet.add(funder); entityList.add(funder); @@ -496,7 +508,8 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso var awardTitle = el.get("awardTitle"); var awardNumber = el.get("awardNumber"); if (awardNumber != null || awardTitle != null || awardUri != null) { - ContextualEntity grant = new ContextualEntity.ContextualEntityBuilder() + ContextualEntity grant = + new ContextualEntity.ContextualEntityBuilder() .addType("Grant") .setId(awardUri == null ? null : awardUri.asText()) .addProperty("name", awardTitle) @@ -520,53 +533,55 @@ private static List getEntitiesFromDataCiteResource(JsonNode jso } } DataEntity dataEntity = new DataEntity.DataEntityBuilder() - .setId(id) - .addType(type) - .addProperty("title", title) - .addProperty("publicationYear", publicationYear) - .addIdProperty("publisher", publisher) - .addIdFromCollectionOfEntities("creator", creatorsList) - .addIdFromCollectionOfEntities("contributor", contributorsList) - .addIdFromCollectionOfEntities("spatialCoverage", geoSet) - .addIdFromCollectionOfEntities("license", licenses) - .addIdFromCollectionOfEntities("funder", funderSet) - .addIdFromCollectionOfEntities("funding", grandSet) - .addIdFromCollectionOfEntities("isPartOf", IsPartOf) - .addIdFromCollectionOfEntities("citation", citation) - .addIdFromCollectionOfEntities("hasPart", hasPart) - .addIdFromCollectionOfEntities("isBasedOn", IsBasedOn) - .addIdFromCollectionOfEntities("sameAs", sameAs) - .addProperty("description", descriptionArray) - .addProperty("dateCreated", dateCreated) - .addProperty("dateModified", dateModified) - .addProperty(PROPTERY_DATE_PUBLISHED, datePublished) - .addProperty("keywords", keyWordsArray) - .addProperty("inLanguage", language) - .addProperty("identifier", alternate) - .addProperty("size", sizes) - .addProperty("encodingFormat", formats) - .addProperty("version", jsonNode.get("version")) - .build(); + .setId(id) + .addType(type) + .addProperty("title", title) + .addProperty("publicationYear", publicationYear) + .addIdProperty("publisher", publisher) + .addIdFromCollectionOfEntities("creator", creatorsList) + .addIdFromCollectionOfEntities("contributor", contributorsList) + .addIdFromCollectionOfEntities("spatialCoverage", geoSet) + .addIdFromCollectionOfEntities("license", licenses) + .addIdFromCollectionOfEntities("funder", funderSet) + .addIdFromCollectionOfEntities("funding", grandSet) + .addIdFromCollectionOfEntities("isPartOf", IsPartOf) + .addIdFromCollectionOfEntities("citation", citation) + .addIdFromCollectionOfEntities("hasPart", hasPart) + .addIdFromCollectionOfEntities("isBasedOn", IsBasedOn) + .addIdFromCollectionOfEntities("sameAs", sameAs) + .addProperty("description", descriptionArray) + .addProperty("dateCreated", dateCreated) + .addProperty("dateModified", dateModified) + .addProperty(PROPTERY_DATE_PUBLISHED, datePublished) + .addProperty("keywords", keyWordsArray) + .addProperty("inLanguage", language) + .addProperty("identifier", alternate) + .addProperty("size", sizes) + .addProperty("encodingFormat", formats) + .addProperty("version", jsonNode.get("version")) + .build(); entityList.add(dataEntity); return entityList; } // here one can map also all the other properties of relatedItem if necessary - private static DataEntity getFromRelatedItem(JsonNode relatedItem) { + private static DataEntity getFromRelatedItem(JsonValue relatedItem) { var relatedId = relatedItem.get("relatedIdentifier"); String relatedIdType = relatedItem.get("relatedIdentifierType").asText(); String relationTypeString = relatedItem.get("relationType").asText(); return new DataEntity.DataEntityBuilder() - .addType("CreativeWork") - .setId(relatedId == null ? null : relatedId.asText()) - .addProperty("description", relatedIdType) - .addProperty("keywords", relationTypeString) - .build(); + .addType("CreativeWork") + .setId(relatedId == null ? null : relatedId.asText()) + .addProperty("description", relatedIdType) + .addProperty("keywords", relationTypeString) + .build(); } - private static AbstractEntity addPersonToListOfEntities(JsonNode personNode, - Collection entities) { + private static AbstractEntity addPersonToListOfEntities( + JsonValue personNode, + Collection entities + ) { // if there is an Orcid provider use it to get the entity directly from orcid var creatorIdentifiers = personNode.get("nameIdentifiers"); PersonEntity person = null; @@ -574,7 +589,9 @@ private static AbstractEntity addPersonToListOfEntities(JsonNode personNode, if (creatorIdentifiers != null && !creatorIdentifiers.isEmpty()) { for (var identifier : creatorIdentifiers) { if (identifier.get("nameIdentifierScheme").asText().equals("ORCID")) { - person = OrcidProvider.getPerson(identifier.get("nameIdentifier").asText()); + person = OrcidProvider.getPerson( + identifier.get("nameIdentifier").asText() + ); } else { personUrl = identifier.get("nameIdentifier").asText(); } @@ -583,11 +600,11 @@ private static AbstractEntity addPersonToListOfEntities(JsonNode personNode, if (person == null) { person = new PersonEntity.PersonEntityBuilder() - .addProperty("name", personNode.get("creatorName")) - .addProperty("givenName", personNode.get("givenName")) - .addProperty("familyName", personNode.get("familyName")) - .addProperty("url", personUrl) - .build(); + .addProperty("name", personNode.get("creatorName")) + .addProperty("givenName", personNode.get("givenName")) + .addProperty("familyName", personNode.get("familyName")) + .addProperty("url", personUrl) + .build(); } // get the person affiliations @@ -605,17 +622,22 @@ private static AbstractEntity addPersonToListOfEntities(JsonNode personNode, organization = RorProvider.getOrganization(affiliationId.asText()); } else { organization = new OrganizationEntity.OrganizationEntityBuilder() - .setId(affiliationId.asText()) - .addProperty("name", affiliationName) - .build(); + .setId(affiliationId.asText()) + .addProperty("name", affiliationName) + .build(); } organizationEntitySet.add(organization); } } - person.addIdListProperties("affiliation", - organizationEntitySet.stream().map(AbstractEntity::getId).collect(Collectors.toList())); + person.addIdListProperties( + "affiliation", + organizationEntitySet + .stream() + .map(AbstractEntity::getId) + .collect(Collectors.toList()) + ); entities.addAll(organizationEntitySet); entities.add(person); return person; } -} \ No newline at end of file +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java similarity index 74% rename from src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java index 4a99ee8a..eb54569f 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/dataentities/ImportFromZenodo.java @@ -3,21 +3,17 @@ import com.apicatalog.jsonld.JsonLd; import com.apicatalog.jsonld.JsonLdError; import com.apicatalog.jsonld.document.JsonDocument; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.Crate; import edu.kit.datamanager.ro_crate.RoCrate; import edu.kit.datamanager.ro_crate.RoCrate.RoCrateBuilder; import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; import java.io.ByteArrayInputStream; import java.io.IOException; import java.nio.charset.StandardCharsets; import java.util.Optional; - import org.apache.http.HttpHeaders; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; @@ -45,12 +41,12 @@ private ImportFromZenodo() {} * @return the created crate. */ public static Crate createCrateWithItem( - String url, - Optional name, - Optional description, - Optional datePublished, - Optional licenseId) { - + String url, + Optional name, + Optional description, + Optional datePublished, + Optional licenseId + ) { RoCrateBuilder builder = new RoCrate.RoCrateBuilder(); name.ifPresent(builder::addName); description.ifPresent(builder::addDescription); @@ -67,40 +63,48 @@ public static void addZenodoToCrate(String ulr, Crate crate) { } private static void addToCrateFromZotero(String url, Crate crate) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); CloseableHttpClient httpClient = HttpClients.createDefault(); HttpGet requestZenodo = new HttpGet(url); // HttpGet requestSchema= new HttpGet("https://www.researchobject.org/ro-crate/1.1/context.jsonld"); - HttpGet requestSchema = new HttpGet("https://schema.org/docs/jsonldcontext.json"); + HttpGet requestSchema = new HttpGet( + "https://schema.org/docs/jsonldcontext.json" + ); requestZenodo.addHeader(HttpHeaders.ACCEPT, "application/ld+json"); - ObjectNode jsonNode; + JsonObject jsonNode; String mainId; try { CloseableHttpResponse response = httpClient.execute(requestZenodo); var stream = response.getEntity().getContent(); // get the item of the main entity - jsonNode = (ObjectNode) objectMapper.readTree(stream); + jsonNode = (JsonObject) Json.parse(stream); mainId = jsonNode.get("@id").asText(); - final var el = JsonLd.flatten(JsonDocument.of( - new ByteArrayInputStream( - jsonNode.toString().getBytes(StandardCharsets.UTF_8)))).get(); + final var el = JsonLd.flatten( + JsonDocument.of( + new ByteArrayInputStream( + jsonNode.toString().getBytes(StandardCharsets.UTF_8) + ) + ) + ).get(); CloseableHttpResponse schema = httpClient.execute(requestSchema); - ObjectNode doc = (ObjectNode) objectMapper.readTree(schema.getEntity().getContent()); - var con = (ObjectNode) doc.get("@context"); + JsonObject doc = (JsonObject) Json.parse(schema.getEntity().getContent()); + var con = (JsonObject) doc.get("@context"); con.remove("type"); con.remove("id"); doc.set("@context", con); var finalVersion = JsonLd.compact( - JsonDocument.of(el), - JsonDocument.of(new ByteArrayInputStream( - doc.toString().getBytes(StandardCharsets.UTF_8)))).get(); - - - jsonNode = (ObjectNode) objectMapper.readTree(finalVersion.toString()); + JsonDocument.of(el), + JsonDocument.of( + new ByteArrayInputStream( + doc.toString().getBytes(StandardCharsets.UTF_8) + ) + ) + ).get(); + + jsonNode = (JsonObject) Json.parse(finalVersion.toString()); } catch (IOException | JsonLdError e) { e.printStackTrace(); return; @@ -112,12 +116,14 @@ private static void addToCrateFromZotero(String url, Crate crate) { for (var entity : graph) { if (entity.get("@id").asText().equals(mainId)) { var dataEntity = new DataEntity.DataEntityBuilder() - .setAllUnsafe((ObjectNode) entity).build(); + .setAllUnsafe((JsonObject) entity) + .build(); crate.addDataEntity(dataEntity); } else { // here we have to think of a way to differentiate between data and contextual entities. var contextualEntity = new ContextualEntity.ContextualEntityBuilder() - .setAllUnsafe((ObjectNode) entity).build(); + .setAllUnsafe((JsonObject) entity) + .build(); crate.addContextualEntity(contextualEntity); } } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java new file mode 100644 index 00000000..910c3d10 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java @@ -0,0 +1,94 @@ +package edu.kit.datamanager.ro_crate.externalproviders.organizationprovider; + +import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import org.apache.http.HttpStatus; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Class providing possibility to import organization entities from ror.com. + */ +public class RorProvider { + + private static final Logger logger = LoggerFactory.getLogger( + RorProvider.class + ); + + private RorProvider() {} + + /** + * The method that parses a ror entry to a crate entity. + * + * @param url the url of the ror entry. + * @return the created Organization entity. + */ + public static OrganizationEntity getOrganization(String url) { + if (!url.startsWith("https://ror.org/")) { + throw new IllegalArgumentException("Should provide ror url"); + } + String newUrl = + "https://api.ror.org/v2/organizations/" + + url.replaceAll("https://ror.org/", ""); + HttpGet request = new HttpGet(newUrl); + + try ( + CloseableHttpClient httpClient = HttpClients.createDefault(); + CloseableHttpResponse response = httpClient.execute(request) + ) { + boolean isError = + response.getStatusLine().getStatusCode() != HttpStatus.SC_OK; + if (isError) { + String errorMessage = String.format( + "Identifier not found: %s", + response.getStatusLine().toString() + ); + logger.error(errorMessage); + return null; + } + JsonObject jsonNode = (JsonObject) Json.parse( + response.getEntity().getContent() + ); + + return new OrganizationEntity.OrganizationEntityBuilder() + .setId(jsonNode.path("id").asText()) + .addProperty("name", getOrganizationNameV2(jsonNode.path("names"))) + .addProperty("email", jsonNode.path("email_address")) + .addProperty("url", jsonNode.path("id").asText()) + .build(); + } catch (IOException e) { + String errorMessage = String.format("IO error: %s", e.getMessage()); + logger.error(errorMessage); + } + return null; + } + + private static String getOrganizationNameV2(JsonValue node) { + if (node.isArray()) { + for (JsonValue n : node) { + if (n.has("types") && n.path("types").isArray()) { + List l = new ArrayList<>(); + for (JsonValue type : n.path("types")) { + l.add(type.asText()); + } + if (l.contains("ror_display")) { + return n.path("value").asText(); + } + } + } + //fallback + return node.path(0).path("value").asText(); + } else { + return node.asText(); + } + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java similarity index 67% rename from src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java index 17207993..0b3da65b 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/personprovider/OrcidProvider.java @@ -1,13 +1,10 @@ package edu.kit.datamanager.ro_crate.externalproviders.personprovider; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.entities.contextual.PersonEntity; import edu.kit.datamanager.ro_crate.entities.validation.EntityValidation; -import edu.kit.datamanager.ro_crate.entities.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.validation.Validation; import java.io.IOException; import org.apache.http.HttpHeaders; import org.apache.http.HttpStatus; @@ -48,23 +45,32 @@ public static PersonEntity getPerson(String url) { CloseableHttpClient httpClient = HttpClients.createDefault(); CloseableHttpResponse response = httpClient.execute(request); ) { - boolean isError = response.getStatusLine().getStatusCode() != HttpStatus.SC_OK; - String receivedMimeType = ContentType.parse(response.getFirstHeader(HttpHeaders.CONTENT_TYPE).getValue()).getMimeType(); - boolean isUnexpectedFormat = response.containsHeader(HttpHeaders.CONTENT_TYPE) - && !receivedMimeType.equals("application/ld+json"); + boolean isError = + response.getStatusLine().getStatusCode() != HttpStatus.SC_OK; + String receivedMimeType = ContentType.parse( + response.getFirstHeader(HttpHeaders.CONTENT_TYPE).getValue() + ).getMimeType(); + boolean isUnexpectedFormat = + response.containsHeader(HttpHeaders.CONTENT_TYPE) && + !receivedMimeType.equals("application/ld+json"); if (isError || isUnexpectedFormat) { - String errorMessage = String.format("Identifier not found: %s", response.getStatusLine().toString()); + String errorMessage = String.format( + "Identifier not found: %s", + response.getStatusLine().toString() + ); logger.error(errorMessage); return null; } - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode jsonNode = objectMapper.readValue(response.getEntity().getContent(), - ObjectNode.class); + JsonObject jsonNode = (JsonObject) Json.parse( + response.getEntity().getContent() + ); jsonNode.remove("@reverse"); jsonNode.remove("@context"); - ObjectNode node = objectMapper.createObjectNode(); - EntityValidation entityValidation = new EntityValidation(new JsonSchemaValidation()); + JsonObject node = Json.objectNode(); + EntityValidation entityValidation = new EntityValidation( + Validation.entityStrategy() + ); var itr = jsonNode.fields(); while (itr.hasNext()) { var element = itr.next(); diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java new file mode 100644 index 00000000..5552972c --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java @@ -0,0 +1,203 @@ +package edu.kit.datamanager.ro_crate.hierarchy; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; +import edu.kit.datamanager.ro_crate.util.FileSystemUtil; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; + +public class HierarchyRecognition { + + protected final Crate crate; + protected final HierarchyRecognitionConfig config; + + public HierarchyRecognition(Crate crate, HierarchyRecognitionConfig config) { + this.crate = crate; + this.config = config; + } + + public HierarchyRecognitionResult buildHierarchy() { + HierarchyRecognitionResult result = new HierarchyRecognitionResult(); + + try { + // Get all data entities to process + Set allEntities = this.crate.getAllDataEntities(); + allEntities.add(crate.getRootDataEntity()); + + // Filter entities with file path IDs (not URLs, DOIs, etc.) + Map pathEntities = new HashMap<>(); + for (DataEntity entity : allEntities) { + String id = entity.getId(); + if (FileSystemUtil.isFilePath(id)) { + pathEntities.put(id, entity); + } else { + result.addSkippedEntity(entity); + } + } + + // Validate hierarchy before making changes + if (!HierarchyRecognition.validateHierarchy(pathEntities, result)) { + return result; + } + + // Create missing intermediate entities if configured + if (config.createMissingIntermediateEntities()) { + this.createMissingIntermediateEntities(pathEntities, result); + } + + // Clear existing relationships if configured + if (config.removeExistingConnections()) { + this.clearExistingRelationships(pathEntities); + } + + // Build hierarchy relationships + this.buildHierarchyRelationships(pathEntities, config, result); + + return result; + } catch (Exception e) { + result.addError( + "Unexpected error during hierarchy recognition: " + e.getMessage() + ); + return result; + } + } + + /** + * Validates that the hierarchy is consistent (no files containing other files/folders). + * + * @param pathEntities map of path IDs to DataEntities + * @param result builder to collect errors + * @return true if valid, false if invalid hierarchy detected + */ + protected static boolean validateHierarchy( + Map pathEntities, + HierarchyRecognitionResult result + ) { + for (Map.Entry entry : pathEntities.entrySet()) { + String childId = entry.getKey(); + String parentPath = FileSystemUtil.getParentPath(childId); + if (parentPath == null || parentPath.equals("./")) { + continue; + } + + // Check both with and without trailing slash since files don't have slash but folders do + DataEntity parentEntity = pathEntities.get(parentPath); + if (parentEntity == null) { + parentEntity = pathEntities.get(parentPath + "/"); + } + + if (parentEntity == null) { + continue; + } + + // Check for invalid hierarchy: file cannot contain another file/folder + if (parentEntity.getTypes().contains("File")) { + result.addError( + "Invalid hierarchy: file '" + + parentEntity.getId() + + "' cannot contain '" + + childId + + "'" + ); + return false; + } + } + return true; + } + + /** + * Creates missing intermediate DataSetEntity instances for folder paths. + * + * @param pathEntities map of path IDs to DataEntities + * @param result builder to collect created entities + */ + protected void createMissingIntermediateEntities( + Map pathEntities, + HierarchyRecognitionResult result + ) { + Set missingPaths = new HashSet<>(); + + // Find all missing intermediate paths + for (String path : pathEntities.keySet()) { + String parentPath = FileSystemUtil.getParentPath(path); + while (parentPath != null && !parentPath.equals("./")) { + String folderPath = parentPath + "/"; + final boolean containsParent = pathEntities.containsKey(parentPath); + final boolean containsFolder = pathEntities.containsKey(folderPath); + if (!containsParent && !containsFolder) { + missingPaths.add(folderPath); + } + parentPath = FileSystemUtil.getParentPath(parentPath); + } + } + + // Create missing DataSetEntity instances + for (String missingPath : missingPaths) { + DataSetEntity newEntity = new DataSetEntity.DataSetBuilder() + .setId(missingPath) + .addProperty("name", "Auto-generated folder: " + missingPath) + .build(); + + this.crate.addDataEntity(newEntity); + pathEntities.put(missingPath, newEntity); + result.addCreatedEntity(newEntity); + } + } + + protected void buildHierarchyRelationships( + Map pathEntities, + HierarchyRecognitionConfig config, + HierarchyRecognitionResult result + ) { + for (Map.Entry entry : pathEntities.entrySet()) { + String childId = entry.getKey(); + DataEntity childEntity = entry.getValue(); + String parentPath = FileSystemUtil.getParentPath(childId); + if (parentPath == null) { + continue; + } + + // Check both with and without trailing slash since files don't have slash but folders do + DataEntity parentEntity = pathEntities.get(parentPath); + String actualParentId = parentPath; + + if (parentEntity == null) { + parentEntity = pathEntities.get(parentPath + "/"); + actualParentId = parentPath + "/"; + } + + if (parentEntity == null) { + continue; + } + + // Add hasPart relationship + if (parentEntity instanceof DataSetEntity) { + ((DataSetEntity) parentEntity).addToHasPart(childId); + result.addProcessedRelationship(actualParentId, childId); + } + + // Add isPartOf relationship if configured + if (config.createInverseRelationships()) { + childEntity.addProperty("isPartOf", actualParentId); + } + + // Remove from root if it has a parent that is not root + if (!parentPath.equals("./")) { + this.crate.getRootDataEntity().removeFromHasPart(childId); + } + } + } + + protected void clearExistingRelationships( + Map pathEntities + ) { + for (DataEntity entity : pathEntities.values()) { + if (entity instanceof DataSetEntity) { + ((DataSetEntity) entity).hasPart.clear(); + } + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java new file mode 100644 index 00000000..28eaa57c --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java @@ -0,0 +1,59 @@ +package edu.kit.datamanager.ro_crate.hierarchy; + +/** + * Configuration class for automatic hierarchy recognition. + * This class provides control over how the hierarchy recognition. + * + *

    + *
  • createMissingIntermediateEntities: Whether missing intermediate folder entities should be automatically created. Default: false
    • + *
  • createInverseRelationships: Whether isPartOf relationships should be added in addition to hasPart. Default: false
    • + *
  • removeExistingConnections: Whether hasPart relationships should be added (false) or remove existing relations in beforehand (true). Default: false
    • + *
+ */ +public record HierarchyRecognitionConfig( + boolean createMissingIntermediateEntities, + boolean createInverseRelationships, + boolean removeExistingConnections +) { + /** + * Creates a new configuration with default values. + *

+ * Default values: + *

    + *
  • createMissingIntermediateEntities: false
    • + *
  • createInverseRelationships: false
    • + *
  • removeExistingConnections: false
    • + *
+ */ + public HierarchyRecognitionConfig() { + this(false, false, false); + } + + public HierarchyRecognitionConfig withCreateMissingIntermediateEntities( + boolean value + ) { + return new HierarchyRecognitionConfig( + value, + this.createInverseRelationships, + this.removeExistingConnections + ); + } + + public HierarchyRecognitionConfig withSetInverseRelationships(boolean value) { + return new HierarchyRecognitionConfig( + this.createMissingIntermediateEntities, + value, + this.removeExistingConnections + ); + } + + public HierarchyRecognitionConfig withRemoveExistingConnections( + boolean value + ) { + return new HierarchyRecognitionConfig( + this.createMissingIntermediateEntities, + this.createInverseRelationships, + value + ); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java new file mode 100644 index 00000000..855cdbab --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java @@ -0,0 +1,56 @@ +package edu.kit.datamanager.ro_crate.hierarchy; + +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; +import java.util.*; + +/** + * Result class containing information about the automatic hierarchy recognition operation. + * This class provides details about what was processed, created, and any issues encountered + * during the hierarchy recognition process. Always contains complete information about the + * operation result, including success/failure and any errors encountered. + */ +public record HierarchyRecognitionResult( + Set createdEntities, + Map> processedRelationships, + Set skippedEntities, + List warnings, + List errors +) { + HierarchyRecognitionResult() { + this( + new HashSet<>(), + new HashMap<>(), + new HashSet<>(), + new ArrayList<>(), + new ArrayList<>() + ); + } + + /** + * Whether there were no errors during the hierarchy recognition operation. + * + * @return true if the operation completed successfully (no errors), false otherwise. + */ + public boolean isSuccessful() { + return this.errors.isEmpty(); + } + + public void addSkippedEntity(DataEntity entity) { + this.skippedEntities.add(entity); + } + + public void addError(String errorMessage) { + this.errors.add(errorMessage); + } + + public void addCreatedEntity(DataSetEntity newEntity) { + this.createdEntities.add(newEntity); + } + + public void addProcessedRelationship(String from, String to) { + this.processedRelationships + .computeIfAbsent(from, k -> new HashSet<>()) + .add(to); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java similarity index 90% rename from src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java index 5d8f119f..6758294e 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/package-info.java @@ -6,4 +6,4 @@ * class, which analyzes the paths of data entities and establishes appropriate * "hasPart" and "isPartOf" relationships to reflect the underlying file system structure. */ -package edu.kit.datamanager.ro_crate.hierarchy; \ No newline at end of file +package edu.kit.datamanager.ro_crate.hierarchy; diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/Json.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/Json.java new file mode 100644 index 00000000..02eabe6a --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/Json.java @@ -0,0 +1,107 @@ +package edu.kit.datamanager.ro_crate.json; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.util.Iterator; +import java.util.ServiceLoader; + +/** + * Static access point to the JSON operations of the neutral tree model. + * + *

The concrete {@link JsonAdapter} (Jackson 2 or Jackson 3) is discovered + * via {@link ServiceLoader}; exactly one adapter must be on the classpath. + * Shading users or special setups can override discovery with + * {@link #setAdapter}. + */ +public final class Json { + + private static volatile JsonAdapter adapter; + + private Json() {} + + public static JsonAdapter adapter() { + JsonAdapter result = adapter; + if (result == null) { + synchronized (Json.class) { + result = adapter; + if (result == null) { + adapter = result = discoverAdapter(); + } + } + } + return result; + } + + /** Overrides adapter discovery; intended for tests and shaded builds. */ + public static void setAdapter(JsonAdapter replacement) { + adapter = replacement; + } + + private static JsonAdapter discoverAdapter() { + return uniqueCandidate( + ServiceLoader.load(JsonAdapter.class).iterator(), + JsonAdapter.class + ); + } + + /** + * Returns the single candidate or throws an exception that names the + * backend artifacts to add or exclude, so users who do not know the module + * layout can fix the classpath themselves. + */ + static T uniqueCandidate(Iterator candidates, Class type) { + if (!candidates.hasNext()) { + throw new IllegalStateException( + "No " + + type.getSimpleName() + + " found on the classpath. Add a JSON " + + "backend as a dependency: edu.kit.datamanager:ro-crate-java " + + "(Jackson 2 backend) or edu.kit.datamanager:ro-crate-java-jackson3 " + + "(Jackson 3 backend)." + ); + } + T discovered = candidates.next(); + if (candidates.hasNext()) { + throw new IllegalStateException( + "Multiple " + + type.getSimpleName() + + " implementations found on the " + + "classpath; ro-crate-java supports only one JSON backend at a " + + "time. Keep the backend matching your Jackson version and exclude " + + "the other one, e.g. exclude edu.kit.datamanager:ro-crate-java " + + "(Jackson 2 backend) and add " + + "edu.kit.datamanager:ro-crate-java-jackson3 (Jackson 3 backend)." + ); + } + return discovered; + } + + public static JsonObject objectNode() { + return adapter().objectNode(); + } + + public static JsonArray arrayNode() { + return adapter().arrayNode(); + } + + public static JsonValue parse(String json) throws IOException { + return adapter().parse(json); + } + + public static JsonValue parse(File file) throws IOException { + return adapter().parse(file); + } + + public static JsonValue parse(InputStream stream) throws IOException { + return adapter().parse(stream); + } + + public static String write(JsonValue value) throws IOException { + return adapter().write(value); + } + + public static String writePretty(JsonValue value) throws IOException { + return adapter().writePretty(value); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonAdapter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonAdapter.java new file mode 100644 index 00000000..0a6fffad --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonAdapter.java @@ -0,0 +1,32 @@ +package edu.kit.datamanager.ro_crate.json; + +import java.io.File; +import java.io.IOException; +import java.io.InputStream; + +/** + * The SPI through which the Jackson-free core talks to a concrete JSON + * implementation (Jackson 2 or Jackson 3). + * + *

Implementations must provide an adapter on the classpath and register it + * via {@code META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter} + * (see {@link Json}). + */ +public interface JsonAdapter { + JsonObject objectNode(); + + JsonArray arrayNode(); + + /** Parses JSON text into the neutral tree model. */ + JsonValue parse(String json) throws IOException; + + JsonValue parse(File file) throws IOException; + + JsonValue parse(InputStream stream) throws IOException; + + /** Serializes a neutral tree to compact JSON text. */ + String write(JsonValue value) throws IOException; + + /** Serializes a neutral tree to pretty-printed JSON text. */ + String writePretty(JsonValue value) throws IOException; +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonArray.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonArray.java new file mode 100644 index 00000000..9553dbb2 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonArray.java @@ -0,0 +1,119 @@ +package edu.kit.datamanager.ro_crate.json; + +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.stream.Stream; + +/** + * The JSON array value: a mutable, order-preserving list of values. Mirrors + * Jackson's {@code ArrayNode} API for the operations the library uses. + */ +public final class JsonArray extends JsonValue { + + private final List items = new ArrayList<>(); + + /** @return a new empty array (the neutral equivalent of createArrayNode) */ + public static JsonArray create() { + return new JsonArray(); + } + + // -- construction / mutation ------------------------------------------------ + + public JsonArray add(JsonValue value) { + // mirrors Jackson's ArrayNode.add: a null argument becomes a null node + items.add(value == null ? JsonNull.INSTANCE : value); + return this; + } + + public JsonArray add(String value) { + return add(value == null ? JsonNull.INSTANCE : new JsonString(value)); + } + + public JsonArray add(long value) { + return add(new JsonNumber(value)); + } + + public JsonArray add(double value) { + return add(new JsonNumber(value)); + } + + public JsonArray add(boolean value) { + return add(JsonBoolean.of(value)); + } + + public JsonArray addAll(JsonArray other) { + items.addAll(other.items); + return this; + } + + /** @return the removed element (mirrors Jackson) */ + public JsonValue remove(int index) { + return items.remove(index); + } + + // -- access ----------------------------------------------------------------- + + public JsonValue get(int index) { + if (index < 0 || index >= items.size()) { + return null; // mirrors Jackson: out-of-bounds yields null + } + return items.get(index); + } + + /** @return the element, or {@link JsonMissing} when out of bounds */ + public JsonValue path(int index) { + JsonValue value = get(index); + return value == null ? JsonMissing.INSTANCE : value; + } + + @Override + public int size() { + return items.size(); + } + + public boolean isEmpty() { + return items.isEmpty(); + } + + @Override + public Iterator iterator() { + return List.copyOf(items).iterator(); + } + + @Override + public Stream valueStream() { + return List.copyOf(items).stream(); + } + + // -- tree operations -------------------------------------------------------- + + @Override + public JsonArray deepCopy() { + JsonArray copy = new JsonArray(); + for (JsonValue item : items) { + copy.add(item.deepCopy()); + } + return copy; + } + + @Override + public boolean isArray() { + return true; + } + + @Override + public String asText() { + return ""; + } + + @Override + public boolean equals(Object obj) { + return obj instanceof JsonArray other && items.equals(other.items); + } + + @Override + public int hashCode() { + return items.hashCode(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonBoolean.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonBoolean.java new file mode 100644 index 00000000..dfb21fb5 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonBoolean.java @@ -0,0 +1,52 @@ +package edu.kit.datamanager.ro_crate.json; + +/** The JSON boolean value. */ +public final class JsonBoolean extends JsonValue { + + public static final JsonBoolean TRUE = new JsonBoolean(true); + public static final JsonBoolean FALSE = new JsonBoolean(false); + + private final boolean value; + + private JsonBoolean(boolean value) { + this.value = value; + } + + public static JsonBoolean of(boolean value) { + return value ? TRUE : FALSE; + } + + public boolean getValue() { + return value; + } + + @Override + public boolean isValueNode() { + return true; + } + + @Override + public boolean isBoolean() { + return true; + } + + @Override + public String asText() { + return Boolean.toString(value); + } + + @Override + public JsonBoolean deepCopy() { + return this; // immutable + } + + @Override + public boolean equals(Object obj) { + return obj instanceof JsonBoolean other && other.value == value; + } + + @Override + public int hashCode() { + return Boolean.hashCode(value); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonMissing.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonMissing.java new file mode 100644 index 00000000..173bc0ec --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonMissing.java @@ -0,0 +1,48 @@ +package edu.kit.datamanager.ro_crate.json; + +/** + * The result of {@link JsonObject#path(String)} for absent keys, mirroring + * Jackson's {@code MissingNode}. + */ +public final class JsonMissing extends JsonValue { + + public static final JsonMissing INSTANCE = new JsonMissing(); + + private JsonMissing() {} + + @Override + public boolean isValueNode() { + return false; + } + + @Override + public boolean isMissing() { + return true; + } + + @Override + public String asText() { + return ""; + } + + /** Mirrors Jackson's {@code MissingNode.asText(default)}: the default. */ + @Override + public String asText(String defaultValue) { + return defaultValue; + } + + @Override + public JsonMissing deepCopy() { + return this; // immutable + } + + @Override + public boolean equals(Object obj) { + return obj instanceof JsonMissing; + } + + @Override + public int hashCode() { + return JsonMissing.class.hashCode(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNull.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNull.java new file mode 100644 index 00000000..11fd51ee --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNull.java @@ -0,0 +1,48 @@ +package edu.kit.datamanager.ro_crate.json; + +/** + * The JSON null value, mirroring Jackson's {@code NullNode}: + * {@link #asText()} returns the string {@code "null"}, while + * {@link #asText(String)} returns the given default. + */ +public final class JsonNull extends JsonValue { + + public static final JsonNull INSTANCE = new JsonNull(); + + private JsonNull() {} + + @Override + public boolean isValueNode() { + return true; + } + + @Override + public boolean isNull() { + return true; + } + + @Override + public String asText() { + return "null"; + } + + @Override + public String asText(String defaultValue) { + return defaultValue; + } + + @Override + public JsonNull deepCopy() { + return this; // immutable + } + + @Override + public boolean equals(Object obj) { + return obj instanceof JsonNull; + } + + @Override + public int hashCode() { + return JsonNull.class.hashCode(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNumber.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNumber.java new file mode 100644 index 00000000..e2e44bb5 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonNumber.java @@ -0,0 +1,61 @@ +package edu.kit.datamanager.ro_crate.json; + +/** + * The JSON number value. + * + *

The original Java number type is preserved (Integer, Long, Double, ...) + * so that serialization stays byte-identical to Jackson's output for the same + * parsed document. Number equality is type-sensitive, mirroring Jackson's + * node equality: {@code 1} (integer) and {@code 1.0} (double) are not equal. + */ +public final class JsonNumber extends JsonValue { + + private final Number value; + + public JsonNumber(Number value) { + if (value == null) { + throw new IllegalArgumentException("JSON numbers cannot be null"); + } + this.value = value; + } + + public Number getValue() { + return value; + } + + @Override + public boolean isValueNode() { + return true; + } + + @Override + public boolean isNumber() { + return true; + } + + @Override + public String asText() { + return String.valueOf(value); + } + + @Override + public JsonNumber deepCopy() { + return this; // immutable + } + + @Override + public boolean equals(Object obj) { + // mirrors Jackson's node equality: numbers are only equal when the Java + // number class matches (IntNode(1) != LongNode(1), != DoubleNode(1.0)) + return ( + obj instanceof JsonNumber other && + value.getClass().equals(other.value.getClass()) && + value.equals(other.value) + ); + } + + @Override + public int hashCode() { + return value.hashCode(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonObject.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonObject.java new file mode 100644 index 00000000..e6175ecf --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonObject.java @@ -0,0 +1,215 @@ +package edu.kit.datamanager.ro_crate.json; + +import java.util.AbstractMap; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Stream; + +/** + * The JSON object value: a mutable, insertion-ordered map from names to + * values. Mirrors Jackson's {@code ObjectNode} API for the operations the + * library uses. + */ +public final class JsonObject extends JsonValue { + + private final List names = new ArrayList<>(); + private final List values = new ArrayList<>(); + + /** @return a new empty object (the neutral equivalent of createObjectNode) */ + public static JsonObject create() { + return new JsonObject(); + } + + // -- construction / mutation ------------------------------------------------ + + public JsonObject put(String name, JsonValue value) { + Objects.requireNonNull(name); + Objects.requireNonNull(value); + int index = names.indexOf(name); + if (index >= 0) { + values.set(index, value); + } else { + names.add(name); + values.add(value); + } + return this; + } + + public JsonObject put(String name, String value) { + return put(name, value == null ? JsonNull.INSTANCE : new JsonString(value)); + } + + public JsonObject put(String name, int value) { + return put(name, new JsonNumber(value)); + } + + public JsonObject put(String name, long value) { + return put(name, new JsonNumber(value)); + } + + public JsonObject put(String name, double value) { + return put(name, new JsonNumber(value)); + } + + public JsonObject put(String name, float value) { + return put(name, new JsonNumber(value)); + } + + public JsonObject put(String name, boolean value) { + return put(name, JsonBoolean.of(value)); + } + + public JsonObject putNull(String name) { + return put(name, JsonNull.INSTANCE); + } + + /** Mirrors Jackson's {@code set}: like {@link #put}, but keeps null values. */ + public JsonObject set(String name, JsonValue value) { + return put(name, value == null ? JsonNull.INSTANCE : value); + } + + /** Copies all entries of {@code other} into this object, in their order. */ + public JsonObject setAll(JsonObject other) { + for (var entry : other.entries()) { + put(entry.getKey(), entry.getValue()); + } + return this; + } + + // -- access ----------------------------------------------------------------- + + /** @return the value, or null when absent (mirrors Jackson's {@code get}) */ + public JsonValue get(String name) { + int index = names.indexOf(name); + return index < 0 ? null : values.get(index); + } + + /** @return the value, or {@link JsonMissing} when absent (mirrors {@code path}) */ + public JsonValue path(String name) { + JsonValue value = get(name); + return value == null ? JsonMissing.INSTANCE : value; + } + + public boolean has(String name) { + return names.contains(name); + } + + /** @return the removed value, or null when absent (mirrors Jackson) */ + public JsonValue remove(String name) { + int index = names.indexOf(name); + if (index < 0) { + return null; + } + names.remove(index); + return values.remove(index); + } + + public void remove(Collection namesToRemove) { + namesToRemove.forEach(this::remove); + } + + public int size() { + return names.size(); + } + + public boolean isEmpty() { + return names.isEmpty(); + } + + /** + * Property names in insertion order, mirroring Jackson's + * {@code fieldNames()} iterator. + */ + public Iterator fieldNames() { + return List.copyOf(names).iterator(); + } + + /** Property names as a list, in insertion order. */ + public List names() { + return List.copyOf(names); + } + + /** Entries in insertion order. */ + public Iterable> entries() { + return new ArrayList<>(namedValues()); + } + + /** + * Mirrors Jackson's {@code fields()}: an iterator over entries in insertion + * order. The iterator does not support removal. + */ + public Iterator> fields() { + return namedValues().iterator(); + } + + /** Property values in insertion order (mirrors Jackson node iteration). */ + @Override + public Iterator iterator() { + return List.copyOf(values).iterator(); + } + + @Override + public Stream valueStream() { + return List.copyOf(values).stream(); + } + + private List> namedValues() { + List> entries = new ArrayList<>(names.size()); + for (int i = 0; i < names.size(); i++) { + entries.add( + new AbstractMap.SimpleImmutableEntry<>(names.get(i), values.get(i)) + ); + } + return entries; + } + + // -- tree operations -------------------------------------------------------- + + @Override + public JsonObject deepCopy() { + JsonObject copy = new JsonObject(); + for (int i = 0; i < names.size(); i++) { + copy.put(names.get(i), values.get(i).deepCopy()); + } + return copy; + } + + @Override + public boolean isObject() { + return true; + } + + @Override + public String asText() { + return ""; + } + + @Override + public boolean equals(Object obj) { + // mirrors Jackson's ObjectNode.equals, which compares the underlying + // LinkedHashMap: order-insensitive, entry-wise structural equality + if (!(obj instanceof JsonObject other) || size() != other.size()) { + return false; + } + for (int i = 0; i < names.size(); i++) { + if (!values.get(i).equals(other.get(names.get(i)))) { + return false; + } + } + return true; + } + + @Override + public int hashCode() { + // mirrors Map.hashCode semantics (order-insensitive) + int hash = 0; + for (int i = 0; i < names.size(); i++) { + hash += names.get(i).hashCode() ^ values.get(i).hashCode(); + } + return hash; + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonString.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonString.java new file mode 100644 index 00000000..cc1ec2c6 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonString.java @@ -0,0 +1,59 @@ +package edu.kit.datamanager.ro_crate.json; + +/** The JSON string value. */ +public final class JsonString extends JsonValue { + + private final String value; + + public JsonString(String value) { + if (value == null) { + throw new IllegalArgumentException("JSON strings cannot be null"); + } + this.value = value; + } + + public String getValue() { + return value; + } + + @Override + public boolean isValueNode() { + return true; + } + + @Override + public boolean isString() { + return true; + } + + @Override + public boolean isTextual() { + return true; + } + + /** Mirrors Jackson's {@code TextNode.isEmpty()}. */ + @Override + public boolean isEmpty() { + return value.isEmpty(); + } + + @Override + public String asText() { + return value; + } + + @Override + public JsonString deepCopy() { + return this; // immutable + } + + @Override + public boolean equals(Object obj) { + return obj instanceof JsonString other && other.value.equals(value); + } + + @Override + public int hashCode() { + return value.hashCode(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonValue.java b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonValue.java new file mode 100644 index 00000000..1eec7e51 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/json/JsonValue.java @@ -0,0 +1,173 @@ +package edu.kit.datamanager.ro_crate.json; + +import java.io.IOException; +import java.util.Collections; +import java.util.Iterator; +import java.util.Map; +import java.util.stream.Stream; + +/** + * A JSON value of the neutral, Jackson-free tree model used inside + * ro-crate-java. + * + *

The API deliberately mirrors the subset of Jackson's {@code JsonNode} + * that the library uses (same method names and semantics), so that domain + * code can be ported mechanically. This is not a general purpose JSON + * library: only the operations the library needs are supported. + * + *

Values are mutable ({@link JsonObject} and {@link JsonArray} can be + * modified in place), preserve insertion order, and implement deep structural + * equality. + */ +public abstract class JsonValue implements Iterable { + + /** + * Returns a deep copy of this value. + * + * @return an independent copy; mutations of the copy do not affect this value + */ + public abstract JsonValue deepCopy(); + + /** + * @return true for string, number, boolean and null values (mirrors Jackson) + */ + public boolean isValueNode() { + return false; + } + + public boolean isObject() { + return false; + } + + public boolean isArray() { + return false; + } + + public boolean isNull() { + return false; + } + + public boolean isString() { + return false; + } + + public boolean isNumber() { + return false; + } + + public boolean isBoolean() { + return false; + } + + /** @return true for the missing value returned by {@link JsonObject#path} */ + public boolean isMissing() { + return false; + } + + /** Mirrors Jackson's {@code isTextual()}. */ + public boolean isTextual() { + return false; + } + + /** + * Mirrors Jackson's {@code get(String)}: null when absent or when this is + * not an object. + */ + public JsonValue get(String name) { + return null; + } + + /** + * Mirrors Jackson's {@code get(int)}: null when out of bounds or when this + * is not an array. + */ + public JsonValue get(int index) { + return null; + } + + /** Mirrors Jackson's {@code has(String)}: false unless this is an object. */ + public boolean has(String name) { + return false; + } + + /** Mirrors Jackson's {@code size()}: 0 unless this is a container. */ + public int size() { + return 0; + } + + /** Mirrors Jackson's {@code isEmpty()}: containers by size, strings by length. */ + public boolean isEmpty() { + return size() == 0; + } + + /** + * Mirrors Jackson's {@code path(String)} on non-container nodes: always the + * missing value. Containers override this. + */ + public JsonValue path(String name) { + return JsonMissing.INSTANCE; + } + + /** + * Mirrors Jackson's {@code path(int)} on non-container nodes: always the + * missing value. Arrays override this. + */ + public JsonValue path(int index) { + return JsonMissing.INSTANCE; + } + + /** + * Mirrors Jackson's {@code fields()}: an entry iterator; empty for + * non-container nodes. + */ + public Iterator> fields() { + return Collections.emptyIterator(); + } + + /** + * Mirrors Jackson's {@code valueStream()}: scalars stream themselves, + * containers stream their values/elements. + */ + public Stream valueStream() { + return Stream.of(this); + } + + /** + * Text representation, mirroring Jackson's {@code asText()} semantics: + * value nodes return their string form, containers return the empty string. + */ + public abstract String asText(); + + /** + * Mirrors Jackson's {@code asText(String defaultValue)}: returns + * {@code defaultValue} when {@link #asText()} would return null, otherwise + * the same as {@link #asText()}. + */ + public String asText(String defaultValue) { + String text = asText(); + return text == null ? defaultValue : text; + } + + /** + * Mirrors Jackson's node iteration (verified against Jackson 2.22.1): + * arrays iterate their elements, objects iterate their values, scalars + * iterate nothing. + */ + @Override + public Iterator iterator() { + return Collections.emptyIterator(); + } + + /** Compact JSON representation, delegated to the active {@link JsonAdapter}. */ + @Override + public String toString() { + try { + return Json.write(this); + } catch (IOException exception) { + throw new java.io.UncheckedIOException( + "Serialization of the JSON tree failed", + exception + ); + } + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java similarity index 92% rename from src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java index 7639ef84..b9b7feca 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/CratePayload.java @@ -1,11 +1,9 @@ package edu.kit.datamanager.ro_crate.payload; -import com.fasterxml.jackson.databind.node.ArrayNode; - import edu.kit.datamanager.ro_crate.entities.AbstractEntity; import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; import edu.kit.datamanager.ro_crate.entities.data.DataEntity; - +import edu.kit.datamanager.ro_crate.json.JsonArray; import java.util.Collection; import java.util.Set; @@ -38,7 +36,7 @@ public interface CratePayload { Set getAllContextualEntities(); - ArrayNode getEntitiesMetadata(); + JsonArray getEntitiesMetadata(); void removeEntityById(String id); } diff --git a/src/main/java/edu/kit/datamanager/ro_crate/payload/EntityObserver.java b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/EntityObserver.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/payload/EntityObserver.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/payload/EntityObserver.java diff --git a/src/main/java/edu/kit/datamanager/ro_crate/payload/Observer.java b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/Observer.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/payload/Observer.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/payload/Observer.java diff --git a/src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java similarity index 78% rename from src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java index bc76d6a2..5db63a61 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/payload/RoCratePayload.java @@ -1,15 +1,11 @@ package edu.kit.datamanager.ro_crate.payload; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - import edu.kit.datamanager.ro_crate.entities.AbstractEntity; import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; - import java.util.*; import java.util.stream.Collectors; @@ -22,8 +18,8 @@ public class RoCratePayload implements CratePayload { private final HashMap contextualEntities; /** - * A map containing for each entity id a set of ids of entities that are linked to it. - * This is used to make the removal of entities from the crate faster. + * A map containing for each entity id a set of ids of entities that are linked to it. + * This is used to make the removal of entities from the crate faster. */ private final HashMap> associatedItems; @@ -123,15 +119,13 @@ public Set getAllContextualEntities() { } @Override - public ArrayNode getEntitiesMetadata() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - - ArrayNode node = objectMapper.createArrayNode(); + public JsonArray getEntitiesMetadata() { + JsonArray node = Json.arrayNode(); for (DataEntity ent : this.getAllDataEntities()) { - node.add(objectMapper.convertValue(ent, ObjectNode.class)); + node.add(ent.toJson()); } for (ContextualEntity ent : this.getAllContextualEntities()) { - node.add(objectMapper.convertValue(ent, ObjectNode.class)); + node.add(ent.toJson()); } return node; } @@ -144,16 +138,19 @@ public void removeEntityById(String id) { } private void removeAllOccurrencesOf(String entityId) { - this.getEntitiesByIds(this.associatedItems.get(entityId)) - .forEach(entity -> JsonUtilFunctions.removeFieldsWith(entityId, entity.getProperties())); + this.getEntitiesByIds(this.associatedItems.get(entityId)).forEach(entity -> + JsonUtilFunctions.removeFieldsWith(entityId, entity.getProperties()) + ); } private Set getEntitiesByIds(Collection ids) { - if (ids == null) { return new HashSet<>(); } - return ids.stream() - .map(this::getEntityById) - .filter(Objects::nonNull) - .collect(Collectors.toSet()); + if (ids == null) { + return new HashSet<>(); + } + return ids + .stream() + .map(this::getEntityById) + .filter(Objects::nonNull) + .collect(Collectors.toSet()); } - } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java new file mode 100644 index 00000000..bb0db62d --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java @@ -0,0 +1,99 @@ +package edu.kit.datamanager.ro_crate.preview; + +import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import net.lingala.zip4j.ZipFile; +import net.lingala.zip4j.exception.ZipException; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import org.apache.commons.io.FileUtils; + +/** + * The default preview should use the + * rochtml tool + * for creating a simple preview file. + * + * @author Nikola Tzotchev on 6.2.2022 г. + * @version 1 + */ +public class AutomaticPreview implements CratePreview { + + public AutomaticPreview() {} + + @Override + public void saveAllToZip(ZipFile zipFile) throws IOException { + if (PreviewGenerator.isRochtmlAvailable()) { + // extract the .json file so we can run the "rochtml" tool on it" + try { + try { + zipFile.extractFile("ro-crate-metadata.json", "temp"); + } catch (ZipException ex) { + throw new IOException( + "ro-crate-metadata.json not found in provided ZIP.", + ex + ); + } + if (PreviewGenerator.isRochtmlAvailable()) { + PreviewGenerator.generatePreview("temp"); + zipFile.addFile("temp/ro-crate-preview.html"); + } + } finally { + try { + FileUtils.deleteDirectory(new File("temp")); + } catch (IOException ex) { + //ignore + } + } + } else { + new CustomPreview().saveAllToZip(zipFile); + } + } + + @Override + public void saveAllToFolder(File folder) throws IOException { + if (folder == null || !folder.exists()) { + throw new IOException( + "Preview target folder " + folder + " does not exist." + ); + } + + if (PreviewGenerator.isRochtmlAvailable()) { + PreviewGenerator.generatePreview(folder.getAbsolutePath()); + } else { + new CustomPreview().saveAllToFolder(folder); + } + } + + @Override + public void saveAllToStream(String metadata, ZipOutputStream stream) + throws IOException { + if (PreviewGenerator.isRochtmlAvailable()) { + try { + FileUtils.forceMkdir(new File("temp")); + try ( + FileWriter writer = new FileWriter("temp/ro-crate-metadata.json") + ) { + writer.write(metadata); + writer.flush(); + } + if (PreviewGenerator.isRochtmlAvailable()) { + PreviewGenerator.generatePreview("temp"); + ZipStreamUtil.addFileToZipStream( + stream, + new File("temp/ro-crate-preview.html"), + "ro-crate-preview.html" + ); + } + } finally { + try { + FileUtils.deleteDirectory(new File("temp")); + } catch (IOException ex) { + //ignore + } + } + } else { + new CustomPreview().saveAllToStream(metadata, stream); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java new file mode 100644 index 00000000..4983fdda --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java @@ -0,0 +1,108 @@ +package edu.kit.datamanager.ro_crate.preview; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.writer.CrateWriter; +import edu.kit.datamanager.ro_crate.writer.WriteFolderStrategy; +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import net.lingala.zip4j.ZipFile; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import org.apache.commons.io.FileUtils; +import org.slf4j.LoggerFactory; + +/** + * Interface for the ROCrate preview. This manages the human-readable + * representation of a crate. + * + * @author Nikola Tzotchev on 6.2.2022 г. + * @author jejkal + * @version 2 + */ +public interface CratePreview { + /** + * Generate a preview of the crate and store it into the given target directory. + * It is the caller's responsibility to handle, e.g. delete after use, the result + * (The caller takes ownership of the result). + *

+ * IMPORTANT NOTE: This method currently has a default implementation that relies + * on deprecated methods. In future, you will have to implement this method directly. + * + * @param crate the crate to generate a preview for. + * @param targetDir the target directory to store the preview in, + * owned by the caller. + * @throws IOException if an error occurs while generating the preview. + */ + default void generate(Crate crate, File targetDir) throws IOException { + // disable preview generation to avoid recursion, + // as this is usually called in the process of writing a crate + // (including preview) + new CrateWriter<>(new WriteFolderStrategy().disablePreview()) + // We assume the caller (e.g. a writer) already stored the provenance. + .withAutomaticProvenance(null) + .save(crate, targetDir.getAbsolutePath()); + this.saveAllToFolder(targetDir); + try (var stream = Files.list(targetDir.toPath())) { + stream + .filter( + path -> !path.getFileName().toString().equals("ro-crate-preview.html") + ) + .filter( + path -> + !path.getFileName().toString().equals("ro-crate-preview_files") + ) + .forEach(path -> { + try { + if (Files.isDirectory(path)) { + FileUtils.deleteDirectory(path.toFile()); + } else { + Files.delete(path); + } + } catch (IOException e) { + // Silently ignore deletion errors + LoggerFactory.getLogger(CratePreview.class).error( + "Failed to delete temporary file {}", + path, + e + ); + } + }); + } + } + + /** + * Takes a crate in form of a zip file and generates a preview of it, + * which will be stored within the crate. + * + * @param zipFile the zip file with the crate, which should receive a preview. + * @throws IOException if an error occurs while saving the preview + * + * @deprecated Use {@link #generate(Crate, File)} instead. + */ + @Deprecated(since = "2.1.0", forRemoval = true) + void saveAllToZip(ZipFile zipFile) throws IOException; + + /** + * Saves the preview, given by the folder, into the given folder. + * + * @param folder the folder (containing a crate) to save the preview in. + * @throws IOException if an error occurs while saving the preview. + * + * @deprecated Use {@link #generate(Crate, File)} instead. + */ + @Deprecated(since = "2.1.0", forRemoval = true) + void saveAllToFolder(File folder) throws IOException; + + /** + * Saves the preview, given by the metadata, into the given stream. + * + * @param metadata the metadata of the crate to save the preview in. + * @param stream the stream to save the preview in. + * @throws IOException if an error occurs while saving the preview. + * + * @deprecated Use {@link #generate(Crate, File)} instead. + */ + @Deprecated(since = "2.1.0", forRemoval = true) + void saveAllToStream(String metadata, ZipOutputStream stream) + throws IOException; +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java new file mode 100644 index 00000000..61c4c67c --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java @@ -0,0 +1,249 @@ +package edu.kit.datamanager.ro_crate.preview; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; +import freemarker.template.Configuration; +import freemarker.template.Template; +import freemarker.template.TemplateException; +import freemarker.template.TemplateExceptionHandler; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.io.Writer; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; +import net.lingala.zip4j.ZipFile; +import net.lingala.zip4j.exception.ZipException; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import org.apache.commons.io.FileUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * This class generates a custom preview without requiring external + * dependencies, i.e., rochtml. Therefore, the FreeMarker template located under + * resources/templates/custom_preview.ftl is used. + * + * @author jejkal + */ +public class CustomPreview implements CratePreview { + + private static final Logger logger = LoggerFactory.getLogger( + CustomPreview.class + ); + + private Template template = null; + + public CustomPreview() { + Configuration cfg = new Configuration(Configuration.VERSION_2_3_34); + cfg.setClassForTemplateLoading(CustomPreview.class, "/"); + cfg.setDefaultEncoding("UTF-8"); + cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER); + try { + template = cfg.getTemplate("templates/custom_preview.ftl"); + } catch (IOException ex) { + logger.error("Failed to read template for CustomPreview.", ex); + } + } + + private CustomPreviewModel mapFromJson(String metadata) throws IOException { + JsonValue root = Json.parse(metadata); + JsonValue graph = root.get("@graph"); + CustomPreviewModel.ROCrate crate = new CustomPreviewModel.ROCrate(); + List datasets = new ArrayList<>(); + List files = new ArrayList<>(); + + if (graph.isArray()) { + for (JsonValue node : graph) { + String id = node.path("@id").asText(); + List types = new LinkedList<>(); + if (node.path("@type").isArray()) { + for (JsonValue type : node.path("@type")) { + types.add(type.asText()); + } + } else { + types.add(node.path("@type").asText()); + } + + if (types.contains("Dataset") && "./".equals(id)) { + crate.name = node.path("name").asText(); + crate.description = node.path("description").asText(null); + crate.type = "Dataset"; + crate.license = node + .path("license") + .path("@id") + .asText(node.path("license").asText(null)); + crate.datePublished = node.path("datePublished").asText(null); + crate.hasPart = new ArrayList<>(); + + for (JsonValue part : node.path("hasPart")) { + CustomPreviewModel.Part p = new CustomPreviewModel.Part(); + String tmpId = part.path("@id").asText(part.asText()); + p.id = tmpId; + p.name = tmpId; // Name will be replaced later + crate.hasPart.add(p); + } + } else if (types.contains("Dataset")) { + CustomPreviewModel.Dataset dataset = new CustomPreviewModel.Dataset(); + dataset.id = id; + dataset.name = node.path("name").asText(); + dataset.description = node.path("description").asText(); + datasets.add(dataset); + } else if (types.contains("File")) { + CustomPreviewModel.File file = new CustomPreviewModel.File(); + file.id = id; + file.name = node.path("name").asText(null); + file.description = node.path("description").asText(null); + file.contentSize = node.path("contentSize").asText(null); + file.encodingFormat = node.path("encodingFormat").asText(null); + files.add(file); + } + } + } + + // Update Part names using dataset and file lists + if (crate.hasPart != null) { + for (CustomPreviewModel.Part part : crate.hasPart) { + for (CustomPreviewModel.Dataset dataset : datasets) { + if (dataset.id.equals(part.id) && dataset.name != null) { + part.name = dataset.name; + } + } + for (CustomPreviewModel.File file : files) { + if (file.id.equals(part.id) && file.name != null) { + part.name = file.name; + } + } + } + } + + CustomPreviewModel model = new CustomPreviewModel(); + model.crate = crate; + model.datasets = datasets; + model.files = files; + return model; + } + + @Override + public void saveAllToZip(ZipFile zipFile) throws IOException { + if (template == null) { + throw new IOException( + "Preview template did not load. Unable to proceed." + ); + } + if (zipFile == null) { + throw new IOException("Argument zipFile must not be null."); + } + try { + zipFile.extractFile("ro-crate-metadata.json", "temp"); + } catch (ZipException ex) { + throw new IOException( + "ro-crate-metadata.json not found in provided ZIP.", + ex + ); + } + + String metadata = FileUtils.readFileToString( + new File("temp/ro-crate-metadata.json"), + "UTF-8" + ); + try { + Map dataModel = new HashMap<>(); + dataModel.put("crateModel", mapFromJson(metadata)); + + try ( + Writer out = new OutputStreamWriter( + new FileOutputStream("temp/ro-crate-preview.html") + ) + ) { + template.process(dataModel, out); + out.flush(); + } + zipFile.addFile("temp/ro-crate-preview.html"); + } catch (TemplateException ex) { + throw new IOException("Failed to generate preview.", ex); + } finally { + try { + FileUtils.deleteDirectory(new File("temp")); + } catch (IOException ex) { + //ignore + } + } + } + + @Override + public void saveAllToFolder(File folder) throws IOException { + if (template == null) { + throw new IOException( + "Preview template did not load. Unable to proceed." + ); + } + if (folder == null || !folder.exists()) { + throw new IOException( + "Preview target folder " + folder + " does not exist." + ); + } + String metadata = FileUtils.readFileToString( + new File(folder, "ro-crate-metadata.json"), + "UTF-8" + ); + try { + Map dataModel = new HashMap<>(); + dataModel.put("crateModel", mapFromJson(metadata)); + try ( + Writer out = new OutputStreamWriter( + new FileOutputStream(new File(folder, "ro-crate-preview.html")) + ) + ) { + template.process(dataModel, out); + out.flush(); + } + } catch (TemplateException ex) { + throw new IOException("Failed to generate preview.", ex); + } + } + + @Override + public void saveAllToStream(String metadata, ZipOutputStream stream) + throws IOException { + if (template == null) { + throw new IOException( + "Preview template did not load. Unable to proceed." + ); + } + try { + //prepare metadata for template + Map dataModel = new HashMap<>(); + dataModel.put("crateModel", mapFromJson(metadata)); + + //prepare output folder and writer + FileUtils.forceMkdir(new File("temp")); + //load and process template + try (FileWriter writer = new FileWriter("temp/ro-crate-preview.html")) { + //load and process template + template.process(dataModel, writer); + writer.flush(); + } + + ZipStreamUtil.addFileToZipStream( + stream, + new File("temp/ro-crate-preview.html"), + "ro-crate-preview.html" + ); + } catch (TemplateException ex) { + throw new IOException("Failed to generate preview.", ex); + } finally { + try { + FileUtils.deleteDirectory(new File("temp")); + } catch (IOException ex) { + //ignore + } + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java new file mode 100644 index 00000000..380251dc --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java @@ -0,0 +1,122 @@ +package edu.kit.datamanager.ro_crate.preview; + +import java.util.List; + +/** + * + * @author jejkal + */ +public class CustomPreviewModel { + + protected ROCrate crate; + protected List datasets; + protected List files; + + public ROCrate getCrate() { + return crate; + } + + public List getDatasets() { + return datasets; + } + + public List getFiles() { + return files; + } + + public static class ROCrate { + + protected String name; + protected String description; + protected String type; + protected String license; + protected String datePublished; + protected List hasPart; + + public String getName() { + return name; + } + + public String getDescription() { + return description; + } + + public String getType() { + return type; + } + + public String getLicense() { + return license; + } + + public String getDatePublished() { + return datePublished; + } + + public List getHasPart() { + return hasPart; + } + } + + public static class Part { + + protected String id; + protected String name; + + public String getId() { + return id; + } + + public String getName() { + return name; + } + } + + public static class Dataset { + + protected String id; + protected String name; + protected String description; + + public String getId() { + return id; + } + + public String getName() { + return name; + } + + public String getDescription() { + return description; + } + } + + public static class File { + + protected String id; + protected String name; + protected String description; + protected String contentSize; + protected String encodingFormat; + + public String getId() { + return id; + } + + public String getName() { + return name; + } + + public String getDescription() { + return description; + } + + public String getContentSize() { + return contentSize; + } + + public String getEncodingFormat() { + return encodingFormat; + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java new file mode 100644 index 00000000..2a729674 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java @@ -0,0 +1,92 @@ +package edu.kit.datamanager.ro_crate.preview; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Class responsible for the generation of the human-readable representation of + * the metadata. For this to work the nodejs library rochtml has to be + * installed. This can be done using: npm install -g ro-crate-html-js or npm + * install ro-crate-html-js + */ +public class PreviewGenerator { + + private static Logger LOG = LoggerFactory.getLogger(PreviewGenerator.class); + private static final String command = "rochtml"; + + public static boolean isRochtmlAvailable() { + ProcessBuilder builder = new ProcessBuilder(); + // this is the equivalent of "rochtml dir/ro-crate-metadata.json" + // check if we are running on windows or unix + String os = System.getProperty("os.name").toLowerCase(); + if (os.contains("win")) { + builder.command("cmd.exe", "/c", command); + } else { + builder.command("sh", "-c", command); + } + Process process; + try { + process = builder.start(); + int exitVal = process.waitFor(); + return exitVal == 0; + } catch (InterruptedException | IOException ex) {} + return false; + } + + /** + * The method that from the location of the crate generates the html file. + * + * @param location the location of the crate in the filesystem. + */ + public static void generatePreview(String location) { + if (!isRochtmlAvailable()) { + LOG.error( + "rochtml is not available. Please install rochtml using npm install -g ro-crate-html-js" + ); + return; + } + ProcessBuilder builder = new ProcessBuilder(); + // this is the equivalent of "rochtml dir/ro-crate-metadata.json" + // check if we are running on windows or unix + String os = System.getProperty("os.name").toLowerCase(); + if (os.contains("win")) { + builder.command( + "cmd.exe", + "/c", + command + " " + location + "/ro-crate-metadata.json" + ); + } else { + builder.command( + "sh", + "-c", + command + " " + location + "/ro-crate-metadata.json" + ); + } + + Process process; + try { + process = builder.start(); + StringBuilder output = new StringBuilder(); + + BufferedReader reader = new BufferedReader( + new InputStreamReader(process.getInputStream()) + ); + + String line; + while ((line = reader.readLine()) != null) { + output.append(line).append("\n"); + } + reader.close(); + int exitVal = process.waitFor(); + if (exitVal != 0) { + //abnormal... + throw new Exception("failed command"); + } + } catch (Exception e) { + LOG.error("Error while generating preview: {}", e.getMessage()); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java new file mode 100644 index 00000000..c4ef2b99 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java @@ -0,0 +1,91 @@ +package edu.kit.datamanager.ro_crate.preview; + +import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; +import java.io.File; +import java.io.IOException; +import net.lingala.zip4j.ZipFile; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import net.lingala.zip4j.model.ZipParameters; +import org.apache.commons.io.FileUtils; + +/** + * This class adds a static preview to the crate, which consists of a + * metadataHtml file and a folder containing other files required to render + * metadataHtml. It will be put unchanged to the writer output, i.e., a zip + * file, folder, or stream. + * + * @author jejkal + */ +public class StaticPreview implements CratePreview { + + private final File metadataHtml; + private final File otherFiles; + + public StaticPreview(File metadataHtml, File otherFiles) { + this.metadataHtml = metadataHtml; + this.otherFiles = otherFiles; + } + + public StaticPreview(File metadataHtml) { + this.metadataHtml = metadataHtml; + this.otherFiles = null; + } + + @Override + public void saveAllToZip(ZipFile zipFile) throws IOException { + if (this.metadataHtml != null) { + ZipParameters zipParameters = new ZipParameters(); + zipParameters.setFileNameInZip("ro-crate-preview.html"); + zipFile.addFile(this.metadataHtml, zipParameters); + } + + if (this.otherFiles != null) { + zipFile.addFolder(this.otherFiles); + zipFile.renameFile( + this.otherFiles.getName() + "/", + "ro-crate-preview_files/" + ); + } + } + + @Override + public void saveAllToFolder(File folder) throws IOException { + if (folder == null || !folder.exists()) { + throw new IOException( + "Preview target folder " + folder + " does not exist." + ); + } + + if (this.metadataHtml != null) { + File fileInCrate = folder + .toPath() + .resolve("ro-crate-preview.html") + .toFile(); + FileUtils.copyFile(this.metadataHtml, fileInCrate); + } + if (this.otherFiles != null) { + File folderName = folder + .toPath() + .resolve("ro-crate-preview_files") + .toFile(); + FileUtils.copyDirectory(this.otherFiles, folderName); + } + } + + @Override + public void saveAllToStream(String metadata, ZipOutputStream stream) + throws IOException { + ZipStreamUtil.addFileToZipStream( + stream, + this.metadataHtml, + "ro-crate-preview.html" + ); + if (this.otherFiles != null) { + ZipStreamUtil.addFolderToZipStream( + stream, + this.otherFiles, + "ro-crate-preview_files" + ); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java new file mode 100644 index 00000000..e230e187 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java @@ -0,0 +1,422 @@ +package edu.kit.datamanager.ro_crate.reader; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.context.CrateMetadataContext; +import edu.kit.datamanager.ro_crate.context.RoCrateMetadataContext; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; +import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.special.IdentifierUtils; +import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; +import edu.kit.datamanager.ro_crate.validation.Validation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; +import java.util.*; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * This class allows reading crates from the outside into the library in order + * to inspect or modify it. + *

+ * The constructor takes a strategy to support different ways of importing the + * crates. (from zip, folder, etc.). + *

+ * The reader considers "hasPart" and "isPartOf" properties and considers all + * entities (in-)directly connected to the root entity ("./") as DataEntities. + * + * @param the type of the location parameter + */ +public class CrateReader { + + private static final Logger logger = LoggerFactory.getLogger( + CrateReader.class + ); + + /** + * This is a private inner class that shall not be exposed. **Do not make it + * public or protected.** It serves only the purpose of unsafe operations + * while reading a crate and may be specific to this implementation. + */ + private static class RoCrateUnsafe extends RoCrate { + + public void addDataEntityWithoutRootHasPart(DataEntity entity) { + this.metadataContext.checkEntity(entity); + this.roCratePayload.addDataEntity(entity); + } + } + + /** + * If the number of JSON entities in the crate is larger than this number, + * parallelization will be used. + */ + private static final int PARALLELIZATION_THRESHOLD = 100; + + private static final String FILE_PREVIEW_FILES = "ro-crate-preview_files"; + private static final String FILE_PREVIEW_HTML = "ro-crate-preview.html"; + private static final String FILE_METADATA_JSON = "ro-crate-metadata.json"; + + protected static final String SPECIFICATION_PREFIX = + "https://w3id.org/ro/crate/"; + + protected static final String PROP_ABOUT = "about"; + protected static final String PROP_CONTEXT = "@context"; + protected static final String PROP_CONFORMS_TO = "conformsTo"; + protected static final String PROP_GRAPH = "@graph"; + protected static final String PROP_HAS_PART = "hasPart"; + protected static final String PROP_ID = "@id"; + + private final GenericReaderStrategy strategy; + + public CrateReader(GenericReaderStrategy strategy) { + this.strategy = strategy; + } + + /** + * This function will read the location (using one of the specified + * strategies) and then build the relation between the entities. + * + * @param location the location of the ro-crate to be read + * @return the read RO-crate + * + * @throws IOException if the crate cannot be read + */ + public RoCrate readCrate(T location) throws IOException { + // get the ro-crate-metadata.json + JsonObject metadataJson = strategy.readMetadataJson(location); + // get the content of the crate + File files = strategy.readContent(location); + + // this set will contain the files that are associated with entities + HashSet usedFiles = new HashSet<>(); + usedFiles.add( + files.toPath().resolve(FILE_METADATA_JSON).toFile().getPath() + ); + usedFiles.add(files.toPath().resolve(FILE_PREVIEW_HTML).toFile().getPath()); + usedFiles.add( + files.toPath().resolve(FILE_PREVIEW_FILES).toFile().getPath() + ); + return rebuildCrate(metadataJson, files, usedFiles).markAsImported(); + } + + private RoCrate rebuildCrate( + JsonObject metadataJson, + File files, + HashSet usedFiles + ) { + Objects.requireNonNull( + metadataJson, + "metadataJson must not be null – did the strategy fail to locate 'ro-crate-metadata.json'?" + ); + Objects.requireNonNull( + files, + "files directory must not be null – check GenericReaderStrategy.readContent()" + ); + JsonValue context = metadataJson.get(PROP_CONTEXT); + + CrateMetadataContext crateContext = new RoCrateMetadataContext(context); + RoCrateUnsafe crate = new RoCrateUnsafe(); + crate.setMetadataContext(crateContext); + JsonValue graph = metadataJson.get(PROP_GRAPH); + + if (graph.isArray()) { + moveRootEntitiesFromGraphToCrate(crate, (JsonArray) graph); + } + RootDataEntity root = crate.getRootDataEntity(); + boolean rootExtractionSuccessful = root != null; + + if (rootExtractionSuccessful) { + Set dataEntityIds = getDataEntityIds(root, graph); + for (JsonValue entityJson : graph) { + String eId = unpackId(entityJson); + JsonObject properties = (JsonObject) entityJson.deepCopy(); + boolean isDataEntity = dataEntityIds.contains(eId); + + if (isDataEntity) { + DataEntity data = null; + boolean isDataSet = + properties.path("@type").asText().equals("Dataset") || + properties + .path("@type") + .valueStream() + .anyMatch(typeString -> typeString.asText().equals("Dataset")); + if (isDataSet) { + data = new DataSetEntity.DataSetBuilder() + .setAllUnsafe(properties) + .build(); + } else { + // data entity + DataEntity.DataEntityBuilder builder = + new DataEntity.DataEntityBuilder().setAllUnsafe(properties); + + // Handle data entities with corresponding file + checkFolderHasFile( + entityJson.get(PROP_ID).asText(), + files + ).ifPresent(file -> { + usedFiles.add(file.getPath()); + builder + .setLocationWithExceptions(file.toPath()) + .setId(file.getName()); + }); + data = builder.build(); + } + crate.addDataEntityWithoutRootHasPart(data); + } else { + // contextual entity + crate.addContextualEntity( + new ContextualEntity.ContextualEntityBuilder() + .setAllUnsafe(properties) + .build() + ); + } + } + } + + Collection untrackedFiles = Arrays.stream( + Optional.ofNullable(files.listFiles()).orElse(new File[0]) + ) + .filter(f -> !usedFiles.contains(f.getPath())) + .collect(Collectors.toSet()); + + crate.setUntrackedFiles(untrackedFiles); + Validator defaultValidation = new Validator(Validation.crateStrategy()); + defaultValidation.validate(crate); + return crate; + } + + /** + * Extracts graph connections from top to bottom. + *

+ * Example: (connections.get(parent) -> children) + * + * @param graph the JsonArray with all Entities. + * @return the graph connections. + */ + protected Map> makeEntityGraph(JsonValue graph) { + Map> connections = new HashMap<>(); + + Map idToNodes = new HashMap<>(); + StreamSupport.stream(graph.spliterator(), false).forEach(jsonNode -> + idToNodes.put(unpackId(jsonNode), jsonNode) + ); + + for (JsonValue entityNode : graph) { + String currentId = unpackId(entityNode); + StreamSupport.stream(entityNode.path("hasPart").spliterator(), false) + .map(this::unpackId) + .map(s -> idToNodes.getOrDefault(s, null)) + .filter(Objects::nonNull) + .forEach(child -> + connections + .computeIfAbsent(currentId, key -> new HashSet<>()) + .add(unpackId(child)) + ); + StreamSupport.stream(entityNode.path("isPartOf").spliterator(), false) + .map(this::unpackId) + .map(s -> idToNodes.getOrDefault(s, null)) + .filter(Objects::nonNull) + .forEach(parent -> + connections + .computeIfAbsent(unpackId(parent), key -> new HashSet<>()) + .add(currentId) + ); + } + return connections; + } + + protected Set getDataEntityIds(RootDataEntity root, JsonValue graph) { + if (root == null) { + return Set.of(); + } + Map> network = makeEntityGraph(graph); + Set directDataEntities = new HashSet<>(root.hasPart); + + Stack processingQueue = new Stack<>(); + processingQueue.addAll(directDataEntities); + Set result = new HashSet<>(); + + while (!processingQueue.empty()) { + String currentId = processingQueue.pop(); + result.add(currentId); + network + .getOrDefault(currentId, new HashSet<>()) + .stream() + .filter(subId -> !result.contains(subId)) // avoid loops! + .forEach(subId -> { + result.add(subId); + processingQueue.add(subId); + }); + } + return result; + } + + protected String unpackId(JsonValue node) { + if (node.isTextual()) { + return node.asText(); + } else /*if (node.isObject())*/ { + return node.path(PROP_ID).asText(); + } + } + + protected Optional checkFolderHasFile( + String filepathOrId, + File folder + ) { + if (IdentifierUtils.isUrl(filepathOrId)) { + return Optional.empty(); + } + return Stream.of( + IdentifierUtils.decode(filepathOrId).orElse(filepathOrId), + filepathOrId + ) + .map(filename -> + folder.toPath().resolve(filename).normalize().toAbsolutePath() + ) + // defence-in-depth: ensure we are still inside the crate folder + .filter(resolved -> resolved.startsWith(folder.toPath())) + .map(Path::toFile) + .filter(File::exists) + .findFirst(); + } + + /** + * Moves the descriptor and the root entity from the graph to the crate. + *

+ * Extracts the root data entity and the Metadata File Descriptor from the + * graph and inserts them into the crate object. It also deletes it from the + * graph. We will need the root dataset to distinguish between data entities + * and contextual entities. + * + * @param crate the crate, which will receive the entities, if available in + * the graph. + * @param graph the graph of the Metadata JSON file, where the entities are + * extracted and removed from. + */ + protected void moveRootEntitiesFromGraphToCrate( + RoCrate crate, + JsonArray graph + ) { + Optional maybeDescriptor = getMetadataDescriptor(graph); + + maybeDescriptor.ifPresent(descriptor -> { + setCrateDescriptor(crate, descriptor); + JsonUtilFunctions.removeJsonNodeFromArrayNode(graph, descriptor); + + Optional maybeRoot = extractRoot(graph, descriptor); + + maybeRoot.ifPresent(root -> { + Set hasPartIds = extractHasPartIds(root); + + crate.setRootDataEntity( + new RootDataEntity.RootDataEntityBuilder() + .setAllUnsafe(root.deepCopy()) + .setHasPart(hasPartIds) + .build() + ); + + JsonUtilFunctions.removeJsonNodeFromArrayNode(graph, root); + }); + }); + } + + /** + * Find the metadata descriptor. + *

+ * Currently prefers algorithm of version 1.1 over the one of 1.2-DRAFT. + * + * @param graph the graph to search the descriptor in. + * @return the metadata descriptor of the crate. + */ + protected Optional getMetadataDescriptor(JsonArray graph) { + boolean isParallel = graph.size() > PARALLELIZATION_THRESHOLD; + // use the algorithm described here: + // https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity + Optional maybeDescriptor = StreamSupport.stream( + graph.spliterator(), + isParallel + ) + // "2. if the conformsTo property is a URI that starts with + // https://w3id.org/ro/crate/" + .filter(node -> + node + .path(PROP_CONFORMS_TO) + .path(PROP_ID) + .asText() + .startsWith(SPECIFICATION_PREFIX) + ) + // "3. from this entity’s about object keep the @id URI as variable root" + .filter(node -> node.path(PROP_ABOUT).path(PROP_ID).isTextual()) + // There should be only one descriptor. If multiple exist, we take the first + // one. + .findFirst(); + return maybeDescriptor.or(() -> + StreamSupport.stream(graph.spliterator(), isParallel) + .filter(node -> node.path(PROP_ID).asText().equals(FILE_METADATA_JSON)) + // from https://www.researchobject.org/ro-crate/1.2-DRAFT/root-data-entity.html#finding-the-root-data-entity + .findFirst() + ); + } + + /** + * Extracts the root entity from the graph, using the information from the + * descriptor. + *

+ * Basically implements step 5 of the algorithm described here: + * + * https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity + * + * + * @param graph the graph from the metadata JSON-LD file + * @param descriptor the RO-Crate descriptor + * @return the root entity, if found + */ + private Optional extractRoot( + JsonArray graph, + JsonValue descriptor + ) { + String rootId = descriptor.get(PROP_ABOUT).get(PROP_ID).asText(); + boolean isParallel = graph.size() > PARALLELIZATION_THRESHOLD; + return StreamSupport.stream(graph.spliterator(), isParallel) + // root is an object (filter + conversion) + .filter(JsonValue::isObject) + .map(node -> (JsonObject) node.deepCopy()) + // "5. if the entity has an @id URI that matches root return it" + .filter(node -> node.path(PROP_ID).asText().equals(rootId)) + .findFirst(); + } + + private Set extractHasPartIds(JsonObject root) { + JsonValue hasPartNode = root.path(PROP_HAS_PART); + boolean isParallel = + hasPartNode.isArray() && hasPartNode.size() > PARALLELIZATION_THRESHOLD; + Set hasPartIds = StreamSupport.stream( + hasPartNode.spliterator(), + isParallel + ) + .map(hasPart -> hasPart.path(PROP_ID).asText()) + .filter(text -> !text.isBlank()) + .collect(Collectors.toSet()); + if (hasPartIds.isEmpty() && hasPartNode.path(PROP_ID).isTextual()) { + hasPartIds.add(hasPartNode.path(PROP_ID).asText()); + } + return hasPartIds; + } + + private void setCrateDescriptor(RoCrate crate, JsonValue descriptor) { + ContextualEntity descriptorEntity = + new ContextualEntity.ContextualEntityBuilder() + .setAllUnsafe((JsonObject) descriptor.deepCopy()) + .build(); + crate.setJsonDescriptor(descriptorEntity); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/FolderReader.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/FolderReader.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/reader/FolderReader.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/reader/FolderReader.java diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java new file mode 100644 index 00000000..d51d6c95 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java @@ -0,0 +1,29 @@ +package edu.kit.datamanager.ro_crate.reader; + +import edu.kit.datamanager.ro_crate.json.JsonObject; +import java.io.File; +import java.io.IOException; + +/** + * Generic interface for the strategy of the reader class. + * This allows for flexible input types when implementing different reading strategies. + * + * @param the type which determines the source of the crate + */ +public interface GenericReaderStrategy { + /** + * Read the metadata.json file from the given location. + * + * @param location the location to read from + * @return the parsed metadata.json as JsonObject + */ + JsonObject readMetadataJson(SOURCE_TYPE location) throws IOException; + + /** + * Read the content from the given location. + * + * @param location the location to read from + * @return the content as a File + */ + File readContent(SOURCE_TYPE location) throws IOException; +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java new file mode 100644 index 00000000..1ceaae48 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java @@ -0,0 +1,31 @@ +package edu.kit.datamanager.ro_crate.reader; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import java.io.File; +import java.io.IOException; +import java.nio.file.Path; + +/** + * A class for reading a crate from a folder. + * + * @author Nikola Tzotchev on 9.2.2022 г. + * @version 1 + */ +public class ReadFolderStrategy implements GenericReaderStrategy { + + @Override + public JsonObject readMetadataJson(String location) throws IOException { + Path metadata = new File(location) + .toPath() + .resolve("ro-crate-metadata.json"); + JsonObject objectNode = Json.objectNode(); + objectNode = (JsonObject) Json.parse(metadata.toFile()).deepCopy(); + return objectNode; + } + + @Override + public File readContent(String location) { + return new File(location); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java similarity index 83% rename from src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java index 5a2474b5..94e1711a 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStrategy.java @@ -1,18 +1,16 @@ package edu.kit.datamanager.ro_crate.reader; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; import edu.kit.datamanager.ro_crate.util.FileSystemUtil; -import net.lingala.zip4j.ZipFile; -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.filefilter.FileFilterUtils; - import java.io.File; import java.io.IOException; import java.nio.file.Path; import java.util.UUID; +import net.lingala.zip4j.ZipFile; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.filefilter.FileFilterUtils; /** * Reads a crate from a ZIP archive (file). @@ -42,7 +40,9 @@ public class ReadZipStrategy implements GenericReaderStrategy { protected final String ID = UUID.randomUUID().toString(); - protected Path temporaryFolder = Path.of(String.format("./.tmp/ro-crate-java/zipReader/%s/", ID)); + protected Path temporaryFolder = Path.of( + String.format("./.tmp/ro-crate-java/zipReader/%s/", ID) + ); protected boolean isExtracted = false; /** @@ -106,29 +106,41 @@ private void readCrate(String location) throws IOException { } @Override - public ObjectNode readMetadataJson(String location) throws IOException { + public JsonObject readMetadataJson(String location) throws IOException { if (!isExtracted) { this.readCrate(location); } - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - File jsonMetadata = this.temporaryFolder.resolve(JsonDescriptor.ID).toFile(); + File jsonMetadata = this.temporaryFolder + .resolve(JsonDescriptor.ID) + .toFile(); if (!jsonMetadata.isFile()) { // Try to find the metadata file in subdirectories File firstSubdir = FileUtils.listFilesAndDirs( - temporaryFolder.toFile(), - FileFilterUtils.directoryFileFilter(), - null // not recursive - ) + temporaryFolder.toFile(), + FileFilterUtils.directoryFileFilter(), + null // not recursive + ) .stream() .limit(50) - .filter(file -> file.toPath().toAbsolutePath().resolve(JsonDescriptor.ID).toFile().isFile()) + .filter(file -> + file + .toPath() + .toAbsolutePath() + .resolve(JsonDescriptor.ID) + .toFile() + .isFile() + ) .findFirst() - .orElseThrow(() -> new IllegalStateException("No %s found in zip file".formatted(JsonDescriptor.ID))); + .orElseThrow(() -> + new IllegalStateException( + "No %s found in zip file".formatted(JsonDescriptor.ID) + ) + ); jsonMetadata = firstSubdir.toPath().resolve(JsonDescriptor.ID).toFile(); } - return objectMapper.readTree(jsonMetadata).deepCopy(); + return (JsonObject) Json.parse(jsonMetadata).deepCopy(); } @Override diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java new file mode 100644 index 00000000..26a748ff --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java @@ -0,0 +1,192 @@ +package edu.kit.datamanager.ro_crate.reader; + +import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.util.FileSystemUtil; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.nio.file.Path; +import java.util.UUID; +import net.lingala.zip4j.io.inputstream.ZipInputStream; +import net.lingala.zip4j.model.LocalFileHeader; +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.filefilter.FileFilterUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Reads a crate from a streamed ZIP archive. + *

+ * This class handles reading and extraction of RO-Crate content from ZIP archives + * into a temporary directory structure on the file system, + * which allows accessing the contained files. + *

+ * Supports ELN-Style crates, + * meaning the crate may be either in the zip archive directly or in a single, + * direct subfolder beneath the root folder (/folder). + *

+ * Note: This implementation checks for up to 50 subdirectories if multiple are present. + * This is to avoid zip bombs, which may contain a lot of subdirectories, + * and at the same time gracefully handle valid crated with hidden subdirectories + * (for example, thumbnails). + *

+ * NOTE: The resulting crate may refer to these temporary files. Therefore, + * these files are only being deleted before the JVM exits. If you need to free + * space because your application is long-running or creates a lot of + * crates, you may use the getters to retrieve information which will help + * you to clean up manually. Keep in mind that crates may refer to this + * folder after extraction. Use RoCrateWriter to export it so some + * persistent location and possibly read it from there, if required. Or use + * the ZipWriter to write it back to its source. + * + * @author jejkal + */ +public class ReadZipStreamStrategy + implements GenericReaderStrategy +{ + + private static final Logger logger = LoggerFactory.getLogger( + ReadZipStreamStrategy.class + ); + protected final String ID = UUID.randomUUID().toString(); + protected Path temporaryFolder = Path.of( + String.format("./.tmp/ro-crate-java/zipStreamReader/%s/", ID) + ); + protected boolean isExtracted = false; + + /** + * Crates an instance with the default configuration. + *

+ * The default configuration is to extract the ZipFile to + * `./.tmp/ro-crate-java/zipStreamReader/%UUID/`. + */ + public ReadZipStreamStrategy() {} + + /** + * Creates a ZipStreamReader which will extract the contents temporary to + * the given location instead of the default location. + * + * @param folderPath the custom directory to extract content to for + * temporary access. + * @param shallAddUuidSubfolder if true, the reader will extract into + * subdirectories of the given directory. These subdirectories will have + * UUIDs as their names. + */ + public ReadZipStreamStrategy(Path folderPath, boolean shallAddUuidSubfolder) { + if (shallAddUuidSubfolder) { + this.temporaryFolder = folderPath.resolve(ID); + } else { + this.temporaryFolder = folderPath; + } + } + + /** + * @return the identifier which may be used as the name for a subfolder in + * the temporary directory. + */ + public String getID() { + return ID; + } + + /** + * @return the folder (considered temporary) where the zipped crate will be + * or has been extracted to. + */ + public Path getTemporaryFolder() { + return temporaryFolder; + } + + /** + * @return whether the crate has already been extracted into the temporary + * folder. + */ + public boolean isExtracted() { + return isExtracted; + } + + /**Read the crate metadata and content from the provided input stream. + * + * @param stream The input stream. + */ + private void readCrate(InputStream stream) throws IOException { + File folder = temporaryFolder.toFile(); + FileSystemUtil.mkdirOrDeleteContent(folder); + + LocalFileHeader localFileHeader; + int readLen; + byte[] readBuffer = new byte[4096]; + + try (ZipInputStream zipInputStream = new ZipInputStream(stream)) { + while ((localFileHeader = zipInputStream.getNextEntry()) != null) { + String fileName = localFileHeader.getFileName(); + File extractedFile = new File(folder, fileName).getCanonicalFile(); + Path targetRoot = folder.toPath().toRealPath(); + if (!extractedFile.toPath().startsWith(targetRoot)) { + throw new IOException( + "Entry is outside of target directory: " + fileName + ); + } + if (localFileHeader.isDirectory()) { + FileUtils.forceMkdir(extractedFile); + continue; + } + FileUtils.forceMkdir(extractedFile.getParentFile()); + try (OutputStream outputStream = new FileOutputStream(extractedFile)) { + while ((readLen = zipInputStream.read(readBuffer)) != -1) { + outputStream.write(readBuffer, 0, readLen); + } + } + } + } + this.isExtracted = true; + // register deletion on exit + FileUtils.forceDeleteOnExit(folder); + } + + @Override + public JsonObject readMetadataJson(InputStream stream) throws IOException { + if (!isExtracted) { + this.readCrate(stream); + } + + File jsonMetadata = temporaryFolder.resolve(JsonDescriptor.ID).toFile(); + if (!jsonMetadata.isFile()) { + // Try to find the metadata file in subdirectories + File firstSubdir = FileUtils.listFilesAndDirs( + temporaryFolder.toFile(), + FileFilterUtils.directoryFileFilter(), + null + ) + .stream() + .limit(50) + .filter(file -> + file + .toPath() + .toAbsolutePath() + .resolve(JsonDescriptor.ID) + .toFile() + .isFile() + ) + .findFirst() + .orElseThrow(() -> + new IllegalStateException( + "No %s found in zip file".formatted(JsonDescriptor.ID) + ) + ); + jsonMetadata = firstSubdir.toPath().resolve(JsonDescriptor.ID).toFile(); + } + return (JsonObject) Json.parse(jsonMetadata).deepCopy(); + } + + @Override + public File readContent(InputStream stream) throws IOException { + if (!isExtracted) { + this.readCrate(stream); + } + return temporaryFolder.toFile(); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReaderStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReaderStrategy.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/reader/ReaderStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/reader/ReaderStrategy.java diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java new file mode 100644 index 00000000..8dc6436e --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java @@ -0,0 +1,87 @@ +package edu.kit.datamanager.ro_crate.reader; + +import java.io.InputStream; +import java.nio.file.Path; + +/** + * Factory for creating common RO-Crate reader instances. + * Provides convenient static methods to instantiate readers with pre-configured strategies. + */ +public class Readers { + + /** + * Private constructor to prevent instantiation of this utility class. + */ + private Readers() {} + + /** + * Creates a reader that reads from ZIP files using input streams. + * + * @return A reader configured for ZIP files + * + * @see ReadZipStreamStrategy#ReadZipStreamStrategy() + */ + public static CrateReader newZipStreamReader() { + return new CrateReader<>(new ReadZipStreamStrategy()); + } + + /** + * Creates a reader that reads from ZIP files using input streams, + * extracting to a custom temporary location. + * + * @param extractPath Path where ZIP contents should be extracted + * @param useUuidSubfolder Whether to create a UUID subfolder under extractPath + * @return A reader configured for ZIP files with custom extraction + * + * @see ReadZipStreamStrategy#ReadZipStreamStrategy(Path, boolean) + */ + public static CrateReader newZipStreamReader( + Path extractPath, + boolean useUuidSubfolder + ) { + return new CrateReader<>( + new ReadZipStreamStrategy(extractPath, useUuidSubfolder) + ); + } + + /** + * Creates a reader that reads from a folder using a string path. + * + * @return A reader configured for folders + * + * @see ReadFolderStrategy + */ + public static CrateReader newFolderReader() { + return new CrateReader<>(new ReadFolderStrategy()); + } + + /** + * Creates a reader that reads from a ZIP file using a string path. + * + * @return A reader configured for ZIP files + * + * @see ReadZipStrategy#ReadZipStrategy() + */ + public static CrateReader newZipPathReader() { + return new CrateReader<>(new ReadZipStrategy()); + } + + /** + * Creates a reader that reads from a ZIP file using a string path, + * extracting to a custom temporary location. + * + * @param extractPath Path where ZIP contents should be extracted + * @param useUuidSubfolder Whether to create a UUID subfolder under extractPath + * @return A reader configured for ZIP files with custom extraction + * + * @see ReadZipStrategy#ReadZipStrategy(Path, boolean) + */ + public static CrateReader newZipPathReader( + Path extractPath, + boolean useUuidSubfolder + ) { + return new CrateReader<>( + new ReadZipStrategy(extractPath, useUuidSubfolder) + ); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java similarity index 86% rename from src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java index d11177c1..9156b9ba 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/RoCrateReader.java @@ -14,7 +14,8 @@ */ @Deprecated(since = "2.1.0", forRemoval = true) public class RoCrateReader extends CrateReader { - public RoCrateReader(GenericReaderStrategy reader) { - super(reader); - } + + public RoCrateReader(GenericReaderStrategy reader) { + super(reader); + } } diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/ZipReader.java b/core/src/main/java/edu/kit/datamanager/ro_crate/reader/ZipReader.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/reader/ZipReader.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/reader/ZipReader.java diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java b/core/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java new file mode 100644 index 00000000..4e7bf749 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java @@ -0,0 +1,111 @@ +package edu.kit.datamanager.ro_crate.special; + +import java.net.URI; +import java.net.URISyntaxException; +import java.util.Optional; + +/** + * Represents a crate version and has information for each version available. + * + * It offers also convenience functionality like version comparison similar to + * numbers. + */ +public enum CrateVersion { + // NOTE: Java defines compareTo for enums to work in the order of the defined + // elements. This means higher versions have to be defined below the lower + // versions. Consider this when adding a new version. + // + // NOTE: To add a new version, simply append a new variant with the correct + // data and read the comment below the versions. + V1P1("https://w3id.org/ro/crate/1.1"), + V1P2_DRAFT("https://w3id.org/ro/crate/1.2-DRAFT"); + + // NOTE: Do not forget to adjust the following when adding a version: + public static final CrateVersion LATEST_STABLE = CrateVersion.V1P1; + public static final CrateVersion LATEST_UNSTABLE = CrateVersion.V1P2_DRAFT; + + /** + * The String which is referred to by the crates conformsTo value. + * Should lead to the specification when resolved as a URL. + */ + public final String conformsTo; + + /** + * The String representation of the version. + * + * Example: assertEquals("1.2-DRAFT", CrateVersion.V1P2_DRAFT); + */ + public final String version; + + /** + * Basically a constructor of a version, if it needs to be created from the spec + * URI. + * + * @param conformsTo the specification URI. Example: + * https://w3id.org/ro/crate/1.1 + * @return the matching CrateVersion enum, if the URI matches any. Empty if not. + */ + public static Optional fromSpecUri(String conformsTo) { + return Optional.ofNullable(crateVersionOfConformsTo(conformsTo)); + } + + /** + * Private constructor which is being used for the internally given information + * above. + * + * @param spec the specification URI / conformsTo value + */ + private CrateVersion(String spec) { + this.conformsTo = spec; + this.version = getVersionFromConformsToString(spec); + } + + public boolean isStable() { + return !this.version.endsWith("-DRAFT"); + } + + public URI getConformsToUri() { + try { + return new URI(this.conformsTo); + } catch (URISyntaxException e) { + // can not happen as the user can not set this string + return null; + } + } + + /** + * Extracts the version from the spec uri. + * + * @param specUri the uri of the spec + * @return the version of the spec + */ + private static String getVersionFromConformsToString(String specUri) { + String[] parts = specUri.split("/"); + return parts[parts.length - 1]; + } + + private static CrateVersion crateVersionOfConformsTo(String conformsTo) { + for (CrateVersion e : values()) { + if (e.conformsTo.equals(conformsTo)) { + return e; + } + } + return null; + } + + public boolean isGreaterThan(CrateVersion other) { + return this.compareTo(other) > 0; + } + + public boolean isGreaterOrEqualThan(CrateVersion other) { + return this.compareTo(other) >= 0; + } + + public boolean isLowerThan(CrateVersion other) { + return this.compareTo(other) < 0; + } + + public boolean isLowerOrEqualThan(CrateVersion other) { + return this.compareTo(other) <= 0; + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java b/core/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java new file mode 100644 index 00000000..d8cebdfc --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java @@ -0,0 +1,161 @@ +package edu.kit.datamanager.ro_crate.special; + +import com.apicatalog.jsonld.uri.UriUtils; +import java.net.MalformedURLException; +import java.net.URI; +import java.net.URISyntaxException; +import java.net.URL; +import java.net.URLDecoder; +import java.net.URLEncoder; +import java.nio.charset.StandardCharsets; +import java.nio.file.InvalidPathException; +import java.nio.file.Path; +import java.util.Optional; + +/** + * This class defines methods regarding URIs in general, which in RO-Crate + * context means usually a valid, resolvable URL or a relative file path. + *

+ * The purpose is to have a simple abstraction where the way e.g. a URL is + * checked can be changed and tested easily for the whole library. + */ +public class IdentifierUtils { + + /** Static class */ + private IdentifierUtils() {} + + /** + * Returns true, if the given String is encoded and can be used as an + * identifier in RO-Crate. + *

+ * Possible identifiers include: + * - a uri + * - a url + * - a valid LD identifier (including blank node identifiers) + * - relative identifiers + * + * @param uri the given URI. Usually a URL or relative file path. + * @return true if the url is encoded, false if it is not. + */ + public static boolean isValidUri(String uri) { + return UriUtils.isURI(uri) || isLdBlankNode(uri); + } + + /** + * Returns true, if the given string is a url. + * + * @param uri the given string + * @return true if it is a url, false otherwise. + */ + public static boolean isUrl(String uri) { + try { + return encode(uri) + .map(encodedUri -> asUrl(encodedUri).isPresent()) + .orElse(false); + } catch (Exception e) { + return false; + } + } + + /** + * Tests if the given String is a URL, and if so, returns it. + * + * @param uriAsString the given String which will be tested. + * @return the url, if it is one. + */ + public static Optional asUrl(String uriAsString) { + try { + URI uri = new URI(uriAsString); + if (uri.isAbsolute()) { + return Optional.of(uri.toURL()); + } + } catch ( + URISyntaxException + | MalformedURLException + | NullPointerException ex + ) { + return Optional.empty(); + } + return Optional.empty(); + } + + /** + * Returns true, if the given string is a file path. + * + * @param uri the given string + * @return true if it is a path, false otherwise. + */ + public static boolean isPath(String uri) { + return asPath(uri).isPresent(); + } + + /** + * Tests if the given String is a file path, and if so, returns it. + * + * @param uri the given String which will be tested. + * @return the path, if it is one. + */ + public static Optional asPath(String uri) { + try { + Path u = Path.of(uri); + if (!isUrl(uri)) { + return Optional.of(u); + } + } catch (InvalidPathException e) { + return Optional.empty(); + } + return Optional.empty(); + } + + /** + * Encodes a string using the description if the ro-crate-specification. + * + * @param uri the string to encode. + * @return the encoded version of the given string, if possible. + */ + public static Optional encode(String uri) { + String result = uri; + // according to + // https://www.researchobject.org/ro-crate/1.1/data-entities.html#encoding-file-paths + // a file path may not be fully encoded and may contain international unicode + // characters. So we try a "soft"-encoding first, and if this is not yet valid, + // we really fully encode it. + + result = result.replace("\\", "/"); // "...express any relative paths using / separator..." + result = result.replace("%", "%25"); // "...escape special characters like space (%25)..." + result = result.replace(" ", "%20"); // "...and percent (%25)..." + if (isValidUri(result)) { + return Optional.of(result); + } + // from here on, our soft-encoding failed and we will fully encode the url or + // path. + result = URLEncoder.encode(uri, StandardCharsets.UTF_8); + result = result.replace("+", "%20"); // UrlEncoder encodes spaces with "+" + result = result.replace("%3A", ":"); // Convert colons back + result = result.replace("%2F", "/"); // Convert slashes back + + if (isValidUri(result)) { + return Optional.of(result); + } else { + return Optional.empty(); + } + } + + public static Optional decode(String uri) { + if (!isValidUri(uri) || isLdBlankNode(uri)) { + return Optional.of(uri); + } + return Optional.of(URLDecoder.decode(uri, StandardCharsets.UTF_8)); + } + + /** + * Returns true if the given string is a blank node identifier in the Linked + * Data world. + * + * @param uri the given String + * @return true if the string is a blank node. False if not. + */ + private static boolean isLdBlankNode(String uri) { + return uri.startsWith("_:") && !uri.contains(" "); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java b/core/src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java similarity index 75% rename from src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java index 1503d87f..bc75557e 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/special/JsonUtilFunctions.java @@ -1,10 +1,10 @@ package edu.kit.datamanager.ro_crate.special; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; import java.util.HashSet; import java.util.Set; @@ -20,8 +20,8 @@ public class JsonUtilFunctions { * @param node the json node that should be unwrapped. * @return the unwrapped Json. */ - public static JsonNode unwrapSingleArray(JsonNode node) { - ObjectNode newNode = MyObjectMapper.getMapper().createObjectNode(); + public static JsonValue unwrapSingleArray(JsonValue node) { + JsonObject newNode = Json.objectNode(); if (node.isObject()) { var itr = node.fields(); while (itr.hasNext()) { @@ -33,7 +33,7 @@ public static JsonNode unwrapSingleArray(JsonNode node) { if (node.size() == 1) { return unwrapSingleArray(node.get(0)); } else { - ArrayNode arrayNode = MyObjectMapper.getMapper().createArrayNode(); + JsonArray arrayNode = Json.arrayNode(); for (var n : node) { arrayNode.add(unwrapSingleArray(n)); } @@ -49,10 +49,10 @@ public static JsonNode unwrapSingleArray(JsonNode node) { * @param id every property with this as id will be removed. * @param node the json from which to remove the properties. */ - public static void removeFieldsWith(String id, JsonNode node) { - //MyObjectMapper.getMapper().createObjectNode(); + public static void removeFieldsWith(String id, JsonValue node) { + //Json.objectNode(); if (node.isObject()) { - ObjectNode newNode = (ObjectNode) node; + JsonObject newNode = (JsonObject) node; var itr = newNode.fields(); while (itr.hasNext()) { var nxt = itr.next(); @@ -65,7 +65,7 @@ public static void removeFieldsWith(String id, JsonNode node) { } } } else if (node.isArray()) { - ArrayNode arrayNode = (ArrayNode) node; + JsonArray arrayNode = (JsonArray) node; for (int i = 0; i < arrayNode.size(); i++) { var p = arrayNode.get(i); if (p.isValueNode()) { @@ -83,10 +83,10 @@ public static void removeFieldsWith(String id, JsonNode node) { * This method extracts from every property of a json objects its id's. * The method is intended for flattened json objects. * - * @param node The JsonNode json object. + * @param node The JsonValue json object. * @return the set containing all the strings. */ - public static Set getIdPropertiesFromJsonNode(JsonNode node) { + public static Set getIdPropertiesFromJsonNode(JsonValue node) { Set set = new HashSet<>(); var itr = node.fields(); while (itr.hasNext()) { @@ -96,14 +96,14 @@ public static Set getIdPropertiesFromJsonNode(JsonNode node) { } /** - * Extracts the id from a JsonNode property. + * Extracts the id from a JsonValue property. * This method is intended for flattened json-ld * that is why it is not recursive * - * @param node the JsonNode property + * @param node the JsonValue property * @return Set containing all the id as string */ - public static Set getIdPropertiesFromProperty(JsonNode node) { + public static Set getIdPropertiesFromProperty(JsonValue node) { Set set = new HashSet<>(); if (node.isArray()) { for (var element : node) { @@ -131,7 +131,7 @@ public static Set getIdPropertiesFromProperty(JsonNode node) { * @return true if an equal node was found and removed, false if no equal node * was found. */ - public static boolean removeJsonNodeFromArrayNode(ArrayNode array, JsonNode node) { + public static boolean removeJsonNodeFromArrayNode(JsonArray array, JsonValue node) { for (int i = 0; i < array.size(); i++) { if (array.get(i).equals(node)) { array.remove(i); diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java b/core/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java new file mode 100644 index 00000000..8431ee44 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java @@ -0,0 +1,47 @@ +package edu.kit.datamanager.ro_crate.util; + +import java.io.IOException; +import java.io.InputStream; +import java.net.URL; +import java.util.Properties; + +public class ClasspathPropertiesVersionProvider implements VersionProvider { + + public static final String VERSION_PROPERTIES = "version.properties"; + + /** + * Cached version to avoid repeated file/resource reads. + */ + private String cachedVersion = null; + + /** + * Constructs a ClasspathPropertiesVersionProvider that reads the version from a properties file in the classpath. + */ + public ClasspathPropertiesVersionProvider() { + // Lazy initialization - version loaded on first access + } + + @Override + public String getVersion() { + if (cachedVersion != null) { + return cachedVersion; + } + + URL resource = this.getClass().getResource("/" + VERSION_PROPERTIES); + assert resource != null : VERSION_PROPERTIES + " not found in classpath"; + + try (InputStream input = resource.openStream()) { + Properties properties = new Properties(); + properties.load(input); + String version = properties.getProperty("version"); + assert version != null : "Version property not found in " + + VERSION_PROPERTIES; + return version.trim(); + } catch (IOException e) { + throw new IllegalStateException( + "Failed to read version from properties file", + e + ); + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java b/core/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java new file mode 100644 index 00000000..2a2a86f8 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java @@ -0,0 +1,128 @@ +package edu.kit.datamanager.ro_crate.util; + +import java.io.File; +import java.io.IOException; +import java.util.Collection; +import java.util.regex.Matcher; +import org.apache.commons.io.FileUtils; + +public class FileSystemUtil { + + private FileSystemUtil() { + // Utility class, no instantiation + } + + /** + * Checks if the given ID appears to be a file path. + *

+ * Specifically excludes IDs starting with "doi:", "http", or "https". + * + * @param id the ID to check + * @return true if it looks like a file path, false otherwise + */ + public static boolean isFilePath(String id) { + return ( + id != null && + !( + id.startsWith("doi:") || + id.startsWith("http://") || + id.startsWith("https://") + ) + ); + } + + /** + * Gets the parent path of a given path. + * @param path the path to evaluate. + * @return the parent path, or null if no parent exists. + */ + public static String getParentPath(String path) { + if (path == null || path.equals("./") || path.isEmpty()) { + return null; + } + + // Normalize path - remove trailing slash for consistency + String normalizedPath = path.endsWith("/") + ? path.substring(0, path.length() - 1) + : path; + + int lastSlash = normalizedPath.lastIndexOf('/'); + if (lastSlash == -1) { + return "./"; // Root directory + } + + String parentPath = normalizedPath.substring(0, lastSlash); + + // If parent is empty, it's root + if (parentPath.isEmpty()) { + return "./"; + } + + // For validation, we need to check both with and without trailing slash + // since files don't have trailing slash but folders do + return parentPath; + } + + /** + * Removes a specific set of given file extensions from a file name, if present. + * The extensions are case-insensitive. Given "ELN", "eln" or "Eln" will also match. + * The dot (.) before the extension is also assumed and removed implicitly: + *

+ * Example: + * filterExtensionsFromFileName("test.eln", Set.of("ELN")) -> "test" + * + * @param filename the file name to filter (must not be null) + * @param extensionsToRemove the extensions to remove (must not be null) + * @return the filtered file name + * @throws NullPointerException if any parameter is null + */ + public static String filterExtensionsFromFileName( + String filename, + Collection extensionsToRemove + ) { + String dot = Matcher.quoteReplacement("."); + String end = Matcher.quoteReplacement("$"); + for (String extension : extensionsToRemove) { + // (?i) removes case sensitivity + filename = filename.replaceFirst("(?i)" + dot + extension + end, ""); + } + return filename; + } + + /** + * Ensures that a given path ends with a trailing slash. + * + * @param path the path to check + * @return the path with a trailing slash if it didn't have one, or the original path + */ + public static String ensureTrailingSlash(String path) { + if (path == null || path.isEmpty()) { + return path; + } + if (!path.endsWith("/")) { + return path + "/"; + } + return path; + } + + /** + * Creates a directory or deletes its content if it already exists. + * + * @param folder the folder to create or delete content from + * @throws IOException if an I/O error occurs + */ + public static void mkdirOrDeleteContent(File folder) throws IOException { + File[] files = folder.listFiles(); + boolean isNonEmptyDir = + folder.exists() && + folder.isDirectory() && + files != null && + files.length > 0; + boolean isFile = folder.exists() && !folder.isDirectory(); + + if (isNonEmptyDir || isFile) { + FileUtils.forceDelete(folder); + } + FileUtils.forceMkdir(folder); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java b/core/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java new file mode 100644 index 00000000..7971b85e --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java @@ -0,0 +1,60 @@ +package edu.kit.datamanager.ro_crate.util; + +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.util.stream.StreamSupport; + +/** + * Utility class for handling operations on RO-Crate graphs. + * Provides methods to find entities by ID or type within a graph. + *

+ * {@see JsonUtilFunctions}. + */ +public class Graph { + + private Graph() { + // Private constructor to prevent instantiation + } + + /** + * Finds an entity in the graph by its ID. + * + * @param graph The JSON node representing the graph. + * @param id The ID of the entity to find. + * @return The entity as a JsonValue if found, null otherwise. + */ + public static JsonValue findEntityById(JsonValue graph, String id) { + for (JsonValue entity : graph) { + if (entity.has("@id") && entity.get("@id").asText().equals(id)) { + return entity; + } + } + return null; + } + + /** + * Finds an entity in the graph by its type. + * + * @param graph The JSON node representing the graph. + * @param type The type of the entity to find. + * @return The entity as a JsonValue if found, null otherwise. + */ + public static JsonValue findEntityByType(JsonValue graph, String type) { + return StreamSupport.stream(graph.spliterator(), false) + .filter(entity -> entity.path("@type").asText().equals(type)) + .findFirst() + .orElse(null); + } + + /** + * Finds all entities in the graph by their type. + * + * @param graph The JSON node representing the graph. + * @param type The type of the entities to find. + * @return An array of JsonValue containing all entities of the specified type. + */ + public static JsonValue[] findEntitiesByType(JsonValue graph, String type) { + return StreamSupport.stream(graph.spliterator(), false) + .filter(entity -> entity.path("@type").asText().equals(type)) + .toArray(JsonValue[]::new); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java b/core/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java new file mode 100644 index 00000000..e14dd222 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java @@ -0,0 +1,10 @@ +package edu.kit.datamanager.ro_crate.util; + +public interface VersionProvider { + /** + * Returns the version of the ro-crate-java library. + * + * @return The version string. + */ + String getVersion(); +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java b/core/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java new file mode 100644 index 00000000..e258b559 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java @@ -0,0 +1,100 @@ +package edu.kit.datamanager.ro_crate.util; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import net.lingala.zip4j.model.ZipParameters; + +/** + * + * @author jejkal + */ +public class ZipStreamUtil { + + /** + * Adds a folder and its contents to a ZipOutputStream. + * + * @param zipOutputStream The ZipOutputStream to which the folder will be added. + * @param folder The folder to be added. + * @param parentPath The path in the zip file where the folder will be added. + * @throws IOException If an I/O error occurs. + */ + public static void addFolderToZipStream( + ZipOutputStream zipOutputStream, + File folder, + String parentPath + ) throws IOException { + if (!folder.exists() || !folder.isDirectory()) { + throw new IllegalArgumentException( + "The provided folder path is not a valid directory: %s".formatted( + folder.getAbsolutePath() + ) + ); + } + + File[] files = folder.listFiles(); + if (files == null) { + return; + } + + for (File file : files) { + String zipEntryPath = parentPath.isEmpty() + ? file.getName() + : parentPath + "/" + file.getName(); + if (file.isDirectory()) { + addFolderToZipStream( + zipOutputStream, + file.getAbsolutePath(), + zipEntryPath + ); + } else { + addFileToZipStream(zipOutputStream, file, zipEntryPath); + } + } + } + + /** + * Adds a folder and its contents to a ZipOutputStream. + * @param zipOutputStream The ZipOutputStream to which the folder will be added. + * @param folderPath The path of the folder to be added. + * @param parentPath The path in the zip file where the folder will be added. + * @throws IOException If an I/O error occurs. + */ + public static void addFolderToZipStream( + ZipOutputStream zipOutputStream, + String folderPath, + String parentPath + ) throws IOException { + addFolderToZipStream(zipOutputStream, new File(folderPath), parentPath); + } + + /** + * Adds a file to a ZipOutputStream. + * + * @param zipOutputStream The ZipOutputStream to which the file will be added. + * @param file The file to be added. + * @param zipEntryPath The path in the zip file where the file will be added. + * @throws IOException If an I/O error occurs. + */ + public static void addFileToZipStream( + ZipOutputStream zipOutputStream, + File file, + String zipEntryPath + ) throws IOException { + ZipParameters zipParameters = new ZipParameters(); + zipParameters.setFileNameInZip(zipEntryPath); + zipOutputStream.putNextEntry(zipParameters); + + try (InputStream inputStream = new FileInputStream(file)) { + byte[] buffer = new byte[4096]; + int len; + while ((len = inputStream.read(buffer)) != -1) { + zipOutputStream.write(buffer, 0, len); + } + } + + zipOutputStream.closeEntry(); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/validation/Validation.java b/core/src/main/java/edu/kit/datamanager/ro_crate/validation/Validation.java new file mode 100644 index 00000000..2dca8024 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/validation/Validation.java @@ -0,0 +1,81 @@ +package edu.kit.datamanager.ro_crate.validation; + +import edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy; +import java.util.Iterator; +import java.util.ServiceLoader; + +/** + * Access point for the JSON-schema validation strategies. + * + *

The concrete implementations live in the JSON backend modules + * (ro-crate-java-jackson2 or ro-crate-java-jackson3) and are discovered via + * {@link ServiceLoader}; exactly one backend must be on the classpath. This + * keeps the core free of any concrete JSON implementation. + */ +public final class Validation { + + private static volatile ValidatorStrategy crateStrategy; + private static volatile EntityValidationStrategy entityStrategy; + + private Validation() {} + + /** + * @return the crate-level JSON-schema validation of the active JSON backend + */ + public static ValidatorStrategy crateStrategy() { + ValidatorStrategy result = crateStrategy; + if (result == null) { + result = discover(ValidatorStrategy.class); + crateStrategy = result; + } + return result; + } + + /** + * @return the entity-level JSON-schema validation of the active JSON backend + */ + public static EntityValidationStrategy entityStrategy() { + EntityValidationStrategy result = entityStrategy; + if (result == null) { + result = discover(EntityValidationStrategy.class); + entityStrategy = result; + } + return result; + } + + private static T discover(Class type) { + return uniqueCandidate(ServiceLoader.load(type).iterator(), type); + } + + /** + * Returns the single candidate or throws an exception that names the + * backend artifacts to add or exclude, so users who do not know the module + * layout can fix the classpath themselves. + */ + static T uniqueCandidate(Iterator candidates, Class type) { + if (!candidates.hasNext()) { + throw new IllegalStateException( + "No " + + type.getSimpleName() + + " found on the classpath. Add a JSON " + + "backend as a dependency: edu.kit.datamanager:ro-crate-java " + + "(Jackson 2 backend) or edu.kit.datamanager:ro-crate-java-jackson3 " + + "(Jackson 3 backend)." + ); + } + T discovered = candidates.next(); + if (candidates.hasNext()) { + throw new IllegalStateException( + "Multiple " + + type.getSimpleName() + + " implementations found on the " + + "classpath; ro-crate-java supports only one JSON backend at a " + + "time. Keep the backend matching your Jackson version and exclude " + + "the other one, e.g. exclude edu.kit.datamanager:ro-crate-java " + + "(Jackson 2 backend) and add " + + "edu.kit.datamanager:ro-crate-java-jackson3 (Jackson 3 backend)." + ); + } + return discovered; + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/validation/Validator.java b/core/src/main/java/edu/kit/datamanager/ro_crate/validation/Validator.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/validation/Validator.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/validation/Validator.java diff --git a/src/main/java/edu/kit/datamanager/ro_crate/validation/ValidatorStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/validation/ValidatorStrategy.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/validation/ValidatorStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/validation/ValidatorStrategy.java diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java new file mode 100644 index 00000000..3aa67f7c --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java @@ -0,0 +1,57 @@ +package edu.kit.datamanager.ro_crate.writer; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.validation.Validation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.io.IOException; + +/** + * The class used for writing (exporting) crates. The class uses a strategy + * pattern for writing crates as different formats. (zip, folders, etc.) + * + * @param the type which determines the destination of the result + */ +public class CrateWriter { + + private final GenericWriterStrategy strategy; + protected ProvenanceManager provenanceManager = new ProvenanceManager(); + + /** + * Constructs a CrateWriter with a specified strategy for writing crates. + * + * @param strategy the strategy to use for writing crates. + */ + public CrateWriter(GenericWriterStrategy strategy) { + this.strategy = strategy; + } + + /** + * Sets the ProvenanceManager to be used for automatic provenance information + * generation when saving the crate. + * + * @param provenanceManager the ProvenanceManager to use. Using null will disable provenance management. + * @return this CrateWriter instance for method chaining. + */ + public CrateWriter withAutomaticProvenance( + ProvenanceManager provenanceManager + ) { + this.provenanceManager = provenanceManager; + return this; + } + + /** + * This method saves the crate to a destination provided. + * + * @param crate the crate to write. + * @param destination the location where the crate should be written. + */ + public void save(Crate crate, DESTINATION_TYPE destination) + throws IOException { + Validator defaultValidation = new Validator(Validation.crateStrategy()); + defaultValidation.validate(crate); + if (this.provenanceManager != null) { + this.provenanceManager.addProvenanceInformation(crate); + } + this.strategy.save(crate, destination); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java new file mode 100644 index 00000000..bb767d1e --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java @@ -0,0 +1,27 @@ +package edu.kit.datamanager.ro_crate.writer; + +/** + * An Interface for {@link GenericWriterStrategy} implementations which support writing + * ELN-Style crates. + * + * @param the type which determines the destination of the result + */ +public interface ElnFormatWriter extends + GenericWriterStrategy { + /** + * Write in ELN format style, meaning with a root subfolder in the zip file. + * Same as {@link #withRootSubdirectory()}. + * + * @return this writer + */ + ElnFormatWriter usingElnStyle(); + + /** + * Alias with more generic name for {@link #usingElnStyle()}. + * + * @return this writer + */ + default ElnFormatWriter withRootSubdirectory() { + return this.usingElnStyle(); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/FolderWriter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/FolderWriter.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/writer/FolderWriter.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/writer/FolderWriter.java diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java similarity index 59% rename from src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java index d06301a0..b0bed7bb 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/GenericWriterStrategy.java @@ -1,7 +1,6 @@ package edu.kit.datamanager.ro_crate.writer; import edu.kit.datamanager.ro_crate.Crate; - import java.io.IOException; /** @@ -11,11 +10,11 @@ * @param the type of the destination parameter */ public interface GenericWriterStrategy { - /** - * Saves the given crate to the specified destination. - * - * @param crate The crate to save - * @param destination The destination where the crate should be saved - */ - void save(Crate crate, DESTINATION_TYPE destination) throws IOException; + /** + * Saves the given crate to the specified destination. + * + * @param crate The crate to save + * @param destination The destination where the crate should be saved + */ + void save(Crate crate, DESTINATION_TYPE destination) throws IOException; } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java new file mode 100644 index 00000000..d6ef92bf --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java @@ -0,0 +1,165 @@ +package edu.kit.datamanager.ro_crate.writer; + +import static edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity.ContextualEntityBuilder; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.util.ClasspathPropertiesVersionProvider; +import edu.kit.datamanager.ro_crate.util.VersionProvider; +import java.time.Instant; + +/** + * Manages provenance information for RO-Crates. + * Handles the creation and updating of ro-crate-java entity and its actions. + */ +public class ProvenanceManager { + + /** + * A record to hold the prefix for the ro-crate-java ID. + * This is used to ensure that the ID is consistent across different versions of the library. + * Having a type for the prefix avoids using it by accident as a full ID. + */ + protected record IdPrefix(String prefix) { + /** + * Constructs a String with the given suffix. + * + * @param suffix The suffix to append to the prefix. + * @return A String combining the prefix and suffix, separated by a hyphen. + * Like this: "$prefix-$suffix". + */ + public String withSuffix(String suffix) { + return prefix + "-" + suffix; + } + + @Override + public String toString() { + return prefix; + } + } + + /** + * The prefix for the ro-crate-java ID. + * This is used to identify the ro-crate-java entity in the crate. + */ + protected static final IdPrefix RO_CRATE_JAVA_ID_PREFIX = new IdPrefix( + "#ro-crate-java" + ); + + /** + * The VersionProvider used to retrieve the version of ro-crate-java. + * This allows for flexibility in how the version is determined, e.g., from a properties file. + */ + protected VersionProvider versionProvider; + + /** + * Constructs a ProvenanceManager with the default ClasspathPropertiesVersionProvider. + */ + public ProvenanceManager() { + this(new ClasspathPropertiesVersionProvider()); + } + + /** + * Constructs a ProvenanceManager with a specified VersionProvider. + * + * @param versionProvider The VersionProvider to use for retrieving the version of ro-crate-java. + */ + public ProvenanceManager(VersionProvider versionProvider) { + this.versionProvider = versionProvider; + } + + /** + * Returns the full ID for the ro-crate-java entity of this library version + * to be used for an entity describing it. + *

+ * The ID is constructed using the RO_CRATE_JAVA_ID_PREFIX and the version from the VersionProvider. + * + * @return The ID for the ro-crate-java entity. + */ + public String getLibraryId() { + return RO_CRATE_JAVA_ID_PREFIX.withSuffix( + versionProvider.getVersion().toLowerCase() + ); + } + + /** + * Adds provenance information to the given crate. + * This includes creating or updating the ro-crate-java entity and its associated action entity. + * + * @param crate The crate to which provenance information will be added. + */ + public void addProvenanceInformation(Crate crate) { + // Determine if this is the first write + boolean isFirstWrite = + crate + .getAllContextualEntities() + .stream() + .noneMatch(entity -> + entity.getId().startsWith(RO_CRATE_JAVA_ID_PREFIX.toString()) + ) && !crate.isImported(); + + String libraryId = this.getLibraryId(); + + // Create action entity first + ContextualEntity actionEntity = buildNewActionEntity( + isFirstWrite, + libraryId + ); + + // Create or update ro-crate-java entity + ContextualEntity roCrateJavaEntity = buildRoCrateJavaEntity( + crate, + actionEntity.getId(), + libraryId + ); + + // Add entities to crate + crate.addContextualEntity(roCrateJavaEntity); + crate.addContextualEntity(actionEntity); + } + + protected ContextualEntity buildNewActionEntity( + boolean isFirstWrite, + String libraryId + ) { + return new ContextualEntityBuilder() + .addType(isFirstWrite ? "CreateAction" : "UpdateAction") + .addIdProperty("result", "./") + .addProperty("startTime", Instant.now().toString()) + .addIdProperty("agent", libraryId) + .build(); + } + + protected ContextualEntity buildRoCrateJavaEntity( + Crate crate, + String newActionId, + String libraryId + ) { + String version = this.versionProvider.getVersion(); + ContextualEntity self = crate + .getAllContextualEntities() + .stream() + .filter(contextualEntity -> libraryId.equals(contextualEntity.getId())) + .findFirst() + .orElseGet(() -> + new ContextualEntityBuilder() + .setId(libraryId) + .addType("SoftwareApplication") + .addProperty("name", "ro-crate-java") + .addProperty( + "url", + "https://github.com/kit-data-manager/ro-crate-java" + ) + .addProperty("version", version) + .addProperty("softwareVersion", version) + .addProperty("license", "Apache-2.0") + .addProperty( + "description", + "A Java library for creating and manipulating RO-Crates" + ) + .addIdProperty("Action", newActionId) + .build() + ); + self.addIdProperty("Action", newActionId); + return self; + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java similarity index 79% rename from src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java index 9337d400..92d34af9 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriter.java @@ -9,7 +9,7 @@ @Deprecated(since = "2.1.0", forRemoval = true) public class RoCrateWriter extends CrateWriter { - public RoCrateWriter(GenericWriterStrategy writer) { - super(writer); - } + public RoCrateWriter(GenericWriterStrategy writer) { + super(writer); + } } diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java new file mode 100644 index 00000000..a15c6627 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java @@ -0,0 +1,100 @@ +package edu.kit.datamanager.ro_crate.writer; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.special.IdentifierUtils; +import java.io.ByteArrayInputStream; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.nio.charset.StandardCharsets; +import java.nio.file.Path; +import org.apache.commons.io.FileUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * A class for writing a crate to a folder. + * + * @author Nikola Tzotchev on 9.2.2022 г. + * @version 1 + */ +public class WriteFolderStrategy implements GenericWriterStrategy { + + private static final Logger logger = LoggerFactory.getLogger( + WriteFolderStrategy.class + ); + + protected boolean writePreview = true; + + /** + * For internal use. Skips the preview generation when writing the crate. + * + * @return this instance of WriteFolderStrategy + * + * @deprecated May be removed in future versions. Not intended for public use. + */ + @Deprecated(since = "2.1.0", forRemoval = true) + public WriteFolderStrategy disablePreview() { + this.writePreview = false; + return this; + } + + @Override + public void save(Crate crate, String destination) throws IOException { + File file = new File(destination); + FileUtils.forceMkdir(file); + JsonValue node = Json.parse(crate.getJsonMetadata()); + String str = Json.writePretty(node); + InputStream inputStream = new ByteArrayInputStream( + str.getBytes(StandardCharsets.UTF_8) + ); + + File json = new File(destination, "ro-crate-metadata.json"); + FileUtils.copyInputStreamToFile(inputStream, json); + inputStream.close(); + // save also the preview files to the crate destination + if (crate.getPreview() != null && this.writePreview) { + crate.getPreview().saveAllToFolder(file); + } + for (var e : crate.getUntrackedFiles()) { + if (e.isDirectory()) { + FileUtils.copyDirectoryToDirectory(e, file); + } else { + FileUtils.copyFileToDirectory(e, file); + } + } + for (DataEntity dataEntity : crate.getAllDataEntities()) { + saveToFile(dataEntity, file); + } + } + + private void saveToFile(DataEntity entity, File file) throws IOException { + if (entity.getPath() != null) { + String id = entity.getId(); + String filename = IdentifierUtils.decode(id).orElse(id); + Path baseFolder = file.toPath().toAbsolutePath().normalize(); + Path destination = baseFolder.resolve(filename).normalize(); + // defence-in-depth: ensure the resolved path remains inside the crate folder + if (!destination.startsWith(baseFolder)) { + logger.warn( + "Skipping entity '{}': resolved path '{}' escapes destination folder '{}'", + id, + destination, + file + ); + return; + } + if (entity.getPath().toFile().isDirectory()) { + FileUtils.copyDirectory( + entity.getPath().toFile(), + destination.toFile() + ); + } else { + FileUtils.copyFile(entity.getPath().toFile(), destination.toFile()); + } + } + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java new file mode 100644 index 00000000..ed336e93 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java @@ -0,0 +1,34 @@ +package edu.kit.datamanager.ro_crate.writer; + +import edu.kit.datamanager.ro_crate.Crate; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.OutputStream; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Implementation of the writing strategy to provide a way of writing crates to + * a zip archive. + */ +public class WriteZipStrategy + implements GenericWriterStrategy, ElnFormatWriter +{ + + private static final Logger logger = LoggerFactory.getLogger( + WriteZipStrategy.class + ); + protected ElnFormatWriter delegate = + new WriteZipStreamStrategy(); + + @Override + public ElnFormatWriter usingElnStyle() { + this.delegate = this.delegate.withRootSubdirectory(); + return this; + } + + @Override + public void save(Crate crate, String destination) throws IOException { + this.delegate.save(crate, new FileOutputStream(destination)); + } +} diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java new file mode 100644 index 00000000..e3dcceb9 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java @@ -0,0 +1,247 @@ +package edu.kit.datamanager.ro_crate.writer; + +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.preview.CratePreview; +import edu.kit.datamanager.ro_crate.special.IdentifierUtils; +import edu.kit.datamanager.ro_crate.util.FileSystemUtil; +import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; +import java.io.*; +import java.nio.charset.StandardCharsets; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.List; +import java.util.Optional; +import java.util.Set; +import java.util.UUID; +import net.lingala.zip4j.io.outputstream.ZipOutputStream; +import net.lingala.zip4j.model.ZipParameters; +import org.apache.commons.io.FileUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Implementation of the writing strategy to provide a way of writing crates to + * a zip archive. + */ +public class WriteZipStreamStrategy + implements GenericWriterStrategy, ElnFormatWriter +{ + + private static final Logger logger = LoggerFactory.getLogger( + WriteZipStreamStrategy.class + ); + public static final String TMP_DIR = + "./.tmp/ro-crate-java/writer-zip-stream-strategy/"; + + /** + * Defines if the zip file will directly contain the crate, + * or if it will contain a subdirectory with the crate. + */ + protected boolean createRootSubdir = false; + + /** + * In streams, we do not have a file name yet (or do not know it), + * so we need to set a default name for the root subdirectory. + */ + protected String rootSubdirName = "content"; + + @Override + public ElnFormatWriter usingElnStyle() { + this.createRootSubdir = true; + return this; + } + + /** + * Sets the name of a root subdirectory in the zip file. + * Implicitly also enables the creation of a root subdirectory. + * If used for ELN files, note the subdirectory name should be the same as the zip + * files name. + * + * @param name the name of the subdirectory + * @return this instance of ReadZipStreamStrategy + */ + public WriteZipStreamStrategy setSubdirectoryName(String name) { + this.rootSubdirName = name; + this.createRootSubdir = true; + return this; + } + + @Override + public void save(Crate crate, OutputStream destination) throws IOException { + String innerFolderName = ""; + if (this.createRootSubdir) { + innerFolderName = FileSystemUtil.filterExtensionsFromFileName( + this.rootSubdirName, + Set.of("ELN", "ZIP") + ); + innerFolderName = FileSystemUtil.ensureTrailingSlash(innerFolderName); + } + try (ZipOutputStream zipFile = new ZipOutputStream(destination)) { + saveMetadataJson(crate, zipFile, innerFolderName); + saveDataEntities(crate, zipFile, innerFolderName); + savePreview(crate, zipFile, innerFolderName); + } + } + + private void saveDataEntities( + Crate crate, + ZipOutputStream zipStream, + String prefix + ) throws IOException { + for (DataEntity dataEntity : crate.getAllDataEntities()) { + this.saveToStream(dataEntity, zipStream, prefix); + } + } + + private void saveMetadataJson( + Crate crate, + ZipOutputStream zipStream, + String prefix + ) throws IOException { + // write the metadata.json file + ZipParameters zipParameters = new ZipParameters(); + zipParameters.setFileNameInZip(prefix + "ro-crate-metadata.json"); + // we create an JsonValue only to have the file written pretty + JsonValue node = Json.parse(crate.getJsonMetadata()); + String str = Json.writePretty(node); + // write the ro-crate-metadata + + byte[] buff = new byte[4096]; + int readLen; + zipStream.putNextEntry(zipParameters); + try ( + InputStream inputStream = new ByteArrayInputStream( + str.getBytes(StandardCharsets.UTF_8) + ) + ) { + while ((readLen = inputStream.read(buff)) != -1) { + zipStream.write(buff, 0, readLen); + } + } + zipStream.closeEntry(); + } + + private void savePreview( + Crate crate, + ZipOutputStream zipStream, + String prefix + ) throws IOException { + Optional preview = Optional.ofNullable(crate.getPreview()); + if (preview.isEmpty()) { + return; + } + final String ID = UUID.randomUUID().toString(); + File tmpPreviewFolder = Path.of(TMP_DIR).resolve(ID).toFile(); + FileUtils.forceMkdir(tmpPreviewFolder); + FileUtils.forceDeleteOnExit(tmpPreviewFolder); + + preview.get().generate(crate, tmpPreviewFolder); + String[] paths = tmpPreviewFolder.list(); + if (paths == null) { + throw new IOException( + "No preview files found in temporary folder. Preview generation failed." + ); + } + for (String path : paths) { + File file = tmpPreviewFolder.toPath().resolve(path).toFile(); + if (file.isDirectory()) { + ZipStreamUtil.addFolderToZipStream(zipStream, file, prefix + path); + } else { + ZipStreamUtil.addFileToZipStream(zipStream, file, prefix + path); + } + } + try { + FileUtils.forceDelete(tmpPreviewFolder); + } catch (IOException e) { + logger.error( + "Could not delete temporary preview folder: {}", + tmpPreviewFolder + ); + } + } + + private void saveToStream( + DataEntity entity, + ZipOutputStream zipStream, + String prefix + ) throws IOException { + if (entity == null) { + return; + } + + boolean isDirectory = entity.getPath().toFile().isDirectory(); + String id = entity.getId(); + String filename = IdentifierUtils.decode(id).orElse(id); + String safeName = sanitizeZipEntryName(filename); + if (safeName.isEmpty()) { + logger.warn( + "Skipping entity '{}': decoded name resolves outside the crate root", + id + ); + return; + } + String entryName = prefix + safeName; + if (isDirectory) { + ZipStreamUtil.addFolderToZipStream( + zipStream, + entity.getPath().toFile(), + entryName + ); + } else { + ZipStreamUtil.addFileToZipStream( + zipStream, + entity.getPath().toFile(), + entryName + ); + } + } + + /** + * Normalizes a decoded entry name into a safe relative path, consistent + * with the containment check in {@link WriteFolderStrategy#saveToFile}. + *

+ * Absolute paths (leading {@code /}) and Windows drive-qualified paths + * (e.g. {@code C:/}) are rejected. Internal {@code .} and {@code ..} + * segments are resolved; if the result escapes the virtual crate root + * the name is rejected. + * + * @param name the raw decoded entry name + * @return a canonical relative entry name, or an empty string if the name + * is absolute, drive-qualified, or escapes the crate root + */ + private static String sanitizeZipEntryName(String name) { + // zip entries always use forward slashes as separators + String normalized = name.replace('\\', '/'); + + // Reject absolute paths and Windows drive-qualified paths (e.g. C:/) + if ( + normalized.startsWith("/") || + (normalized.length() >= 2 && + normalized.charAt(1) == ':' && + Character.isLetter(normalized.charAt(0))) + ) { + return ""; + } + + // Normalize "." and ".." segments, rejecting paths that escape the root + String[] segments = normalized.split("/"); + List stack = new ArrayList<>(); + for (String segment : segments) { + if (segment.isEmpty() || segment.equals(".")) { + continue; + } + if (segment.equals("..")) { + if (stack.isEmpty()) { + return ""; + } + stack.remove(stack.size() - 1); + } else { + stack.add(segment); + } + } + return String.join("/", stack); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriterStrategy.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriterStrategy.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/writer/WriterStrategy.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/writer/WriterStrategy.java diff --git a/core/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java new file mode 100644 index 00000000..729403c2 --- /dev/null +++ b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java @@ -0,0 +1,42 @@ +package edu.kit.datamanager.ro_crate.writer; + +import java.io.OutputStream; + +/** + * Utility class for creating instances of different crate writers. + * This class is not meant to be instantiated. + */ +public class Writers { + + /** + * Prevents instantiation of this utility class. + */ + private Writers() {} + + /** + * Creates a new instance of a crate writer that writes to a folder. + * + * @return a new instance of {@link CrateWriter} for writing to a folder + */ + public static CrateWriter newFolderWriter() { + return new CrateWriter<>(new WriteFolderStrategy()); + } + + /** + * Creates a new instance of a crate writer that writes to a zip stream. + * + * @return a new instance of {@link CrateWriter} for writing to a zip stream + */ + public static CrateWriter newZipStreamWriter() { + return new CrateWriter<>(new WriteZipStreamStrategy()); + } + + /** + * Creates a new instance of a crate writer that writes to a zip file. + * + * @return a new instance of {@link CrateWriter} for writing to a zip file + */ + public static CrateWriter newZipPathWriter() { + return new CrateWriter<>(new WriteZipStrategy()); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/ZipWriter.java b/core/src/main/java/edu/kit/datamanager/ro_crate/writer/ZipWriter.java similarity index 100% rename from src/main/java/edu/kit/datamanager/ro_crate/writer/ZipWriter.java rename to core/src/main/java/edu/kit/datamanager/ro_crate/writer/ZipWriter.java diff --git a/src/main/resources/default_context/version1.1.json b/core/src/main/resources/default_context/version1.1.json similarity index 100% rename from src/main/resources/default_context/version1.1.json rename to core/src/main/resources/default_context/version1.1.json diff --git a/src/main/resources/templates/custom_preview.ftl b/core/src/main/resources/templates/custom_preview.ftl similarity index 100% rename from src/main/resources/templates/custom_preview.ftl rename to core/src/main/resources/templates/custom_preview.ftl diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesBenchmark.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesBenchmark.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesBenchmark.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesBenchmark.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesWriteAndRead.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesWriteAndRead.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesWriteAndRead.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/multiplecrates/MultipleCratesWriteAndRead.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/ContextualEntitiesPerformance.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/ContextualEntitiesPerformance.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/ContextualEntitiesPerformance.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/ContextualEntitiesPerformance.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/DeletionEntitiesPerformance.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/DeletionEntitiesPerformance.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/DeletionEntitiesPerformance.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/DeletionEntitiesPerformance.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/LocalDataEntitiesPerformance.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/LocalDataEntitiesPerformance.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/LocalDataEntitiesPerformance.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/LocalDataEntitiesPerformance.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/MixtureOfEntitiesPerformance.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/MixtureOfEntitiesPerformance.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/MixtureOfEntitiesPerformance.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/MixtureOfEntitiesPerformance.java diff --git a/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/RemoteDataEntitiesPerformance.java b/core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/RemoteDataEntitiesPerformance.java similarity index 100% rename from src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/RemoteDataEntitiesPerformance.java rename to core/src/performanceTest/java/edu/kit/datamanager/ro_crate/singlecratebenchmarks/RemoteDataEntitiesPerformance.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/GoldenCrateRoundTripTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/GoldenCrateRoundTripTest.java new file mode 100644 index 00000000..1fded937 --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/GoldenCrateRoundTripTest.java @@ -0,0 +1,153 @@ +package edu.kit.datamanager.ro_crate; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.writer.Writers; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; +import java.util.stream.Stream; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.MethodSource; + +/** + * Golden tests locking down the exact behavior of the library as a safety net + * for the Jackson-free-core conversion. + * + *

For every fixture crate this test asserts: + *

    + *
  1. {@code getJsonMetadata()} of a freshly read crate is byte-identical to + * the committed golden file ({@code /golden/<name>.metadata.json}).
    2. + *
  2. Writing the crate to disk and reading it back yields structurally + * identical metadata (write/read idempotence, compared with the same + * comparator the existing test suite uses).
    3. + *
  3. The set of data entities survives the round trip unchanged.
    4. + *
+ * + *

If a behavior change is intentional, regenerate the golden files with + * {@code ./gradlew test -Drocrate.golden.update=true} and review the diff — + * it must be limited to the intended change. + */ +class GoldenCrateRoundTripTest { + + /** Fixtures must be plain crate folders (no network access on read). */ + static Stream fixtureCrates() { + return Stream.of( + "crates/extendedContextExample", + "crates/hasPartHierarchy", + "crates/simple_crate", + "crates/other/idrc_project", + "crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array" + ); + } + + /** + * Canonicalizes metadata for byte-level comparison: entities in the graph + * are sorted by their {@code @id}. The library does not specify the order + * of entities in the output graph (it follows Java hash iteration, which is + * not stable across JVM runs), so entity order is excluded from the lock; + * everything else — entity content, property order, formatting — is locked. + */ + static String canonicalize(String metadata) throws IOException { + JsonObject root = (JsonObject) Json.parse(metadata); + JsonValue graph = root.path("@graph"); + if (graph.isArray()) { + List entities = new ArrayList<>(); + graph.forEach(entities::add); + entities.sort( + Comparator.comparing( + node -> node.path("@id").asText(""), + String.CASE_INSENSITIVE_ORDER + ) + ); + JsonArray graphArray = (JsonArray) graph; + while (!graphArray.isEmpty()) { + graphArray.remove(0); + } + entities.forEach(graphArray::add); + } + return Json.write(root); + } + + @ParameterizedTest + @MethodSource("fixtureCrates") + void goldenMetadataIsStableThroughWriteReadRoundTrip(String fixture) + throws IOException { + Path crateDir = Path.of("src/test/resources", fixture); + String name = Path.of(fixture).getFileName().toString(); + + RoCrate read = Readers.newFolderReader().readCrate(crateDir.toString()); + String originalMetadata = read.getJsonMetadata(); + + Path goldenPath = Path.of( + "src/test/resources/golden", + name + ".metadata.json" + ); + if (System.getProperty("rocrate.golden.update") != null) { + Files.createDirectories(goldenPath.getParent()); + Files.writeString( + goldenPath, + canonicalize(originalMetadata), + StandardCharsets.UTF_8 + ); + } else { + assertTrue( + Files.exists(goldenPath), + "missing golden file " + + goldenPath + + " — run with -Drocrate.golden.update=true to generate" + ); + assertEquals( + Files.readString(goldenPath, StandardCharsets.UTF_8), + canonicalize(originalMetadata), + "metadata of freshly read crate '" + + name + + "' drifted from the golden file" + ); + } + + Path writtenDir = Files.createTempDirectory("golden-roundtrip"); + Writers.newFolderWriter().save(read, writtenDir.toString()); + RoCrate roundTripped = Readers.newFolderReader().readCrate( + writtenDir.toString() + ); + + // structural comparison: the reader normalizes formatting, so byte equality + // across a write/read round trip is not an invariant of the current library + HelpFunctions.compareTwoCrateJson(read, roundTripped); + + if (System.getProperty("rocrate.golden.update") != null) { + // golden files are regenerated; no additional assertions in this mode + } else { + } + + assertEquals( + read + .getAllDataEntities() + .stream() + .map(DataEntity::getId) + .sorted() + .toList(), + roundTripped + .getAllDataEntities() + .stream() + .map(DataEntity::getId) + .sorted() + .toList(), + "data entities changed across the write/read round trip for '" + + name + + "'" + ); + } +} diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java b/core/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java new file mode 100644 index 00000000..b640351c --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java @@ -0,0 +1,196 @@ +package edu.kit.datamanager.ro_crate; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import edu.kit.datamanager.ro_crate.entities.AbstractEntity; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; +import io.json.compare.JSONCompare; +import io.json.compare.JsonComparator; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Map; +import java.util.function.Function; +import java.util.stream.Collectors; +import org.apache.commons.io.FileUtils; +import org.opentest4j.AssertionFailedError; + +public class HelpFunctions { + + public static void compareEntityWithFile(AbstractEntity entity, String string) + throws IOException { + InputStream inputStream = HelpFunctions.class.getResourceAsStream(string); + JsonValue expectedJson = Json.parse(inputStream); + JsonValue node = entity.toJson(); + //compare the size of the expected and actual node. Both nodes should have the same number of properties. + assertEquals(expectedJson.size(), node.size()); + compare(expectedJson, node, true); + } + + public static void compare(JsonValue node1, JsonValue node2, Boolean equals) { + var comparator = new JsonComparator() { + public boolean compareValues(Object expected, Object actual) { + return expected.equals(actual); + } + + public boolean compareFields(String expected, String actual) { + return expected.equals(actual); + } + }; + + // json-compare works on JSON documents; hand it the string form of the + // neutral trees (produced by the active adapter) + if (equals) { + JSONCompare.assertMatches(node1.toString(), node2.toString(), comparator); + } else { + JSONCompare.assertNotMatches( + node1.toString(), + node2.toString(), + comparator + ); + } + } + + public static void compareTwoMetadataJsonNotEqual(Crate crate1, Crate crate2) + throws IOException { + JsonValue node1 = Json.parse(crate1.getJsonMetadata()); + JsonValue node2 = Json.parse(crate2.getJsonMetadata()); + compare(node1, node2, false); + } + + public static void compareTwoMetadataJsonNotEqual( + Crate crate1, + String jsonFileString + ) throws IOException { + InputStream inputStream = HelpFunctions.class.getResourceAsStream( + jsonFileString + ); + JsonValue node1 = Json.parse(crate1.getJsonMetadata()); + JsonValue node2 = JsonUtilFunctions.unwrapSingleArray( + Json.parse(inputStream) + ); + compare(node1, node2, false); + } + + public static void compareTwoCrateJson(Crate crate1, Crate crate2) + throws IOException { + JsonValue node1 = Json.parse(crate1.getJsonMetadata()); + JsonValue node2 = Json.parse(crate2.getJsonMetadata()); + compare(node1, node2, true); + } + + public static void prettyPrintJsonString(String minimalJsonMetadata) { + try { + JsonValue jsonNode = Json.parse(minimalJsonMetadata); + System.out.println(Json.writePretty(jsonNode)); + } catch (IOException e) { + throw new AssertionFailedError("Not able to process string as JSON!", e); + } + } + + public static void printAndAssertEquals( + RoCrate crate, + String pathToResource + ) { + // So you get something to see + prettyPrintJsonString(crate.getJsonMetadata()); + // Compare with the example from the specification + try { + HelpFunctions.compareCrateJsonToFileInResources(crate, pathToResource); + } catch (IOException e) { + throw new AssertionFailedError("Missing resources file!", e); + } + } + + public static void compareCrateJsonToFileInResources(File file1, File file2) + throws IOException { + JsonValue node1 = JsonUtilFunctions.unwrapSingleArray(Json.parse(file1)); + JsonValue node2 = JsonUtilFunctions.unwrapSingleArray(Json.parse(file2)); + compare(node1, node2, true); + } + + /** + * Compares the JSON metadata of a Crate object with a JSON file in the resources directory. + * + * @param crate1 The Crate object to compare. + * @param jsonFileString The path to the JSON file in the resources directory. + * @throws IOException If an error occurs while reading the JSON file. + */ + public static void compareCrateJsonToFileInResources( + Crate crate1, + String jsonFileString + ) throws IOException { + InputStream inputStream = HelpFunctions.class.getResourceAsStream( + jsonFileString + ); + JsonValue node1 = Json.parse(crate1.getJsonMetadata()); + JsonValue node2 = JsonUtilFunctions.unwrapSingleArray( + Json.parse(inputStream) + ); + compare(node1, node2, true); + } + + public static boolean compareTwoDir(File dir1, File dir2) throws IOException { + // compare the content of the two directories + Map compareWithMe = FileUtils.listFiles(dir1, null, true) + .stream() + .collect(Collectors.toMap(java.io.File::getName, Function.identity())); + + Map testMe = FileUtils.listFiles(dir2, null, true) + .stream() + .collect(Collectors.toMap(java.io.File::getName, Function.identity())); + + if (compareWithMe.size() != testMe.size()) { + return false; + } + for (String filename : testMe.keySet()) { + // we do that because the ro-crate-metadata.json can be differently formatted, + // or the order of the entities may be different + // the same holds for the html file + if ( + filename.equals("ro-crate-preview.html") || + filename.equals("ro-crate-metadata.json") + ) { + if (!compareWithMe.containsKey(filename)) { + return false; + } + } else if ( + !FileUtils.contentEqualsIgnoreEOL( + testMe.get(filename), + compareWithMe.get(filename), + null + ) + ) { + return false; + } + } + return true; + } + + /** + * Prints the file tree of the given directory for debugging and understanding + * a test more quickly. + * + * @param directoryToPrint the directory to print + * @throws IOException if an error occurs while printing the file tree + */ + @SuppressWarnings("resource") + public static void printFileTree(Path directoryToPrint) throws IOException { + // Print all files recursively in a tree structure for debugging + System.out.printf( + "Files in %s:%n", + directoryToPrint.getFileName().toString() + ); + Files.walk(directoryToPrint).forEach(path -> { + if (!path.toAbsolutePath().equals(directoryToPrint.toAbsolutePath())) { + int depth = path.relativize(directoryToPrint).getNameCount(); + String prefix = " ".repeat(depth); + System.out.printf("%s%s%s%n", prefix, "└── ", path.getFileName()); + } + }); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java similarity index 67% rename from src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java index 1fb7b574..4329bf84 100644 --- a/src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java @@ -1,25 +1,20 @@ package edu.kit.datamanager.ro_crate.context; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; +import static org.junit.jupiter.api.Assertions.*; import edu.kit.datamanager.ro_crate.HelpFunctions; import edu.kit.datamanager.ro_crate.RoCrate; import edu.kit.datamanager.ro_crate.entities.AbstractEntity; import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; import java.io.IOException; import java.util.List; import java.util.Set; - -import static org.junit.jupiter.api.Assertions.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; public class RoCrateMetadataContextTest { @@ -31,44 +26,45 @@ void initContext() throws IOException { // this will load the default context this.context = new RoCrateMetadataContext(); - final String crateManifestPath = "/crates/extendedContextExample/ro-crate-metadata.json"; - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode jsonNode = objectMapper.readTree(RoCrateMetadataContextTest.class.getResourceAsStream(crateManifestPath)); + final String crateManifestPath = + "/crates/extendedContextExample/ro-crate-metadata.json"; + JsonObject jsonNode = (JsonObject) Json.parse( + RoCrateMetadataContextTest.class.getResourceAsStream(crateManifestPath) + ); this.complexContext = new RoCrateMetadataContext(jsonNode.get("@context")); } @Test void testContext() { - var entity = this.context.getContextJsonEntity(); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); // we expect the default RO-crate context; - var expected = objectMapper.createObjectNode(); + var expected = Json.objectNode(); expected.put("@context", "https://w3id.org/ro/crate/1.1/context"); HelpFunctions.compare(entity, expected, true); // this entity is not correct // there is no type blabla in schema.org var contextualEntity = new ContextualEntity.ContextualEntityBuilder() - .setId("dkfaj") - .addType("blabla") - .build(); + .setId("dkfaj") + .addType("blabla") + .build(); assertFalse(this.context.checkEntity(contextualEntity)); // this entity is correct the type Accommodation exists in schema.org, // so it should be valid var contextualEntityCorrect = new ContextualEntity.ContextualEntityBuilder() - .setId("dkfaj") - .addType("Accommodation") - .addProperty("name", "ffjkjk") - .build(); + .setId("dkfaj") + .addType("Accommodation") + .addProperty("name", "ffjkjk") + .build(); assertTrue(this.context.checkEntity(contextualEntityCorrect)); // this entity has correct types but wrong field - var contextualEntityWrongField = new ContextualEntity.ContextualEntityBuilder() + var contextualEntityWrongField = + new ContextualEntity.ContextualEntityBuilder() .setId("dkfaj") .addType("Accommodation") .addProperty("notExisting", "kfdjfk") @@ -80,9 +76,11 @@ void testContext() { @Test void creationUrlTest() { RoCrateMetadataContext newContext = new RoCrateMetadataContext( - List.of("www.example.com", "www.example.com/context")); + List.of("www.example.com", "www.example.com/context") + ); - var contextualEntityWrongField = new ContextualEntity.ContextualEntityBuilder() + var contextualEntityWrongField = + new ContextualEntity.ContextualEntityBuilder() .setId("dkfaj") .addType("Accommodation") .build(); @@ -96,13 +94,11 @@ void creationUrlTest() { @Test void creationFromPairsJsonTest() { - var objectMapper = MyObjectMapper.getMapper(); - - ObjectNode rawContext = objectMapper.createObjectNode(); + JsonObject rawContext = Json.objectNode(); rawContext.put("house", "www.example.com/house"); rawContext.put("road", "www.example.com/road"); - ObjectNode rawCrate = objectMapper.createObjectNode(); + JsonObject rawCrate = Json.objectNode(); rawCrate.set("@context", rawContext); RoCrateMetadataContext newContext = new RoCrateMetadataContext(rawContext); assertNotNull(newContext); @@ -110,10 +106,10 @@ void creationFromPairsJsonTest() { HelpFunctions.compare(newContext.getContextJsonEntity(), rawCrate, true); var entityWithTerms = new ContextualEntity.ContextualEntityBuilder() - .setId("dkfaj") - .addType("house") - .addType("road") - .build(); + .setId("dkfaj") + .addType("house") + .addType("road") + .build(); assertTrue(newContext.checkEntity(entityWithTerms)); } @@ -126,7 +122,11 @@ void deletePairTest() { context.deleteValuePairFromContext("key"); - HelpFunctions.compare(context.getContextJsonEntity(), emptyContext.getContextJsonEntity(), true); + HelpFunctions.compare( + context.getContextJsonEntity(), + emptyContext.getContextJsonEntity(), + true + ); } @Test @@ -136,7 +136,11 @@ void deleteNonExistingPairTest() { context.deleteValuePairFromContext("key"); - HelpFunctions.compare(context.getContextJsonEntity(), emptyContext.getContextJsonEntity(), true); + HelpFunctions.compare( + context.getContextJsonEntity(), + emptyContext.getContextJsonEntity(), + true + ); } @Test @@ -148,8 +152,11 @@ void deleteUrlTest() { context.deleteUrlFromContext("www.example.com"); - HelpFunctions.compare(context.getContextJsonEntity(), emptyContext.getContextJsonEntity(), true); - + HelpFunctions.compare( + context.getContextJsonEntity(), + emptyContext.getContextJsonEntity(), + true + ); } @Test @@ -163,13 +170,21 @@ void doubledContextUrlsTest() { RoCrateMetadataContext contextDoubled = new RoCrateMetadataContext(); contextDoubled.addToContextFromUrl(url); contextDoubled.addToContextFromUrl(url); - - HelpFunctions.compare(context.getContextJsonEntity(), contextDoubled.getContextJsonEntity(), true); + + HelpFunctions.compare( + context.getContextJsonEntity(), + contextDoubled.getContextJsonEntity(), + true + ); RoCrateMetadataContext emptyContext = new RoCrateMetadataContext(); contextDoubled.deleteUrlFromContext(url); - HelpFunctions.compare(emptyContext.getContextJsonEntity(), contextDoubled.getContextJsonEntity(), true); + HelpFunctions.compare( + emptyContext.getContextJsonEntity(), + contextDoubled.getContextJsonEntity(), + true + ); } @Test @@ -179,18 +194,19 @@ void deleteNonExistentUrlTest() { context.deleteUrlFromContext("www.example.com"); - HelpFunctions.compare(context.getContextJsonEntity(), emptyContext.getContextJsonEntity(), true); + HelpFunctions.compare( + context.getContextJsonEntity(), + emptyContext.getContextJsonEntity(), + true + ); } @Test void creationFromUrlAndPairsTest() { + JsonObject res = Json.objectNode(); + JsonArray arr = Json.arrayNode(); - var objectMapper = MyObjectMapper.getMapper(); - - ObjectNode res = objectMapper.createObjectNode(); - ArrayNode arr = objectMapper.createArrayNode(); - - ObjectNode node = objectMapper.createObjectNode(); + JsonObject node = Json.objectNode(); node.put("house", "www.example.con/house"); node.put("road", "www.example.con/road"); arr.add(node); @@ -201,9 +217,9 @@ void creationFromUrlAndPairsTest() { HelpFunctions.compare(newContext.getContextJsonEntity(), res, true); var data = new DataEntity.DataEntityBuilder() - .addType("house") - .setId("https://www.example.com/entity") - .build(); + .addType("house") + .setId("https://www.example.com/entity") + .build(); // house is in the context assertTrue(newContext.checkEntity(data)); } @@ -211,33 +227,33 @@ void creationFromUrlAndPairsTest() { @Test void testIdType() { AbstractEntity validEntity = new DataEntity.DataEntityBuilder() - .setId("Airline") // this is defined in the context! - .addType("@id") // this is a JSON-LD feature to refer to the ID ("Airline") as a type - .addType("@json") // this is a JSON-LD built-in type - .build(); + .setId("Airline") // this is defined in the context! + .addType("@id") // this is a JSON-LD feature to refer to the ID ("Airline") as a type + .addType("@json") // this is a JSON-LD built-in type + .build(); assertTrue(this.context.checkEntity(validEntity)); AbstractEntity invalidEntity = new DataEntity.DataEntityBuilder() - .setId("Something which is definitely not in the context") - .addType("@id") - .build(); + .setId("Something which is definitely not in the context") + .addType("@id") + .build(); assertFalse(this.context.checkEntity(invalidEntity)); } @Test void testJsonType() { AbstractEntity validEntity = new DataEntity.DataEntityBuilder() - .addType("@json") // this is a JSON-LD built-in type - .build(); + .addType("@json") // this is a JSON-LD built-in type + .build(); assertTrue(this.context.checkEntity(validEntity)); } @Test void testAbsoluteUrlType() { AbstractEntity validEntity = new DataEntity.DataEntityBuilder() - .addType("http://example.org/Person") // this is not in the context! - .addProperty("http://example.org/Thing", "Some thing") - .build(); + .addType("http://example.org/Person") // this is not in the context! + .addProperty("http://example.org/Thing", "Some thing") + .build(); assertTrue(this.context.checkEntity(validEntity)); } @@ -267,10 +283,15 @@ void testReadKeys() { var expected = Set.of("custom", "owl", "datacite", "xsd", "rdfs"); var given = this.complexContext.getKeys(); for (String key : expected) { - assertTrue(given.contains(key), "Key " + key + " not found in the context"); + assertTrue( + given.contains(key), + "Key " + key + " not found in the context" + ); } // prove immutability - assertThrows(UnsupportedOperationException.class, () -> given.add("newKey")); + assertThrows(UnsupportedOperationException.class, () -> + given.add("newKey") + ); } @Test @@ -280,11 +301,18 @@ void testReadPairs() { var keys = given.keySet(); var values = given.values(); for (String key : expected) { - assertTrue(keys.contains(key), "Key " + key + " not found in the context"); - values.forEach(s -> assertFalse(s.isEmpty(), "Value for key " + key + " is empty")); + assertTrue( + keys.contains(key), + "Key " + key + " not found in the context" + ); + values.forEach(s -> + assertFalse(s.isEmpty(), "Value for key " + key + " is empty") + ); } // prove immutability - assertThrows(UnsupportedOperationException.class, () -> given.put("newKey", "newValue")); + assertThrows(UnsupportedOperationException.class, () -> + given.put("newKey", "newValue") + ); } @Test @@ -292,13 +320,13 @@ void checkEntity_withDefinedPrefixedType_succeeds() throws IOException { // assume we read a crate just for demonstration RoCrate crate = new RoCrate(); // and we extend the context - RoCrateMetadataContext context = new RoCrateMetadataContext(); + RoCrateMetadataContext context = new RoCrateMetadataContext(); context.addToContext("rdfs", "https://www.w3.org/2000/01/rdf-schema#"); crate.setMetadataContext(context); // then we use the new context DataEntity entity = new DataEntity.DataEntityBuilder() - .addType("rdfs:Property") - .build(); + .addType("rdfs:Property") + .build(); crate.addDataEntity(entity); // Then we expect this to work assertTrue(context.checkEntity(entity)); diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java new file mode 100644 index 00000000..55343b9c --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java @@ -0,0 +1,88 @@ +package edu.kit.datamanager.ro_crate.crate; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.special.CrateVersion; +import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.io.IOException; +import java.net.URI; +import java.net.URISyntaxException; +import java.util.Collection; +import org.junit.jupiter.api.Test; + +class BuilderSpec12Test { + + private URI profile1; + private URI profile2; + + @Test + void testAppendConformsTo() throws URISyntaxException { + Crate crate = new RoCrate.BuilderWithDraftFeatures() + .alsoConformsTo(new URI("https://w3id.org/ro/wfrun/process/0.1")) + .alsoConformsTo(new URI("https://example.com/myprofile/1.0")) + .build(); + JsonValue conformsTo = crate.getJsonDescriptor().getProperty("conformsTo"); + assertTrue(conformsTo.isArray()); + // one version and two profiles + assertEquals(1 + 2, conformsTo.size()); + } + + @Test + void testModificationOfDraftCrate() throws URISyntaxException, IOException { + String path = this.getClass() + .getResource("/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array") + .getPath(); + RoCrate crate = Readers.newFolderReader().readCrate(path); + Collection existingProfiles = crate.getProfiles(); + profile1 = new URI("https://example.com/myprofile/1.0"); + profile2 = new URI("https://example.com/myprofile/2.0"); + // the loaded crate has at least one profile + assertFalse(existingProfiles.isEmpty()); + // and the ones we will add later are not part of it + assertFalse(existingProfiles.contains(profile1.toString())); + assertFalse(existingProfiles.contains(profile2.toString())); + + // add profiles + RoCrate modifiedCrate = new RoCrate.BuilderWithDraftFeatures(crate) + .alsoConformsTo(profile1) + .alsoConformsTo(profile2) + .addContextualEntity( + new ContextualEntity.ContextualEntityBuilder() + .addType("CreativeWork") + .build() + ) + .build(); + + // sanity checks + Validator defaultValidation = new Validator(new JsonSchemaValidation()); + assertTrue(defaultValidation.validate(modifiedCrate)); + assertEquals(CrateVersion.LATEST_UNSTABLE, crate.getVersion().get()); + assertEquals( + CrateVersion.LATEST_UNSTABLE, + modifiedCrate.getVersion().get() + ); + + // number of profiles increased by 2 + Collection newProfileState = modifiedCrate.getProfiles(); + assertEquals(existingProfiles.size() + 2, newProfileState.size()); + // new profiles are present + assertTrue(newProfileState.contains(profile1.toString())); + assertTrue(newProfileState.contains(profile2.toString())); + // old profiles are present + assertEquals( + 0, + existingProfiles + .stream() + .filter(txt -> !newProfileState.contains(txt)) + .count() + ); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java similarity index 95% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java index d4fed2a9..76ec126a 100644 --- a/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderTest.java @@ -5,7 +5,6 @@ import org.junit.jupiter.api.Test; -import com.fasterxml.jackson.core.JsonProcessingException; import edu.kit.datamanager.ro_crate.HelpFunctions; import edu.kit.datamanager.ro_crate.RoCrate; @@ -14,7 +13,7 @@ class BuilderTest { @Test - void testReadBuilder() throws JsonProcessingException { + void testReadBuilder() throws IOException { ContextualEntity license = new ContextualEntity.ContextualEntityBuilder() .addType("CreativeWork") .setId("https://creativecommons.org/licenses/by-nc-sa/3.0/au/") @@ -56,7 +55,7 @@ void testAddCrateWithOnlyRootDataEntity() throws IOException { } @Test - void testEmptyCrates() throws JsonProcessingException { + void testEmptyCrates() throws IOException { RoCrate built = new RoCrate.RoCrateBuilder().build(); RoCrate constructed = new RoCrate(); diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/HasPartTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/HasPartTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/HasPartTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/HasPartTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/OtherFilesTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/OtherFilesTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/OtherFilesTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/OtherFilesTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/SerializationTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/SerializationTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/SerializationTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/SerializationTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java similarity index 93% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java index 31c0dc8e..9b051d99 100644 --- a/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddContext.java @@ -4,7 +4,6 @@ import edu.kit.datamanager.ro_crate.HelpFunctions; import edu.kit.datamanager.ro_crate.RoCrate; -import com.fasterxml.jackson.core.JsonProcessingException; import java.io.IOException; import java.util.Objects; @@ -25,7 +24,7 @@ void setup() throws IOException { } @Test - void testAddRemoveValuePair() throws JsonProcessingException { + void testAddRemoveValuePair() throws IOException { RoCrate crate = new RoCrate.RoCrateBuilder().addValuePairToContext("key", "value").build(); RoCrate defaultCrate = new RoCrate.RoCrateBuilder().build(); @@ -36,7 +35,7 @@ void testAddRemoveValuePair() throws JsonProcessingException { } @Test - void testAddRemoveUrl() throws JsonProcessingException { + void testAddRemoveUrl() throws IOException { RoCrate crate = new RoCrate.RoCrateBuilder().addUrlToContext("https://example.com").build(); RoCrate defaultCrate = new RoCrate.RoCrateBuilder().build(); diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java new file mode 100644 index 00000000..037d306f --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java @@ -0,0 +1,213 @@ +package edu.kit.datamanager.ro_crate.crate; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.PersonEntity; +import edu.kit.datamanager.ro_crate.entities.contextual.PlaceEntity; +import edu.kit.datamanager.ro_crate.entities.data.FileEntity; +import java.io.IOException; +import org.junit.jupiter.api.Test; + +public class TestRemoveAddEntity { + + @Test + void testAddRemoveEntity() throws IOException { + RoCrate roCrate = new RoCrate.RoCrateBuilder( + "minimal", + "minimal RO_crate", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addDataEntity( + new FileEntity.FileEntityBuilder() + .setId("survey-responses-2019.csv") + .addProperty("name", "Survey responses") + .addProperty("contentSize", "26452") + .addProperty("encodingFormat", "text/csv") + .build() + ) + .build(); + HelpFunctions.compareCrateJsonToFileInResources( + roCrate, + "/json/crate/onlyOneFile.json" + ); + + assertEquals(0, roCrate.getAllContextualEntities().size()); + assertEquals(1, roCrate.getAllDataEntities().size()); + + // remove entity and check if equals to the basic crate + roCrate.deleteEntityById("survey-responses-2019.csv"); + assertEquals(0, roCrate.getAllDataEntities().size()); + HelpFunctions.compareCrateJsonToFileInResources( + roCrate, + "/json/crate/simple.json" + ); + } + + @Test + void withTwoFiles() throws IOException { + PlaceEntity place = new PlaceEntity.PlaceEntityBuilder() + .setId("http://sws.geonames.org/8152662/") + .addProperty("name", "Catalina Park") + .build(); + + PersonEntity person = new PersonEntity.PersonEntityBuilder() + .setId("#alice") + .addProperty("name", "Alice") + .addProperty("description", "One of hopefully many Contextual Entities") + .build(); + + FileEntity file = new FileEntity.FileEntityBuilder() + .setId("data1.txt") + .addProperty("description", "One of hopefully many Data Entities") + .setContentLocation(place.getId()) + .addAuthor(person.getId()) + .build(); + + RoCrate roCrate = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addContextualEntity(place) + .addContextualEntity(person) + .addDataEntity(file) + .addDataEntity( + new FileEntity.FileEntityBuilder().setId("data2.txt").build() + ) + .build(); + + HelpFunctions.compareCrateJsonToFileInResources( + roCrate, + "/json/crate/twoFiles.json" + ); + + assertEquals(2, roCrate.getAllDataEntities().size()); + assertEquals(2, roCrate.getAllContextualEntities().size()); + + roCrate.deleteEntityById("data1.txt"); + assertEquals(1, roCrate.getAllDataEntities().size()); + + roCrate.deleteEntityById("data2.txt"); + assertEquals(0, roCrate.getAllDataEntities().size()); + + roCrate.deleteEntityById("#alice"); + assertEquals(1, roCrate.getAllContextualEntities().size()); + + roCrate.deleteEntityById("http://sws.geonames.org/8152662/"); + assertEquals(0, roCrate.getAllContextualEntities().size()); + + RoCrate roCrate2 = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ).build(); + HelpFunctions.compareTwoCrateJson(roCrate, roCrate2); + } + + @Test + void removeOtherOccur() throws IOException { + PlaceEntity place = new PlaceEntity.PlaceEntityBuilder() + .setId("http://sws.geonames.org/8152662/") + .addProperty("name", "Catalina Park") + .build(); + + PersonEntity person = new PersonEntity.PersonEntityBuilder() + .setId("#alice") + .addProperty("name", "Alice") + .addProperty("description", "One of hopefully many Contextual Entities") + .build(); + + FileEntity file = new FileEntity.FileEntityBuilder() + .setId("data1.txt") + .addProperty("description", "One of hopefully many Data Entities") + .setContentLocation(place.getId()) + .addAuthor(person.getId()) + .addAuthor(person.getId()) + .build(); + + RoCrate roCrate = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addContextualEntity(place) + .addContextualEntity(person) + .addDataEntity(file) + .build(); + + assertEquals(1, roCrate.getAllDataEntities().size()); + assertEquals(2, roCrate.getAllContextualEntities().size()); + + roCrate.deleteEntityById(person.getId()); + assertEquals(1, roCrate.getAllContextualEntities().size()); + + roCrate.deleteEntityById(place.getId()); + assertEquals(0, roCrate.getAllContextualEntities().size()); + assertEquals(1, roCrate.getAllDataEntities().size()); + + FileEntity file2 = new FileEntity.FileEntityBuilder() + .setId("data1.txt") + .addProperty("description", "One of hopefully many Data Entities") + .build(); + RoCrate second2 = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addDataEntity(file2) + .build(); + + HelpFunctions.compareTwoCrateJson(roCrate, second2); + } + + @Test + void testAddEntitiesWithSameId() throws IOException { + PersonEntity person = new PersonEntity.PersonEntityBuilder() + .setId("person") + .addProperty("name", "Alice") + .addProperty("description", "One of hopefully many Contextual Entities") + .build(); + + RoCrate roCrate = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addContextualEntity(person) + .build(); + + RoCrate roCrateNew = new RoCrate.RoCrateBuilder( + "Example RO-Crate", + "The RO-Crate Root Data Entity", + "2023", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addContextualEntity(person) + .build(); + + assertEquals(1, roCrate.getAllContextualEntities().size()); + assertEquals(1, roCrateNew.getAllContextualEntities().size()); + + PersonEntity personNew = new PersonEntity.PersonEntityBuilder() + .setId("person") + .addProperty("name", "Peter Sefton") + .addProperty("email", "peter.sefton@uts.edu.au") + .build(); + + roCrateNew.addContextualEntity(personNew); + + assertEquals(1, roCrate.getAllContextualEntities().size()); + assertEquals(1, roCrateNew.getAllContextualEntities().size()); + + assertEquals(roCrate.getContextualEntityById("person"), person); + assertEquals(roCrateNew.getContextualEntityById("person"), personNew); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/preview/PreviewCrateTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/preview/PreviewCrateTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/preview/PreviewCrateTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/preview/PreviewCrateTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/RealTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/RealTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/RealTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/RealTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/WorkflowHubTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/WorkflowHubTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/WorkflowHubTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/realexamples/WorkflowHubTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java similarity index 61% rename from src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java index 170ff09c..f681f1e1 100644 --- a/src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/crate/validation/ValidationTest.java @@ -1,46 +1,49 @@ package edu.kit.datamanager.ro_crate.crate.validation; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; import edu.kit.datamanager.ro_crate.Crate; import edu.kit.datamanager.ro_crate.RoCrate; import edu.kit.datamanager.ro_crate.entities.data.WorkflowEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; import edu.kit.datamanager.ro_crate.validation.Validator; - -import org.junit.jupiter.api.Test; - import java.io.IOException; import java.io.InputStream; import java.net.URISyntaxException; import java.net.URL; import java.util.Objects; - -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertTrue; +import org.junit.jupiter.api.Test; public class ValidationTest { @Test void jsonSchemaValidationTest() throws IOException, URISyntaxException { - Crate crate = new RoCrate.RoCrateBuilder("workflowCrate", "this is a test", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addDataEntity( - new WorkflowEntity.WorkflowEntityBuilder() - .setId("https://www.example.com/entity") - .build() - ) - .build(); - - InputStream inputStream = - ValidationTest.class.getResourceAsStream("/crates/validation/workflowschema.json"); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode expectedJson = objectMapper.readTree(inputStream); + Crate crate = new RoCrate.RoCrateBuilder( + "workflowCrate", + "this is a test", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + .addDataEntity( + new WorkflowEntity.WorkflowEntityBuilder() + .setId("https://www.example.com/entity") + .build() + ) + .build(); + + InputStream inputStream = ValidationTest.class.getResourceAsStream( + "/crates/validation/workflowschema.json" + ); + JsonValue expectedJson = Json.parse(inputStream); Validator validator = new Validator(new JsonSchemaValidation(expectedJson)); assertTrue(validator.validate(crate)); - URL schemaUrl = Objects.requireNonNull(ValidationTest.class.getResource("/crates/validation/workflowschema.json")); + URL schemaUrl = Objects.requireNonNull( + ValidationTest.class.getResource("/crates/validation/workflowschema.json") + ); String schemaPath = schemaUrl.getPath(); // test with string file location validator = new Validator(new JsonSchemaValidation(schemaPath)); diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java new file mode 100644 index 00000000..efc32a7b --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java @@ -0,0 +1,148 @@ +package edu.kit.datamanager.ro_crate.entities; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonString; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.util.Optional; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.NullAndEmptySource; +import org.junit.jupiter.params.provider.ValueSource; + +class AbstractEntityTest { + + @ParameterizedTest + @NullAndEmptySource + @ValueSource(strings = { " ", "\t", "\n" }) + void mergeIdIntoValue_withInvalidId_returnsEmpty(String invalidId) { + Optional result = AbstractEntity.mergeIdIntoValue( + invalidId, + null + ); + assertTrue(result.isEmpty(), "Should return empty Optional for invalid ID"); + + Optional result2 = AbstractEntity.mergeIdIntoValue( + invalidId, + Json.objectNode() + ); + assertTrue( + result2.isEmpty(), + "Should return empty Optional for invalid ID" + ); + } + + @Test + void mergeIdIntoValue_withNullCurrentValue_returnsIdObject() { + String id = "test-id"; + Optional result = AbstractEntity.mergeIdIntoValue(id, null); + + // Should return a value for valid ID + JsonValue node = result.orElseThrow(); + assertTrue(node.isObject(), "Should return an object"); + assertEquals(id, node.get("@id").asText(), "Should contain the ID"); + } + + @Test + void mergeIdIntoValue_withExistingIdAsString_returnsEmpty() { + String id = "test-id"; + JsonValue currentValue = new JsonString(id); + + Optional result = AbstractEntity.mergeIdIntoValue( + id, + currentValue + ); + assertTrue( + result.isEmpty(), + "Should return empty when ID already exists as string" + ); + } + + @Test + void mergeIdIntoValue_withExistingIdObject_returnsEmpty() { + String id = "test-id"; + JsonObject currentValue = Json.objectNode(); + currentValue.put("@id", id); + + Optional result = AbstractEntity.mergeIdIntoValue( + id, + currentValue + ); + assertTrue( + result.isEmpty(), + "Should return empty when ID already exists as object" + ); + } + + @Test + void mergeIdIntoValue_withNonArrayValue_createsArray() { + String id = "new-id"; + String existingId = "existing-id"; + JsonObject existingValue = Json.objectNode(); + existingValue.put("@id", existingId); + + Optional result = AbstractEntity.mergeIdIntoValue( + id, + existingValue + ); + + assertTrue(result.isPresent(), "Should return a value"); + JsonValue node = result.get(); + assertTrue(node.isArray(), "Should be converted to array"); + assertEquals(2, node.size(), "Should contain both values"); + assertEquals( + existingId, + node.get(0).get("@id").asText(), + "Should contain existing ID" + ); + assertEquals(id, node.get(1).get("@id").asText(), "Should contain new ID"); + } + + @Test + void mergeIdIntoValue_withExistingArray_addsToArray() { + String id = "new-id"; + String existingId = "existing-id"; + + JsonArray currentValue = Json.arrayNode(); + JsonObject existingIdObj = Json.objectNode(); + existingIdObj.put("@id", existingId); + currentValue.add(existingIdObj); + + Optional result = AbstractEntity.mergeIdIntoValue( + id, + currentValue + ); + + assertTrue(result.isPresent(), "Should return a value"); + JsonValue node = result.get(); + assertTrue(node.isArray(), "Should remain an array"); + assertEquals(2, node.size(), "Should contain both values"); + assertEquals( + existingId, + node.get(0).get("@id").asText(), + "Should contain existing ID" + ); + assertEquals(id, node.get(1).get("@id").asText(), "Should contain new ID"); + } + + @Test + void mergeIdIntoValue_withExistingArrayContainingId_returnsEmpty() { + String id = "test-id"; + JsonArray currentValue = Json.arrayNode(); + JsonObject existingIdObj = Json.objectNode(); + existingIdObj.put("@id", id); + currentValue.add(existingIdObj); + + Optional result = AbstractEntity.mergeIdIntoValue( + id, + currentValue + ); + assertTrue( + result.isEmpty(), + "Should return empty when ID already exists in array" + ); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntityTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java new file mode 100644 index 00000000..c990de6f --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java @@ -0,0 +1,148 @@ +package edu.kit.datamanager.ro_crate.entities.contextual; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import java.io.IOException; +import org.junit.jupiter.api.Test; + +/** + * @author Nikola Tzotchev on 5.2.2022 г. + * @version 1 + */ +public class ContextualEntityTest { + + /** + * This is exactly the same test as the PlaceEntityTest it shows again (similarly to the + * DataEntityTest) that we can also just use this class for the creation of our Contextual + * Entities + */ + @Test + void testSerialization() throws IOException { + // this does not make any difference for our testcase it just shows how the GeoCoordinates entity will look + ContextualEntity geo = new ContextualEntity.ContextualEntityBuilder() + .setId("#b4168a98-8534-4c6d-a568-64a55157b656") + .addType("GeoCoordinates") + .addProperty("latitude", "-33.7152") + .addProperty("longitude", "150.30119") + .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") + .build(); + + ContextualEntity place = new ContextualEntity.ContextualEntityBuilder() + .addType("Place") + .setId("https://sws.geonames.org/8152662/") + .addProperty( + "description", + "Catalina Park is a disused motor racing venue, located at Katoomba ..." + ) + .addProperty("identifier", "https://sws.geonames.org/8152662/") + .addProperty("uri", "https://www.geonames.org/8152662/catalina-park.html") + .addProperty("name", "Catalina Park") + // here we can also do .setGeo(geo) + .addIdProperty("geo", geo) + .build(); + + assertTrue(place.getLinkedTo().contains(geo.getId())); + HelpFunctions.compareEntityWithFile( + place, + "/json/entities/contextual/place.json" + ); + } + + @Test + void testAddAllValidCase() throws IOException { + ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() + .setId("#b4168a98-8534-4c6d-a568-64a55157b656") + .addType("GeoCoordinates") + .addProperty("latitude", "-33.7152") + .addProperty("longitude", "150.30119") + .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") + .build(); + + String allProperties = """ + { + "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", + "@type": "GeoCoordinates", + "latitude": "-33.7152", + "longitude": "150.30119", + "name": "Latitude: -33.7152 Longitude: 150.30119" + } + """; + + JsonObject properties = (JsonObject) Json.parse(allProperties); + ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() + .setAllIfValid(properties) + .build(); + assertEquals(second.getProperties(), first.getProperties()); + } + + @Test + void testAddAllInvalidCase() throws IOException { + ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() + .setId("#b4168a98-8534-4c6d-a568-64a55157b656") + .addType("GeoCoordinates") + .addProperty("latitude", "-33.7152") + .addProperty("longitude", "150.30119") + .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") + .build(); + + String allProperties = """ + { + "wrong property": {"any": "value"}, + "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", + "@type": "GeoCoordinates", + "latitude": "-33.7152", + "longitude": "150.30119", + "name": "Latitude: -33.7152 Longitude: 150.30119" + } + """; + + JsonObject properties = (JsonObject) Json.parse(allProperties); + ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() + .setId("second") + .setAllIfValid(properties) + .build(); + assertNotEquals(second.getProperties(), first.getProperties()); + JsonObject empty = new ContextualEntity.ContextualEntityBuilder() + .setId("second") + .build() + .getProperties(); + assertEquals(empty, second.getProperties()); + } + + @Test + void testAddAllUnsafeDoesInvalidCase() throws IOException { + ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() + .setId("#b4168a98-8534-4c6d-a568-64a55157b656") + .addType("GeoCoordinates") + .addProperty("latitude", "-33.7152") + .addProperty("longitude", "150.30119") + .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") + .build(); + + String allProperties = """ + { + "wrong property": {"any": "value"}, + "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", + "@type": "GeoCoordinates", + "latitude": "-33.7152", + "longitude": "150.30119", + "name": "Latitude: -33.7152 Longitude: 150.30119" + } + """; + + JsonObject properties = (JsonObject) Json.parse(allProperties); + ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() + .setId("second") + .setAllUnsafe(properties) + .build(); + assertNotEquals(second.getProperties(), first.getProperties()); + JsonObject empty = new ContextualEntity.ContextualEntityBuilder() + .setId("second") + .build() + .getProperties(); + assertNotEquals(empty, second.getProperties()); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/OrganizationEntityTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PersonEntityTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/PlaceEntityTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java new file mode 100644 index 00000000..bddc3ba7 --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java @@ -0,0 +1,257 @@ +package edu.kit.datamanager.ro_crate.entities.data; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity.DataEntityBuilder; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonNull; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.io.IOException; +import java.net.URI; +import java.net.URISyntaxException; +import java.net.URL; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Arrays; +import java.util.List; +import java.util.stream.Stream; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.MethodSource; + +/** + * @author Nikola Tzotchev on 4.2.2022 г. + * @version 1 + */ +class DataEntityTest { + + @Test + void testSerialization() throws IOException { + JsonObject bigJson = Json.objectNode(); + bigJson.put("onefield", "dalkfa"); + JsonObject address = Json.objectNode(); + address.put("street", "x"); + address.put("city", "other"); + address.put("state", "this"); + address.put("zipCode", 66439); + bigJson.set("nestedObject", address); + + DataEntity file = new DataEntityBuilder() + .addType("File") + .setId("https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf") + .addProperty("name", "RO-Crate specification") + .addProperty("encodingFormat", "application/pdf") + .addProperty("url", "https://zenodo.org/record/3541888") + // this should not be included since it does not follow the json flatten form of the RO-Crate + .addProperty("test", bigJson) + .build(); + assertNull(file.getProperty("test")); + HelpFunctions.compareEntityWithFile( + file, + "/json/entities/data/fileEntity.json" + ); + } + + @Test + void testSerializationOutside() throws IOException { + JsonObject json = Json.objectNode(); + json.put("name", "RO-Crate specification"); + json.put("encodingFormat", "application/pdf"); + json.put("url", "https://zenodo.org/record/3541888"); + json.put( + "@id", + "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf" + ); + json.put("@type", "File"); + + DataEntity data = new DataEntity.DataEntityBuilder().build(); + data.setProperties(json); + HelpFunctions.compareEntityWithFile( + data, + "/json/entities/data/fileEntity.json" + ); + + JsonObject address = Json.objectNode(); + address.put("street", "x"); + address.put("city", "other"); + address.put("state", "this"); + address.put("zipCode", 66439); + json.set("nestedObject", address); + // this should not be included into the entity since it does not follow the basic RO-Crate structure + data.setProperties(json); + assertNotEquals("", data.getId()); + HelpFunctions.compareEntityWithFile( + data, + "/json/entities/data/fileEntity.json" + ); + } + + @Test + void testUriCheck() { + //this entity id is a valid URL so there should not be any console information + DataEntity dataEntity = new DataEntity.DataEntityBuilder() + .addType("File") + .setLocation(URI.create("https://www.example.com/19")) + .build(); + + assertNotNull(dataEntity); + + Exception exception = assertThrows(IllegalArgumentException.class, () -> + new DataEntity.DataEntityBuilder() + .addType("File") + .setLocationWithExceptions(URI.create("zzz://wrong/url")) + .build() + ); + + assertEquals( + "This Data Entity remote ID does not resolve to a valid URL.", + exception.getMessage() + ); + + assertNotNull(dataEntity); + } + + @Test + void testPathCheck() throws IOException { + FileEntity dataEntity = new FileEntity.FileEntityBuilder() + .setLocationWithExceptions(Paths.get("example.json")) + .setId("example.json") + .addProperty("name", "RO-Crate specification") + .setEncodingFormat("application/json") + .build(); + assertEquals("example.json", dataEntity.getId()); + HelpFunctions.compareEntityWithFile( + dataEntity, + "/json/entities/data/localFile.json" + ); + + String fileName = "cp7glop.ai"; + Path filePath = Paths.get(fileName); + + dataEntity = new FileEntity.FileEntityBuilder() + .setLocationWithExceptions(filePath) + .setId(fileName) + .addProperty("name", "Diagram showing trend to increase") + .setEncodingFormat("application/pdf") + .build(); + assertEquals(fileName, dataEntity.getId()); + assertEquals(dataEntity.getPath(), filePath); + assertEquals( + "application/pdf", + dataEntity.getProperty("encodingFormat").asText() + ); + } + + @Test + void testEncodedUrl() throws URISyntaxException { + //this entity id is a valid URL so there should not be any console information + DataEntity dataEntity = new DataEntity.DataEntityBuilder() + .addType("File") + .setLocation( + URI.create("https://github.com/kit-data-manager/ro-crate-java/issues/5") + ) + .build(); + + assertEquals( + "https://github.com/kit-data-manager/ro-crate-java/issues/5", + dataEntity.getId() + ); + + URL url = HelpFunctions.class.getResource("/json/crate/simple2.json"); + assert url != null; + dataEntity = new DataEntity.DataEntityBuilder() + .addType("File") + .setLocationWithExceptions(Paths.get(url.toURI())) + .setId("simple2.json") + .build(); + + assertNotNull(dataEntity); + + dataEntity = new DataEntity.DataEntityBuilder() + .addType("File") + .setLocationWithExceptions( + Paths.get("/json/crate/Results%20and%20Diagrams/almost-50%25.json") + ) + .setId("almost-50%25.json") + .build(); + + assertTrue(dataEntity.getTypes().contains("File")); + assertEquals("almost-50%25.json", dataEntity.getId()); + + // even if the Path is not correctly encoded, the data entity will be added with an encoded Path. + dataEntity = new DataEntity.DataEntityBuilder() + .addType("File") + .setLocationWithExceptions( + Paths.get("/json/crate/Results and Diagrams/almost-50%.json") + ) + .setId("almost-50%.json") + .build(); + assertEquals("almost-50%25.json", dataEntity.getId()); + } + + @Test + void testRemoveProperty() { + FileEntity dataEntity = new FileEntity.FileEntityBuilder() + .addProperty("name", "RO-Crate specification") + .setEncodingFormat("application/json") + .addProperty("url", "https://zenodo.org/record/3541888") + .addProperty( + "@id", + "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf" + ) + .build(); + + dataEntity.removeProperty("url"); + assertNull(dataEntity.getProperty("url")); + assertEquals(4, dataEntity.getProperties().size()); + + List keyList = Arrays.asList("encodingFormat", "name"); + dataEntity.removeProperties(keyList); + assertEquals(2, dataEntity.getProperties().size()); + } + + @Test + void testMixedArrayProperties() { + JsonArray propertyValue = Json.arrayNode(); + propertyValue + .add(1) + .add("2") + .add(3.14) + .add(true) + .add((JsonValue) null) + .add(JsonNull.INSTANCE); + String propertyName = "mixedArray"; + + DataEntity entity = new DataEntityBuilder() + .addProperty(propertyName, propertyValue) + .build(); + assertEquals(propertyValue, entity.getProperty(propertyName)); + } + + @ParameterizedTest + @MethodSource("provideInvalidPropertyValues") + void testNestedArrayProperties(JsonArray propertyValue) { + String propertyName = "invalidArray"; + DataEntity entity = new DataEntityBuilder() + .addProperty(propertyName, propertyValue) + .build(); + assertNull(entity.getProperty(propertyName)); + } + + private static Stream provideInvalidPropertyValues() { + JsonArray withSubArray = Json.arrayNode().add(1).add("2"); + withSubArray.add(JsonArray.create()); + JsonArray withSubObject = Json.arrayNode().add(1).add("2"); + withSubObject.add(JsonObject.create()); + + return Stream.of(withSubArray, withSubObject); + } +} diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java new file mode 100644 index 00000000..b0fb17eb --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java @@ -0,0 +1,115 @@ +package edu.kit.datamanager.ro_crate.entities.data; + +import static org.junit.jupiter.api.Assertions.*; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import java.io.IOException; +import java.net.URI; +import java.nio.file.Paths; +import org.junit.jupiter.api.Test; + +/** + * @author Nikola Tzotchev on 5.2.2022 г. + * @version 1 + */ +public class DataSetEntityTest { + + @Test + void testImpossibleRootId() { + DataSetEntity e = new DataSetEntity.DataSetBuilder() + .setId("./") + .addProperty("not_root", true) + .build(); + assertNotNull(e.getId()); + assertFalse(e.getId().isBlank()); + assertNotEquals(RootDataEntity.ID, e.getId()); + } + + @Test + void testSimpleDirDeserialization() throws IOException { + String id = "lots_of_little_files/"; + DataSetEntity dir = new DataSetEntity.DataSetBuilder() + // this does not change anything, but it shows that the entity contains a physical file + .setLocationWithExceptions(Paths.get("invalid_file")) + .setId(id) + .addProperty("name", "Too many files") + .addProperty( + "description", + "This directory contains many small files, that we're not going to describe in detail." + ) + .build(); + + assertEquals(id, dir.getId()); + HelpFunctions.compareEntityWithFile( + dir, + "/json/entities/data/directory.json" + ); + } + + /** + * This is a test with a directory that is located on the web. It is + * recommended that such a dir list all of its files in the hasPart property + * https://www.researchobject.org/ro-crate/1.1/data-entities.html#directories-on-the-web-dataset-distributions + */ + @Test + void testDirWithHasPartDeserialization() throws IOException { + String id = "second_content"; + DataEntity second_content = new DataEntity.DataEntityBuilder() + .setLocationWithExceptions(Paths.get("does_not_matter")) + .setId(id) + .addProperty( + "description", + "This entity just describes one of the contents in the Dir" + ) + .build(); + + // we can add to hasPart using directly the id, or passing the entity to it + DataSetEntity dir = new DataSetEntity.DataSetBuilder() + .setLocation(URI.create("https://www.example.com/urltodir")) + .addProperty("name", "Directory that is located on the web") + .addToHasPart("first_content") + .addToHasPart(second_content) + .build(); + + assertTrue(dir.hasPart(id)); + HelpFunctions.compareEntityWithFile( + dir, + "/json/entities/data/directoryWeb.json" + ); + } + + @Test + void testWebDir() { + JsonObject propertyValue = Json.objectNode(); + propertyValue.put( + "@id", + "http://example.com/downloads/2020/lots_of_little_files.zip" + ); + + DataSetEntity dir = new DataSetEntity.DataSetBuilder() + .setLocationWithExceptions(Paths.get("lots_of_little_files/")) + .setId("lots_of_little_files/") + .addProperty("name", "Too many files") + .addProperty( + "description", + "This directory contains many small files, that we're not going to describe in detail." + ) + .addProperty("distribution", propertyValue) + .build(); + + assertEquals(dir.getProperty("distribution"), propertyValue); + + DataEntity webDir = new DataEntity.DataEntityBuilder() + .setLocation( + URI.create("http://example.com/downloads/2020/lots_of_little_files.zip") + ) + .addType("DataDownload") + .addProperty("encodingFormat", "application/zip") + .addProperty("contentSize", "82818928") + .build(); + + assertNotNull(webDir); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/FileEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/FileEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/data/FileEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/FileEntityTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java new file mode 100644 index 00000000..a16aae6c --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java @@ -0,0 +1,81 @@ +package edu.kit.datamanager.ro_crate.entities.data; + +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.json.Json; +import java.io.IOException; +import java.nio.file.Paths; +import org.junit.jupiter.api.Test; + +/** + * @author Nikola Tzotchev on 5.2.2022 г. + * @version 1 + */ +public class RootDataEntityTest { + + @Test + void testSerialization() throws IOException { + String id1 = "file1_id"; + FileEntity file1 = new FileEntity.FileEntityBuilder() + .setLocationWithExceptions(Paths.get("does_not_matter")) + .setId(id1) + .build(); + + String id2 = "file2_id"; + FileEntity file2 = new FileEntity.FileEntityBuilder() + .addIdProperty("name", "dsklfajs") + .addIdProperty("name", "11111111") + .setLocationWithExceptions(Paths.get("does_not_matter")) + .setId(id2) + .build(); + + RootDataEntity rootDataEntity = new RootDataEntity.RootDataEntityBuilder() + .addProperty("identifier", "https://doi.org/10.4225/59/59672c09f4a4b") + .addProperty("datePublished", "2000-02-01T00:00:00Z") + .addProperty( + "name", + "Data files associated with the manuscript:Effects of facilitated family case conferencing for ..." + ) + .addProperty( + "description", + "Palliative care planning for nursing home residents with advanced dementia ..." + ) + .addToHasPart(file1) + .addToHasPart(file2) + .addAuthor("a1") + .addAuthor("a2") + .build(); + + assertTrue(rootDataEntity.hasPart(id1)); + assertTrue(rootDataEntity.hasPart(id2)); + HelpFunctions.compareEntityWithFile( + rootDataEntity, + "/json/entities/data/root.json" + ); + } + + @Test + void testSerializationMinimalExample() + throws IOException, IllegalArgumentException { + RootDataEntity rootDataEntity = new RootDataEntity.RootDataEntityBuilder() + .addProperty("name", "Data files") + .addProperty("description", "Palliative care planning...") + .addDateTimePropertyWithExceptions( + "datePublished", + "2024-02-09T08:21:41Z" + ) + .addProperty( + "license", + Json.objectNode().put( + "@id", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ) + ) + .build(); + HelpFunctions.compareEntityWithFile( + rootDataEntity, + "/json/entities/data/rootMinimalExample.json" + ); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntityTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntityTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntityTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/entities/data/WorkflowEntityTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java b/core/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/examples/ExamplesOfSpecificationV1p1Test.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/examples/LearnByExampleTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java similarity index 58% rename from src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java index 8ab685fa..ca8451b1 100644 --- a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/DataCiteImportTest.java @@ -1,78 +1,81 @@ package edu.kit.datamanager.ro_crate.externalproviders; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; +import static org.junit.jupiter.api.Assertions.assertTrue; import edu.kit.datamanager.ro_crate.RoCrate; import edu.kit.datamanager.ro_crate.externalproviders.dataentities.ImportFromDataCite; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; import edu.kit.datamanager.ro_crate.validation.Validator; - +import java.io.IOException; +import java.util.Optional; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpGet; import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.HttpClients; import org.junit.jupiter.api.Test; -import java.io.IOException; -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.assertTrue; - class DataCiteImportTest { @Test void dataCiteImportNewCrate() { - var crate = ImportFromDataCite - .createCrateFromDataCiteResource( - "https://api.datacite.org/application/vnd.datacite.datacite+json/10.1594/pangaea.149669", - Optional.of("importedCrate"), - Optional.of("description"), - Optional.of("2024"), - Optional.of("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")); + var crate = ImportFromDataCite.createCrateFromDataCiteResource( + "https://api.datacite.org/application/vnd.datacite.datacite+json/10.1594/pangaea.149669", + Optional.of("importedCrate"), + Optional.of("description"), + Optional.of("2024"), + Optional.of("https://creativecommons.org/licenses/by-nc-sa/3.0/au/") + ); Validator validator = new Validator(new JsonSchemaValidation()); assertTrue(validator.validate(crate)); } @Test void dataCiteImportToExistingCrate() { - var crate = new RoCrate.RoCrateBuilder("name", "description", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/").build(); - ImportFromDataCite.addDataCiteToCrate("https://api.datacite.org/application/vnd.datacite.datacite+json/10.1594/pangaea.149669", crate); + var crate = new RoCrate.RoCrateBuilder( + "name", + "description", + "2024", + "https://creativecommons.org/licenses/by-nc-sa/3.0/au/" + ).build(); + ImportFromDataCite.addDataCiteToCrate( + "https://api.datacite.org/application/vnd.datacite.datacite+json/10.1594/pangaea.149669", + crate + ); Validator validator = new Validator(new JsonSchemaValidation()); assertTrue(validator.validate(crate)); } @Test void dataCiteImportFromExistingJson() { - String url = "https://api.datacite.org/application/vnd.datacite.datacite+json/10.5061/dryad.91741"; + String url = + "https://api.datacite.org/application/vnd.datacite.datacite+json/10.5061/dryad.91741"; CloseableHttpClient httpClient = HttpClients.createDefault(); HttpGet request = new HttpGet(url); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode jsonNode; + JsonValue jsonNode; try { CloseableHttpResponse response = httpClient.execute(request); - jsonNode = objectMapper.readValue(response.getEntity().getContent(), - JsonNode.class); + jsonNode = Json.parse(response.getEntity().getContent()); var crate = ImportFromDataCite.createCrateFromDataCiteJson( jsonNode, Optional.of("importedCrate"), Optional.of("description"), Optional.of("2024"), - Optional.of("https://creativecommons.org/licenses/by-nc-sa/3.0/au/")); + Optional.of("https://creativecommons.org/licenses/by-nc-sa/3.0/au/") + ); Validator validator = new Validator(new JsonSchemaValidation()); assertTrue(validator.validate(crate)); - String anotherUrl = "https://api.datacite.org/application/vnd.datacite.datacite+json/10.5061/dryad.dr554m2"; + String anotherUrl = + "https://api.datacite.org/application/vnd.datacite.datacite+json/10.5061/dryad.dr554m2"; request = new HttpGet(anotherUrl); response = httpClient.execute(request); - jsonNode = objectMapper.readValue(response.getEntity().getContent(), - JsonNode.class); + jsonNode = Json.parse(response.getEntity().getContent()); assertTrue(validator.validate(crate)); ImportFromDataCite.addDataCiteToCrateFromJson(jsonNode, crate); - } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/OrcidProviderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/OrcidProviderTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/externalproviders/OrcidProviderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/OrcidProviderTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java new file mode 100644 index 00000000..f26861e0 --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java @@ -0,0 +1,53 @@ +package edu.kit.datamanager.ro_crate.externalproviders; + +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertThrows; + +import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity; +import edu.kit.datamanager.ro_crate.externalproviders.organizationprovider.RorProvider; +import java.io.IOException; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +/** + * @author Nikola Tzotchev on 11.2.2022 г. + * @version 1 + */ +public class RorProviderTest { + + @Test + void testExternalRorProvider() throws IOException { + OrganizationEntity organizationEntity = RorProvider.getOrganization( + "https://ror.org/04t3en479" + ); + assertNotNull(organizationEntity); + Assertions.assertEquals( + "https://ror.org/04t3en479", + organizationEntity.getProperty("@id").asText() + ); + Assertions.assertEquals( + "https://ror.org/04t3en479", + organizationEntity.getProperty("url").asText() + ); + Assertions.assertEquals( + "Karlsruhe Institute of Technology", + organizationEntity.getProperty("name").asText() + ); + } + + @Test + void testInvalidRorUrl() { + assertThrows(IllegalArgumentException.class, () -> { + RorProvider.getOrganization("https://notror.org/04t3en479"); + }); + } + + @Test + void testInvalidRorId() { + OrganizationEntity organizationEntity = RorProvider.getOrganization( + "https://ror.org/42" + ); + assertNull(organizationEntity); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/ZenodoImportTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/ZenodoImportTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/externalproviders/ZenodoImportTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/ZenodoImportTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/json/JsonDiscoveryTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/json/JsonDiscoveryTest.java new file mode 100644 index 00000000..5f2a6a1c --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/json/JsonDiscoveryTest.java @@ -0,0 +1,96 @@ +package edu.kit.datamanager.ro_crate.json; + +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.File; +import java.io.InputStream; +import java.util.Collections; +import java.util.List; +import org.junit.jupiter.api.Test; + +/** + * The discovery failures must tell a user who does not know the module layout + * exactly what to add or exclude, so the messages must name the backend + * artifacts. + */ +class JsonDiscoveryTest { + + private static JsonAdapter stubAdapter() { + return new JsonAdapter() { + @Override + public JsonObject objectNode() { + return null; + } + + @Override + public JsonArray arrayNode() { + return null; + } + + @Override + public JsonValue parse(String json) { + return null; + } + + @Override + public JsonValue parse(File file) { + return null; + } + + @Override + public JsonValue parse(InputStream stream) { + return null; + } + + @Override + public String write(JsonValue value) { + return null; + } + + @Override + public String writePretty(JsonValue value) { + return null; + } + }; + } + + @Test + void missingBackendMessageNamesTheBackendArtifacts() { + var exception = assertThrows( + IllegalStateException.class, + () -> Json.uniqueCandidate( + Collections.emptyIterator(), + JsonAdapter.class + ) + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java"), + "message should name the Jackson 2 artifact: " + exception.getMessage() + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java-jackson3"), + "message should name the Jackson 3 artifact: " + exception.getMessage() + ); + } + + @Test + void multipleBackendsMessageSuggestsTheFix() { + JsonAdapter adapter = stubAdapter(); + var exception = assertThrows( + IllegalStateException.class, + () -> Json.uniqueCandidate( + List.of(adapter, adapter).iterator(), + JsonAdapter.class + ) + ); + assertTrue( + exception.getMessage().contains("exclude"), + "message should suggest excluding one backend: " + exception.getMessage() + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java-jackson3"), + "message should name the Jackson 3 artifact: " + exception.getMessage() + ); + } +} diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/json/NeutralJsonModelTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/json/NeutralJsonModelTest.java new file mode 100644 index 00000000..e650d1eb --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/json/NeutralJsonModelTest.java @@ -0,0 +1,153 @@ +package edu.kit.datamanager.ro_crate.json; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertNotEquals; +import static org.junit.jupiter.api.Assertions.assertNull; +import static org.junit.jupiter.api.Assertions.assertSame; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.IOException; +import org.junit.jupiter.api.Test; + +/** Unit tests for the neutral, Jackson-free JSON tree model. */ +class NeutralJsonModelTest { + + @Test + void objectPreservesInsertionOrderAndOverwritesInPlace() { + JsonObject object = JsonObject.create(); + object.put("b", "second").put("a", "first"); + assertEquals("b", object.names().get(0)); + object.put("b", "changed"); + assertEquals(2, object.size()); + assertEquals("changed", object.get("b").asText()); + } + + @Test + void accessorsMirrorJacksonSemantics() { + JsonObject object = JsonObject.create().put("name", "crate"); + assertNull(object.get("absent")); + assertTrue(object.path("absent").isMissing()); + assertEquals("", object.path("absent").asText()); + assertEquals("DEF", object.path("absent").asText("DEF")); + assertTrue(object.has("name")); + assertFalse(object.has("absent")); + assertEquals("crate", object.get("name").asText()); + assertEquals("", object.asText()); // containers mirror Jackson: "" + } + + @Test + void putNullStoresJsonNull() { + JsonObject object = JsonObject.create().putNull("x"); + assertTrue(object.get("x").isNull()); + } + + @Test + void removeWorksByIndexAndName() { + JsonArray array = JsonArray.create().add("a").add("b").add("c"); + assertEquals(new JsonString("b"), array.remove(1)); + assertEquals(2, array.size()); + + JsonObject object = JsonObject.create().put("x", 1).put("y", 2); + assertEquals(new JsonNumber(2), object.remove("y")); + assertNull(object.get("y")); + } + + @Test + void numbersKeepTheirJavaType() throws IOException { + JsonValue parsed = Json.parse("{\"i\": 1, \"l\": 2147483648, \"d\": 1.5}"); + JsonObject object = (JsonObject) parsed; + assertTrue(object.get("i").isNumber()); + assertEquals(1, ((JsonNumber) object.get("i")).getValue()); + assertEquals(2147483648L, ((JsonNumber) object.get("l")).getValue()); + assertEquals(1.5, ((JsonNumber) object.get("d")).getValue()); + } + + @Test + void equalityIsStructuralAndTypeSensitiveForNumbers() { + JsonObject first = JsonObject.create().put("a", JsonArray.create().add(1)); + JsonObject second = JsonObject.create().put("a", JsonArray.create().add(1)); + assertEquals(first, second); + assertEquals(first.hashCode(), second.hashCode()); + + // Jackson numeric node equality is class-strict (verified against + // Jackson 2.22.1: IntNode(1) != LongNode(1), != DoubleNode(1.0)) + assertNotEquals(new JsonNumber(1), new JsonNumber(1.0)); + assertNotEquals(new JsonNumber(1), new JsonNumber(1L)); + assertNotEquals(new JsonNumber(1), new JsonNumber(2147483648L)); + assertNotEquals(new JsonNumber(1), new JsonString("1")); + + // object equality is order-insensitive, mirroring Jackson's LinkedHashMap + JsonObject ordered = JsonObject.create().put("a", 1).put("b", 2); + JsonObject reordered = JsonObject.create().put("b", 2).put("a", 1); + assertEquals(ordered, reordered); + assertEquals(ordered.hashCode(), reordered.hashCode()); + } + + @Test + void deepCopyIsIndependent() { + JsonObject original = JsonObject.create().put( + "nested", + JsonObject.create().put("x", 1) + ); + JsonObject copy = original.deepCopy(); + ((JsonObject) copy.get("nested")).put("x", 2); + assertEquals( + 1, + ((JsonNumber) original.path("nested").path("x")).getValue() + ); + assertEquals(original, original.deepCopy()); + } + + @Test + void valueNodeSemanticsMirrorJackson() { + assertTrue(new JsonString("x").isValueNode()); + assertTrue(JsonNull.INSTANCE.isValueNode()); + assertTrue(JsonNull.INSTANCE.isNull()); + assertFalse(JsonNull.INSTANCE.isString()); + assertEquals("null", JsonNull.INSTANCE.asText()); + assertEquals("default", JsonNull.INSTANCE.asText("default")); + assertEquals("true", JsonBoolean.of(true).asText()); + assertSame(JsonBoolean.TRUE, JsonBoolean.of(true)); + assertTrue(JsonMissing.INSTANCE.isMissing()); + } + + @Test + void setAllCopiesInOrder() { + JsonObject source = JsonObject.create().put("a", 1).put("b", 2); + JsonObject target = JsonObject.create().put("b", 9).put("c", 3); + target.setAll(source); + assertEquals(3, target.size()); + assertEquals(new JsonNumber(2), target.get("b")); + assertEquals(new JsonNumber(1), target.get("a")); + assertEquals(new JsonNumber(3), target.get("c")); + } + + @Test + void fieldsAndIterationExposeValues() { + JsonObject object = JsonObject.create().put("x", "1").put("y", "2"); + var iterator = object.fields(); + assertEquals("x", iterator.next().getKey()); + assertEquals("y", iterator.next().getKey()); + assertFalse(iterator.hasNext()); + + int count = 0; + for (JsonValue value : object) { + count++; + assertTrue(value.isString()); + } + assertEquals(2, count); + } + + @Test + void writeProducesCompactJsonViaAdapter() throws IOException { + JsonObject object = JsonObject.create() + .put("name", "crate") + .put("count", 3) + .putNull("missing"); + assertEquals( + "{\"name\":\"crate\",\"count\":3,\"missing\":null}", + Json.write(object) + ); + } +} diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java new file mode 100644 index 00000000..3640e735 --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java @@ -0,0 +1,82 @@ +package edu.kit.datamanager.ro_crate.other; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; +import io.json.compare.JSONCompare; +import java.io.IOException; +import java.io.InputStream; +import org.junit.jupiter.api.Test; + +public class UtilFunctionsTest { + + @Test + void testUnwrapSimple() throws IOException { + InputStream fileJson = UtilFunctionsTest.class.getResourceAsStream( + "/json/unwrap/simple.json" + ); + + JsonValue node = JsonUtilFunctions.unwrapSingleArray(Json.parse(fileJson)); + JsonValue expectedResult = Json.parse( + UtilFunctionsTest.class.getResourceAsStream( + "/json/unwrap/simpleResult.json" + ) + ); + JSONCompare.assertMatches(node.toString(), expectedResult.toString()); + } + + @Test + void testGettingIdEntriesFromJsonProperty() { + JsonObject jsonNode = Json.objectNode(); + jsonNode.put("@id", "string1"); + + var result = JsonUtilFunctions.getIdPropertiesFromProperty(jsonNode); + assertEquals(1, result.size()); + assertEquals("string1", result.stream().findFirst().get()); + + JsonArray arrayNode = Json.arrayNode(); + arrayNode.add(Json.objectNode().put("@id", "string1")); + arrayNode.add(Json.objectNode().put("@id", "string2")); + + result = JsonUtilFunctions.getIdPropertiesFromProperty(arrayNode); + assertEquals(2, result.size()); + assertTrue(result.contains("string1")); + assertTrue(result.contains("string2")); + } + + @Test + void testGettingIdFromObject() { + JsonObject jsonNode = Json.objectNode(); + + jsonNode.put("random", "not id"); + jsonNode.set("other", Json.arrayNode().add("kdfjdlk").add("kdfjalkfj")); + + jsonNode.set("test", Json.objectNode().put("@id", "test1")); + + jsonNode.set("another", Json.objectNode().put("@id", "test2")); + + jsonNode.set( + "singleArray", + Json.arrayNode().add(Json.objectNode().put("@id", "test3")) + ); + jsonNode.set( + "multipleArrayEl", + Json.arrayNode() + .add(Json.objectNode().put("@id", "test4")) + .add(Json.objectNode().put("@id", "test5")) + ); + + var set = JsonUtilFunctions.getIdPropertiesFromJsonNode(jsonNode); + + assertEquals(5, set.size()); + + for (int i = 1; i <= 5; i++) { + assertTrue(set.contains("test" + i)); + } + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/payload/PayloadTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/payload/PayloadTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/payload/PayloadTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/payload/PayloadTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/preview/PreviewTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/preview/PreviewTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/preview/PreviewTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/preview/PreviewTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/ElnFileFormatTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/ElnFileFormatTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/ElnFileFormatTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/ElnFileFormatTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java new file mode 100644 index 00000000..00b0289f --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java @@ -0,0 +1,48 @@ +package edu.kit.datamanager.ro_crate.reader; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.Crate; +import java.io.IOException; +import java.util.stream.StreamSupport; +import org.junit.jupiter.api.Test; + +/** + * These reading tests are specific for reading 1.2 compliant crates. + * + * They will refer to 1.2-DRAFT as long as the specification is not final. + * Base for these tests are usually examples from the specification, but may + * contain modifications if no example for a certain property is given. + * + * Current specification: https://www.researchobject.org/ro-crate/1.2-DRAFT/ + */ +public class RoCrateReaderSpec12Test { + + /** + * Test reading a minimal crate with multiple conformsTo values, as described in + * https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles.html#declaring-conformance-of-an-ro-crate-profile + */ + @Test + void testReadingCrateWithConformsToArray() throws IOException { + String path = this.getClass() + .getResource("/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array") + .getPath(); + Crate crate = Readers.newFolderReader().readCrate(path); + JsonValue conformsTo = crate.getJsonDescriptor().getProperty("conformsTo"); + assertTrue(conformsTo.isArray()); + assertEquals(2, conformsTo.size()); + // filter the list to only contain the two expected values and expect no changes + long numFiltered = StreamSupport.stream(conformsTo.spliterator(), false) + .filter(node -> { + String asText = node.path("@id").asText(); + return ( + asText.equals("https://w3id.org/ro/crate/1.2-DRAFT") || + asText.equals("https://example.com/my/profile/1.0-TEST") + ); + }) + .count(); + assertEquals(2, numFiltered); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/TestableReaderStrategy.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/TestableReaderStrategy.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/TestableReaderStrategy.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/TestableReaderStrategy.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/special/CrateVersionTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/special/CrateVersionTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/special/CrateVersionTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/special/CrateVersionTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/special/IdentifierUtilsTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/special/IdentifierUtilsTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/special/IdentifierUtilsTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/special/IdentifierUtilsTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/util/FileSystemUtilTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/util/FileSystemUtilTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/util/FileSystemUtilTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/util/FileSystemUtilTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/validation/ValidationDiscoveryTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/validation/ValidationDiscoveryTest.java new file mode 100644 index 00000000..e339c802 --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/validation/ValidationDiscoveryTest.java @@ -0,0 +1,55 @@ +package edu.kit.datamanager.ro_crate.validation; + +import static org.junit.jupiter.api.Assertions.assertThrows; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.util.Collections; +import java.util.List; +import org.junit.jupiter.api.Test; + +/** + * The discovery failures must tell a user who does not know the module layout + * exactly what to add or exclude, so the messages must name the backend + * artifacts. + */ +class ValidationDiscoveryTest { + + @Test + void missingBackendMessageNamesTheBackendArtifacts() { + var exception = assertThrows( + IllegalStateException.class, + () -> Validation.uniqueCandidate( + Collections.emptyIterator(), + ValidatorStrategy.class + ) + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java"), + "message should name the Jackson 2 artifact: " + exception.getMessage() + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java-jackson3"), + "message should name the Jackson 3 artifact: " + exception.getMessage() + ); + } + + @Test + void multipleBackendsMessageSuggestsTheFix() { + ValidatorStrategy strategy = crate -> true; + var exception = assertThrows( + IllegalStateException.class, + () -> Validation.uniqueCandidate( + List.of(strategy, strategy).iterator(), + ValidatorStrategy.class + ) + ); + assertTrue( + exception.getMessage().contains("exclude"), + "message should suggest excluding one backend: " + exception.getMessage() + ); + assertTrue( + exception.getMessage().contains("edu.kit.datamanager:ro-crate-java-jackson3"), + "message should name the Jackson 3 artifact: " + exception.getMessage() + ); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/CommonWriterTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/CommonWriterTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/CommonWriterTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/CommonWriterTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/ElnFileWriterTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/ElnFileWriterTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/ElnFileWriterTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/ElnFileWriterTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java diff --git a/core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java new file mode 100644 index 00000000..7d8a877e --- /dev/null +++ b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java @@ -0,0 +1,558 @@ +package edu.kit.datamanager.ro_crate.writer; + +import static edu.kit.datamanager.ro_crate.util.Graph.*; +import static org.junit.jupiter.api.Assertions.*; + +import edu.kit.datamanager.ro_crate.HelpFunctions; +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; + +class RoCrateMetadataGenerationTest { + + private final String currentVersionId = + new ProvenanceManager().getLibraryId(); + + private Validator validator; + + @BeforeEach + void setUp() { + validator = new Validator(new JsonSchemaValidation()); + } + + private void validateCrate(RoCrate crate) { + assertTrue( + validator.validate(crate), + "Crate should validate against the JSON schema" + ); + } + + @Test + void should_ContainRoCrateJavaEntities_When_WritingEmptyCrate( + @TempDir Path tempDir + ) throws IOException { + // Create and write crate + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + + // Re-read the crate to verify it's still valid after writing + RoCrate readCrate = Readers.newFolderReader().readCrate( + outputPath.toString() + ); + validateCrate(readCrate); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue graph = rootNode.get("@graph"); + + // Find ro-crate-java entity + JsonValue roCrateJavaEntity = findEntityById(graph, this.currentVersionId); + assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); + assertEquals( + "SoftwareApplication", + roCrateJavaEntity.get("@type").asText(), + "ro-crate-java should be of type SoftwareApplication" + ); + + // Find CreateAction entity + JsonValue createActionEntity = findEntityByType(graph, "CreateAction"); + assertNotNull(createActionEntity, "CreateAction entity should exist"); + assertNotNull( + createActionEntity.get("startTime"), + "CreateAction should have startTime" + ); + assertEquals( + this.currentVersionId, + createActionEntity.get("agent").get("@id").asText(), + "CreateAction should reference ro-crate-java as agent" + ); + } + + @Test + void should_HaveRequiredPropertiesInRoCrateJavaEntity_When_WritingCrate( + @TempDir Path tempDir + ) throws IOException { + // Create and write crate + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + + RoCrate readCrate = Readers.newFolderReader().readCrate( + outputPath.toString() + ); + validateCrate(readCrate); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue roCrateJavaEntity = findEntityById( + rootNode.get("@graph"), + this.currentVersionId + ); + + assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); + assertEquals( + "ro-crate-java", + roCrateJavaEntity.get("name").asText(), + "should have correct name" + ); + assertEquals( + "https://github.com/kit-data-manager/ro-crate-java", + roCrateJavaEntity.get("url").asText(), + "should have correct repository URL" + ); + assertNotNull( + roCrateJavaEntity.get("version"), + "should have version property" + ); + } + + @Test + void should_HaveBidirectionalRelation_Between_RoCrateJavaAndItsAction( + @TempDir Path tempDir + ) throws IOException { + // Create and write crate + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + + RoCrate readCrate = Readers.newFolderReader().readCrate( + outputPath.toString() + ); + validateCrate(readCrate); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue graph = rootNode.get("@graph"); + + // Get both entities + JsonValue roCrateJavaEntity = findEntityById(graph, this.currentVersionId); + JsonValue createActionEntity = findEntityByType(graph, "CreateAction"); + + assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); + assertNotNull(createActionEntity, "CreateAction entity should exist"); + + // Test CreateAction -> ro-crate-java reference + JsonValue agentRef = createActionEntity.get("agent"); + assertNotNull(agentRef, "CreateAction should have agent property"); + assertEquals( + this.currentVersionId, + agentRef.get("@id").asText(), + "CreateAction's agent should reference ro-crate-java" + ); + + // Test ro-crate-java -> CreateAction reference + JsonValue actionRef = roCrateJavaEntity.get("Action"); + assertNotNull(actionRef, "ro-crate-java should have action property"); + assertEquals( + createActionEntity.get("@id").asText(), + actionRef.get("@id").asText(), + "ro-crate-java's action should reference the CreateAction" + ); + } + + @Test + void should_AccumulateActions_When_WritingMultipleTimes(@TempDir Path tempDir) + throws IOException, InterruptedException { + // Create and write crate first time + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); + Thread.sleep(10); + + // Write same crate two more times to simulate updates + Writers.newFolderWriter().save(crate, outputPath.toString()); + Thread.sleep(10); + Writers.newFolderWriter().save(crate, outputPath.toString()); + validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); + Thread.sleep(10); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue graph = rootNode.get("@graph"); + + // Get ro-crate-java entity + JsonValue roCrateJavaEntity = findEntityById(graph, this.currentVersionId); + assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); + + // Verify actions array exists and has three entries + assertTrue( + roCrateJavaEntity.get("Action").isArray(), + "ro-crate-java should have an array of actions" + ); + assertEquals( + 3, + roCrateJavaEntity.get("Action").size(), + "should have three actions after three writes" + ); + + // Find all action entities + JsonValue createAction = findEntityByType(graph, "CreateAction"); + assertNotNull(createAction, "should have one CreateAction"); + + JsonValue[] createActions = findEntitiesByType(graph, "CreateAction"); + assertEquals( + 1, + createActions.length, + "should have exactly one CreateAction" + ); + + JsonValue[] updateActions = findEntitiesByType(graph, "UpdateAction"); + assertEquals(2, updateActions.length, "should have two UpdateActions"); + + // Verify CreateAction properties + assertNotNull( + createAction.get("startTime"), + "CreateAction should have startTime" + ); + assertEquals( + this.currentVersionId, + createAction.get("agent").get("@id").asText(), + "CreateAction should reference ro-crate-java as agent" + ); + + // Verify UpdateAction properties + for (JsonValue updateAction : updateActions) { + assertNotNull( + updateAction.get("startTime"), + "UpdateAction should have startTime" + ); + assertEquals( + this.currentVersionId, + updateAction.get("agent").get("@id").asText(), + "UpdateAction should reference ro-crate-java as agent" + ); + } + + // Verify chronological order of timestamps + String createTime = createAction.get("startTime").asText(); + String updateTime1 = updateActions[0].get("startTime").asText(); + String updateTime2 = updateActions[1].get("startTime").asText(); + // The order of updates is not the order in the graph. + // But we can check that creation happened before the updates: + assertTrue( + createTime.compareTo(updateTime1) < 0, + "First update should be after creation" + ); + assertTrue( + createTime.compareTo(updateTime2) < 0, + "Second update should be after creation" + ); + } + + @Test + void should_HaveValidVersionFormat_When_WritingCrate(@TempDir Path tempDir) + throws IOException { + // Create and write crate + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue roCrateJavaEntity = findEntityById( + rootNode.get("@graph"), + this.currentVersionId + ); + + // Version format validation + @SuppressWarnings("DataFlowIssue") + String version = roCrateJavaEntity.get("version").asText(); + + // Semantic versioning regex pattern that allows: + // - Required: major.minor.patch (e.g., 1.2.3) + // - Optional: pre-release identifier (e.g., -rc1, -RC1, -beta.1, -SNAPSHOT) + // - Optional: build metadata (e.g., +build.123) + String semverPattern = + "(?i)^\\d+\\.\\d+\\.\\d+(?:-(?:rc\\d+|alpha|beta|snapshot)(?:\\.\\d+)?)?(?:\\+[0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*)?$"; + + assertTrue( + version.matches(semverPattern), + String.format( + "Version '%s' should match semantic versioning format: major.minor.patch[-prerelease][+build]%n" + + "Examples: 1.2.3, 1.2.3-rc1, 1.2.3-SNAPSHOT, 1.2.3-beta.1, 1.2.3+build.123", + version + ) + ); + } + + @SuppressWarnings("DataFlowIssue") + @Test + void should_HaveCompleteMetadata_When_WritingCrate(@TempDir Path tempDir) + throws IOException { + // Create and write crate + RoCrate crate = new RoCrate.RoCrateBuilder().build(); + validateCrate(crate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(crate, outputPath.toString()); + validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); + + // Read and print metadata for debugging + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + // Parse metadata file + JsonValue rootNode = Json.parse(metadata); + JsonValue roCrateJavaEntity = findEntityById( + rootNode.get("@graph"), + this.currentVersionId + ); + + // Required properties with specific values + assertEquals( + "ro-crate-java", + roCrateJavaEntity.get("name").asText(), + "should have correct name" + ); + assertEquals( + "https://github.com/kit-data-manager/ro-crate-java", + roCrateJavaEntity.get("url").asText(), + "should have correct repository URL" + ); + assertEquals( + "SoftwareApplication", + roCrateJavaEntity.get("@type").asText(), + "should have correct type" + ); + + // Optional but recommended properties + assertNotNull( + roCrateJavaEntity.get("description"), + "should have a description" + ); + assertFalse( + roCrateJavaEntity.get("description").asText().isEmpty(), + "description should not be empty" + ); + + assertNotNull(roCrateJavaEntity.get("license"), "should have a license"); + assertTrue( + roCrateJavaEntity.has("softwareVersion"), + "should have softwareVersion as an alias for version" + ); + assertEquals( + roCrateJavaEntity.get("version").asText(), + roCrateJavaEntity.get("softwareVersion").asText(), + "version and softwareVersion should match" + ); + } + + @Test + void should_AddProvenanceInfo_When_ModifyingExistingCrateWithoutProvenance( + @TempDir Path tempDir + ) throws IOException { + // First create a crate without provenance information + RoCrate originalCrate = new RoCrate.RoCrateBuilder().build(); + validateCrate(originalCrate); + + Path outputPath = tempDir.resolve("test-crate"); + + // Use writer with disabled provenance (not implemented yet) + Writers.newFolderWriter() + .withAutomaticProvenance(null) + .save(originalCrate, outputPath.toString()); + + // Verify the original crate has no provenance information + String originalMetadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(originalMetadata); + + JsonValue originalRoot = Json.parse(originalMetadata); + JsonValue originalGraph = originalRoot.get("@graph"); + assertNull( + findEntityById(originalGraph, this.currentVersionId), + "Original crate should not have ro-crate-java entity" + ); + assertNull( + findEntityByType(originalGraph, "CreateAction"), + "Original crate should not have CreateAction" + ); + assertNull( + findEntityByType(originalGraph, "UpdateAction"), + "Original crate should not have UpdateAction" + ); + + // Now read and modify the crate + RoCrate modifiedCrate = Readers.newFolderReader().readCrate( + outputPath.toString() + ); + validateCrate(modifiedCrate); + modifiedCrate + .getRootDataEntity() + .addProperty("description", "Modified crate"); + validateCrate(modifiedCrate); + + // Write the modified crate with provenance enabled (default) + Path modifiedPath = tempDir.resolve("modified-crate"); + Writers.newFolderWriter().save(modifiedCrate, modifiedPath.toString()); + + // Read and verify the modified crate's metadata + String modifiedMetadata = Files.readString( + modifiedPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(modifiedMetadata); + + JsonValue modifiedRoot = Json.parse(modifiedMetadata); + JsonValue modifiedGraph = modifiedRoot.get("@graph"); + + // Verify ro-crate-java entity was added + JsonValue roCrateJavaEntity = findEntityById( + modifiedGraph, + this.currentVersionId + ); + assertNotNull(roCrateJavaEntity, "ro-crate-java entity should be added"); + + // Should only have UpdateAction, no CreateAction + assertNull( + findEntityByType(modifiedGraph, "CreateAction"), + "Modified crate should not have CreateAction" + ); + + JsonValue updateAction = findEntityByType(modifiedGraph, "UpdateAction"); + assertNotNull(updateAction, "Should have UpdateAction"); + + // Verify update action properties + assertNotNull( + updateAction.get("startTime"), + "UpdateAction should have startTime" + ); + assertEquals( + this.currentVersionId, + updateAction.get("agent").get("@id").asText(), + "UpdateAction should reference ro-crate-java as agent" + ); + + // Verify ro-crate-java references the action + assertTrue( + roCrateJavaEntity.get("Action").isObject(), + "ro-crate-java should have a single reference to an UpdateAction" + ); + assertEquals( + updateAction.get("@id").asText(), + roCrateJavaEntity.get("Action").get("@id").asText(), + "ro-crate-java should reference the UpdateAction" + ); + } + + @Test + void should_PreserveExistingProvenance_When_ModifyingCrate( + @TempDir Path tempDir + ) throws IOException, InterruptedException { + // First create a crate with normal provenance + RoCrate originalCrate = new RoCrate.RoCrateBuilder().build(); + validateCrate(originalCrate); + + Path outputPath = tempDir.resolve("test-crate"); + Writers.newFolderWriter().save(originalCrate, outputPath.toString()); + Thread.sleep(10); + + // Now read and modify the crate + RoCrate modifiedCrate = Readers.newFolderReader().readCrate( + outputPath.toString() + ); + validateCrate(modifiedCrate); + modifiedCrate + .getRootDataEntity() + .addProperty("description", "Modified crate"); + validateCrate(modifiedCrate); + + // Write the modified crate + Writers.newFolderWriter().save(modifiedCrate, outputPath.toString()); + + // Read and verify the metadata + String metadata = Files.readString( + outputPath.resolve("ro-crate-metadata.json") + ); + HelpFunctions.prettyPrintJsonString(metadata); + + JsonValue root = Json.parse(metadata); + JsonValue graph = root.get("@graph"); + + // Should have both CreateAction and UpdateAction + JsonValue createAction = findEntityByType(graph, "CreateAction"); + assertNotNull(createAction, "Original CreateAction should be preserved"); + + JsonValue[] updateActions = findEntitiesByType(graph, "UpdateAction"); + assertEquals( + 1, + updateActions.length, + "Should have exactly one UpdateAction" + ); + + // Verify chronological order + String createTime = createAction.get("startTime").asText(); + String updateTime = updateActions[0].get("startTime").asText(); + assertTrue( + createTime.compareTo(updateTime) < 0, + "Update should be after creation" + ); + + // Verify ro-crate-java entity references both actions + JsonValue roCrateJavaEntity = findEntityById(graph, this.currentVersionId); + //noinspection DataFlowIssue + assertTrue( + roCrateJavaEntity.get("Action").isArray(), + "ro-crate-java should have an array of actions" + ); + assertEquals( + 2, + roCrateJavaEntity.get("Action").size(), + "should have both actions" + ); + } +} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/TestableWriterStrategy.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/TestableWriterStrategy.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/TestableWriterStrategy.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/TestableWriterStrategy.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipWriterTest.java b/core/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipWriterTest.java similarity index 100% rename from src/test/java/edu/kit/datamanager/ro_crate/writer/ZipWriterTest.java rename to core/src/test/java/edu/kit/datamanager/ro_crate/writer/ZipWriterTest.java diff --git a/src/test/resources/crates/extendedContextExample/ro-crate-metadata.json b/core/src/test/resources/crates/extendedContextExample/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/extendedContextExample/ro-crate-metadata.json rename to core/src/test/resources/crates/extendedContextExample/ro-crate-metadata.json diff --git a/src/test/resources/crates/hasPartHierarchy/README.md b/core/src/test/resources/crates/hasPartHierarchy/README.md similarity index 100% rename from src/test/resources/crates/hasPartHierarchy/README.md rename to core/src/test/resources/crates/hasPartHierarchy/README.md diff --git a/src/test/resources/crates/hasPartHierarchy/ro-crate-metadata.json b/core/src/test/resources/crates/hasPartHierarchy/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/hasPartHierarchy/ro-crate-metadata.json rename to core/src/test/resources/crates/hasPartHierarchy/ro-crate-metadata.json diff --git a/src/test/resources/crates/other/idrc_project/ro-crate-metadata.json b/core/src/test/resources/crates/other/idrc_project/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/other/idrc_project/ro-crate-metadata.json rename to core/src/test/resources/crates/other/idrc_project/ro-crate-metadata.json diff --git a/src/test/resources/crates/simple_crate/ro-crate-metadata.json b/core/src/test/resources/crates/simple_crate/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/simple_crate/ro-crate-metadata.json rename to core/src/test/resources/crates/simple_crate/ro-crate-metadata.json diff --git a/src/test/resources/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array/ro-crate-metadata.json b/core/src/test/resources/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array/ro-crate-metadata.json rename to core/src/test/resources/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array/ro-crate-metadata.json diff --git a/src/test/resources/crates/validation/workflowschema.json b/core/src/test/resources/crates/validation/workflowschema.json similarity index 100% rename from src/test/resources/crates/validation/workflowschema.json rename to core/src/test/resources/crates/validation/workflowschema.json diff --git a/src/test/resources/crates/workflowhub/workflow-109-5.crate.zip b/core/src/test/resources/crates/workflowhub/workflow-109-5.crate.zip similarity index 100% rename from src/test/resources/crates/workflowhub/workflow-109-5.crate.zip rename to core/src/test/resources/crates/workflowhub/workflow-109-5.crate.zip diff --git a/src/test/resources/crates/workflowhub/workflow1/CHANGELOG.md b/core/src/test/resources/crates/workflowhub/workflow1/CHANGELOG.md similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/CHANGELOG.md rename to core/src/test/resources/crates/workflowhub/workflow1/CHANGELOG.md diff --git a/src/test/resources/crates/workflowhub/workflow1/README.md b/core/src/test/resources/crates/workflowhub/workflow1/README.md similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/README.md rename to core/src/test/resources/crates/workflowhub/workflow1/README.md diff --git a/src/test/resources/crates/workflowhub/workflow1/ro-crate-metadata.json b/core/src/test/resources/crates/workflowhub/workflow1/ro-crate-metadata.json similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/ro-crate-metadata.json rename to core/src/test/resources/crates/workflowhub/workflow1/ro-crate-metadata.json diff --git a/src/test/resources/crates/workflowhub/workflow1/ro-crate-preview.html b/core/src/test/resources/crates/workflowhub/workflow1/ro-crate-preview.html similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/ro-crate-preview.html rename to core/src/test/resources/crates/workflowhub/workflow1/ro-crate-preview.html diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/by_variant_report.tsv b/core/src/test/resources/crates/workflowhub/workflow1/test-data/by_variant_report.tsv similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/by_variant_report.tsv rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/by_variant_report.tsv diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/combined_variant_report.tsv b/core/src/test/resources/crates/workflowhub/workflow1/test-data/combined_variant_report.tsv similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/combined_variant_report.tsv rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/combined_variant_report.tsv diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/ont-artic.vcf b/core/src/test/resources/crates/workflowhub/workflow1/test-data/ont-artic.vcf similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/ont-artic.vcf rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/ont-artic.vcf diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/pe-artic.vcf b/core/src/test/resources/crates/workflowhub/workflow1/test-data/pe-artic.vcf similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/pe-artic.vcf rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/pe-artic.vcf diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/pe-illumina-wgs.vcf b/core/src/test/resources/crates/workflowhub/workflow1/test-data/pe-illumina-wgs.vcf similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/pe-illumina-wgs.vcf rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/pe-illumina-wgs.vcf diff --git a/src/test/resources/crates/workflowhub/workflow1/test-data/se-illumina-wgs.vcf b/core/src/test/resources/crates/workflowhub/workflow1/test-data/se-illumina-wgs.vcf similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/test-data/se-illumina-wgs.vcf rename to core/src/test/resources/crates/workflowhub/workflow1/test-data/se-illumina-wgs.vcf diff --git a/src/test/resources/crates/workflowhub/workflow1/variation-reporting-test.yml b/core/src/test/resources/crates/workflowhub/workflow1/variation-reporting-test.yml similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/variation-reporting-test.yml rename to core/src/test/resources/crates/workflowhub/workflow1/variation-reporting-test.yml diff --git a/src/test/resources/crates/workflowhub/workflow1/variation-reporting.ga b/core/src/test/resources/crates/workflowhub/workflow1/variation-reporting.ga similarity index 100% rename from src/test/resources/crates/workflowhub/workflow1/variation-reporting.ga rename to core/src/test/resources/crates/workflowhub/workflow1/variation-reporting.ga diff --git a/core/src/test/resources/golden/extendedContextExample.metadata.json b/core/src/test/resources/golden/extendedContextExample.metadata.json new file mode 100644 index 00000000..34e0d425 --- /dev/null +++ b/core/src/test/resources/golden/extendedContextExample.metadata.json @@ -0,0 +1 @@ +{"@context":["https://w3id.org/ro/crate/1.1/context",{"owl":"https://www.w3.org/TR/owl-ref/#","custom":"_:","datacite":"http://datacite.org/schema/kernel-4#","xsd":"http://www.w3.org/2001/XMLSchema#","rdfs":"https://www.w3.org/2000/01/rdf-schema#"}],"@graph":[{"@id":"./","@type":"Dataset","name":"minimal","description":"minimal RO_crate","datePublished":"2024","license":{"@id":"https://creativecommons.org/licenses/by-nc-sa/3.0/au/"}},{"@type":"CreativeWork","@id":"ro-crate-metadata.json","conformsTo":{"@id":"https://w3id.org/ro/crate/1.1"},"about":{"@id":"./"}}]} \ No newline at end of file diff --git a/core/src/test/resources/golden/hasPartHierarchy.metadata.json b/core/src/test/resources/golden/hasPartHierarchy.metadata.json new file mode 100644 index 00000000..7e0634e7 --- /dev/null +++ b/core/src/test/resources/golden/hasPartHierarchy.metadata.json @@ -0,0 +1 @@ +{"@context":"https://w3id.org/ro/crate/1.1/context","@graph":[{"@id":"./","@type":"Dataset","name":"Root element","description":"Description","license":{"@id":"https://creativecommons.org/licenses/by-nc-sa/3.0/au/"},"hasPart":[{"@id":"sub-b.file"},{"@id":"sub-a.file"}]},{"@id":"https://creativecommons.org/licenses/by-nc-sa/3.0/au/","@type":"CreativeWork","description":"Contextual entity (license)","identifier":"https://creativecommons.org/licenses/by-nc-sa/3.0/au/","name":"Attribution-NonCommercial-ShareAlike 3.0 Australia (CC BY-NC-SA 3.0 AU)"},{"@id":"looper-isPartOf.file","@type":"File","hasPart":{"@id":"sub-b.file"},"isPartOf":{"@id":"sub-b.file"}},{"@id":"looper.file","@type":"File","hasPart":{"@id":"sub-b.file"}},{"@type":"CreativeWork","@id":"ro-crate-metadata.json","conformsTo":{"@id":"https://w3id.org/ro/crate/1.1"},"about":{"@id":"./"}},{"@id":"sub-a.file","@type":"File"},{"@id":"sub-b-sub-a.file","@type":"File","hasPart":{"@id":"looper.file"}},{"@id":"sub-b-sub-b.file","@type":"File","isPartOf":{"@id":"sub-b.file"}},{"@id":"sub-b.file","@type":"File","hasPart":{"@id":"sub-b-sub-a.file"}}]} \ No newline at end of file diff --git a/core/src/test/resources/golden/idrc_project.metadata.json b/core/src/test/resources/golden/idrc_project.metadata.json new file mode 100644 index 00000000..885aa1fc --- /dev/null +++ b/core/src/test/resources/golden/idrc_project.metadata.json @@ -0,0 +1 @@ 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a/src/test/resources/json/crate/onlyOneFile.json b/core/src/test/resources/json/crate/onlyOneFile.json similarity index 100% rename from src/test/resources/json/crate/onlyOneFile.json rename to core/src/test/resources/json/crate/onlyOneFile.json diff --git a/src/test/resources/json/crate/simple.json b/core/src/test/resources/json/crate/simple.json similarity index 100% rename from src/test/resources/json/crate/simple.json rename to core/src/test/resources/json/crate/simple.json diff --git a/src/test/resources/json/crate/simple2.json b/core/src/test/resources/json/crate/simple2.json similarity index 100% rename from src/test/resources/json/crate/simple2.json rename to core/src/test/resources/json/crate/simple2.json diff --git a/src/test/resources/json/crate/twoFiles.json b/core/src/test/resources/json/crate/twoFiles.json similarity index 100% rename from src/test/resources/json/crate/twoFiles.json rename to core/src/test/resources/json/crate/twoFiles.json diff --git a/src/test/resources/json/entities/contextual/createActionExample.json b/core/src/test/resources/json/entities/contextual/createActionExample.json similarity index 100% rename from src/test/resources/json/entities/contextual/createActionExample.json rename to core/src/test/resources/json/entities/contextual/createActionExample.json diff --git a/src/test/resources/json/entities/contextual/createActionExampleSoftware.json b/core/src/test/resources/json/entities/contextual/createActionExampleSoftware.json similarity index 100% rename from src/test/resources/json/entities/contextual/createActionExampleSoftware.json rename to core/src/test/resources/json/entities/contextual/createActionExampleSoftware.json diff --git a/src/test/resources/json/entities/contextual/equipment.json b/core/src/test/resources/json/entities/contextual/equipment.json similarity index 100% rename from src/test/resources/json/entities/contextual/equipment.json rename to core/src/test/resources/json/entities/contextual/equipment.json diff --git a/src/test/resources/json/entities/contextual/orcidperson.json b/core/src/test/resources/json/entities/contextual/orcidperson.json similarity index 100% rename from src/test/resources/json/entities/contextual/orcidperson.json rename to core/src/test/resources/json/entities/contextual/orcidperson.json diff --git a/src/test/resources/json/entities/contextual/organization.json b/core/src/test/resources/json/entities/contextual/organization.json similarity index 100% rename from src/test/resources/json/entities/contextual/organization.json rename to core/src/test/resources/json/entities/contextual/organization.json diff --git a/src/test/resources/json/entities/contextual/person.json b/core/src/test/resources/json/entities/contextual/person.json similarity index 100% rename from src/test/resources/json/entities/contextual/person.json rename to core/src/test/resources/json/entities/contextual/person.json diff --git a/src/test/resources/json/entities/contextual/place.json b/core/src/test/resources/json/entities/contextual/place.json similarity index 100% rename from src/test/resources/json/entities/contextual/place.json rename to core/src/test/resources/json/entities/contextual/place.json diff --git a/src/test/resources/json/entities/contextual/software.json b/core/src/test/resources/json/entities/contextual/software.json similarity index 100% rename from src/test/resources/json/entities/contextual/software.json rename to core/src/test/resources/json/entities/contextual/software.json diff --git a/src/test/resources/json/entities/contextual/updateAction.json b/core/src/test/resources/json/entities/contextual/updateAction.json similarity index 100% rename from src/test/resources/json/entities/contextual/updateAction.json rename to core/src/test/resources/json/entities/contextual/updateAction.json diff --git a/src/test/resources/json/entities/data/directory.json b/core/src/test/resources/json/entities/data/directory.json similarity index 100% rename from src/test/resources/json/entities/data/directory.json rename to core/src/test/resources/json/entities/data/directory.json diff --git a/src/test/resources/json/entities/data/directoryWeb.json b/core/src/test/resources/json/entities/data/directoryWeb.json similarity index 100% rename from src/test/resources/json/entities/data/directoryWeb.json rename to core/src/test/resources/json/entities/data/directoryWeb.json diff --git a/src/test/resources/json/entities/data/fileEntity.json b/core/src/test/resources/json/entities/data/fileEntity.json similarity index 100% rename from src/test/resources/json/entities/data/fileEntity.json rename to core/src/test/resources/json/entities/data/fileEntity.json diff --git a/src/test/resources/json/entities/data/license.json b/core/src/test/resources/json/entities/data/license.json similarity index 100% rename from src/test/resources/json/entities/data/license.json rename to core/src/test/resources/json/entities/data/license.json diff --git a/src/test/resources/json/entities/data/localFile.json b/core/src/test/resources/json/entities/data/localFile.json similarity index 100% rename from src/test/resources/json/entities/data/localFile.json rename to core/src/test/resources/json/entities/data/localFile.json diff --git a/src/test/resources/json/entities/data/localFileWithLicense.json b/core/src/test/resources/json/entities/data/localFileWithLicense.json similarity index 100% rename from src/test/resources/json/entities/data/localFileWithLicense.json rename to core/src/test/resources/json/entities/data/localFileWithLicense.json diff --git a/src/test/resources/json/entities/data/root.json b/core/src/test/resources/json/entities/data/root.json similarity index 100% rename from src/test/resources/json/entities/data/root.json rename to core/src/test/resources/json/entities/data/root.json diff --git a/src/test/resources/json/entities/data/rootMinimalExample.json b/core/src/test/resources/json/entities/data/rootMinimalExample.json similarity index 100% rename from src/test/resources/json/entities/data/rootMinimalExample.json rename to core/src/test/resources/json/entities/data/rootMinimalExample.json diff --git a/src/test/resources/json/entities/data/script1.json b/core/src/test/resources/json/entities/data/script1.json similarity index 100% rename from src/test/resources/json/entities/data/script1.json rename to core/src/test/resources/json/entities/data/script1.json diff --git a/src/test/resources/json/entities/data/workflow.json b/core/src/test/resources/json/entities/data/workflow.json similarity index 100% rename from src/test/resources/json/entities/data/workflow.json rename to core/src/test/resources/json/entities/data/workflow.json diff --git a/src/test/resources/json/unwrap/simple.json b/core/src/test/resources/json/unwrap/simple.json similarity index 100% rename from src/test/resources/json/unwrap/simple.json rename to core/src/test/resources/json/unwrap/simple.json diff --git a/src/test/resources/json/unwrap/simpleResult.json b/core/src/test/resources/json/unwrap/simpleResult.json similarity index 100% rename from src/test/resources/json/unwrap/simpleResult.json rename to core/src/test/resources/json/unwrap/simpleResult.json diff --git a/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json b/core/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json similarity index 100% rename from src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json rename to core/src/test/resources/spec-v1.1-example-json-files/complete-workflow-example.json diff --git a/src/test/resources/spec-v1.1-example-json-files/file-author-location.json b/core/src/test/resources/spec-v1.1-example-json-files/file-author-location.json similarity index 100% rename from src/test/resources/spec-v1.1-example-json-files/file-author-location.json rename to core/src/test/resources/spec-v1.1-example-json-files/file-author-location.json diff --git a/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json b/core/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json similarity index 100% rename from src/test/resources/spec-v1.1-example-json-files/files-and-folders.json rename to core/src/test/resources/spec-v1.1-example-json-files/files-and-folders.json diff --git a/src/test/resources/spec-v1.1-example-json-files/minimal.json b/core/src/test/resources/spec-v1.1-example-json-files/minimal.json similarity index 100% rename from src/test/resources/spec-v1.1-example-json-files/minimal.json rename to core/src/test/resources/spec-v1.1-example-json-files/minimal.json diff --git a/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json b/core/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json similarity index 100% rename from src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json rename to core/src/test/resources/spec-v1.1-example-json-files/web-based-data-entities.json diff --git a/examples/build.gradle b/examples/build.gradle new file mode 100644 index 00000000..7831d264 --- /dev/null +++ b/examples/build.gradle @@ -0,0 +1,125 @@ +/* + * Executable examples for ro-crate-java that double as a behavior-comparison + * test suite. + * + * How it works: + * + * - src/main the examples written against the current API. They are + * backend-agnostic: they compile against :core only and run + * with whichever JSON backend is on the classpath. + * - src/legacy the same examples written against the released 2.1.2 + * artifact (pre-port Jackson API). Kept in a separate source + * set so the two classpaths never mix. + * + * - Every example is a main() that receives an output file path and writes + * deterministic, canonical content there. + * + * - For each example and variant (see the `variants` map below) a JavaExec + * task runs the example in its own JVM — required, because the JSON + * backends register via ServiceLoader and must not share a classpath — + * and writes build/examples//.txt. + * + * - The parity test (ParityTest) then asserts that consecutive variants + * produce byte-identical output: legacy == current-jackson2 == + * current-jackson3. It derives the variant names from the same `variants` + * map (passed as the rocrate.parity.variants system property) and the + * example list from the output files, so new examples are covered by just + * adding a class and registering it in `exampleClasses` below. + */ + +plugins { + id 'java' +} + +ext { + legacyVersion = '2.1.2' +} + +repositories { + mavenCentral() +} + +sourceSets { + // compiled and run against the released artifact; deliberately not + // sharing a classpath with the current code + legacy +} + +configurations { + // runtime-only backend jars for the current examples; deliberately not on + // the compile classpath so the examples stay backend-agnostic + jackson2Backend + jackson3Backend +} + +dependencies { + implementation project(':core') + // the released artifact exposes Jackson only at runtime scope, so the + // legacy source set declares the same versions for compilation + legacyImplementation "edu.kit.datamanager:ro-crate-java:${legacyVersion}" + legacyImplementation "com.fasterxml.jackson.core:jackson-databind:2.22.1" + jackson2Backend project(':jackson2') + jackson3Backend project(':jackson3') + + testImplementation(platform("org.junit:junit-bom:6.1.3")) + testImplementation('org.junit.jupiter:junit-jupiter') + testRuntimeOnly('org.junit.platform:junit-platform-launcher') +} + +/* + * The variants to compare. The key is the variant name and is used as + * - the output directory: build/examples//.txt, + * - the task name fragment: run, and + * - the variant list handed to ParityTest (in map order). + * The classpath closure defines the JVM classpath of the variant; classesTask + * is the task that produces the compiled example classes for it. + */ +def variants = [ + legacy: [ + classesTask: 'legacyClasses', + classpath : { sourceSets.legacy.runtimeClasspath }, + ], + 'current-jackson2': [ + classesTask: 'classes', + classpath : { sourceSets.main.runtimeClasspath + configurations.jackson2Backend }, + ], + 'current-jackson3': [ + classesTask: 'classes', + classpath : { sourceSets.main.runtimeClasspath + configurations.jackson3Backend }, + ], +] + +// register every new example here; the parity test picks it up automatically +def exampleClasses = [ + 'CreateMinimalCrate', + 'ReadCrate', + 'ModifyCrate', + 'WriteCrate', + 'ValidateCrate', +] + +exampleClasses.each { example -> + variants.each { variant, setup -> + tasks.register("run${variant.capitalize()}${example}", JavaExec) { + group = 'examples' + description = "Runs the ${example} example with the ${variant} variant." + dependsOn setup.classesTask + classpath = setup.classpath() + mainClass = "examples.${example}" + def outputFile = layout.buildDirectory.file("examples/${variant}/${example}.txt") + args outputFile.get().asFile.absolutePath + doFirst { + outputFile.get().asFile.parentFile.mkdirs() + } + outputs.file(outputFile) + } + } +} + +tasks.named('test') { + dependsOn exampleClasses.collectMany { example -> + variants.keySet().collect { variant -> tasks.named("run${variant.capitalize()}${example}") } + } + // single source of truth for the variant names used by ParityTest + systemProperty 'rocrate.parity.variants', variants.keySet().join(',') +} diff --git a/examples/src/legacy/java/examples/CanonicalJson.java b/examples/src/legacy/java/examples/CanonicalJson.java new file mode 100644 index 00000000..f195a472 --- /dev/null +++ b/examples/src/legacy/java/examples/CanonicalJson.java @@ -0,0 +1,45 @@ +package examples; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ArrayNode; +import com.fasterxml.jackson.databind.node.ObjectNode; +import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; + +/** + * Canonical form of crate metadata, used to compare runs of different library + * versions byte-for-byte: the {@code @graph} entities are sorted by their + * {@code @id} (the entity order follows Java hash iteration and is + * unspecified) and the JSON is written compactly. + * + *

Legacy Jackson implementation for the 2.1.2 examples; the current + * examples ({@code src/main}) use an equivalent neutral-JSON implementation + * of the same class name. + */ +final class CanonicalJson { + + private CanonicalJson() {} + + static String canonicalize(String metadata) throws Exception { + ObjectMapper mapper = MyObjectMapper.getMapper(); + ObjectNode root = (ObjectNode) mapper.readTree(metadata); + JsonNode graph = root.path("@graph"); + if (graph.isArray()) { + List entities = new ArrayList<>(); + graph.forEach(entities::add); + entities.sort( + Comparator.comparing( + entity -> entity.path("@id").asText(""), + String.CASE_INSENSITIVE_ORDER + ) + ); + ArrayNode graphArray = (ArrayNode) graph; + graphArray.removeAll(); + entities.forEach(graphArray::add); + } + return mapper.writeValueAsString(root); + } +} diff --git a/examples/src/legacy/java/examples/CreateMinimalCrate.java b/examples/src/legacy/java/examples/CreateMinimalCrate.java new file mode 100644 index 00000000..682eb8f2 --- /dev/null +++ b/examples/src/legacy/java/examples/CreateMinimalCrate.java @@ -0,0 +1,47 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Legacy variant of {@code CreateMinimalCrate}, written against the released + * 2.1.2 API. The example code is identical to the current variant; only + * {@link CanonicalJson} uses the Jackson API instead of the neutral JSON + * model. + */ +public class CreateMinimalCrate { + + public static void main(String[] args) throws Exception { + RoCrate crate = new RoCrate.RoCrateBuilder( + "Example crate", + "An example crate built with ro-crate-java", + "2024", + "https://creativecommons.org/licenses/by/4.0/" + ) + .addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("survey-responses-2019.csv") + .addType("File") + .addProperty("name", "Survey responses") + .addProperty("contentSize", "26452") + .addProperty("encodingFormat", "text/csv") + .build() + ) + .addContextualEntity( + new ContextualEntity.ContextualEntityBuilder() + .setId("https://orcid.org/0000-0002-1825-0097") + .addType("Person") + .addProperty("name", "Josiah Carberry") + .build() + ) + .build(); + + Files.writeString( + Path.of(args[0]), + CanonicalJson.canonicalize(crate.getJsonMetadata()) + ); + } +} diff --git a/examples/src/legacy/java/examples/ModifyCrate.java b/examples/src/legacy/java/examples/ModifyCrate.java new file mode 100644 index 00000000..1ca59245 --- /dev/null +++ b/examples/src/legacy/java/examples/ModifyCrate.java @@ -0,0 +1,95 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.reader.Readers; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Legacy variant of {@code ModifyCrate}, written against the released 2.1.2 + * API. The example code is identical to the current variant; only + * {@link CanonicalJson} uses the Jackson API instead of the neutral JSON + * model. + */ +public class ModifyCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + RoCrate crate = Readers.newFolderReader().readCrate(FIXTURE.toString()); + StringBuilder report = new StringBuilder(); + + report + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add a data entity, then delete it again + crate.addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("data.txt") + .addType("File") + .addProperty("name", "Some data") + .build() + ); + report + .append("after addDataEntity(data.txt)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + crate.deleteEntityById("data.txt"); + report + .append("after deleteEntityById(data.txt)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add it back with different properties + crate.addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("data.txt") + .addType("File") + .addProperty("name", "Some other data") + .addProperty("encodingFormat", "text/plain") + .build() + ); + report + .append("after re-adding data.txt with different properties\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // modify properties of the root data entity + crate.getRootDataEntity().removeProperty("datePublished"); + crate.getRootDataEntity().addProperty("keywords", "testing, parity"); + report + .append("after root data entity property changes\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add and remove a contextual entity + ContextualEntity organization = + new ContextualEntity.ContextualEntityBuilder() + .setId("https://ror.org/04jsmm180") + .addType("Organization") + .addProperty("name", "Karlsruhe Institute of Technology") + .build(); + crate.addContextualEntity(organization); + report + .append("after addContextualEntity(organization)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + crate.deleteEntityById("https://ror.org/04jsmm180"); + report + .append("after deleteEntityById(organization)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())); + + Files.writeString(Path.of(args[0]), report.toString()); + } +} diff --git a/examples/src/legacy/java/examples/ReadCrate.java b/examples/src/legacy/java/examples/ReadCrate.java new file mode 100644 index 00000000..d732fcd4 --- /dev/null +++ b/examples/src/legacy/java/examples/ReadCrate.java @@ -0,0 +1,51 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.writer.Writers; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Legacy variant of {@code ReadCrate}, written against the released 2.1.2 + * API. The example code is identical to the current variant; only + * {@link CanonicalJson} uses the Jackson API instead of the neutral JSON + * model. + */ +public class ReadCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + Path output = Path.of(args[0]); + Path zip = output.getParent().resolve("simple_crate.zip"); + RoCrate folderCrate = Readers.newFolderReader().readCrate( + FIXTURE.toString() + ); + // suppress provenance: it would stamp library version and creation time + // into the metadata and is not part of the comparison + Writers.newZipPathWriter() + .withAutomaticProvenance(null) + .save(folderCrate, zip.toAbsolutePath().toString()); + RoCrate zipCrate = Readers.newZipPathReader().readCrate( + zip.toAbsolutePath().toString() + ); + + StringBuilder report = new StringBuilder(); + report + .append("from folder\n") + .append(CanonicalJson.canonicalize(folderCrate.getJsonMetadata())) + .append("\n\nfrom zip\n") + .append(CanonicalJson.canonicalize(zipCrate.getJsonMetadata())) + .append("\n"); + Files.writeString(output, report.toString()); + } +} diff --git a/examples/src/legacy/java/examples/ValidateCrate.java b/examples/src/legacy/java/examples/ValidateCrate.java new file mode 100644 index 00000000..c38f4c34 --- /dev/null +++ b/examples/src/legacy/java/examples/ValidateCrate.java @@ -0,0 +1,35 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +/** + * Legacy variant of {@code ValidateCrate}, written against the released + * 2.1.2 API. The released version has no {@code Validation} entry point, so + * the JSON-schema validator is instantiated directly; the current code uses + * the backend-agnostic {@code Validation.crateStrategy()} instead. + */ +public class ValidateCrate { + + static final Path CRATES = Path.of("..", "core", "src", "test", "resources", "crates"); + + public static void main(String[] args) throws Exception { + Validator validator = new Validator(new JsonSchemaValidation()); + StringBuilder report = new StringBuilder(); + for (String fixture : List.of("simple_crate", "extendedContextExample", "hasPartHierarchy")) { + RoCrate crate = Readers.newFolderReader() + .readCrate(CRATES.resolve(fixture).toString()); + report + .append(fixture) + .append(": ") + .append(validator.validate(crate)) + .append("\n"); + } + Files.writeString(Path.of(args[0]), report.toString()); + } +} diff --git a/examples/src/legacy/java/examples/WriteCrate.java b/examples/src/legacy/java/examples/WriteCrate.java new file mode 100644 index 00000000..7d078635 --- /dev/null +++ b/examples/src/legacy/java/examples/WriteCrate.java @@ -0,0 +1,119 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.writer.Writers; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.security.MessageDigest; +import java.util.Comparator; +import java.util.List; +import java.util.stream.Stream; +import java.util.zip.ZipEntry; +import java.util.zip.ZipFile; + +/** + * Legacy variant of {@code WriteCrate}, written against the released 2.1.2 + * API. The example code is identical to the current variant; only + * {@link CanonicalJson} uses the Jackson API instead of the neutral JSON + * model. + */ +public class WriteCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + Path workDir = Path.of(args[0]).getParent(); + Path folder = workDir.resolve("written-crate"); + Path zip = workDir.resolve("written-crate.zip"); + + RoCrate crate = Readers.newFolderReader().readCrate(FIXTURE.toString()); + Writers.newFolderWriter() + .withAutomaticProvenance(null) + .save(crate, folder.toAbsolutePath().toString()); + Writers.newZipPathWriter() + .withAutomaticProvenance(null) + .save(crate, zip.toAbsolutePath().toString()); + + StringBuilder report = new StringBuilder(); + report + .append("metadata\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\nfolder files (name: sha256)\n") + .append(folderFileDigests(folder)) + .append("\nzip entries (name: sha256)\n") + .append(zipEntryDigests(zip)) + .append("\n"); + Files.writeString(Path.of(args[0]), report.toString()); + } + + static String folderFileDigests(Path folder) throws Exception { + List files; + try (Stream walk = Files.walk(folder)) { + files = walk + .filter(Files::isRegularFile) + .sorted(Comparator.comparing(Path::toString)) + .toList(); + } + StringBuilder report = new StringBuilder(); + for (Path file : files) { + report + .append(folder.relativize(file).toString()) + .append(": ") + .append(digest(file)) + .append("\n"); + } + return report.toString(); + } + + static String zipEntryDigests(Path zip) throws Exception { + StringBuilder report = new StringBuilder(); + try (ZipFile zipFile = new ZipFile(zip.toFile())) { + List entries = zipFile + .stream() + .sorted(Comparator.comparing(ZipEntry::getName)) + .toList(); + for (ZipEntry entry : entries) { + report + .append(entry.getName()) + .append(": ") + .append(digest(() -> zipFile.getInputStream(entry))) + .append("\n"); + } + } + return report.toString(); + } + + static String digest(Path file) throws Exception { + return digest(() -> Files.newInputStream(file)); + } + + static String digest(InputStreamSupplier supplier) throws Exception { + MessageDigest sha256 = MessageDigest.getInstance("SHA-256"); + try (InputStream stream = supplier.open()) { + byte[] buffer = new byte[8192]; + int read; + while ((read = stream.read(buffer)) != -1) { + sha256.update(buffer, 0, read); + } + } + StringBuilder hex = new StringBuilder(); + for (byte b : sha256.digest()) { + hex.append(String.format("%02x", b)); + } + return hex.toString(); + } + + interface InputStreamSupplier { + InputStream open() throws Exception; + } +} diff --git a/examples/src/main/java/examples/CanonicalJson.java b/examples/src/main/java/examples/CanonicalJson.java new file mode 100644 index 00000000..f5bbb77a --- /dev/null +++ b/examples/src/main/java/examples/CanonicalJson.java @@ -0,0 +1,46 @@ +package examples; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.List; + +/** + * Canonical form of crate metadata, used to compare runs of different library + * versions byte-for-byte: the {@code @graph} entities are sorted by their + * {@code @id} (the entity order follows Java hash iteration and is + * unspecified) and the JSON is written compactly. + * + *

This class exists once per source set: this neutral-JSON implementation + * is used by the current examples ({@code src/main}); the legacy 2.1.2 + * examples ({@code src/legacy}) use an equivalent Jackson implementation of + * the same class name. + */ +final class CanonicalJson { + + private CanonicalJson() {} + + static String canonicalize(String metadata) throws Exception { + JsonObject root = (JsonObject) Json.parse(metadata); + JsonValue graph = root.path("@graph"); + if (graph.isArray()) { + List entities = new ArrayList<>(); + graph.forEach(entities::add); + entities.sort( + Comparator.comparing( + entity -> entity.path("@id").asText(""), + String.CASE_INSENSITIVE_ORDER + ) + ); + JsonArray graphArray = (JsonArray) graph; + while (!graphArray.isEmpty()) { + graphArray.remove(0); + } + entities.forEach(graphArray::add); + } + return Json.write(root); + } +} diff --git a/examples/src/main/java/examples/CreateMinimalCrate.java b/examples/src/main/java/examples/CreateMinimalCrate.java new file mode 100644 index 00000000..865010e2 --- /dev/null +++ b/examples/src/main/java/examples/CreateMinimalCrate.java @@ -0,0 +1,49 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Builds a small crate programmatically and writes its metadata in canonical + * form (see {@link CanonicalJson}). + * + *

Run with any backend on the classpath — the example itself is + * backend-agnostic; the ServiceLoader picks up whichever JSON backend + * (jackson2 or jackson3) is present. + */ +public class CreateMinimalCrate { + + public static void main(String[] args) throws Exception { + RoCrate crate = new RoCrate.RoCrateBuilder( + "Example crate", + "An example crate built with ro-crate-java", + "2024", + "https://creativecommons.org/licenses/by/4.0/" + ) + .addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("survey-responses-2019.csv") + .addType("File") + .addProperty("name", "Survey responses") + .addProperty("contentSize", "26452") + .addProperty("encodingFormat", "text/csv") + .build() + ) + .addContextualEntity( + new ContextualEntity.ContextualEntityBuilder() + .setId("https://orcid.org/0000-0002-1825-0097") + .addType("Person") + .addProperty("name", "Josiah Carberry") + .build() + ) + .build(); + + Files.writeString( + Path.of(args[0]), + CanonicalJson.canonicalize(crate.getJsonMetadata()) + ); + } +} diff --git a/examples/src/main/java/examples/ModifyCrate.java b/examples/src/main/java/examples/ModifyCrate.java new file mode 100644 index 00000000..8820ee8f --- /dev/null +++ b/examples/src/main/java/examples/ModifyCrate.java @@ -0,0 +1,95 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; +import edu.kit.datamanager.ro_crate.entities.data.DataEntity; +import edu.kit.datamanager.ro_crate.reader.Readers; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Reads a fixture crate from disk and modifies it: adds and removes entities, + * adds and removes properties. Writes the canonical metadata after each step + * (see {@link CanonicalJson}), so the comparison covers the mutation paths of + * the library. + */ +public class ModifyCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + RoCrate crate = Readers.newFolderReader().readCrate(FIXTURE.toString()); + StringBuilder report = new StringBuilder(); + + report + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add a data entity, then delete it again + crate.addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("data.txt") + .addType("File") + .addProperty("name", "Some data") + .build() + ); + report + .append("after addDataEntity(data.txt)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + crate.deleteEntityById("data.txt"); + report + .append("after deleteEntityById(data.txt)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add it back with different properties + crate.addDataEntity( + new DataEntity.DataEntityBuilder() + .setId("data.txt") + .addType("File") + .addProperty("name", "Some other data") + .addProperty("encodingFormat", "text/plain") + .build() + ); + report + .append("after re-adding data.txt with different properties\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // modify properties of the root data entity + crate.getRootDataEntity().removeProperty("datePublished"); + crate.getRootDataEntity().addProperty("keywords", "testing, parity"); + report + .append("after root data entity property changes\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + + // add and remove a contextual entity + ContextualEntity organization = + new ContextualEntity.ContextualEntityBuilder() + .setId("https://ror.org/04jsmm180") + .addType("Organization") + .addProperty("name", "Karlsruhe Institute of Technology") + .build(); + crate.addContextualEntity(organization); + report + .append("after addContextualEntity(organization)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\n"); + crate.deleteEntityById("https://ror.org/04jsmm180"); + report + .append("after deleteEntityById(organization)\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())); + + Files.writeString(Path.of(args[0]), report.toString()); + } +} diff --git a/examples/src/main/java/examples/ReadCrate.java b/examples/src/main/java/examples/ReadCrate.java new file mode 100644 index 00000000..8976409f --- /dev/null +++ b/examples/src/main/java/examples/ReadCrate.java @@ -0,0 +1,50 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.writer.Writers; +import java.nio.file.Files; +import java.nio.file.Path; + +/** + * Reads a crate from a folder and from a zip archive (the archive is created + * from the fixture with the library's own zip writer) and writes the + * canonical metadata for both paths (see {@link CanonicalJson}). + */ +public class ReadCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + Path output = Path.of(args[0]); + Path zip = output.getParent().resolve("simple_crate.zip"); + RoCrate folderCrate = Readers.newFolderReader().readCrate( + FIXTURE.toString() + ); + // suppress provenance: it would stamp library version and creation time + // into the metadata and is not part of the comparison + Writers.newZipPathWriter() + .withAutomaticProvenance(null) + .save(folderCrate, zip.toAbsolutePath().toString()); + RoCrate zipCrate = Readers.newZipPathReader().readCrate( + zip.toAbsolutePath().toString() + ); + + StringBuilder report = new StringBuilder(); + report + .append("from folder\n") + .append(CanonicalJson.canonicalize(folderCrate.getJsonMetadata())) + .append("\n\nfrom zip\n") + .append(CanonicalJson.canonicalize(zipCrate.getJsonMetadata())) + .append("\n"); + Files.writeString(output, report.toString()); + } +} diff --git a/examples/src/main/java/examples/ValidateCrate.java b/examples/src/main/java/examples/ValidateCrate.java new file mode 100644 index 00000000..390846ba --- /dev/null +++ b/examples/src/main/java/examples/ValidateCrate.java @@ -0,0 +1,48 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.validation.Validation; +import edu.kit.datamanager.ro_crate.validation.Validator; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +/** + * Validates fixture crates with the default schema and prints the result + * (the boolean only; the human-readable problems go to the error stream and + * are not part of the comparison). The validator is the one provided by the + * JSON backend module on the classpath, obtained through the core's + * {@code Validation} entry point. + */ +public class ValidateCrate { + + static final Path CRATES = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates" + ); + + public static void main(String[] args) throws Exception { + Validator validator = new Validator(Validation.crateStrategy()); + StringBuilder report = new StringBuilder(); + for (String fixture : List.of( + "simple_crate", + "extendedContextExample", + "hasPartHierarchy" + )) { + RoCrate crate = Readers.newFolderReader().readCrate( + CRATES.resolve(fixture).toString() + ); + report + .append(fixture) + .append(": ") + .append(validator.validate(crate)) + .append("\n"); + } + Files.writeString(Path.of(args[0]), report.toString()); + } +} diff --git a/examples/src/main/java/examples/WriteCrate.java b/examples/src/main/java/examples/WriteCrate.java new file mode 100644 index 00000000..36824d45 --- /dev/null +++ b/examples/src/main/java/examples/WriteCrate.java @@ -0,0 +1,120 @@ +package examples; + +import edu.kit.datamanager.ro_crate.RoCrate; +import edu.kit.datamanager.ro_crate.reader.Readers; +import edu.kit.datamanager.ro_crate.writer.Writers; +import java.io.InputStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.security.MessageDigest; +import java.util.Comparator; +import java.util.List; +import java.util.stream.Stream; +import java.util.zip.ZipEntry; +import java.util.zip.ZipFile; + +/** + * Reads the fixture crate, writes it to a folder and to a zip archive, and + * reports the written files: the canonical metadata (see + * {@link CanonicalJson}) plus, for every written file and zip entry, its + * name and sha256 hash. Zip entry timestamps and order are deliberately + * excluded (they are not part of the comparison). + */ +public class WriteCrate { + + static final Path FIXTURE = Path.of( + "..", + "core", + "src", + "test", + "resources", + "crates", + "simple_crate" + ); + + public static void main(String[] args) throws Exception { + Path workDir = Path.of(args[0]).getParent(); + Path folder = workDir.resolve("written-crate"); + Path zip = workDir.resolve("written-crate.zip"); + + RoCrate crate = Readers.newFolderReader().readCrate(FIXTURE.toString()); + Writers.newFolderWriter() + .withAutomaticProvenance(null) + .save(crate, folder.toAbsolutePath().toString()); + Writers.newZipPathWriter() + .withAutomaticProvenance(null) + .save(crate, zip.toAbsolutePath().toString()); + + StringBuilder report = new StringBuilder(); + report + .append("metadata\n") + .append(CanonicalJson.canonicalize(crate.getJsonMetadata())) + .append("\n\nfolder files (name: sha256)\n") + .append(folderFileDigests(folder)) + .append("\nzip entries (name: sha256)\n") + .append(zipEntryDigests(zip)) + .append("\n"); + Files.writeString(Path.of(args[0]), report.toString()); + } + + static String folderFileDigests(Path folder) throws Exception { + List files; + try (Stream walk = Files.walk(folder)) { + files = walk + .filter(Files::isRegularFile) + .sorted(Comparator.comparing(Path::toString)) + .toList(); + } + StringBuilder report = new StringBuilder(); + for (Path file : files) { + report + .append(folder.relativize(file).toString()) + .append(": ") + .append(digest(file)) + .append("\n"); + } + return report.toString(); + } + + static String zipEntryDigests(Path zip) throws Exception { + StringBuilder report = new StringBuilder(); + try (ZipFile zipFile = new ZipFile(zip.toFile())) { + List entries = zipFile + .stream() + .sorted(Comparator.comparing(ZipEntry::getName)) + .toList(); + for (ZipEntry entry : entries) { + report + .append(entry.getName()) + .append(": ") + .append(digest(() -> zipFile.getInputStream(entry))) + .append("\n"); + } + } + return report.toString(); + } + + static String digest(Path file) throws Exception { + return digest(() -> Files.newInputStream(file)); + } + + static String digest(InputStreamSupplier supplier) throws Exception { + MessageDigest sha256 = MessageDigest.getInstance("SHA-256"); + try (InputStream stream = supplier.open()) { + byte[] buffer = new byte[8192]; + int read; + while ((read = stream.read(buffer)) != -1) { + sha256.update(buffer, 0, read); + } + } + StringBuilder hex = new StringBuilder(); + for (byte b : sha256.digest()) { + hex.append(String.format("%02x", b)); + } + return hex.toString(); + } + + interface InputStreamSupplier { + InputStream open() throws Exception; + } +} diff --git a/examples/src/test/java/examples/ParityTest.java b/examples/src/test/java/examples/ParityTest.java new file mode 100644 index 00000000..7fbee032 --- /dev/null +++ b/examples/src/test/java/examples/ParityTest.java @@ -0,0 +1,115 @@ +package examples; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.stream.Stream; +import org.junit.jupiter.api.Test; + +/** + * Compares the outputs of the example runs. Each example is executed once per + * variant (see the {@code variants} map in build.gradle; each run happens in + * its own JVM) and writes {@code build/examples//.txt}. + * + *

This test asserts that consecutive variants produce byte-identical + * output: the released 2.1.2 artifact ({@code legacy}) matches the current + * code with the jackson2 backend, which matches the current code with the + * jackson3 backend. + * + *

New examples are covered automatically: the example list is derived from + * the output files, and the variant names are passed in from the build via + * the {@code rocrate.parity.variants} system property (single source of + * truth: the {@code variants} map in build.gradle). + */ +class ParityTest { + + private static final Path EXAMPLES_DIR = Path.of("build", "examples"); + private static final String VARIANTS_PROPERTY = "rocrate.parity.variants"; + private static final String OUTPUT_SUFFIX = ".txt"; + + private static List variants() { + String value = System.getProperty(VARIANTS_PROPERTY); + assertTrue( + value != null, + "missing system property " + + VARIANTS_PROPERTY + + " — run the tests through the Gradle build" + ); + return List.of(value.split(",")); + } + + /** + * The example names as found in the output of the first variant; also + * asserts that every variant produced the same set of examples. + */ + private static List examples() throws IOException { + List expected = exampleNames(variants().get(0)); + for (String variant : variants()) { + assertEquals( + expected, + exampleNames(variant), + "variant '" + variant + "' produced a different set of examples" + ); + } + return expected; + } + + private static List exampleNames(String variant) throws IOException { + Path dir = EXAMPLES_DIR.resolve(variant); + assertTrue( + Files.isDirectory(dir), + "missing output directory " + + dir + + " — the run tasks should have produced it" + ); + try (Stream files = Files.list(dir)) { + return files + .map(file -> file.getFileName().toString()) + .filter(name -> name.endsWith(OUTPUT_SUFFIX)) + .map(name -> name.substring(0, name.length() - OUTPUT_SUFFIX.length())) + .sorted() + .toList(); + } + } + + private static String output(String variant, String example) + throws IOException { + Path file = EXAMPLES_DIR.resolve(variant).resolve(example + OUTPUT_SUFFIX); + assertTrue( + Files.exists(file), + "missing output " + file + " — the run tasks should have produced it" + ); + return Files.readString(file); + } + + @Test + void everyVariantProducedTheSameExamples() throws IOException { + examples(); + } + + @Test + void consecutiveVariantsProduceIdenticalOutput() throws IOException { + List variants = variants(); + for (String example : examples()) { + for (int i = 0; i < variants.size() - 1; i++) { + String previous = variants.get(i); + String next = variants.get(i + 1); + assertEquals( + output(previous, example), + output(next, example), + "output of '" + + example + + "' differs between '" + + previous + + "' and '" + + next + + "'" + ); + } + } + } +} diff --git a/gradle/module-common.gradle b/gradle/module-common.gradle new file mode 100644 index 00000000..2ec59c21 --- /dev/null +++ b/gradle/module-common.gradle @@ -0,0 +1,44 @@ +/* + * Common configuration applied to every module of ro-crate-java. + */ + +apply plugin: 'java' + +println "Building ${name} version: ${version}" +println "Profile (system property): ${System.getProperty('profile')}" + +java { + //package JavaDoc as part of publication + withJavadocJar() + //package Sources as part of publication + withSourcesJar() + // set java version compatibility + sourceCompatibility = JavaVersion.VERSION_17 + targetCompatibility = JavaVersion.VERSION_17 +} + +if (JavaVersion.current() == JavaVersion.VERSION_17) { + println "Setting encoding to UTF-8 manually" + compileJava.options.encoding = "UTF-8" + compileTestJava.options.encoding = "UTF-8" +} + +// enable -Xlint:deprecation +tasks.withType(JavaCompile).configureEach { + options.compilerArgs << "-Xlint:deprecation" +} + +javadoc { + if (JavaVersion.current().isJava9Compatible()) { + options.addBooleanOption('html5', true) + } +} + +tasks.withType(Test).configureEach { + useJUnitPlatform() +} + +tasks.withType(Test).configureEach { + // make flags like -Drocrate.golden.update=true visible to the test JVM + systemProperties System.getProperties().findAll { it.key.toString().startsWith('rocrate.') } +} diff --git a/gradle/module-publishing.gradle b/gradle/module-publishing.gradle new file mode 100644 index 00000000..4e33a1bb --- /dev/null +++ b/gradle/module-publishing.gradle @@ -0,0 +1,67 @@ +/* + * Publishing configuration shared by the backend modules. + * + * The publication name is provided by the applying module via the + * 'publishedArtifactId' extra property (defaults to the project name). + */ + +apply plugin: 'maven-publish' +apply plugin: 'signing' + +publishing { + publications { + maven(MavenPublication) { + artifactId = project.findProperty('publishedArtifactId') ?: project.name + from components.java + //set elements in generated pom.xml according to requirements + //by Sonatype (see https://central.sonatype.org/pages/requirements.html) + pom { + name = project['name'] + description = project['description'] + url = 'https://github.com/kit-data-manager/ro-crate-java' + licenses { + license { + name = 'The Apache License, Version 2.0' + url = 'http://www.apache.org/licenses/LICENSE-2.0.txt' + } + } + developers { + developer { + id = 'Pfeil' + name = 'Andreas Pfeil' + email = 'webmaster@datamanager.kit.edu' + } + } + scm { + connection = 'scm:git:github.com/kit-data-manager/ro-crate-java' + developerConnection = 'scm:git:github.com/kit-data-manager/ro-crate-java' + url = 'https://github.com/kit-data-manager/ro-crate-java' + } + } + } + } +} + +signing { + //make signing required unless for SNAPSHOT releases or if signing is explicitly skipped + required { !project.version.endsWith("-SNAPSHOT") && !project.hasProperty("skipSigning") } + + //look for property 'signingKey' + if (project.findProperty("signingKey")) { + //read property 'signingKey' + def signingKey = findProperty("signingKey") + //read property 'signingPassword' + def signingPassword = findProperty("signingPassword") + //use in-memory ascii-armored keys + useInMemoryPgpKeys(signingKey, signingPassword) + //sign publication identity 'publishing.publications.maven' + sign publishing.publications.maven + } else { + println 'WARNING: No property \'signingKey\' found. Artifact signing will be skipped.' + } +} + +def signingTasks = tasks.withType(Sign) +tasks.withType(AbstractPublishToMaven).configureEach { + mustRunAfter(signingTasks) +} diff --git a/gradle/profile-release.gradle b/gradle/profile-release.gradle deleted file mode 100644 index b9a0d003..00000000 --- a/gradle/profile-release.gradle +++ /dev/null @@ -1,123 +0,0 @@ -/* - * Copyright 2021 Karlsruhe Institute of Technology. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -apply plugin: 'net.researchgate.release' -apply plugin: 'maven-publish' -apply plugin: 'signing' - -//for plugin net.researchgate.release -//see https://github.com/researchgate/gradle-release -release { - //define template for tagging, e.g. v1.0.0 - tagTemplate = 'v${version}' -} - -//for java plugin -//see https://docs.gradle.org/current/userguide/java_plugin.html -java { - //package JavaDoc as part of publication - withJavadocJar() - //package Sources as part of publication - withSourcesJar() - // set java version compatibility - sourceCompatibility = JavaVersion.VERSION_17 - targetCompatibility = JavaVersion.VERSION_17 -} - -//for javadoc task -//see https://docs.gradle.org/current/dsl/org.gradle.api.tasks.javadoc.Javadoc.html -javadoc { - if(JavaVersion.current().isJava9Compatible()) { - options.addBooleanOption('html5', true) - } -} - -//for plugin io.github.gradle-nexus.publish-plugin -//see https://github.com/gradle-nexus/publish-plugin -nexusPublishing { - repositories { - //select sonatype repository as publication destination - sonatype { - nexusUrl.set(uri("https://ossrh-staging-api.central.sonatype.com/service/local/")) - snapshotRepositoryUrl.set(uri("https://central.sonatype.com/repository/maven-snapshots/")) - } - } -} - -//for plugin maven-publish/io.github.gradle-nexus.publish-plugin -//see https://docs.gradle.org/current/userguide/publishing_maven.html -publishing { - publications { - //define publication identity, e.g. maven, which will be used - //by the signing plugin, e.g. sign publishing.publications.maven - maven(MavenPublication) { - //select component to publish, e.g. java including JavaDoc - //and sources (see above) - from components.java - //set elements in generated pom.xml according to requirements - //by Sonatype (see https://central.sonatype.org/pages/requirements.html) - pom { - name = project['name'] - description = project['description'] - url = 'https://github.com/kit-data-manager/ro-crate-java' - licenses { - license { - name = 'The Apache License, Version 2.0' - url = 'http://www.apache.org/licenses/LICENSE-2.0.txt' - } - } - developers { - developer { - id = 'Pfeil' - name = 'Andreas Pfeil' - email = 'webmaster@datamanager.kit.edu' - } - } - scm { - connection = 'scm:git:github.com/kit-data-manager/ro-crate-java' - developerConnection = 'scm:git:github.com/kit-data-manager/ro-crate-java' - url = 'https://github.com/kit-data-manager/ro-crate-java' - } - } - } - } -} - -//for plugin signing -//see https://docs.gradle.org/current/userguide/signing_plugin.html -signing { - //make signing required unless for SNAPSHOT releases or if signing is explicitly skipped - required { !project.version.endsWith("-SNAPSHOT") && !project.hasProperty("skipSigning") } - - //look for property 'signingKey' - if (project.findProperty("signingKey")) { - //If required, read a sub-key specified by its ID in property signingKeyId - //def signingKeyId = findProperty("signingKeyId") - //read property 'signingKey' - def signingKey = findProperty("signingKey") - //read property 'signingPassword' - def signingPassword = findProperty("signingPassword") - //Select to use in-memory ascii-armored keys - useInMemoryPgpKeys(signingKey, signingPassword) - //Only if also using signingKeyId - //useInMemoryPgpKeys(signingKeyId, signingKey, signingPassword) - - //Apply signing to publication identity 'publishing.publications.maven' - sign publishing.publications.maven - }else { - println 'WARNING: No property \'signingKey\' found. Artifact signing will be skipped.' - } -} diff --git a/jackson2/build.gradle b/jackson2/build.gradle new file mode 100644 index 00000000..a303cf60 --- /dev/null +++ b/jackson2/build.gradle @@ -0,0 +1,40 @@ +/* + * The Jackson 2 backend of ro-crate-java. + * + * Publishes under the historical artifact coordinates (edu.kit.datamanager: + * ro-crate-java), so consumers of the library keep resolving the same + * artifact; it transitively pulls in the Jackson-free core. + */ + +plugins { + id 'java-library' + id "maven-publish" + id "io.freefair.maven-publish-java" version "9.8.2" +} + +ext { + jacksonVersion = '2.22.4' + // this module publishes under the historical library coordinates + publishedArtifactId = 'ro-crate-java' +} + +description = "A library for easy creation and modification of valid RO-Crates (Jackson 2 backend)." + +repositories { + mavenCentral() +} + +dependencies { + api project(':core') + // JSON object mapping / (de-)serialization + implementation "com.fasterxml.jackson.core:jackson-databind:${jacksonVersion}" + // metadata validation, profiles based on JSON schema + implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.9" + + // test parity reference + testImplementation(platform("org.junit:junit-bom:6.1.3")) + testImplementation('org.junit.jupiter:junit-jupiter') + testRuntimeOnly('org.junit.platform:junit-platform-launcher') +} + +apply from: rootProject.file('gradle/module-publishing.gradle') diff --git a/jackson2/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java new file mode 100644 index 00000000..51850bf8 --- /dev/null +++ b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java @@ -0,0 +1,101 @@ +package edu.kit.datamanager.ro_crate.entities.validation; + +import com.networknt.schema.JsonSchema; +import com.networknt.schema.JsonSchemaFactory; +import com.networknt.schema.SpecVersion; +import com.networknt.schema.ValidationMessage; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson2.Jackson2JsonAdapter; +import java.net.URISyntaxException; +import java.net.URL; +import java.util.Objects; +import java.util.Set; + +/** + * Implementation of the entity validation strategy that uses json schema. + * + *

The neutral JSON model is converted to the native tree of the validation + * backend at this boundary; in the split build this class moves to the + * Jackson 2 adapter module. + */ +public class JsonSchemaValidation implements EntityValidationStrategy { + + private static final URL entitySchemaDefault = Objects.requireNonNull( + JsonSchemaValidation.class + .getClassLoader() + .getResource("json_schemas/entity_schema.json") + ); + private static final URL fieldSchemaDefault = Objects.requireNonNull( + JsonSchemaValidation.class + .getClassLoader() + .getResource("json_schemas/entity_field_structure_schema.json") + ); + + private JsonSchema entitySchema; + private JsonSchema entityFieldSchema; + + /** + * Default constructor that uses the default schemas. + */ + public JsonSchemaValidation() { + JsonSchemaFactory factory = JsonSchemaFactory.getInstance( + SpecVersion.VersionFlag.V201909 + ); + try { + this.entitySchema = factory.getSchema(entitySchemaDefault.toURI()); + this.entityFieldSchema = factory.getSchema(fieldSchemaDefault.toURI()); + } catch (URISyntaxException e) { + e.printStackTrace(); + } + } + + /** + * Constructor that uses custom schemas present as Json files. + * + * @param entitySchema schema for the entities validation. + * @param fieldSchema schema for the field validation. + */ + public JsonSchemaValidation(JsonValue entitySchema, JsonValue fieldSchema) { + JsonSchemaFactory factory = JsonSchemaFactory.getInstance( + SpecVersion.VersionFlag.V201909 + ); + this.entitySchema = factory.getSchema( + Jackson2JsonAdapter.toJackson(entitySchema) + ); + this.entityFieldSchema = factory.getSchema( + Jackson2JsonAdapter.toJackson(fieldSchema) + ); + } + + @Override + public boolean validateEntity(JsonValue entity) { + Set errors = this.entitySchema.validate( + Jackson2JsonAdapter.toJackson(entity) + ); + if (errors.size() != 0) { + System.err.println( + "This entity does not comply to the basic RO-Crate entity structure." + ); + errors.forEach(error -> System.err.println(error.getMessage())); + return false; + } + return true; + } + + @Override + public boolean validateFieldOfEntity(JsonValue field) { + Set errors = this.entityFieldSchema.validate( + Jackson2JsonAdapter.toJackson(field) + ); + if (!errors.isEmpty()) { + System.err.println("The property: "); + System.err.println(field.toString()); + System.err.println( + "does not comply with the flattened structure" + + " of the RO-Crate json document." + ); + return false; + } + return true; + } +} diff --git a/jackson2/src/main/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapter.java b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapter.java new file mode 100644 index 00000000..72d6bf61 --- /dev/null +++ b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapter.java @@ -0,0 +1,204 @@ +package edu.kit.datamanager.ro_crate.json.jackson2; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.node.ArrayNode; +import com.fasterxml.jackson.databind.node.ObjectNode; +import edu.kit.datamanager.ro_crate.json.JsonAdapter; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonBoolean; +import edu.kit.datamanager.ro_crate.json.JsonMissing; +import edu.kit.datamanager.ro_crate.json.JsonNull; +import edu.kit.datamanager.ro_crate.json.JsonNumber; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonString; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.math.BigDecimal; +import java.math.BigInteger; + +/** + * Jackson 2 implementation of the {@link JsonAdapter} SPI. + * + *

Serialization and parsing are delegated to Jackson 2, so the produced + * JSON is byte-identical to what the library emitted before the conversion. + * The mapper keeps the parse features the library historically enabled on its + * shared mapper (see the former {@code MyObjectMapper}). + */ +public final class Jackson2JsonAdapter implements JsonAdapter { + + private static final ObjectMapper MAPPER = new ObjectMapper() + .enable( + com.fasterxml.jackson.databind.DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY + ) + .enable( + com.fasterxml.jackson.databind.DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS + ); + + @Override + public JsonObject objectNode() { + return JsonObject.create(); + } + + @Override + public JsonArray arrayNode() { + return JsonArray.create(); + } + + @Override + public JsonValue parse(String json) throws IOException { + return toNeutral(MAPPER.readTree(json)); + } + + @Override + public JsonValue parse(File file) throws IOException { + return toNeutral(MAPPER.readTree(file)); + } + + @Override + public JsonValue parse(InputStream stream) throws IOException { + return toNeutral(MAPPER.readTree(stream)); + } + + @Override + public String write(JsonValue value) throws IOException { + return MAPPER.writeValueAsString(toJackson(value)); + } + + @Override + public String writePretty(JsonValue value) throws IOException { + return MAPPER.writerWithDefaultPrettyPrinter().writeValueAsString( + toJackson(value) + ); + } + + /** Converts a Jackson 2 tree into the neutral model. */ + public static JsonValue toNeutral(JsonNode node) { + if (node == null || node.isMissingNode()) { + return JsonMissing.INSTANCE; + } + if (node.isObject()) { + JsonObject object = JsonObject.create(); + for (var field : node.properties()) { + object.put(field.getKey(), toNeutral(field.getValue())); + } + return object; + } + if (node.isArray()) { + JsonArray array = JsonArray.create(); + for (JsonNode element : node) { + array.add(toNeutral(element)); + } + return array; + } + if (node.isNull()) { + return JsonNull.INSTANCE; + } + if (node.isTextual()) { + return new JsonString(node.textValue()); + } + if (node.isBoolean()) { + return JsonBoolean.of(node.booleanValue()); + } + if (node.isNumber()) { + return new JsonNumber(numberOf(node)); + } + throw new IllegalArgumentException( + "Unsupported Jackson node type: " + node.getNodeType() + ); + } + + private static Number numberOf(JsonNode node) { + if (node.isInt()) { + return node.intValue(); + } + if (node.isLong()) { + return node.longValue(); + } + if (node.isShort()) { + return node.shortValue(); + } + if (node.isBigInteger()) { + return node.bigIntegerValue(); + } + if (node.isDouble()) { + return node.doubleValue(); + } + if (node.isFloat()) { + return node.floatValue(); + } + if (node.isBigDecimal()) { + return node.decimalValue(); + } + return node.doubleValue(); + } + + /** Converts the neutral model into a Jackson 2 tree. */ + public static JsonNode toJackson(JsonValue value) { + if (value instanceof JsonObject object) { + ObjectNode node = MAPPER.createObjectNode(); + for (var entry : object.entries()) { + node.set(entry.getKey(), toJackson(entry.getValue())); + } + return node; + } + if (value instanceof JsonArray array) { + ArrayNode node = MAPPER.createArrayNode(); + for (JsonValue element : array) { + node.add(toJackson(element)); + } + return node; + } + if (value instanceof JsonString string) { + return MAPPER.getNodeFactory().textNode(string.getValue()); + } + if (value instanceof JsonBoolean bool) { + return bool.getValue() + ? MAPPER.getNodeFactory().booleanNode(true) + : MAPPER.getNodeFactory().booleanNode(false); + } + if (value instanceof JsonNull) { + return MAPPER.getNodeFactory().nullNode(); + } + if (value instanceof JsonMissing) { + return MAPPER.getNodeFactory().missingNode(); + } + if (value instanceof JsonNumber number) { + return numberNode(number.getValue()); + } + throw new IllegalArgumentException( + "Unsupported neutral JSON value: " + value.getClass() + ); + } + + private static JsonNode numberNode(Number number) { + if (number instanceof Integer n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Long n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Short n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Byte n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Double n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Float n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof BigInteger n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof BigDecimal n) { + return MAPPER.getNodeFactory().numberNode(n); + } + // fallback for exotic Number implementations + return MAPPER.getNodeFactory().numberNode(number.doubleValue()); + } +} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java similarity index 60% rename from src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java rename to jackson2/src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java index 1aed8400..ce64f014 100644 --- a/src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java +++ b/jackson2/src/main/java/edu/kit/datamanager/ro_crate/validation/JsonSchemaValidation.java @@ -1,15 +1,13 @@ package edu.kit.datamanager.ro_crate.validation; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; import com.networknt.schema.JsonSchema; import com.networknt.schema.JsonSchemaFactory; import com.networknt.schema.SpecVersion; import com.networknt.schema.ValidationMessage; - import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson2.Jackson2JsonAdapter; import java.io.File; import java.io.IOException; import java.net.URI; @@ -26,7 +24,9 @@ public class JsonSchemaValidation implements ValidatorStrategy { private JsonSchema schema; private void getSchema(URI schemaUri) { - JsonSchemaFactory factory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V201909); + JsonSchemaFactory factory = JsonSchemaFactory.getInstance( + SpecVersion.VersionFlag.V201909 + ); this.schema = factory.getSchema(schemaUri); } @@ -36,7 +36,8 @@ private void getSchema(URI schemaUri) { public JsonSchemaValidation() { try { URI schemaUri = Objects.requireNonNull( - getClass().getClassLoader().getResource(defaultSchema)).toURI(); + getClass().getClassLoader().getResource(defaultSchema) + ).toURI(); getSchema(schemaUri); } catch (URISyntaxException e) { e.printStackTrace(); @@ -52,23 +53,28 @@ public JsonSchemaValidation(String schema) { getSchema(schemaUri); } - public JsonSchemaValidation(JsonNode schema) { - JsonSchemaFactory factory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V201909); - this.schema = factory.getSchema(schema); + public JsonSchemaValidation(JsonValue schema) { + JsonSchemaFactory factory = JsonSchemaFactory.getInstance( + SpecVersion.VersionFlag.V201909 + ); + this.schema = factory.getSchema(Jackson2JsonAdapter.toJackson(schema)); } @Override public boolean validate(Crate crate) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); try { - final JsonNode good = objectMapper.readTree(crate.getJsonMetadata()); - Set errors = this.schema.validate(good); + final JsonValue good = Json.parse(crate.getJsonMetadata()); + Set errors = this.schema.validate( + Jackson2JsonAdapter.toJackson(good) + ); if (errors.size() == 0) { return true; } else { - System.err.println("This crate does not validate against the this schema." - + " If you haven't provided any schemas," - + " then it does not validate against the default one."); + System.err.println( + "This crate does not validate against the this schema." + + " If you haven't provided any schemas," + + " then it does not validate against the default one." + ); for (var e : errors) { System.err.println(e.getMessage()); } diff --git a/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy new file mode 100644 index 00000000..07c2eba0 --- /dev/null +++ b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.entities.validation.JsonSchemaValidation diff --git a/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter new file mode 100644 index 00000000..e5e0a8aa --- /dev/null +++ b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.json.jackson2.Jackson2JsonAdapter diff --git a/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy new file mode 100644 index 00000000..f9121276 --- /dev/null +++ b/jackson2/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation diff --git a/src/main/resources/json_schemas/default.json b/jackson2/src/main/resources/json_schemas/default.json similarity index 100% rename from src/main/resources/json_schemas/default.json rename to jackson2/src/main/resources/json_schemas/default.json diff --git a/src/main/resources/json_schemas/entity_field_structure_schema.json b/jackson2/src/main/resources/json_schemas/entity_field_structure_schema.json similarity index 100% rename from src/main/resources/json_schemas/entity_field_structure_schema.json rename to jackson2/src/main/resources/json_schemas/entity_field_structure_schema.json diff --git a/src/main/resources/json_schemas/entity_schema.json b/jackson2/src/main/resources/json_schemas/entity_schema.json similarity index 100% rename from src/main/resources/json_schemas/entity_schema.json rename to jackson2/src/main/resources/json_schemas/entity_schema.json diff --git a/jackson2/src/test/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapterParityTest.java b/jackson2/src/test/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapterParityTest.java new file mode 100644 index 00000000..fe9879d6 --- /dev/null +++ b/jackson2/src/test/java/edu/kit/datamanager/ro_crate/json/jackson2/Jackson2JsonAdapterParityTest.java @@ -0,0 +1,83 @@ +package edu.kit.datamanager.ro_crate.json.jackson2; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import com.fasterxml.jackson.databind.ObjectMapper; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import java.io.IOException; +import org.junit.jupiter.api.Test; + +/** + * Parity tests: the Jackson 2 adapter must behave like the ObjectMapper the + * library used before the conversion (former {@code MyObjectMapper}), + * byte-for-byte on output and feature-for-feature on parsing. + */ +class Jackson2JsonAdapterParityTest { + + private static final ObjectMapper LEGACY_MAPPER = new ObjectMapper() + .enable( + com.fasterxml.jackson.databind.DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY + ) + .enable( + com.fasterxml.jackson.databind.DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS + ); + + @Test + void parseMatchesLegacyMapperTree() throws IOException { + String json = + "{\"name\":\"crate\",\"items\":[\"one\"],\"nested\":{\"a\":1}}"; + assertEquals( + Jackson2JsonAdapter.toNeutral(LEGACY_MAPPER.readTree(json)), + Json.parse(json) + ); + } + + @Test + void writeMatchesLegacyMapperOutput() throws IOException { + JsonObject object = JsonObject.create() + .put("z", "last") + .put("a", "first") + .put("n", 1) + .put("d", 2.5) + .put("b", true) + .putNull("nil") + .set("items", JsonArray.create().add("x").add("y")); + assertEquals( + LEGACY_MAPPER.writeValueAsString(Jackson2JsonAdapter.toJackson(object)), + Json.write(object) + ); + } + + @Test + void readTreeBehaviorIsIdenticalToLegacyMapper() throws IOException { + // readTree does NOT unwrap single-element arrays even with the legacy + // features enabled (verified against Jackson 2.22.1) — the adapter must + // behave exactly the same + String json = "{\"hasPart\": [{\"@id\": \"a\"}],\"tags\": \"one\"}"; + assertEquals( + Jackson2JsonAdapter.toNeutral(LEGACY_MAPPER.readTree(json)), + Json.parse(json) + ); + assertTrue( + ((JsonObject) Json.parse(json)).get("hasPart").isArray(), + "readTree keeps single-element arrays as arrays" + ); + } + + @Test + void roundTripThroughAdapterIsStable() throws IOException { + String json = + "{\"@context\":\"https://w3id.org/ro/crate/1.1/context\"," + + "\"@graph\":[{\"@id\":\"./\",\"name\":\"m\\\"in\",\"num\":1.0," + + "\"unicode\":\"äöü €\"}]}"; + assertEquals(json, Json.write(Json.parse(json))); + } + + @Test + void adapterIsDiscoverableViaServiceLoader() { + assertEquals(Jackson2JsonAdapter.class, Json.adapter().getClass()); + } +} diff --git a/jackson3/build.gradle b/jackson3/build.gradle new file mode 100644 index 00000000..deee2c63 --- /dev/null +++ b/jackson3/build.gradle @@ -0,0 +1,44 @@ +/* + * The Jackson 3 backend of ro-crate-java (tools.jackson, new package/group). + * + * The Jackson 3 version follows the requirement of the json-schema-validator + * backend (networknt 3.0.x builds against Jackson 3.2.x). + */ + +plugins { + id 'java-library' +} + +ext { + jackson3Version = '3.2.1' + networknt3Version = '3.0.8' + // this module publishes under its own artifact coordinates + publishedArtifactId = 'ro-crate-java-jackson3' +} + +description = "A library for easy creation and modification of valid RO-Crates (Jackson 3 backend)." + +repositories { + mavenCentral() +} + +dependencies { + api project(':core') + // JSON object mapping / (de-)serialization + implementation "tools.jackson.core:jackson-databind:${jackson3Version}" + // metadata validation, profiles based on JSON schema + implementation group: "com.networknt", name: "json-schema-validator", version: networknt3Version + + testImplementation(platform("org.junit:junit-bom:6.1.3")) + testImplementation('org.junit.jupiter:junit-jupiter') + testRuntimeOnly('org.junit.platform:junit-platform-launcher') +} + +apply from: rootProject.file('gradle/module-publishing.gradle') + +test { + // the golden files live in the core test resources; make them visible so + // the parity test can compare the Jackson 3 output against the same + // goldens the Jackson 2 backend is verified against + sourceSets.test.resources.srcDir file('../core/src/test/resources') +} diff --git a/jackson3/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/jackson3/JsonSchemaValidation.java b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/jackson3/JsonSchemaValidation.java new file mode 100644 index 00000000..715cdb63 --- /dev/null +++ b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/jackson3/JsonSchemaValidation.java @@ -0,0 +1,95 @@ +package edu.kit.datamanager.ro_crate.entities.validation.jackson3; + +import com.networknt.schema.Error; +import com.networknt.schema.Schema; +import com.networknt.schema.SchemaLocation; +import com.networknt.schema.SchemaRegistry; +import com.networknt.schema.SpecificationVersion; +import edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson3.Jackson3JsonAdapter; +import java.util.List; + +/** + * Implementation of the entity validation strategy that uses json schema, + * backed by the Jackson 3 version of the networknt validator (networknt 3.x + * API with the SchemaRegistry). + */ +public class JsonSchemaValidation implements EntityValidationStrategy { + + private static final String entitySchemaDefault = + "classpath:json_schemas/entity_schema.json"; + private static final String fieldSchemaDefault = + "classpath:json_schemas/entity_field_structure_schema.json"; + + private Schema entitySchema; + private Schema entityFieldSchema; + + /** + * Default constructor that uses the default schemas. + */ + public JsonSchemaValidation() { + SchemaRegistry registry = SchemaRegistry.withDefaultDialect( + SpecificationVersion.DRAFT_2019_09 + ); + // the schema files use relative $refs, so they must be loaded with a + // proper base location; the classpath: scheme resolves those correctly + // and works both from folders and jars + this.entitySchema = registry.getSchema( + SchemaLocation.of(entitySchemaDefault) + ); + this.entityFieldSchema = registry.getSchema( + SchemaLocation.of(fieldSchemaDefault) + ); + } + + /** + * Constructor that uses custom schemas present as Json files. + * + * @param entitySchema schema for the entities validation. + * @param fieldSchema schema for the field validation. + */ + public JsonSchemaValidation(JsonValue entitySchema, JsonValue fieldSchema) { + SchemaRegistry registry = SchemaRegistry.withDefaultDialect( + SpecificationVersion.DRAFT_2019_09 + ); + this.entitySchema = registry.getSchema( + Jackson3JsonAdapter.toJackson(entitySchema) + ); + this.entityFieldSchema = registry.getSchema( + Jackson3JsonAdapter.toJackson(fieldSchema) + ); + } + + @Override + public boolean validateEntity(JsonValue entity) { + List errors = this.entitySchema.validate( + Jackson3JsonAdapter.toJackson(entity) + ); + if (!errors.isEmpty()) { + System.err.println( + "This entity does not comply to the basic RO-Crate entity structure." + ); + errors.forEach(error -> System.err.println(error.getMessage())); + return false; + } + return true; + } + + @Override + public boolean validateFieldOfEntity(JsonValue field) { + List errors = this.entityFieldSchema.validate( + Jackson3JsonAdapter.toJackson(field) + ); + if (!errors.isEmpty()) { + System.err.println("The property: "); + System.err.println(field.toString()); + System.err.println( + "does not comply with the flattened structure" + + " of the RO-Crate json document." + ); + return false; + } + return true; + } +} diff --git a/jackson3/src/main/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3JsonAdapter.java b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3JsonAdapter.java new file mode 100644 index 00000000..4ce22654 --- /dev/null +++ b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3JsonAdapter.java @@ -0,0 +1,209 @@ +package edu.kit.datamanager.ro_crate.json.jackson3; + +import edu.kit.datamanager.ro_crate.json.JsonAdapter; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonBoolean; +import edu.kit.datamanager.ro_crate.json.JsonMissing; +import edu.kit.datamanager.ro_crate.json.JsonNull; +import edu.kit.datamanager.ro_crate.json.JsonNumber; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonString; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.math.BigDecimal; +import java.math.BigInteger; +import tools.jackson.databind.JsonNode; +import tools.jackson.databind.json.JsonMapper; +import tools.jackson.databind.node.ArrayNode; +import tools.jackson.databind.node.ObjectNode; + +/** + * Jackson 3 implementation of the {@link JsonAdapter} SPI. + * + *

Serialization and parsing are delegated to Jackson 3 + * ({@code tools.jackson}), producing byte-identical output to the Jackson 2 + * backend for the same document. The mapper keeps the parse features the + * library historically enabled on its shared mapper (see the former + * {@code MyObjectMapper}). + * + *

Note on exceptions: Jackson 3 throws unchecked exceptions; the checked + * {@link IOException} in the SPI is kept for interface compatibility. + */ +public final class Jackson3JsonAdapter implements JsonAdapter { + + private static final JsonMapper MAPPER = JsonMapper.builder() + .enable( + tools.jackson.databind.DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY + ) + .enable( + tools.jackson.databind.DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS + ) + .build(); + + @Override + public JsonObject objectNode() { + return JsonObject.create(); + } + + @Override + public JsonArray arrayNode() { + return JsonArray.create(); + } + + @Override + public JsonValue parse(String json) { + return toNeutral(MAPPER.readTree(json)); + } + + @Override + public JsonValue parse(File file) throws IOException { + return toNeutral(MAPPER.readTree(file)); + } + + @Override + public JsonValue parse(InputStream stream) throws IOException { + return toNeutral(MAPPER.readTree(stream)); + } + + @Override + public String write(JsonValue value) { + return MAPPER.writeValueAsString(toJackson(value)); + } + + @Override + public String writePretty(JsonValue value) { + return MAPPER.writerWithDefaultPrettyPrinter().writeValueAsString( + toJackson(value) + ); + } + + /** Converts a Jackson 3 tree into the neutral model. */ + public static JsonValue toNeutral(JsonNode node) { + if (node == null || node.isMissingNode()) { + return JsonMissing.INSTANCE; + } + if (node.isObject()) { + JsonObject object = JsonObject.create(); + for (var field : node.properties()) { + object.put(field.getKey(), toNeutral(field.getValue())); + } + return object; + } + if (node.isArray()) { + JsonArray array = JsonArray.create(); + for (JsonNode element : node) { + array.add(toNeutral(element)); + } + return array; + } + if (node.isNull()) { + return JsonNull.INSTANCE; + } + if (node.isString()) { + return new JsonString(node.stringValue()); + } + if (node.isBoolean()) { + return JsonBoolean.of(node.booleanValue()); + } + if (node.isNumber()) { + return new JsonNumber(numberOf(node)); + } + throw new IllegalArgumentException( + "Unsupported Jackson node type: " + node.getNodeType() + ); + } + + private static Number numberOf(JsonNode node) { + if (node.isInt()) { + return node.intValue(); + } + if (node.isLong()) { + return node.longValue(); + } + if (node.isShort()) { + return node.shortValue(); + } + if (node.isBigInteger()) { + return node.bigIntegerValue(); + } + if (node.isDouble()) { + return node.doubleValue(); + } + if (node.isFloat()) { + return node.floatValue(); + } + if (node.isBigDecimal()) { + return node.decimalValue(); + } + return node.doubleValue(); + } + + /** Converts the neutral model into a Jackson 3 tree. */ + public static JsonNode toJackson(JsonValue value) { + if (value instanceof JsonObject object) { + ObjectNode node = MAPPER.createObjectNode(); + for (var entry : object.entries()) { + node.set(entry.getKey(), toJackson(entry.getValue())); + } + return node; + } + if (value instanceof JsonArray array) { + ArrayNode node = MAPPER.createArrayNode(); + for (JsonValue element : array) { + node.add(toJackson(element)); + } + return node; + } + if (value instanceof JsonString string) { + return MAPPER.getNodeFactory().textNode(string.getValue()); + } + if (value instanceof JsonBoolean bool) { + return bool.getValue() + ? MAPPER.getNodeFactory().booleanNode(true) + : MAPPER.getNodeFactory().booleanNode(false); + } + if (value instanceof JsonNull) { + return MAPPER.getNodeFactory().nullNode(); + } + if (value instanceof JsonMissing) { + return MAPPER.getNodeFactory().missingNode(); + } + if (value instanceof JsonNumber number) { + return numberNode(number.getValue()); + } + throw new IllegalArgumentException( + "Unsupported neutral JSON value: " + value.getClass() + ); + } + + private static JsonNode numberNode(Number number) { + if (number instanceof Integer n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Long n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Short n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Byte n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Double n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof Float n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof BigInteger n) { + return MAPPER.getNodeFactory().numberNode(n); + } + if (number instanceof BigDecimal n) { + return MAPPER.getNodeFactory().numberNode(n); + } + // fallback for exotic Number implementations + return MAPPER.getNodeFactory().numberNode(number.doubleValue()); + } +} diff --git a/jackson3/src/main/java/edu/kit/datamanager/ro_crate/validation/jackson3/JsonSchemaValidation.java b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/validation/jackson3/JsonSchemaValidation.java new file mode 100644 index 00000000..b6c89418 --- /dev/null +++ b/jackson3/src/main/java/edu/kit/datamanager/ro_crate/validation/jackson3/JsonSchemaValidation.java @@ -0,0 +1,89 @@ +package edu.kit.datamanager.ro_crate.validation.jackson3; + +import com.networknt.schema.Error; +import com.networknt.schema.Schema; +import com.networknt.schema.SchemaLocation; +import com.networknt.schema.SchemaRegistry; +import com.networknt.schema.SpecificationVersion; +import edu.kit.datamanager.ro_crate.Crate; +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import edu.kit.datamanager.ro_crate.json.jackson3.Jackson3JsonAdapter; +import edu.kit.datamanager.ro_crate.validation.ValidatorStrategy; +import java.io.File; +import java.io.IOException; +import java.net.URI; +import java.util.List; + +/** + * Validation of the crate metadata using JSON-schema, backed by the Jackson 3 + * version of the networknt validator (networknt 3.x API with the + * SchemaRegistry). + */ +public class JsonSchemaValidation implements ValidatorStrategy { + + private static final String defaultSchema = "json_schemas/default.json"; + private Schema schema; + + private void getSchema(URI schemaUri) { + SchemaRegistry registry = SchemaRegistry.withDefaultDialect( + SpecificationVersion.DRAFT_2019_09 + ); + this.schema = registry.getSchema(SchemaLocation.of(schemaUri.toString())); + } + + /** + * Default constructor for the JSON-schema validation. + */ + public JsonSchemaValidation() { + // the classpath: scheme resolves relative $refs correctly and works + // both from folders and jars + SchemaRegistry registry = SchemaRegistry.withDefaultDialect( + SpecificationVersion.DRAFT_2019_09 + ); + this.schema = registry.getSchema( + SchemaLocation.of("classpath:" + defaultSchema) + ); + } + + public JsonSchemaValidation(URI schemaUri) { + getSchema(schemaUri); + } + + public JsonSchemaValidation(String schema) { + URI schemaUri = new File(schema).toURI(); + getSchema(schemaUri); + } + + public JsonSchemaValidation(JsonValue schema) { + SchemaRegistry registry = SchemaRegistry.withDefaultDialect( + SpecificationVersion.DRAFT_2019_09 + ); + this.schema = registry.getSchema(Jackson3JsonAdapter.toJackson(schema)); + } + + @Override + public boolean validate(Crate crate) { + try { + final JsonValue good = Json.parse(crate.getJsonMetadata()); + List errors = this.schema.validate( + Jackson3JsonAdapter.toJackson(good) + ); + if (errors.isEmpty()) { + return true; + } else { + System.err.println( + "This crate does not validate against the this schema." + + " If you haven't provided any schemas," + + " then it does not validate against the default one." + ); + for (var e : errors) { + System.err.println(e.getMessage()); + } + } + } catch (IOException e) { + e.printStackTrace(); + } + return false; + } +} diff --git a/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy new file mode 100644 index 00000000..301835a1 --- /dev/null +++ b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.entities.validation.EntityValidationStrategy @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.entities.validation.jackson3.JsonSchemaValidation diff --git a/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter new file mode 100644 index 00000000..ec4080aa --- /dev/null +++ b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.json.JsonAdapter @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.json.jackson3.Jackson3JsonAdapter diff --git a/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy new file mode 100644 index 00000000..7c716296 --- /dev/null +++ b/jackson3/src/main/resources/META-INF/services/edu.kit.datamanager.ro_crate.validation.ValidatorStrategy @@ -0,0 +1 @@ +edu.kit.datamanager.ro_crate.validation.jackson3.JsonSchemaValidation diff --git a/jackson3/src/main/resources/json_schemas/default.json b/jackson3/src/main/resources/json_schemas/default.json new file mode 100644 index 00000000..5d404f94 --- /dev/null +++ b/jackson3/src/main/resources/json_schemas/default.json @@ -0,0 +1,20 @@ +{ + "$schema": "https://json-schema.org/draft/2019-09/schema", + "required": [ + "@context", + "@graph" + ], + "properties": { + "@graph": { + "type": "array", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "$ref": "entity_field_structure_schema.json" + } + } + } + } + } +} \ No newline at end of file diff --git a/jackson3/src/main/resources/json_schemas/entity_field_structure_schema.json b/jackson3/src/main/resources/json_schemas/entity_field_structure_schema.json new file mode 100644 index 00000000..d2112ebb --- /dev/null +++ b/jackson3/src/main/resources/json_schemas/entity_field_structure_schema.json @@ -0,0 +1,46 @@ +{ + "$schema": "https://json-schema.org/draft/2019-09/schema", + "title": "Core schema meta-schema", + "anyOf": [ + { + "type": "array", + "items": { + "anyOf": [ + { "$ref": "#/$defs/idProperty"}, + {"type": "string"}, + {"type": "number"}, + {"type": "boolean"}, + {"type": "null"} + ] + } + }, + { + "$ref": "#/$defs/idProperty" + }, + { + "type": "string" + }, + { + "type": "number" + }, + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "$defs" : { + "idProperty": { + "type": ["object"], + "properties": { + "@id": { + "type": ["string"] + } + }, + "required": ["@id"], + "additionalProperties": false + } + + } +} \ No newline at end of file diff --git a/jackson3/src/main/resources/json_schemas/entity_schema.json b/jackson3/src/main/resources/json_schemas/entity_schema.json new file mode 100644 index 00000000..f8388bd7 --- /dev/null +++ b/jackson3/src/main/resources/json_schemas/entity_schema.json @@ -0,0 +1,10 @@ +{ + "$schema": "https://json-schema.org/draft/2019-09/schema", + "title": "Schema for the structure of the whole entity", + "type": "object", + "patternProperties": { + ".*": { + "$ref": "entity_field_structure_schema.json" + } + } +} diff --git a/jackson3/src/test/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3BackendParityTest.java b/jackson3/src/test/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3BackendParityTest.java new file mode 100644 index 00000000..84c12c96 --- /dev/null +++ b/jackson3/src/test/java/edu/kit/datamanager/ro_crate/json/jackson3/Jackson3BackendParityTest.java @@ -0,0 +1,144 @@ +package edu.kit.datamanager.ro_crate.json.jackson3; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import edu.kit.datamanager.ro_crate.json.Json; +import edu.kit.datamanager.ro_crate.json.JsonArray; +import edu.kit.datamanager.ro_crate.json.JsonObject; +import edu.kit.datamanager.ro_crate.json.JsonValue; +import java.io.IOException; +import java.nio.file.Path; +import java.util.stream.Stream; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.MethodSource; +import tools.jackson.databind.json.JsonMapper; + +/** + * Parity tests for the Jackson 3 backend: output must be byte-identical to + * what the Jackson 2 backend produces (and to the committed golden files, + * which were generated with the original Jackson 2 based library). + */ +class Jackson3BackendParityTest { + + private static final JsonMapper REFERENCE_MAPPER = JsonMapper.builder() + .enable( + tools.jackson.databind.DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY + ) + .enable( + tools.jackson.databind.DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS + ) + .build(); + + @Test + void parseMatchesJackson3Tree() throws IOException { + String json = + "{\"name\":\"crate\",\"items\":[\"one\"],\"nested\":{\"a\":1}}"; + assertEquals( + Jackson3JsonAdapter.toNeutral(REFERENCE_MAPPER.readTree(json)), + Json.parse(json) + ); + } + + @Test + void writeMatchesJackson3Output() throws IOException { + JsonObject object = JsonObject.create() + .put("z", "last") + .put("a", "first") + .put("n", 1) + .put("d", 2.5) + .put("b", true) + .putNull("nil") + .set("items", JsonArray.create().add("x").add("y")); + assertEquals( + REFERENCE_MAPPER.writeValueAsString( + Jackson3JsonAdapter.toJackson(object) + ), + Json.write(object) + ); + } + + @Test + void roundTripThroughAdapterIsStable() throws IOException { + String json = + "{\"@context\":\"https://w3id.org/ro/crate/1.1/context\"," + + "\"@graph\":[{\"@id\":\"./\",\"name\":\"m\\\"in\",\"num\":1.0," + + "\"unicode\":\"äöü €\"}]}"; + assertEquals(json, Json.write(Json.parse(json))); + } + + @Test + void adapterIsDiscoverableViaServiceLoader() { + assertEquals(Jackson3JsonAdapter.class, Json.adapter().getClass()); + } + + /** + * The Jackson 3 backend must produce the same crate metadata as the + * golden files locked in by the core test suite (which were generated + * with the original Jackson 2 based library). + */ + @ParameterizedTest + @MethodSource("fixtureCrates") + void crateMetadataMatchesGoldenFiles(String fixture) throws IOException { + Path crateDir = Path.of("../core/src/test/resources", fixture); + String name = Path.of(fixture).getFileName().toString(); + + edu.kit.datamanager.ro_crate.RoCrate read = + edu.kit.datamanager.ro_crate.reader.Readers.newFolderReader().readCrate( + crateDir.toString() + ); + String metadata = read.getJsonMetadata(); + + Path goldenPath = Path.of( + "../core/src/test/resources/golden", + name + ".metadata.json" + ); + assertTrue( + java.nio.file.Files.exists(goldenPath), + "missing golden file " + goldenPath + ); + String golden = java.nio.file.Files.readString(goldenPath); + assertEquals( + canonicalize(golden), + canonicalize(metadata), + "Jackson 3 backend output drifted from the golden file for '" + name + "'" + ); + } + + /** + * Canonicalizes metadata for byte-level comparison by sorting the + * {@code @graph} entities by their {@code @id} (entity order is unspecified + * in the library). Same semantics as the core golden test's canonicalizer. + */ + private static String canonicalize(String metadata) throws IOException { + JsonObject root = (JsonObject) Json.parse(metadata); + JsonValue graph = root.path("@graph"); + if (graph.isArray()) { + java.util.List entities = new java.util.ArrayList<>(); + graph.forEach(entities::add); + entities.sort( + java.util.Comparator.comparing( + node -> node.path("@id").asText(""), + String.CASE_INSENSITIVE_ORDER + ) + ); + JsonArray graphArray = (JsonArray) graph; + while (!graphArray.isEmpty()) { + graphArray.remove(0); + } + entities.forEach(graphArray::add); + } + return Json.write(root); + } + + static Stream fixtureCrates() { + return Stream.of( + "crates/extendedContextExample", + "crates/hasPartHierarchy", + "crates/simple_crate", + "crates/other/idrc_project", + "crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array" + ); + } +} diff --git a/settings.gradle b/settings.gradle index 2bc86c66..3e70723e 100644 --- a/settings.gradle +++ b/settings.gradle @@ -1,2 +1,3 @@ rootProject.name = 'ro-crate-java' +include 'core', 'jackson2', 'jackson3', 'examples' diff --git a/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java b/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java deleted file mode 100644 index cb960b4a..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java +++ /dev/null @@ -1,693 +0,0 @@ -package edu.kit.datamanager.ro_crate; - -import com.fasterxml.jackson.core.TreeNode; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.context.CrateMetadataContext; -import edu.kit.datamanager.ro_crate.context.RoCrateMetadataContext; -import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognition; -import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionConfig; -import edu.kit.datamanager.ro_crate.hierarchy.HierarchyRecognitionResult; -import edu.kit.datamanager.ro_crate.entities.AbstractEntity; -import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; -import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; -import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; -import edu.kit.datamanager.ro_crate.externalproviders.dataentities.ImportFromDataCite; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.payload.CratePayload; -import edu.kit.datamanager.ro_crate.payload.RoCratePayload; -import edu.kit.datamanager.ro_crate.preview.CratePreview; -import edu.kit.datamanager.ro_crate.preview.CustomPreview; -import edu.kit.datamanager.ro_crate.special.CrateVersion; -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; -import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.validation.Validator; -import java.io.File; -import java.net.URI; -import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.StreamSupport; - -/** - * The class that represents a single ROCrate. - *

- * To build or modify it, use a instance of {@link RoCrateBuilder}. In the case - * features of RO-Crate DRAFT specifications are needed, refer to - * {@link BuilderWithDraftFeatures} and its documentation. - * - * @author Nikola Tzotchev on 6.2.2022 г. - * @version 1 - */ -public class RoCrate implements Crate { - - protected final CratePayload roCratePayload; - protected CrateMetadataContext metadataContext; - protected CratePreview roCratePreview; - protected RootDataEntity rootDataEntity; - protected ContextualEntity jsonDescriptor; - - protected Collection untrackedFiles; - - /** - * Indicates whether this crate has been imported from an external source. - * This is used to determine if ro-crate-java should add a CreateAction - * or an UpdateAction in the provenance on export. - */ - protected boolean isImported = false; - - @Override - public RoCrate markAsImported() { - this.isImported = true; - return this; - } - - @Override - public boolean isImported() { - return this.isImported; - } - - @Override - public CratePreview getPreview() { - return this.roCratePreview; - } - - public void setRoCratePreview(CratePreview preview) { - this.roCratePreview = preview; - } - - @Override - public void setMetadataContext(CrateMetadataContext metadataContext) { - this.metadataContext = metadataContext; - } - - @Override - public String getMetadataContextValueOf(String key) { - return this.metadataContext.getValueOf(key); - } - - @Override - public Set getMetadataContextKeys() { - return this.metadataContext.getKeys(); - } - - @Override - public Map getMetadataContextPairs() { - return this.metadataContext.getPairs(); - } - - public ContextualEntity getJsonDescriptor() { - return jsonDescriptor; - } - - @Override - public void setJsonDescriptor(ContextualEntity jsonDescriptor) { - this.jsonDescriptor = jsonDescriptor; - } - - @Override - public RootDataEntity getRootDataEntity() { - return rootDataEntity; - } - - @Override - public void setRootDataEntity(RootDataEntity rootDataEntity) { - this.rootDataEntity = rootDataEntity; - } - - /** - * Default constructor for creation of an empty crate. - */ - public RoCrate() { - this.roCratePayload = new RoCratePayload(); - this.untrackedFiles = new HashSet<>(); - this.metadataContext = new RoCrateMetadataContext(); - rootDataEntity = new RootDataEntity.RootDataEntityBuilder().build(); - jsonDescriptor = new JsonDescriptor(); - } - - /** - * A constructor for creating the crate using a Crate builder for easier - * creation. - * - * @param roCrateBuilder the builder to use. - */ - public RoCrate(RoCrateBuilder roCrateBuilder) { - this.roCratePayload = roCrateBuilder.payload; - this.metadataContext = roCrateBuilder.metadataContext; - this.roCratePreview = roCrateBuilder.preview; - this.rootDataEntity = roCrateBuilder.rootDataEntity; - this.jsonDescriptor = roCrateBuilder.descriptorBuilder.build(); - this.untrackedFiles = roCrateBuilder.untrackedFiles; - Validator defaultValidation = new Validator(new JsonSchemaValidation()); - defaultValidation.validate(this); - } - - @Override - public Optional getVersion() { - JsonNode conformsTo = this.jsonDescriptor.getProperty("conformsTo"); - if (conformsTo.isArray()) { - return StreamSupport.stream(conformsTo.spliterator(), false) - .filter(TreeNode::isObject) - .map(obj -> obj.path("@id").asText()) - .map(CrateVersion::fromSpecUri) - .filter(Optional::isPresent) - .map(Optional::get) - .findFirst(); - } else if (conformsTo.isObject()) { - return CrateVersion.fromSpecUri(conformsTo.get("@id").asText()); - } else { - return Optional.empty(); - } - } - - @Override - public Collection getProfiles() { - JsonNode conformsTo = this.jsonDescriptor.getProperty("conformsTo"); - if (conformsTo.isArray()) { - return StreamSupport.stream(conformsTo.spliterator(), false) - .filter(TreeNode::isObject) - .map(obj -> obj.path("@id").asText()) - .collect(Collectors.toSet()); - } else { - return Collections.emptySet(); - } - } - - @Override - public String getJsonMetadata() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode node = objectMapper.createObjectNode(); - - node.setAll(this.metadataContext.getContextJsonEntity()); - - var graph = objectMapper.createArrayNode(); - ObjectNode root = objectMapper.convertValue( - this.rootDataEntity, - ObjectNode.class - ); - graph.add(root); - - graph.add( - objectMapper.convertValue(this.jsonDescriptor, JsonNode.class) - ); - if ( - this.roCratePayload != null && - this.roCratePayload.getEntitiesMetadata() != null - ) { - graph.addAll(this.roCratePayload.getEntitiesMetadata()); - } - node.set("@graph", graph); - return node.toString(); - } - - @Override - public DataEntity getDataEntityById(String id) { - return this.roCratePayload.getDataEntityById(id); - } - - @Override - public Optional getDataSetById(String id) { - DataEntity data = this.roCratePayload.getDataEntityById(id); - if (data instanceof DataSetEntity) { - return Optional.of((DataSetEntity) data); - } - return Optional.empty(); - } - - @Override - public Set getAllDataEntities() { - return new HashSet<>(this.roCratePayload.getAllDataEntities()); - } - - @Override - public ContextualEntity getContextualEntityById(String id) { - return this.roCratePayload.getContextualEntityById(id); - } - - @Override - public Set getAllContextualEntities() { - return new HashSet<>(this.roCratePayload.getAllContextualEntities()); - } - - @Override - public AbstractEntity getEntityById(String id) { - return this.roCratePayload.getEntityById(id); - } - - /** - * {@inheritDoc} - *

- * Note: This will also link the DataEntity to the root node using the root - * nodes hasPart property. - * - * @param entity the DataEntity to add to this crate. - */ - @Override - public void addDataEntity(DataEntity entity) { - this.metadataContext.checkEntity(entity); - this.roCratePayload.addDataEntity(entity); - this.rootDataEntity.addToHasPart(entity.getId()); - } - - @Override - public void addDataEntity(DataEntity entity, String parentId) - throws IllegalArgumentException { - if (parentId == null) { - throw new IllegalArgumentException("Parent ID is null."); - } - - DataEntity parentEntity = parentId.equals("./") - ? this.getRootDataEntity() - : this.getDataEntityById(parentId); - - if (parentEntity == null) { - throw new IllegalArgumentException( - "Parent ID not found in the crate." - ); - } - - if (parentEntity.getTypes().contains("File")) { - throw new IllegalArgumentException( - "Parent entity cannot be a File." - ); - } - - if (!parentEntity.getTypes().contains("Dataset")) { - throw new IllegalArgumentException( - "Parent entity must be a Dataset in order to contain another DataEntity as a part." - ); - } - - this.metadataContext.checkEntity(entity); - - if (parentEntity instanceof DataSetEntity) { - ((DataSetEntity) parentEntity).addToHasPart(entity.getId()); - } else { - parentEntity.addProperty("hasPart", entity.getId()); - } - this.roCratePayload.addDataEntity(entity); - } - - @Override - public void addContextualEntity(ContextualEntity entity) { - this.metadataContext.checkEntity(entity); - this.roCratePayload.addContextualEntity(entity); - } - - @Override - public void deleteEntityById(String entityId) { - // delete the entity firstly - this.roCratePayload.removeEntityById(entityId); - // remove from the root data entity hasPart - this.rootDataEntity.removeFromHasPart(entityId); - // remove from the root entity and the file descriptor - JsonUtilFunctions.removeFieldsWith( - entityId, - this.rootDataEntity.getProperties() - ); - JsonUtilFunctions.removeFieldsWith( - entityId, - this.jsonDescriptor.getProperties() - ); - } - - @Override - public void setUntrackedFiles(Collection files) { - this.untrackedFiles = files; - } - - @Override - public void deleteValuePairFromContext(String key) { - this.metadataContext.deleteValuePairFromContext(key); - } - - @Override - public void deleteUrlFromContext(String key) { - this.metadataContext.deleteUrlFromContext(key); - } - - @Override - public void addFromCollection( - Collection entities - ) { - this.roCratePayload.addEntities(entities); - } - - @Override - public void addItemFromDataCite(String locationUrl) { - ImportFromDataCite.addDataCiteToCrate(locationUrl, this); - } - - @Override - public Collection getUntrackedFiles() { - return this.untrackedFiles; - } - - @Override - public HierarchyRecognitionResult createDataEntityFileStructure( - boolean addInverseRelationships - ) { - HierarchyRecognitionConfig config = new HierarchyRecognitionConfig() - .withSetInverseRelationships(addInverseRelationships); - return this.createDataEntityFileStructure(config); - } - - @Override - public HierarchyRecognitionResult createDataEntityFileStructure( - HierarchyRecognitionConfig config - ) { - return new HierarchyRecognition(this, config).buildHierarchy(); - } - - /** - * The inner class builder for the easier creation of a ROCrate. - */ - public static class RoCrateBuilder { - - private static final String PROPERTY_DESCRIPTION = "description"; - - CratePayload payload; - CratePreview preview = new CustomPreview(); - CrateMetadataContext metadataContext; - ContextualEntity license; - RootDataEntity rootDataEntity; - Collection untrackedFiles = new HashSet<>(); - - JsonDescriptor.Builder descriptorBuilder = new JsonDescriptor.Builder(); - - /** - * The default constructor of a builder. - * - * @param name the name of the crate. - * @param description the description of the crate. - * @param datePublished the published date of the crate. - * @param licenseId the license identifier of the crate. - */ - public RoCrateBuilder( - String name, - String description, - String datePublished, - String licenseId - ) { - this.payload = new RoCratePayload(); - this.metadataContext = new RoCrateMetadataContext(); - this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder() - .addProperty("name", name) - .addProperty(PROPERTY_DESCRIPTION, description) - .build(); - this.setLicense(licenseId); - this.addDatePublishedWithExceptions(datePublished); - } - - /** - * The default constructor of a builder. - * - * @param name the name of the crate. - * @param description the description of the crate. - * @param datePublished the published date of the crate. - * @param license the license entity of the crate. - */ - public RoCrateBuilder( - String name, - String description, - String datePublished, - ContextualEntity license - ) { - this.payload = new RoCratePayload(); - this.metadataContext = new RoCrateMetadataContext(); - this.rootDataEntity = new RootDataEntity.RootDataEntityBuilder() - .addProperty("name", name) - .addProperty(PROPERTY_DESCRIPTION, description) - .build(); - this.setLicense(license); - this.addDatePublishedWithExceptions(datePublished); - } - - /** - * A default constructor without any params where the root data entity - * will be plain. - */ - public RoCrateBuilder() { - this.payload = new RoCratePayload(); - this.metadataContext = new RoCrateMetadataContext(); - rootDataEntity = new RootDataEntity.RootDataEntityBuilder().build(); - } - - /** - * A constructor with a crate as template. - * - * @param crate the crate to copy. - */ - public RoCrateBuilder(RoCrate crate) { - this.payload = crate.roCratePayload; - this.preview = crate.roCratePreview; - this.metadataContext = crate.metadataContext; - this.rootDataEntity = crate.rootDataEntity; - this.untrackedFiles = crate.untrackedFiles; - this.descriptorBuilder = new JsonDescriptor.Builder(crate); - } - - public RoCrateBuilder addName(String name) { - this.rootDataEntity.addProperty("name", name); - return this; - } - - /** - * Adds an "identifier" property to the root data entity. - *

- * This is useful e.g. to assign e.g. a DOI to this crate. - * @param identifier the identifier to add. - * @return this builder. - */ - public RoCrateBuilder addIdentifier(String identifier) { - this.rootDataEntity.addProperty("identifier", identifier.strip()); - return this; - } - - public RoCrateBuilder addDescription(String description) { - this.rootDataEntity.addProperty(PROPERTY_DESCRIPTION, description); - return this; - } - - /** - * Adds a data entity to the crate. - *

- * Note: This will also link the DataEntity to the root node using the - * root nodes hasPart property. - * - * @param dataEntity the DataEntity to add to this crate. - * @return returns the builder for further usage. - */ - public RoCrateBuilder addDataEntity(DataEntity dataEntity) { - this.metadataContext.checkEntity(dataEntity); - this.payload.addDataEntity(dataEntity); - this.rootDataEntity.addToHasPart(dataEntity.getId()); - return this; - } - - public void addDataEntity(DataEntity entity, String parentId) - throws IllegalArgumentException { - if (parentId == null) { - throw new IllegalArgumentException("Parent ID is null."); - } - - DataEntity parentEntity = parentId.equals("./") - ? this.rootDataEntity - : this.payload.getDataEntityById(parentId); - - if (parentEntity == null) { - throw new IllegalArgumentException( - "Parent ID not found in the crate." - ); - } - - if (parentEntity.getTypes().contains("File")) { - throw new IllegalArgumentException( - "Parent entity cannot be a File." - ); - } - - if (!parentEntity.getTypes().contains("Dataset")) { - throw new IllegalArgumentException( - "Parent entity must be a Dataset in order to contain another DataEntity as a part." - ); - } - - this.metadataContext.checkEntity(entity); - - if (parentEntity instanceof DataSetEntity) { - ((DataSetEntity) parentEntity).addToHasPart(entity.getId()); - } else { - parentEntity.addProperty("hasPart", entity.getId()); - } - this.payload.addDataEntity(entity); - } - - public RoCrateBuilder addContextualEntity( - ContextualEntity contextualEntity - ) { - this.metadataContext.checkEntity(contextualEntity); - this.payload.addContextualEntity(contextualEntity); - return this; - } - - /** - * Setting the license of the crate. - * - * @param license the license to set. - * @return this builder. - */ - public RoCrateBuilder setLicense(ContextualEntity license) { - this.license = license; - // From our tests, it seems like if we only have the ID for our license, we do - // not need to add an extra entity. - if (license.getProperties().size() > 1) { - this.addContextualEntity(license); - } - this.rootDataEntity.addIdProperty("license", license.getId()); - return this; - } - - /** - * Setting the license of the crate using only a license identifier. - * - * @param licenseId the licenses identifier. Should be a resolveable - * URI. - * @return the builder - */ - public RoCrateBuilder setLicense(String licenseId) { - ContextualEntity licenseEntity = - new ContextualEntity.ContextualEntityBuilder() - .setId(licenseId) - .build(); - this.setLicense(licenseEntity); - return this; - } - - /** - * Adds a property with date time format. The property should match the - * ISO 8601 date format. - * - * @param dateValue time string in ISO 8601 format - * @return this builder - * @throws IllegalArgumentException if format is not ISO 8601 - */ - public RoCrateBuilder addDatePublishedWithExceptions(String dateValue) - throws IllegalArgumentException { - this.rootDataEntity.addDateTimePropertyWithExceptions( - "datePublished", - dateValue - ); - return this; - } - - public RoCrateBuilder setContext(CrateMetadataContext context) { - this.metadataContext = context; - return this; - } - - public RoCrateBuilder addUrlToContext(String url) { - this.metadataContext.addToContextFromUrl(url); - return this; - } - - public RoCrateBuilder addValuePairToContext(String key, String value) { - this.metadataContext.addToContext(key, value); - return this; - } - - public RoCrateBuilder setPreview(CratePreview preview) { - this.preview = preview; - return this; - } - - public RoCrateBuilder addUntrackedFile(File file) { - this.untrackedFiles.add(file); - return this; - } - - /** - * @return a crate with the information from this builder. - */ - public RoCrate build() { - return new RoCrate(this); - } - } - - /** - * Builder for Crates, supporting features which are not in a final - * specification yet. - *

- * NOTE: This will change the specification version of your crate. - *

- * We only add features we expect to be in the new specification in the end. - * In case a feature will not make it into the specification, we will mark - * it as deprecated and remove it in new major versions. If a feature is - * finalized, it will be added to the stable {@link RoCrateBuilder} and - * marked as deprecated in this class. - */ - public static class BuilderWithDraftFeatures extends RoCrateBuilder { - - /** - * @see RoCrateBuilder#RoCrateBuilder() - */ - public BuilderWithDraftFeatures() { - super(); - } - - /** - * @see RoCrateBuilder#RoCrateBuilder(String, String, String, String) - */ - public BuilderWithDraftFeatures( - String name, - String description, - String datePublished, - String licenseId - ) { - super(name, description, datePublished, licenseId); - } - - /** - * @see RoCrateBuilder#RoCrateBuilder(String, String, String, - * ContextualEntity) - */ - public BuilderWithDraftFeatures( - String name, - String description, - String datePublished, - ContextualEntity licenseId - ) { - super(name, description, datePublished, licenseId); - } - - /** - * @see RoCrateBuilder#RoCrateBuilder(RoCrate) - */ - public BuilderWithDraftFeatures(RoCrate crate) { - super(crate); - this.descriptorBuilder = new JsonDescriptor.Builder(crate); - } - - /** - * Indicate this crate also conforms to the given specification, in - * addition to the version this builder adds. - *

- * This is helpful for profiles or other specifications the crate - * conforms to. Can be called multiple times to add more specifications. - * - * @param specification a specification or profile this crate conforms - * to. - * @return the builder - */ - public BuilderWithDraftFeatures alsoConformsTo(URI specification) { - descriptorBuilder - .addConformsTo(specification) - // usage of a draft feature results in draft version numbers of the crate - .setVersion(CrateVersion.LATEST_UNSTABLE); - return this; - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java deleted file mode 100644 index e978b199..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java +++ /dev/null @@ -1,648 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities; - -import com.fasterxml.jackson.annotation.JsonIgnore; -import com.fasterxml.jackson.annotation.JsonUnwrapped; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - -import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; -import edu.kit.datamanager.ro_crate.entities.serializers.ObjectNodeSerializer; -import edu.kit.datamanager.ro_crate.entities.validation.EntityValidation; -import edu.kit.datamanager.ro_crate.entities.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.payload.Observer; -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; -import edu.kit.datamanager.ro_crate.special.IdentifierUtils; - -import java.util.*; -import java.util.regex.Matcher; -import java.util.regex.Pattern; - -/** - * Abstract Entity parent class of every singe item in the json metadata file. - * - * @author Nikola Tzotchev on 3.2.2022 г. - * @version 1 - */ -public class AbstractEntity { - - /** - * This set contains the types of an entity (ex. File, Dataset, ect.) It is - * a set because it does not make sense to have duplicates - */ - @JsonIgnore - private Set types; - - /** - * Contains the whole list of properties of the entity It uses a custom - * serializer because of cases where a single array element should be - * displayed as a single value. ex: "key" : ["value"] - * <=> "key" : "value" - */ - @JsonUnwrapped - @JsonSerialize(using = ObjectNodeSerializer.class) - private ObjectNode properties; - - private static final EntityValidation entityValidation - = new EntityValidation(new JsonSchemaValidation()); - - /** - * This set contains all the ids of the entities that are linked by - * this entity. This information is provided to crate payloads to make - * the removal of entities faster. - */ - @JsonIgnore - private final Set linkedTo; - - @JsonIgnore - private final Set observers; - - public void addObserver(Observer observer) { - this.observers.add(observer); - } - - private void notifyObservers() { - this.observers.forEach(observer -> observer.update(this.getId())); - } - - /** - * Constructor that takes a builder and instantiates all the fields from it. - * - * @param entityBuilder the entity builder passed to the constructor. - */ - public AbstractEntity(AbstractEntityBuilder entityBuilder) { - this.types = entityBuilder.types; - this.properties = entityBuilder.properties; - this.linkedTo = entityBuilder.relatedItems; - this.observers = new HashSet<>(); - if (this.properties.get("@id") == null) { - if (entityBuilder.id == null) { - this.properties.put("@id", UUID.randomUUID().toString()); - } else { - this.properties.put("@id", entityBuilder.id); - } - } - } - - public Set getLinkedTo() { - return linkedTo; - } - - /** - * Returns the types of this entity. - * - * @return a set of type strings. - */ - public Set getTypes() { - return types; - } - - /** - * Returns a Json object containing the properties of the entity. - * - * @return ObjectNode representing the properties. - */ - public ObjectNode getProperties() { - if (this.types != null) { - JsonNode node = MyObjectMapper.getMapper().valueToTree(this.types); - this.properties.set("@type", node); - } - return properties; - } - - public JsonNode getProperty(String propertyKey) { - return this.properties.get(propertyKey); - } - - /** - * Returns the value of the property with the given key as a String. - * If the property is not found, it returns null. - * - * @param propertyKey the key of the property. - * @return the value of the property as a String or null if not found. - */ - public String getIdProperty(String propertyKey) { - return Optional.ofNullable(this.properties.get(propertyKey)) - .map(jsonNode -> jsonNode.path("@id").asText(null)) - .orElse(null); - } - - @JsonIgnore - public String getId() { - JsonNode id = this.properties.get("@id"); - return id == null ? null : id.asText(); - } - - /** - * Set all the properties from a Json object to the Entity. The entities are - * first validated to filter any invalid entity properties. - * - * @param obj the object that contains all the json properties that should - * be added. - */ - public void setProperties(JsonNode obj) { - // validate whole entity - if (entityValidation.entityValidation(obj)) { - this.properties = obj.deepCopy(); - this.notifyObservers(); - } - } - - protected void setId(String id) { - this.properties.put("@id", id); - } - - /** - * removes one property from an entity. - * - * @param key the key of the entity, which will be removed. - */ - public void removeProperty(String key) { - this.getProperties().remove(key); - this.notifyObservers(); - } - - /** - * Removes a collection of properties from an entity. - * - * @param keys collection of keys, which will be removed. - */ - public void removeProperties(Collection keys) { - this.getProperties().remove(keys); - this.notifyObservers(); - } - - /** - * Adds a property to the entity. - *

- * It may override values, if the key already exists. - * - * @param key the key of the property. - * @param value value of the property. - */ - public void addProperty(String key, String value) { - if (key != null && value != null) { - this.properties.put(key, value); - this.notifyObservers(); - } - } - - /** - * Adds a property to the entity. - *

- * It may override values, if the key already exists. - * - * @param key the key of the property. - * @param value value of the property. - */ - public void addProperty(String key, long value) { - if (key != null) { - this.properties.put(key, value); - this.notifyObservers(); - } - } - - /** - * Adds a property to the entity. - *

- * It may override values, if the key already exists. - * - * @param key the key of the property. - * @param value value of the property. - */ - public void addProperty(String key, double value) { - if (key != null) { - this.properties.put(key, value); - this.notifyObservers(); - } - } - - /** - * Adds a generic property to the entity. - *

- * It may fail with an error message on stdout, in which case the - * value is not added. - * It may override values, if the key already exists. - * This is the most generic way to add a property. The value is a - * JsonNode that could contain anything possible. It is limited to - * objects allowed to flattened documents, which means any literal, - * an array of literals, or an object with an @id property. - * - * @param key String key of the property. - * @param value The JsonNode representing the value. - */ - public void addProperty(String key, JsonNode value) { - if (addProperty(this.properties, key, value)) { - notifyObservers(); - } - } - - private static boolean addProperty(ObjectNode whereToAdd, String key, JsonNode value) { - boolean validInput = key != null && value != null; - if (validInput && entityValidation.fieldValidation(value)) { - whereToAdd.set(key, value); - return true; - } - return false; - } - - /** - * Add a property that looks like this: "name" : {"@id" : "id"} If the - * name property already exists add a second @id to it. - * - * @param name the "key" of the property. - * @param id the "id" of the property. - */ - public void addIdProperty(String name, String id) { - if (id == null || id.isBlank()) { return; } - mergeIdIntoValue(id, this.properties.get(name)) - .ifPresent(newValue -> this.properties.set(name, newValue)); - this.linkedTo.add(id); - this.notifyObservers(); - } - - /** - * Merges the given id into the current value, - * using this representation: {"@id" : "id"}. - *

- * The current value can be null without errors. - * Only the id will be considered in this case. - *

- * If the id is null-ish, it will not be added, similar to a null-ish value. - * If the id is already present, nothing will be done. - * If it is not an array and the id is not present, an array will be applied. - * - * @param id the id to add. - * @param currentValue the current value of the property. - * @return The updated value of the property. - * Empty if value does not change! - */ - protected static Optional mergeIdIntoValue(String id, JsonNode currentValue) { - if (id == null || id.isBlank()) { return Optional.empty(); } - - ObjectMapper jsonBuilder = MyObjectMapper.getMapper(); - ObjectNode newIdObject = jsonBuilder.createObjectNode().put("@id", id); - if (currentValue == null || currentValue.isNull() || currentValue.isMissingNode()) { - return Optional.ofNullable(newIdObject); - } - - boolean isIdAlready = currentValue.asText().equals(id); - boolean isIdObjectAlready = currentValue.path("@id").asText().equals(id); - boolean isArrayWithIdPresent = currentValue.valueStream() - .anyMatch(node -> node - .path("@id") - .asText() - .equals(id)); - if (isIdAlready || isIdObjectAlready || isArrayWithIdPresent) { - return Optional.empty(); - } - - if (currentValue.isArray() && currentValue instanceof ArrayNode currentValueAsArray) { - currentValueAsArray.add(newIdObject); - return Optional.of(currentValueAsArray); - } else { - // property is not an array, so we make it an array - ArrayNode newNodes = jsonBuilder.createArrayNode(); - newNodes.add(currentValue); - newNodes.add(newIdObject); - return Optional.of(newNodes); - } - } - - /** - * Adds everything from the properties to the property "name" as id. - * - * @param name the key of the property. - * @param properties a collection containing all the id as String. - */ - public void addIdListProperties(String name, Collection properties) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ArrayNode node = objectMapper.createArrayNode(); - if (this.properties.get(name) == null) { - node = objectMapper.createArrayNode(); - } else { - if (!this.properties.get(name).isArray()) { - node.add(this.properties.get(name)); - } - } - for (String s : properties) { - this.linkedTo.add(s); - node.add(objectMapper.createObjectNode().put("@id", s)); - } - if (node.size() == 1) { - this.properties.set(name, node.get(0)); - } else { - this.properties.set(name, node); - } - notifyObservers(); - } - - /** - * Adding new type to the property (which may have multiple such ones). - * - * @param type the String representing the type. - */ - public void addType(String type) { - if (this.types == null) { - this.types = new HashSet<>(); - } - this.types.add(type); - JsonNode node = MyObjectMapper.getMapper().valueToTree(this.types); - this.properties.set("@type", node); - } - - /** - * Checks if the date matches the ISO 8601 date format. - * - * @param date the date as a string - * @throws IllegalArgumentException if format does not match - */ - private static void checkFormatISO8601(String date) throws IllegalArgumentException { - String regex = "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$"; - Pattern pattern = Pattern.compile(regex); - Matcher matcher = pattern.matcher(date); - if (!matcher.matches()) { - throw new IllegalArgumentException("Date MUST be a string in ISO 8601 format"); - } - } - - /** - * Adds a property with date time format. The property should match the ISO 8601 - * date format. - *

- * Same as {@link #addProperty(String, String)} but with internal check. - * - * @param key key of the property (e.g. datePublished) - * @param value time string in ISO 8601 format - * @throws IllegalArgumentException if format is not ISO 8601 - */ - public void addDateTimePropertyWithExceptions(String key, String value) throws IllegalArgumentException { - if (value != null) { - checkFormatISO8601(value); - this.properties.put(key, value); - this.notifyObservers(); - } - } - - /** - * This a builder inner class that should allow for an easier creating of - * entities. - * - * @param The type of the child builders so that they to can use the - * methods provided here. - */ - public abstract static class AbstractEntityBuilder> { - - private Set types; - protected Set relatedItems; - private ObjectNode properties; - private String id; - - protected AbstractEntityBuilder() { - this.properties = MyObjectMapper.getMapper().createObjectNode(); - this.relatedItems = new HashSet<>(); - } - - protected String getId() { - return this.id; - } - - /** - * Setting the id property of the entity, if the given value is not - * null. If the id is not encoded, the encoding will be done. - *

- * NOTE: IDs are not just names! The ID may have effects - * on parts of your crate! For example: If the entity represents a - * file which will be copied into the crate, writers must use the - * ID as filename. - * - * @param id the String representing the id. - * @return the generic builder. - */ - public T setId(String id) { - if (id != null && !id.equals(RootDataEntity.ID)) { - if (IdentifierUtils.isValidUri(id)) { - this.id = id; - } else { - this.id = IdentifierUtils.encode(id).orElse(this.id); - } - } - return self(); - } - - /** - * Adding a type to the builder types. - * - * @param type the type to add. - * @return the generic builder. - */ - public T addType(String type) { - if (this.types == null) { - this.types = new HashSet<>(); - } - if (type != null && !type.isEmpty()) { - this.types.add(type); - } - return self(); - } - - /** - * Adds multiple types in one call. - * - * @param types the types to add. - * @return the generic builder. - */ - public T addTypes(Collection types) { - if (this.types == null) { - this.types = new HashSet<>(); - } - this.types.addAll(types); - return self(); - } - - /** - * Adds a property with date time format. The property should match the ISO 8601 - * date format. - *

- * Same as {@link #addProperty(String, String)} but with internal check. - * - * @param key key of the property (e.g. datePublished) - * @param value time string in ISO 8601 format - * @return this builder - * @throws IllegalArgumentException if format is not ISO 8601 - */ - public T addDateTimePropertyWithExceptions(String key, String value) throws IllegalArgumentException { - if (value != null) { - checkFormatISO8601(value); - this.properties.put(key, value); - } - return self(); - } - - /** - * Adding a property to the builder. - * - * @param key the key of the property in a string. - * @param value the JsonNode value of te property. - * @return the generic builder. - */ - public T addProperty(String key, JsonNode value) { - if (AbstractEntity.addProperty(this.properties, key, value)) { - this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromProperty(value)); - } - return self(); - } - - /** - * Adding a property to the builder. - * - * @param key the key of the property as a string. - * @param value the value of the property as a string. - * @return the generic builder. - */ - public T addProperty(String key, String value) { - this.properties.put(key, value); - return self(); - } - - public T addProperty(String key, int value) { - this.properties.put(key, value); - return self(); - } - - public T addProperty(String key, double value) { - this.properties.put(key, value); - return self(); - } - - public T addProperty(String key, boolean value) { - this.properties.put(key, value); - return self(); - } - - /** - * ID properties are often used when referencing other entities within - * the ROCrate. This method adds automatically such one. - *

- * Instead of {@code "name": "id" } - * this will add {@code "name" : {"@id": "id"} } - * - * Does nothing if name or id are null. - * - * @param name the name of the ID property. - * @param id the ID. - * @return the generic builder - */ - public T addIdProperty(String name, String id) { - AbstractEntity.mergeIdIntoValue(id, this.properties.get(name)) - .ifPresent(newValue -> { - this.properties.set(name, newValue); - this.relatedItems.add(id); - }); - return self(); - } - - /** - * This is another way of adding the ID property, this time the whole - * other Entity is provided. - * - * @param name the name of the property. - * @param entity the other entity that is referenced. - * @return the generic builder. - */ - public T addIdProperty(String name, AbstractEntity entity) { - if (entity != null) { - return addIdProperty(name, entity.getId()); - } - return self(); - } - - /** - * This adds multiple id entities to a single key. - * - * @param name the name of the property. - * @param entities the Collection containing the multiple entities. - * @return the generic builder. - */ - public T addIdFromCollectionOfEntities(String name, Collection entities) { - if (entities != null) { - for (var e : entities) { - addIdProperty(name, e); - } - } - return self(); - } - - /** - * Deprecated. Equivalent to {@link #setAllIfValid(ObjectNode)}. - * - * @param properties the Json representing all the properties. - * @return the generic builder, either including all given properties - * * or unchanged. - * - * @deprecated To enforce the user know what this method does, - * we want the user to use one of the more explicitly named - * methods {@link #setAllIfValid(ObjectNode)} or - * {@link #setAllIfValid(ObjectNode)}. - * @see #setAllIfValid(ObjectNode) - */ - @Deprecated(since = "2.1.0", forRemoval = true) - public T setAll(ObjectNode properties) { - return setAllIfValid(properties); - } - - /** - * This sets everything from a json object to the property, - * if the result is valid. Otherwise, it will do nothing. - *

- * Valid means here that the json object needs to be flat as specified - * in the RO-Crate specification. In principle, this means that - * primitives and objects referencing an ID are allowed, - * as well as arrays of these. - * - * @param properties the Json representing all the properties. - * @return the generic builder, either including all given properties - * or unchanged. - */ - public T setAllIfValid(ObjectNode properties) { - if (AbstractEntity.entityValidation.entityValidation(properties)) { - this.properties = properties; - this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties)); - } - return self(); - } - - /** - * This sets everything from a json object to the property. Can be - * useful when the entity is already available somewhere. - *

- * Errors on validation are printed, but everything will be added. - * For more about validation, see {@link #setAllIfValid(ObjectNode)}. - * - * @param properties the Json representing all the properties. - * @return the generic builder with all properties added. - */ - public T setAllUnsafe(ObjectNode properties) { - // This will currently only print errors. - AbstractEntity.entityValidation.entityValidation(properties); - this.properties = properties; - JsonNode typeProps = properties.path("@type"); - if (typeProps.isArray()) { - typeProps.valueStream() - .forEach(value -> this.addType(value.asText())); - } else if (typeProps.isTextual()) { - this.addType(typeProps.asText()); - } - this.relatedItems.addAll(JsonUtilFunctions.getIdPropertiesFromJsonNode(properties)); - return self(); - } - - public abstract T self(); - - public abstract AbstractEntity build(); - } - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java deleted file mode 100644 index 8136052a..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionEntity.java +++ /dev/null @@ -1,191 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.contextual; - -import java.util.Collection; -import java.util.HashSet; -import java.util.Optional; - -/** - * This class represents a detailing provenance of entities. - * - * Relevant specification link: Provenance - * of entities - * - * @author sabrinechelbi - */ -public class ActionEntity extends ContextualEntity { - - public ActionEntity(AbstractActionEntityBuilder entityBuilder) { - super(entityBuilder); - this.addType(entityBuilder.type.getName()); - this.addProperty("name", entityBuilder.name); - this.addProperty("description", entityBuilder.description); - - this.addDateTimePropertyWithExceptions("startTime", entityBuilder.startTime); - this.addDateTimePropertyWithExceptions("endTime", entityBuilder.endTime); - - entityBuilder.status.ifPresent(status -> this.addIdProperty("actionStatus", status.getId())); - this.addIdProperty("agent", entityBuilder.agent); - this.addIdListProperties("instrument", entityBuilder.instruments); - this.addIdListProperties("result", entityBuilder.results); - this.addIdListProperties("object", entityBuilder.objects); - } - - abstract static class AbstractActionEntityBuilder> - extends AbstractContextualEntityBuilder { - - protected ActionType type; - protected String description; - protected String name; - protected String startTime; - protected String endTime; - protected String agent; - protected Optional status = Optional.empty(); - - protected Collection objects = new HashSet<>(); - protected Collection results = new HashSet<>(); - protected Collection instruments = new HashSet<>(); - - protected AbstractActionEntityBuilder(ActionType type) { - this.type = type; - } - - public T setDescription(String description) { - this.description = description; - return self(); - } - - public T setName(String name) { - this.name = name; - return self(); - } - - public T setStartTime(String startTime) { - this.startTime = startTime; - return self(); - } - - public T setEndTime(String endTime) { - this.endTime = endTime; - return self(); - } - - public T setAgent(String agent) { - this.agent = agent; - return self(); - } - - public T setStatus(ActionStatus status) { - this.status = Optional.ofNullable(status); - return self(); - } - - /** - * Same as calling {@link #addObject(String)} with each element of the - * collection. - * - * From the specification: "A curation Action MUST have at least one object - * which associates it with either the root data entity Dataset or one of its - * components." - * - * @param objects see {@link #addObject(String)} - * @return this builder - */ - public T addObjects(Collection objects) { - this.objects.addAll(objects); - return self(); - } - - /** - * Adds a object to the collection of objects of this ActionEntity. - * - * From the specification: "A curation Action MUST have at least one object - * which associates it with either the root data entity Dataset or one of its - * components." - * - * @param object the object to add to this ActionEntity. Duplicates will be - * ignored/removed. "The object upon which the action is carried - * out, whose state is kept intact or changed. Also known as the - * semantic roles patient, affected or undergoer (which change - * their state) or theme (which doesn't). E.g. John read a book." - * (Schema.org definition) - * @return this builder - */ - public T addObject(String object) { - this.objects.add(object); - return self(); - } - - /** - * Same as calling {@link #addResult(String)} with each element of the - * collection. - * - * @param results see {@link #addResult(String)} - * @return this builder - */ - public T addResults(Collection results) { - this.results.addAll(results); - return self(); - } - - /** - * Adds a result to the collection of results of this ActionEntity. - * - * @param result the result to add to this ActionEntity. Duplicates will be - * ignored/removed. "The result produced in the action. E.g. John - * wrote a book." (Schema.org definition) - * @return this builder - */ - public T addResult(String result) { - this.results.add(result); - return self(); - } - - /** - * Same as calling {@link #addInstrument(String)} with each element of the - * collection. - * - * @param instruments see {@link #addInstrument(String)} - * @return this builder - */ - public T addInstruments(Collection instruments) { - this.instruments.addAll(instruments); - return self(); - } - - /** - * Adds a instrument to the collection of instruments of this ActionEntity. - * - * @param instrument the instrument to add to this ActionEntity. Duplicates will - * be ignored/removed. "The object that helped the agent - * perform the action. E.g. John wrote a book with a pen." - * (Schema.org definition) - * @return this builder - */ - public T addInstrument(String instrument) { - this.instruments.add(instrument); - return self(); - } - - @Override - public abstract ActionEntity build(); - } - - public static final class ActionEntityBuilder - extends AbstractActionEntityBuilder { - - public ActionEntityBuilder(ActionType type) { - super(type); - } - - @Override - public ActionEntityBuilder self() { - return this; - } - - @Override - public ActionEntity build() { - return new ActionEntity(this); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java deleted file mode 100644 index f107dcac..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionStatus.java +++ /dev/null @@ -1,18 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.contextual; - -public enum ActionStatus { - ACTIVE_ACTION_STATUS("http://schema.org/ActiveActionStatus"), - COMPLETED_ACTION_STATUS("http://schema.org/CompletedActionStatus"), - FAILED_ACTION_STATUS("http://schema.org/FailedActionStatus"), - POTENTIAL_ACTION_STATUS("http://schema.org/PotentialActionStatus"); - - private final String id; - - ActionStatus(String id) { - this.id = id; - } - - public String getId() { - return id; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java deleted file mode 100644 index 02cff8dd..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/ActionType.java +++ /dev/null @@ -1,21 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.contextual; - -/** - * Enumeration class representing action types. - * @author sabrinechelbi - */ -public enum ActionType { - - CREATE("CreateAction"), - UPDATE("UpdateAction"); - - private final String name; - - ActionType(String name) { - this.name = name; - } - - public String getName(){ - return name; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java deleted file mode 100644 index 88aaf89e..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/contextual/JsonDescriptor.java +++ /dev/null @@ -1,95 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.contextual; - -import java.net.URI; -import java.util.HashSet; -import java.util.Set; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.special.CrateVersion; - -public class JsonDescriptor extends ContextualEntity { - - protected static final String CONFORMS_TO = "conformsTo"; - public static final String ID = "ro-crate-metadata.json"; - - /** - * Returns a JsonDescriptor with the conformsTo value set to the latest stable - * version. - */ - public JsonDescriptor() { - super( - staticPropertiesPrefilledBuilder() - .addIdProperty(CONFORMS_TO, CrateVersion.LATEST_STABLE.conformsTo)); - } - - protected static ContextualEntityBuilder staticPropertiesPrefilledBuilder() { - return new ContextualEntity.ContextualEntityBuilder() - .setId(ID) - .addType("CreativeWork") - .addIdProperty("about", "./"); - } - - private JsonDescriptor(ContextualEntityBuilder builder) { - super(builder); - } - - /** - * Builder for the JsonDescriptor. - *

- * Defaults to the latest stable crate version and no other conformsTo values. - */ - public static final class Builder { - CrateVersion version = CrateVersion.LATEST_STABLE; - Set otherConformsToValues = new HashSet<>(); - - public Builder() { - // default - } - - public Builder(Crate crate) { - crate.getVersion().ifPresent(v -> this.version = v); - this.otherConformsToValues.addAll(crate.getProfiles()); - } - - public Builder setVersion(CrateVersion version) { - this.version = version; - return this; - } - - public Builder addConformsTo(String uri) { - this.otherConformsToValues.add(uri); - return this; - } - - public Builder addConformsTo(URI uri) { - this.otherConformsToValues.add(uri.toString()); - return this; - } - - public JsonDescriptor build() { - if (this.otherConformsToValues.isEmpty()) { - // in this case we do not need an array - ContextualEntityBuilder entityBuilder = staticPropertiesPrefilledBuilder() - .addIdProperty(CONFORMS_TO, this.version.conformsTo); - return new JsonDescriptor(entityBuilder); - } else { - // use an array to collect all values into an array of simple @id objects. - ObjectMapper mapper = MyObjectMapper.getMapper(); - ArrayNode array = mapper.createArrayNode(); - array.add( - mapper.createObjectNode().put("@id", this.version.conformsTo)); - for (String other : this.otherConformsToValues) { - array.add( - mapper.createObjectNode().put("@id", other)); - } - ContextualEntityBuilder entityBuilder = staticPropertiesPrefilledBuilder() - .addProperty(CONFORMS_TO, array); - return new JsonDescriptor(entityBuilder); - } - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java deleted file mode 100644 index 829ee9c2..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataEntity.java +++ /dev/null @@ -1,187 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.data; - -import com.fasterxml.jackson.annotation.JsonIgnore; - -import edu.kit.datamanager.ro_crate.entities.AbstractEntity; -import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; -import static edu.kit.datamanager.ro_crate.special.IdentifierUtils.isUrl; - -import java.net.URI; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.List; - -/** - * The base class of every data entity. - * - * @author Nikola Tzotchev on 4.2.2022 г. - * @version 1 - */ -public class DataEntity extends AbstractEntity { - - @JsonIgnore - private Path path; - - /** - * The constructor that takes an DataEntity builder and instantiates the - * entity. - * - * @param entityBuilder the builder passed as argument. - */ - public DataEntity(AbstractDataEntityBuilder entityBuilder) { - super(entityBuilder); - if (!entityBuilder.authors.isEmpty()) { - this.addIdListProperties("author", entityBuilder.authors); - } - this.path = entityBuilder.location; - } - - /** - * Adds an author ID to the entity. - *

- * Calling this multiple times will add multiple author IDs. - * - * @param id the identifier of the author. - */ - @SuppressWarnings("unused") - public void addAuthorId(String id) { - this.addIdProperty("author", id); - } - - /** - * Gets the path of this entity. - *

- * When reading a crate, this will point to the entity's file within the crate. - * When creating a new entity or crate, it might point to a file outside the crate, - * as set by {@link DataEntityBuilder#setLocation(Path)}. - * Such a file will be copied into the crate when writing. - * - * @return the path to the file this entity represents. - */ - @JsonIgnore - public Path getPath() { - return path; - } - - abstract static class AbstractDataEntityBuilder> extends - AbstractEntityBuilder { - - private Path location; - private List authors = new ArrayList<>(); - - /** - * Sets the location of the data entity to make a copy from when writing the crate. - *

- * Use this if you want to copy the associated file to the crate. - * Do not use it if the file should already be considered (e.g. - * as part of a DataSetEntity). - *

- * If the ID has not been set manually in beforehand, it will be derived - * from the path. Use {@link #setId(String)} to override it or set it in - * beforehand. Note that another call of this method will - * not override the ID as it has been set by the previous call! - * - * @param path the location of the data. May be null, in which case - * nothing happens. - * @return this builder - */ - public T setLocation(Path path) { - if (path != null) { - if (this.getId() == null) { - this.setId(path.getFileName().toString()); - } - this.location = path; - } - return self(); - } - - /** - * A variant of {@link #setLocation(Path)} which may throw exceptions. - * - * @param path the location of the data - * @return this builder - * @throws IllegalArgumentException if path is null - */ - public T setLocationWithExceptions(Path path) throws IllegalArgumentException { - if (path == null) { - throw new IllegalArgumentException("The given path should not be null."); - } - return setLocation(path); - } - - /** - * Same as {@link #setLocation(Path)} but instead of associating this - * entity with a file, it will point to some place on the internet. - *

- * Via the specification, this means the uri will be set as the ID. This - * call is therefore equivalent to {@link #setId(String)}. - * - * @param uri the URI, should point at the data reachable on the - * internet. - * @return this builder - */ - public T setLocation(URI uri) { - if (uri != null && this.getId() == null) { - this.setId(uri.toString()); - } - return self(); - } - - /** - * A variant of {@link #setLocation(URI)} which may throw exceptions. - * - * @param uri the given uri - * @return this builder - * @throws IllegalArgumentException if uri is null or not a valid URL - */ - public T setLocationWithExceptions(URI uri) throws IllegalArgumentException { - if (!isUrl(uri.toString())) { - throw new IllegalArgumentException("This Data Entity remote ID does not resolve to a valid URL."); - } - return setLocation(uri); - } - - public T setLicense(String id) { - this.addIdProperty("license", id); - return self(); - } - - public T setLicense(ContextualEntity license) { - this.addIdProperty("license", license.getId()); - return self(); - } - - public T addAuthor(String id) { - this.authors.add(id); - return self(); - } - - public T setContentLocation(String id) { - this.addIdProperty("contentLocation", id); - return self(); - } - - @Override - public abstract DataEntity build(); - } - - /** - * Data Entity builder class that allows for easier data entity creation. - *

- * If not explicitly mentioned, all methods avoid Exceptions and will - * silently ignore null-parameters, in which case nothing will happen. Use - * the available *WithExceptions-methods in case you need them. - */ - public static final class DataEntityBuilder extends AbstractDataEntityBuilder { - - @Override - public DataEntityBuilder self() { - return this; - } - - @Override - public DataEntity build() { - return new DataEntity(this); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java deleted file mode 100644 index 8030c04c..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntity.java +++ /dev/null @@ -1,146 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.data; - -import com.fasterxml.jackson.annotation.JsonInclude; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.annotation.JsonSerialize; - -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.entities.serializers.HasPartSerializer; - -import java.util.HashSet; -import java.util.Set; -import java.util.stream.Collectors; - -/** - * A helping class for the creating of Data entities of type Dataset. - * - * @author Nikola Tzotchev on 5.2.2022 г. - * @version 1 - */ -public class DataSetEntity extends DataEntity { - - public static final String TYPE = "Dataset"; - - /** - * Points to the parts of this dataset. - *

- * This will be serialized to and deserialized from the "hasPart" property - * and exists for convenience to represent the additional capabilities of - * a DataSetEntity over a normal DataEntity. - */ - @JsonSerialize(using = HasPartSerializer.class) - @JsonInclude(JsonInclude.Include.NON_EMPTY) - public Set hasPart; - - /** - * Constructor for instantiating a Dataset entity from the builder. - * - * @param entityBuilder the builder passed as argument. - */ - public DataSetEntity(AbstractDataSetBuilder entityBuilder) { - super(entityBuilder); - this.hasPart = entityBuilder.hasPart.stream() - .filter(s -> !s.isBlank()) - .collect(Collectors.toSet()); - this.addType(TYPE); - } - - public void removeFromHasPart(String str) { - this.hasPart.remove(str); - } - - public void addToHasPart(String id) { - if (id != null && !id.isEmpty()) { - this.hasPart.add(id); - } - } - - /** - * Check if the hasPart property contains a specific id. - * - * @deprecated use {@link #hasPart(String)} instead. - * - * @param id the id to check for - * @return true if the id is present, false otherwise - */ - @Deprecated(forRemoval = true) - public boolean hasInHasPart(String id) { - return this.hasPart.contains(id); - } - - /** - * Check if the hasPart property contains a specific id. - * @param id the id to check for - * @return true if the id is present, false otherwise - */ - public boolean hasPart(String id) { - return this.hasPart.contains(id); - } - - abstract static class AbstractDataSetBuilder> extends - AbstractDataEntityBuilder { - - Set hasPart; - - public AbstractDataSetBuilder() { - this.hasPart = new HashSet<>(); - } - - public T setHasPart(Set hasPart) { - this.hasPart = hasPart; - return self(); - } - - public T addToHasPart(DataEntity dataEntity) { - if (dataEntity != null) { - this.hasPart.add(dataEntity.getId()); - this.relatedItems.add(dataEntity.getId()); - } - return self(); - } - - public T addToHasPart(String dataEntity) { - if (dataEntity != null) { - this.hasPart.add(dataEntity); - this.relatedItems.add(dataEntity); - } - return self(); - } - - @Override - public T setAllUnsafe(ObjectNode properties) { - super.setAllUnsafe(properties); - JsonNode hasPart = properties.path("hasPart"); - String txt = hasPart.asText(); - if (!txt.isBlank()) { - this.hasPart.add(txt); - } - hasPart.valueStream() - .map(JsonNode::asText) - .filter(value -> !value.isBlank()) - .forEach( - value -> this.hasPart.add(value) - ); - return self(); - } - - @Override - public abstract DataSetEntity build(); - } - - /** - * Builder for the helping class DataSetEntity. - */ - public static final class DataSetBuilder extends AbstractDataSetBuilder { - - @Override - public DataSetBuilder self() { - return this; - } - - @Override - public DataSetEntity build() { - return new DataSetEntity(this); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/HasPartSerializer.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/HasPartSerializer.java deleted file mode 100644 index d8189958..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/HasPartSerializer.java +++ /dev/null @@ -1,48 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.serializers; - -import com.fasterxml.jackson.core.JsonGenerator; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.SerializerProvider; -import com.fasterxml.jackson.databind.node.ObjectNode; -import com.fasterxml.jackson.databind.ser.std.StdSerializer; - -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import java.io.IOException; -import java.util.Set; - -/** - * Class for serializing the hasPart property of a entity. - */ -public class HasPartSerializer extends StdSerializer> { - - public HasPartSerializer() { - this(null); - } - - public HasPartSerializer(Class> t) { - super(t); - } - - @Override - public boolean isEmpty(SerializerProvider provider, Set value) { - return value.size() == 0; - } - - @Override - public void serialize(Set value, JsonGenerator gen, SerializerProvider provider) - throws IOException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - if (value.size() > 1) { - gen.writeStartArray(); - for (String str : value) { - ObjectNode node = objectMapper.createObjectNode(); - node.put("@id", str); - gen.writeObject(node); - } - gen.writeEndArray(); - } else if (value.size() == 1) { - gen.writeObject(objectMapper.createObjectNode().put("@id", value.iterator().next())); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/ObjectNodeSerializer.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/ObjectNodeSerializer.java deleted file mode 100644 index d9ca1245..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/serializers/ObjectNodeSerializer.java +++ /dev/null @@ -1,78 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.serializers; - -import com.fasterxml.jackson.core.JsonGenerator; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.SerializerProvider; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import com.fasterxml.jackson.databind.ser.std.StdSerializer; - -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; - -import java.io.IOException; -import java.util.Iterator; -import java.util.Map; -import java.util.Map.Entry; - -/** - * Serialization class used with jackson to serialize the entity. - * - * @author Nikola Tzotchev on 4.2.2022 г. - * @version 1 - */ -public class ObjectNodeSerializer extends StdSerializer { - - public ObjectNodeSerializer() { - this(null); - } - - protected ObjectNodeSerializer(Class t) { - super(t); - } - - @Override - public void serialize(ObjectNode value, JsonGenerator jgen, SerializerProvider provider) - throws IOException { - - JsonNode node = JsonUtilFunctions.unwrapSingleArray(value); - final Iterator> fields = node.fields(); - - while (fields.hasNext()) { - Map.Entry field = fields.next(); - final String fieldName = field.getKey(); - JsonNode fieldValue = field.getValue(); - if (fieldValue.isObject() && fieldValue.size() == 0) { - continue; - } - if (fieldValue.isNull()) { - continue; - } - // if the type array contains only one type set it as String - // if (fieldName.equals("@type")) { - if (fieldValue.isArray()) { - if (fieldValue.isEmpty()) { - continue; - } - ArrayNode arrayNode = (ArrayNode) fieldValue; - int size = arrayNode.size(); - for (int i = size - 1; i >= 0; i--) { - var element = arrayNode.get(i); - if (element.isObject() && element.isEmpty()) { - arrayNode.remove(i); - } - } - if (arrayNode.isEmpty()) { - continue; - } - } - jgen.writeFieldName(fieldName); - jgen.writeTree(fieldValue); - } - } - - @Override - public boolean isUnwrappingSerializer() { - return true; - } - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java b/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java deleted file mode 100644 index 18e9624a..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/entities/validation/JsonSchemaValidation.java +++ /dev/null @@ -1,86 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.validation; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.networknt.schema.JsonSchema; -import com.networknt.schema.JsonSchemaFactory; -import com.networknt.schema.SpecVersion; -import com.networknt.schema.ValidationMessage; - -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import java.net.URISyntaxException; -import java.net.URL; -import java.util.Objects; -import java.util.Set; - -/** - * Implementation of the entity validation strategy that uses json schema. - */ -public class JsonSchemaValidation implements EntityValidationStrategy { - - private static final URL entitySchemaDefault - = Objects.requireNonNull(JsonSchemaValidation.class.getClassLoader() - .getResource("json_schemas/entity_schema.json")); - private static final URL fieldSchemaDefault - = Objects.requireNonNull(JsonSchemaValidation.class.getClassLoader() - .getResource("json_schemas/entity_field_structure_schema.json")); - - private JsonSchema entitySchema; - private JsonSchema entityFieldSchema; - - /** - * Default constructor that uses the default schemas. - */ - public JsonSchemaValidation() { - JsonSchemaFactory factory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V201909); - try { - this.entitySchema = factory.getSchema(entitySchemaDefault.toURI()); - this.entityFieldSchema = factory.getSchema(fieldSchemaDefault.toURI()); - } catch (URISyntaxException e) { - e.printStackTrace(); - } - } - - /** - * Constructor that uses custom schemas present as Json files. - * - * @param entitySchema schema for the entities validation. - * @param fieldSchema schema for the field validation. - */ - public JsonSchemaValidation(JsonNode entitySchema, JsonNode fieldSchema) { - JsonSchemaFactory factory = JsonSchemaFactory.getInstance(SpecVersion.VersionFlag.V201909); - this.entitySchema = factory.getSchema(entitySchema); - this.entityFieldSchema = factory.getSchema(fieldSchema); - } - - @Override - public boolean validateEntity(JsonNode entity) { - Set errors = this.entitySchema.validate(entity); - if (errors.size() != 0) { - System.err.println("This entity does not comply to the basic RO-Crate entity structure."); - errors.forEach(error -> System.err.println(error.getMessage())); - return false; - } - return true; - } - - @Override - public boolean validateFieldOfEntity(JsonNode field) { - Set errors = this.entityFieldSchema.validate(field); - if (!errors.isEmpty()) { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - System.err.println("The property: "); - try { - System.err.println(objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(field)); - } catch (JsonProcessingException e) { - e.printStackTrace(); - } - System.err.println("does not comply with the flattened structure" - + " of the RO-Crate json document."); - return false; - } - return true; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java b/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java deleted file mode 100644 index 350fdad6..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/externalproviders/organizationprovider/RorProvider.java +++ /dev/null @@ -1,85 +0,0 @@ -package edu.kit.datamanager.ro_crate.externalproviders.organizationprovider; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; - -import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import java.io.IOException; -import java.util.ArrayList; - -import org.apache.http.HttpStatus; -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpGet; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.impl.client.HttpClients; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Class providing possibility to import organization entities from ror.com. - */ -public class RorProvider { - - private static final Logger logger = LoggerFactory.getLogger(RorProvider.class); - - private RorProvider() { - } - - /** - * The method that parses a ror entry to a crate entity. - * - * @param url the url of the ror entry. - * @return the created Organization entity. - */ - public static OrganizationEntity getOrganization(String url) { - if (!url.startsWith("https://ror.org/")) { - throw new IllegalArgumentException("Should provide ror url"); - } - String newUrl = "https://api.ror.org/v2/organizations/" + url.replaceAll("https://ror.org/", ""); - HttpGet request = new HttpGet(newUrl); - - try ( - CloseableHttpClient httpClient = HttpClients.createDefault(); CloseableHttpResponse response = httpClient.execute(request)) { - boolean isError = response.getStatusLine().getStatusCode() != HttpStatus.SC_OK; - if (isError) { - String errorMessage = String.format("Identifier not found: %s", response.getStatusLine().toString()); - logger.error(errorMessage); - return null; - } - ObjectNode jsonNode = MyObjectMapper.getMapper().readValue(response.getEntity().getContent(), - ObjectNode.class); - - return new OrganizationEntity.OrganizationEntityBuilder() - .setId(jsonNode.path("id").asText()) - .addProperty("name", getOrganizationNameV2(jsonNode.path("names"))) - .addProperty("email", jsonNode.path("email_address")) - .addProperty("url", jsonNode.path("id").asText()) - .build(); - } catch (IOException e) { - String errorMessage = String.format("IO error: %s", e.getMessage()); - logger.error(errorMessage); - } - return null; - } - - private static String getOrganizationNameV2(JsonNode node) { - if (node.isArray()) { - for (JsonNode n : node) { - if (n.has("types") && n.path("types").isArray()) { - ArrayList l = new ObjectMapper().convertValue(n.path("types"), ArrayList.class); - if (l.contains("ror_display")) { - return n.path("value").asText(); - } - } - } - //fallback - return node.path(0).path("value").asText(); - } else { - return node.asText(); - } - } - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java b/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java deleted file mode 100644 index 46a278c7..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognition.java +++ /dev/null @@ -1,208 +0,0 @@ -package edu.kit.datamanager.ro_crate.hierarchy; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; -import edu.kit.datamanager.ro_crate.util.FileSystemUtil; - -import java.util.HashMap; -import java.util.HashSet; -import java.util.Map; -import java.util.Set; - -public class HierarchyRecognition { - protected final Crate crate; - protected final HierarchyRecognitionConfig config; - - public HierarchyRecognition(Crate crate, HierarchyRecognitionConfig config) { - this.crate = crate; - this.config = config; - } - - public HierarchyRecognitionResult buildHierarchy() { - HierarchyRecognitionResult result = new HierarchyRecognitionResult(); - - try { - // Get all data entities to process - Set allEntities = this.crate.getAllDataEntities(); - allEntities.add(crate.getRootDataEntity()); - - // Filter entities with file path IDs (not URLs, DOIs, etc.) - Map pathEntities = new HashMap<>(); - for (DataEntity entity : allEntities) { - String id = entity.getId(); - if (FileSystemUtil.isFilePath(id)) { - pathEntities.put(id, entity); - } else { - result.addSkippedEntity(entity); - } - } - - - // Validate hierarchy before making changes - if (!HierarchyRecognition.validateHierarchy(pathEntities, result)) { - return result; - } - - // Create missing intermediate entities if configured - if (config.createMissingIntermediateEntities()) { - this.createMissingIntermediateEntities(pathEntities, result); - } - - // Clear existing relationships if configured - if (config.removeExistingConnections()) { - this.clearExistingRelationships(pathEntities); - } - - // Build hierarchy relationships - this.buildHierarchyRelationships(pathEntities, config, result); - - return result; - } catch (Exception e) { - result.addError( - "Unexpected error during hierarchy recognition: " + - e.getMessage() - ); - return result; - } - } - - /** - * Validates that the hierarchy is consistent (no files containing other files/folders). - * - * @param pathEntities map of path IDs to DataEntities - * @param result builder to collect errors - * @return true if valid, false if invalid hierarchy detected - */ - protected static boolean validateHierarchy( - Map pathEntities, - HierarchyRecognitionResult result - ) { - for (Map.Entry entry : pathEntities.entrySet()) { - String childId = entry.getKey(); - String parentPath = FileSystemUtil.getParentPath(childId); - if (parentPath == null || parentPath.equals("./")) { - continue; - } - - // Check both with and without trailing slash since files don't have slash but folders do - DataEntity parentEntity = pathEntities.get(parentPath); - if (parentEntity == null) { - parentEntity = pathEntities.get(parentPath + "/"); - } - - if (parentEntity == null) { - continue; - } - - // Check for invalid hierarchy: file cannot contain another file/folder - if (parentEntity.getTypes().contains("File")) { - result.addError( - "Invalid hierarchy: file '" + - parentEntity.getId() + - "' cannot contain '" + - childId + - "'" - ); - return false; - } - } - return true; - } - - /** - * Creates missing intermediate DataSetEntity instances for folder paths. - * - * @param pathEntities map of path IDs to DataEntities - * @param result builder to collect created entities - */ - protected void createMissingIntermediateEntities( - Map pathEntities, - HierarchyRecognitionResult result - ) { - Set missingPaths = new HashSet<>(); - - // Find all missing intermediate paths - for (String path : pathEntities.keySet()) { - String parentPath = FileSystemUtil.getParentPath(path); - while (parentPath != null && !parentPath.equals("./")) { - String folderPath = parentPath + "/"; - final boolean containsParent = pathEntities.containsKey(parentPath); - final boolean containsFolder = pathEntities.containsKey(folderPath); - if (!containsParent && !containsFolder) { - missingPaths.add(folderPath); - } - parentPath = FileSystemUtil.getParentPath(parentPath); - } - } - - // Create missing DataSetEntity instances - for (String missingPath : missingPaths) { - DataSetEntity newEntity = new DataSetEntity.DataSetBuilder() - .setId(missingPath) - .addProperty("name", "Auto-generated folder: " + missingPath) - .build(); - - this.crate.addDataEntity(newEntity); - pathEntities.put(missingPath, newEntity); - result.addCreatedEntity(newEntity); - } - } - - protected void buildHierarchyRelationships( - Map pathEntities, - HierarchyRecognitionConfig config, - HierarchyRecognitionResult result - ) { - for (Map.Entry entry : pathEntities.entrySet()) { - String childId = entry.getKey(); - DataEntity childEntity = entry.getValue(); - String parentPath = FileSystemUtil.getParentPath(childId); - if (parentPath == null) { - continue; - } - - // Check both with and without trailing slash since files don't have slash but folders do - DataEntity parentEntity = pathEntities.get(parentPath); - String actualParentId = parentPath; - - if (parentEntity == null) { - parentEntity = pathEntities.get(parentPath + "/"); - actualParentId = parentPath + "/"; - } - - if (parentEntity == null) { - continue; - } - - // Add hasPart relationship - if (parentEntity instanceof DataSetEntity) { - ((DataSetEntity) parentEntity).addToHasPart(childId); - result.addProcessedRelationship( - actualParentId, - childId - ); - } - - // Add isPartOf relationship if configured - if (config.createInverseRelationships()) { - childEntity.addProperty("isPartOf", actualParentId); - } - - // Remove from root if it has a parent that is not root - if (!parentPath.equals("./")) { - this.crate.getRootDataEntity().removeFromHasPart(childId); - } - } - } - - protected void clearExistingRelationships( - Map pathEntities - ) { - for (DataEntity entity : pathEntities.values()) { - if (entity instanceof DataSetEntity) { - ((DataSetEntity) entity).hasPart.clear(); - } - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java b/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java deleted file mode 100644 index c37372d0..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionConfig.java +++ /dev/null @@ -1,43 +0,0 @@ -package edu.kit.datamanager.ro_crate.hierarchy; - -/** - * Configuration class for automatic hierarchy recognition. - * This class provides control over how the hierarchy recognition. - * - *

    - *
  • createMissingIntermediateEntities: Whether missing intermediate folder entities should be automatically created. Default: false
    • - *
  • createInverseRelationships: Whether isPartOf relationships should be added in addition to hasPart. Default: false
    • - *
  • removeExistingConnections: Whether hasPart relationships should be added (false) or remove existing relations in beforehand (true). Default: false
    • - *
- */ -public record HierarchyRecognitionConfig( - boolean createMissingIntermediateEntities, - boolean createInverseRelationships, - boolean removeExistingConnections -) { - /** - * Creates a new configuration with default values. - *

- * Default values: - *

    - *
  • createMissingIntermediateEntities: false
    • - *
  • createInverseRelationships: false
    • - *
  • removeExistingConnections: false
    • - *
- */ - public HierarchyRecognitionConfig() { - this(false, false, false); - } - - public HierarchyRecognitionConfig withCreateMissingIntermediateEntities(boolean value) { - return new HierarchyRecognitionConfig(value, this.createInverseRelationships, this.removeExistingConnections); - } - - public HierarchyRecognitionConfig withSetInverseRelationships(boolean value) { - return new HierarchyRecognitionConfig(this.createMissingIntermediateEntities, value, this.removeExistingConnections); - } - - public HierarchyRecognitionConfig withRemoveExistingConnections(boolean value) { - return new HierarchyRecognitionConfig(this.createMissingIntermediateEntities, this.createInverseRelationships, value); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java b/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java deleted file mode 100644 index ce4eab50..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/hierarchy/HierarchyRecognitionResult.java +++ /dev/null @@ -1,51 +0,0 @@ -package edu.kit.datamanager.ro_crate.hierarchy; - -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; - -import java.util.*; - -/** - * Result class containing information about the automatic hierarchy recognition operation. - * This class provides details about what was processed, created, and any issues encountered - * during the hierarchy recognition process. Always contains complete information about the - * operation result, including success/failure and any errors encountered. - */ -public record HierarchyRecognitionResult( - Set createdEntities, - Map> processedRelationships, - Set skippedEntities, - List warnings, - List errors -) { - HierarchyRecognitionResult() { - this(new HashSet<>(), new HashMap<>(), new HashSet<>(), new ArrayList<>(), new ArrayList<>()); - } - - /** - * Whether there were no errors during the hierarchy recognition operation. - * - * @return true if the operation completed successfully (no errors), false otherwise. - */ - public boolean isSuccessful() { - return this.errors.isEmpty(); - } - - public void addSkippedEntity(DataEntity entity) { - this.skippedEntities.add(entity); - } - - public void addError(String errorMessage) { - this.errors.add(errorMessage); - } - - public void addCreatedEntity(DataSetEntity newEntity) { - this.createdEntities.add(newEntity); - } - - public void addProcessedRelationship(String from, String to) { - this.processedRelationships - .computeIfAbsent(from, k -> new HashSet<>()) - .add(to); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/objectmapper/MyObjectMapper.java b/src/main/java/edu/kit/datamanager/ro_crate/objectmapper/MyObjectMapper.java deleted file mode 100644 index 7e711848..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/objectmapper/MyObjectMapper.java +++ /dev/null @@ -1,27 +0,0 @@ -package edu.kit.datamanager.ro_crate.objectmapper; - -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.SerializationFeature; - -/** - * Singleton pattern for the object mapper used everywhere in the library. - * - * @author Nikola Tzotchev on 4.2.2022 г. - * @version 1 - */ -public class MyObjectMapper { - - private static final ObjectMapper mapper = new ObjectMapper() - .enable(SerializationFeature.WRITE_SINGLE_ELEM_ARRAYS_UNWRAPPED) - .enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY) - .enable(DeserializationFeature.UNWRAP_SINGLE_VALUE_ARRAYS); - - private MyObjectMapper() { - - } - - public static ObjectMapper getMapper() { - return mapper; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java deleted file mode 100644 index c403ab1c..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/AutomaticPreview.java +++ /dev/null @@ -1,89 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import net.lingala.zip4j.ZipFile; -import net.lingala.zip4j.exception.ZipException; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import org.apache.commons.io.FileUtils; - -/** - * The default preview should use the - * rochtml tool - * for creating a simple preview file. - * - * @author Nikola Tzotchev on 6.2.2022 г. - * @version 1 - */ -public class AutomaticPreview implements CratePreview { - - public AutomaticPreview() { - } - - @Override - public void saveAllToZip(ZipFile zipFile) throws IOException { - if (PreviewGenerator.isRochtmlAvailable()) { - // extract the .json file so we can run the "rochtml" tool on it" - try { - try { - zipFile.extractFile("ro-crate-metadata.json", "temp"); - } catch (ZipException ex) { - throw new IOException("ro-crate-metadata.json not found in provided ZIP.", ex); - } - if (PreviewGenerator.isRochtmlAvailable()) { - PreviewGenerator.generatePreview("temp"); - zipFile.addFile("temp/ro-crate-preview.html"); - } - } finally { - try { - FileUtils.deleteDirectory(new File("temp")); - } catch (IOException ex) { - //ignore - } - } - } else { - new CustomPreview().saveAllToZip(zipFile); - } - } - - @Override - public void saveAllToFolder(File folder) throws IOException { - if (folder == null || !folder.exists()) { - throw new IOException("Preview target folder " + folder + " does not exist."); - } - - if (PreviewGenerator.isRochtmlAvailable()) { - PreviewGenerator.generatePreview(folder.getAbsolutePath()); - } else { - new CustomPreview().saveAllToFolder(folder); - } - } - - @Override - public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException { - if (PreviewGenerator.isRochtmlAvailable()) { - try { - FileUtils.forceMkdir(new File("temp")); - try (FileWriter writer = new FileWriter("temp/ro-crate-metadata.json")) { - writer.write(metadata); - writer.flush(); - } - if (PreviewGenerator.isRochtmlAvailable()) { - PreviewGenerator.generatePreview("temp"); - ZipStreamUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html"); - } - } finally { - try { - FileUtils.deleteDirectory(new File("temp")); - } catch (IOException ex) { - //ignore - } - } - } else { - new CustomPreview().saveAllToStream(metadata, stream); - } - } - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java deleted file mode 100644 index e966b4af..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java +++ /dev/null @@ -1,102 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.writer.CrateWriter; -import edu.kit.datamanager.ro_crate.writer.WriteFolderStrategy; -import net.lingala.zip4j.ZipFile; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import org.apache.commons.io.FileUtils; -import org.slf4j.LoggerFactory; - -/** - * Interface for the ROCrate preview. This manages the human-readable - * representation of a crate. - * - * @author Nikola Tzotchev on 6.2.2022 г. - * @author jejkal - * @version 2 - */ -public interface CratePreview { - - /** - * Generate a preview of the crate and store it into the given target directory. - * It is the caller's responsibility to handle, e.g. delete after use, the result - * (The caller takes ownership of the result). - *

- * IMPORTANT NOTE: This method currently has a default implementation that relies - * on deprecated methods. In future, you will have to implement this method directly. - * - * @param crate the crate to generate a preview for. - * @param targetDir the target directory to store the preview in, - * owned by the caller. - * @throws IOException if an error occurs while generating the preview. - */ - default void generate(Crate crate, File targetDir) throws IOException { - // disable preview generation to avoid recursion, - // as this is usually called in the process of writing a crate - // (including preview) - new CrateWriter<>(new WriteFolderStrategy().disablePreview()) - // We assume the caller (e.g. a writer) already stored the provenance. - .withAutomaticProvenance(null) - .save(crate, targetDir.getAbsolutePath()); - this.saveAllToFolder(targetDir); - try (var stream = Files.list(targetDir.toPath())) { - stream - .filter(path -> !path.getFileName().toString().equals("ro-crate-preview.html")) - .filter(path -> !path.getFileName().toString().equals("ro-crate-preview_files")) - .forEach(path -> { - try { - if (Files.isDirectory(path)) { - FileUtils.deleteDirectory(path.toFile()); - } else { - Files.delete(path); - } - } catch (IOException e) { - // Silently ignore deletion errors - LoggerFactory.getLogger(CratePreview.class) - .error("Failed to delete temporary file {}", path, e); - } - }); - } - } - - /** - * Takes a crate in form of a zip file and generates a preview of it, - * which will be stored within the crate. - * - * @param zipFile the zip file with the crate, which should receive a preview. - * @throws IOException if an error occurs while saving the preview - * - * @deprecated Use {@link #generate(Crate, File)} instead. - */ - @Deprecated(since = "2.1.0", forRemoval = true) - void saveAllToZip(ZipFile zipFile) throws IOException; - - /** - * Saves the preview, given by the folder, into the given folder. - * - * @param folder the folder (containing a crate) to save the preview in. - * @throws IOException if an error occurs while saving the preview. - * - * @deprecated Use {@link #generate(Crate, File)} instead. - */ - @Deprecated(since = "2.1.0", forRemoval = true) - void saveAllToFolder(File folder) throws IOException; - - /** - * Saves the preview, given by the metadata, into the given stream. - * - * @param metadata the metadata of the crate to save the preview in. - * @param stream the stream to save the preview in. - * @throws IOException if an error occurs while saving the preview. - * - * @deprecated Use {@link #generate(Crate, File)} instead. - */ - @Deprecated(since = "2.1.0", forRemoval = true) - void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException; - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java deleted file mode 100644 index 77300a87..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreview.java +++ /dev/null @@ -1,217 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; -import freemarker.template.Configuration; -import freemarker.template.Template; -import freemarker.template.TemplateException; -import freemarker.template.TemplateExceptionHandler; -import java.io.File; -import java.io.FileOutputStream; -import java.io.FileWriter; -import java.io.IOException; -import java.io.OutputStreamWriter; -import java.io.Writer; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; -import net.lingala.zip4j.ZipFile; -import net.lingala.zip4j.exception.ZipException; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import org.apache.commons.io.FileUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * This class generates a custom preview without requiring external - * dependencies, i.e., rochtml. Therefore, the FreeMarker template located under - * resources/templates/custom_preview.ftl is used. - * - * @author jejkal - */ -public class CustomPreview implements CratePreview { - - private final static Logger logger = LoggerFactory.getLogger(CustomPreview.class); - - private Template template = null; - - public CustomPreview() { - Configuration cfg = new Configuration(Configuration.VERSION_2_3_34); - cfg.setClassForTemplateLoading(CustomPreview.class, "/"); - cfg.setDefaultEncoding("UTF-8"); - cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER); - try { - template = cfg.getTemplate("templates/custom_preview.ftl"); - } catch (IOException ex) { - logger.error("Failed to read template for CustomPreview.", ex); - } - } - - private CustomPreviewModel mapFromJson(String metadata) throws IOException { - ObjectMapper mapper = new ObjectMapper(); - JsonNode root = mapper.readValue(metadata, JsonNode.class); - JsonNode graph = root.get("@graph"); - CustomPreviewModel.ROCrate crate = new CustomPreviewModel.ROCrate(); - List datasets = new ArrayList<>(); - List files = new ArrayList<>(); - - if (graph.isArray()) { - - for (JsonNode node : graph) { - String id = node.path("@id").asText(); - List types = new LinkedList<>(); - if (node.path("@type").isArray()) { - - Collections.addAll(types, mapper.convertValue(node.path("@type"), String[].class)); - } else { - types.add(node.path("@type").asText()); - } - - if (types.contains("Dataset") && "./".equals(id)) { - crate.name = node.path("name").asText(); - crate.description = node.path("description").asText(null); - crate.type = "Dataset"; - crate.license = node.path("license").path("@id").asText(node.path("license").asText(null)); - crate.datePublished = node.path("datePublished").asText(null); - crate.hasPart = new ArrayList<>(); - - for (JsonNode part : node.path("hasPart")) { - CustomPreviewModel.Part p = new CustomPreviewModel.Part(); - String tmpId = part.path("@id").asText(part.asText()); - p.id = tmpId; - p.name = tmpId; // Name will be replaced later - crate.hasPart.add(p); - } - } else if (types.contains("Dataset")) { - CustomPreviewModel.Dataset dataset = new CustomPreviewModel.Dataset(); - dataset.id = id; - dataset.name = node.path("name").asText(); - dataset.description = node.path("description").asText(); - datasets.add(dataset); - } else if (types.contains("File")) { - CustomPreviewModel.File file = new CustomPreviewModel.File(); - file.id = id; - file.name = node.path("name").asText(null); - file.description = node.path("description").asText(null); - file.contentSize = node.path("contentSize").asText(null); - file.encodingFormat = node.path("encodingFormat").asText(null); - files.add(file); - } - } - } - - // Update Part names using dataset and file lists - if (crate.hasPart != null) { - for (CustomPreviewModel.Part part : crate.hasPart) { - for (CustomPreviewModel.Dataset dataset : datasets) { - if (dataset.id.equals(part.id) && dataset.name != null) { - part.name = dataset.name; - } - } - for (CustomPreviewModel.File file : files) { - if (file.id.equals(part.id) && file.name != null) { - part.name = file.name; - } - } - } - } - - CustomPreviewModel model = new CustomPreviewModel(); - model.crate = crate; - model.datasets = datasets; - model.files = files; - return model; - } - - @Override - public void saveAllToZip(ZipFile zipFile) throws IOException { - if (template == null) { - throw new IOException("Preview template did not load. Unable to proceed."); - } - if (zipFile == null) { - throw new IOException("Argument zipFile must not be null."); - } - try { - zipFile.extractFile("ro-crate-metadata.json", "temp"); - } catch (ZipException ex) { - throw new IOException("ro-crate-metadata.json not found in provided ZIP.", ex); - } - - String metadata = FileUtils.readFileToString(new File("temp/ro-crate-metadata.json"), "UTF-8"); - try { - Map dataModel = new HashMap<>(); - dataModel.put("crateModel", mapFromJson(metadata)); - - try (Writer out = new OutputStreamWriter(new FileOutputStream("temp/ro-crate-preview.html"))) { - template.process(dataModel, out); - out.flush(); - } - zipFile.addFile("temp/ro-crate-preview.html"); - } catch (TemplateException ex) { - throw new IOException("Failed to generate preview.", ex); - } finally { - try { - FileUtils.deleteDirectory(new File("temp")); - } catch (IOException ex) { - //ignore - } - } - } - - @Override - public void saveAllToFolder(File folder) throws IOException { - if (template == null) { - throw new IOException("Preview template did not load. Unable to proceed."); - } - if (folder == null || !folder.exists()) { - throw new IOException("Preview target folder " + folder + " does not exist."); - } - String metadata = FileUtils.readFileToString(new File(folder, "ro-crate-metadata.json"), "UTF-8"); - try { - Map dataModel = new HashMap<>(); - dataModel.put("crateModel", mapFromJson(metadata)); - try (Writer out = new OutputStreamWriter(new FileOutputStream(new File(folder, "ro-crate-preview.html")))) { - template.process(dataModel, out); - out.flush(); - } - } catch (TemplateException ex) { - throw new IOException("Failed to generate preview.", ex); - } - } - - @Override - public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException { - if (template == null) { - throw new IOException("Preview template did not load. Unable to proceed."); - } - try { - //prepare metadata for template - Map dataModel = new HashMap<>(); - dataModel.put("crateModel", mapFromJson(metadata)); - - //prepare output folder and writer - FileUtils.forceMkdir(new File("temp")); - //load and process template - try (FileWriter writer = new FileWriter("temp/ro-crate-preview.html")) { - //load and process template - template.process(dataModel, writer); - writer.flush(); - } - - ZipStreamUtil.addFileToZipStream(stream, new File("temp/ro-crate-preview.html"), "ro-crate-preview.html"); - } catch (TemplateException ex) { - throw new IOException("Failed to generate preview.", ex); - } finally { - try { - FileUtils.deleteDirectory(new File("temp")); - } catch (IOException ex) { - //ignore - } - } - } - -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java deleted file mode 100644 index 21dbd802..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/CustomPreviewModel.java +++ /dev/null @@ -1,126 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import java.util.List; - -/** - * - * @author jejkal - */ -public class CustomPreviewModel { - - protected ROCrate crate; - protected List datasets; - protected List files; - - public ROCrate getCrate() { - return crate; - } - - public List getDatasets() { - return datasets; - } - - public List getFiles() { - return files; - } - - public static class ROCrate { - - protected String name; - protected String description; - protected String type; - protected String license; - protected String datePublished; - protected List hasPart; - - public String getName() { - return name; - } - - public String getDescription() { - return description; - } - - public String getType() { - return type; - } - - public String getLicense() { - return license; - } - - public String getDatePublished() { - return datePublished; - } - - public List getHasPart() { - return hasPart; - } - - } - - public static class Part { - - protected String id; - protected String name; - - public String getId() { - return id; - } - - public String getName() { - return name; - } - - } - - public static class Dataset { - - protected String id; - protected String name; - protected String description; - - public String getId() { - return id; - } - - public String getName() { - return name; - } - - public String getDescription() { - return description; - } - - } - - public static class File { - - protected String id; - protected String name; - protected String description; - protected String contentSize; - protected String encodingFormat; - - public String getId() { - return id; - } - - public String getName() { - return name; - } - - public String getDescription() { - return description; - } - - public String getContentSize() { - return contentSize; - } - - public String getEncodingFormat() { - return encodingFormat; - } - - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java deleted file mode 100644 index 60e8e19e..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/PreviewGenerator.java +++ /dev/null @@ -1,85 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStreamReader; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Class responsible for the generation of the human-readable representation of - * the metadata. For this to work the nodejs library rochtml has to be - * installed. This can be done using: npm install -g ro-crate-html-js or npm - * install ro-crate-html-js - */ -public class PreviewGenerator { - - private static Logger LOG = LoggerFactory.getLogger(PreviewGenerator.class); - private static final String command = "rochtml"; - - public static boolean isRochtmlAvailable() { - ProcessBuilder builder = new ProcessBuilder(); - // this is the equivalent of "rochtml dir/ro-crate-metadata.json" - // check if we are running on windows or unix - String os = System.getProperty("os.name").toLowerCase(); - if (os.contains("win")) { - builder.command("cmd.exe", "/c", command); - - } else { - builder.command("sh", "-c", command); - } - Process process; - try { - process = builder.start(); - int exitVal = process.waitFor(); - return exitVal == 0; - } catch (InterruptedException | IOException ex) { - } - return false; - } - - /** - * The method that from the location of the crate generates the html file. - * - * @param location the location of the crate in the filesystem. - */ - public static void generatePreview(String location) { - if (!isRochtmlAvailable()) { - LOG.error("rochtml is not available. Please install rochtml using npm install -g ro-crate-html-js"); - return; - } - ProcessBuilder builder = new ProcessBuilder(); - // this is the equivalent of "rochtml dir/ro-crate-metadata.json" - // check if we are running on windows or unix - String os = System.getProperty("os.name").toLowerCase(); - if (os.contains("win")) { - builder.command("cmd.exe", "/c", command + " " + location + "/ro-crate-metadata.json"); - - } else { - builder.command("sh", "-c", command + " " + location + "/ro-crate-metadata.json"); - } - - Process process; - try { - process = builder.start(); - StringBuilder output = new StringBuilder(); - - BufferedReader reader = new BufferedReader( - new InputStreamReader(process.getInputStream())); - - String line; - while ((line = reader.readLine()) != null) { - output.append(line).append("\n"); - } - reader.close(); - int exitVal = process.waitFor(); - if (exitVal != 0) { - //abnormal... - throw new Exception("failed command"); - } - } catch (Exception e) { - LOG.error("Error while generating preview: {}", e.getMessage()); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java b/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java deleted file mode 100644 index c3a93629..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/preview/StaticPreview.java +++ /dev/null @@ -1,72 +0,0 @@ -package edu.kit.datamanager.ro_crate.preview; - -import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; -import java.io.File; -import java.io.IOException; - -import net.lingala.zip4j.ZipFile; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import net.lingala.zip4j.model.ZipParameters; -import org.apache.commons.io.FileUtils; - -/** - * This class adds a static preview to the crate, which consists of a - * metadataHtml file and a folder containing other files required to render - * metadataHtml. It will be put unchanged to the writer output, i.e., a zip - * file, folder, or stream. - * - * @author jejkal - */ -public class StaticPreview implements CratePreview { - - private final File metadataHtml; - private final File otherFiles; - - public StaticPreview(File metadataHtml, File otherFiles) { - this.metadataHtml = metadataHtml; - this.otherFiles = otherFiles; - } - - public StaticPreview(File metadataHtml) { - this.metadataHtml = metadataHtml; - this.otherFiles = null; - } - - @Override - public void saveAllToZip(ZipFile zipFile) throws IOException { - if (this.metadataHtml != null) { - ZipParameters zipParameters = new ZipParameters(); - zipParameters.setFileNameInZip("ro-crate-preview.html"); - zipFile.addFile(this.metadataHtml, zipParameters); - } - - if (this.otherFiles != null) { - zipFile.addFolder(this.otherFiles); - zipFile.renameFile(this.otherFiles.getName() + "/", "ro-crate-preview_files/"); - } - } - - @Override - public void saveAllToFolder(File folder) throws IOException { - if (folder == null || !folder.exists()) { - throw new IOException("Preview target folder " + folder + " does not exist."); - } - - if (this.metadataHtml != null) { - File fileInCrate = folder.toPath().resolve("ro-crate-preview.html").toFile(); - FileUtils.copyFile(this.metadataHtml, fileInCrate); - } - if (this.otherFiles != null) { - File folderName = folder.toPath().resolve("ro-crate-preview_files").toFile(); - FileUtils.copyDirectory(this.otherFiles, folderName); - } - } - - @Override - public void saveAllToStream(String metadata, ZipOutputStream stream) throws IOException { - ZipStreamUtil.addFileToZipStream(stream, this.metadataHtml, "ro-crate-preview.html"); - if (this.otherFiles != null) { - ZipStreamUtil.addFolderToZipStream(stream, this.otherFiles, "ro-crate-preview_files"); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java deleted file mode 100644 index c63ba21a..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java +++ /dev/null @@ -1,362 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.RoCrate; -import edu.kit.datamanager.ro_crate.context.CrateMetadataContext; -import edu.kit.datamanager.ro_crate.context.RoCrateMetadataContext; -import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.entities.data.DataSetEntity; -import edu.kit.datamanager.ro_crate.entities.data.RootDataEntity; -import edu.kit.datamanager.ro_crate.special.IdentifierUtils; -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; -import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.validation.Validator; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Path; -import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; -import java.util.stream.StreamSupport; - -/** - * This class allows reading crates from the outside into the library in order - * to inspect or modify it. - *

- * The constructor takes a strategy to support different ways of importing the - * crates. (from zip, folder, etc.). - *

- * The reader considers "hasPart" and "isPartOf" properties and considers all - * entities (in-)directly connected to the root entity ("./") as DataEntities. - * - * @param the type of the location parameter - */ -public class CrateReader { - - private static final Logger logger = LoggerFactory.getLogger(CrateReader.class); - - /** - * This is a private inner class that shall not be exposed. **Do not make it - * public or protected.** It serves only the purpose of unsafe operations - * while reading a crate and may be specific to this implementation. - */ - private static class RoCrateUnsafe extends RoCrate { - - public void addDataEntityWithoutRootHasPart(DataEntity entity) { - this.metadataContext.checkEntity(entity); - this.roCratePayload.addDataEntity(entity); - } - } - - /** - * If the number of JSON entities in the crate is larger than this number, - * parallelization will be used. - */ - private static final int PARALLELIZATION_THRESHOLD = 100; - - private static final String FILE_PREVIEW_FILES = "ro-crate-preview_files"; - private static final String FILE_PREVIEW_HTML = "ro-crate-preview.html"; - private static final String FILE_METADATA_JSON = "ro-crate-metadata.json"; - - protected static final String SPECIFICATION_PREFIX = "https://w3id.org/ro/crate/"; - - protected static final String PROP_ABOUT = "about"; - protected static final String PROP_CONTEXT = "@context"; - protected static final String PROP_CONFORMS_TO = "conformsTo"; - protected static final String PROP_GRAPH = "@graph"; - protected static final String PROP_HAS_PART = "hasPart"; - protected static final String PROP_ID = "@id"; - - private final GenericReaderStrategy strategy; - - public CrateReader(GenericReaderStrategy strategy) { - this.strategy = strategy; - } - - /** - * This function will read the location (using one of the specified - * strategies) and then build the relation between the entities. - * - * @param location the location of the ro-crate to be read - * @return the read RO-crate - * - * @throws IOException if the crate cannot be read - */ - public RoCrate readCrate(T location) throws IOException { - // get the ro-crate-metadata.json - ObjectNode metadataJson = strategy.readMetadataJson(location); - // get the content of the crate - File files = strategy.readContent(location); - - // this set will contain the files that are associated with entities - HashSet usedFiles = new HashSet<>(); - usedFiles.add(files.toPath().resolve(FILE_METADATA_JSON).toFile().getPath()); - usedFiles.add(files.toPath().resolve(FILE_PREVIEW_HTML).toFile().getPath()); - usedFiles.add(files.toPath().resolve(FILE_PREVIEW_FILES).toFile().getPath()); - return rebuildCrate(metadataJson, files, usedFiles).markAsImported(); - } - - private RoCrate rebuildCrate(ObjectNode metadataJson, File files, HashSet usedFiles) { - Objects.requireNonNull(metadataJson, - "metadataJson must not be null – did the strategy fail to locate 'ro-crate-metadata.json'?"); - Objects.requireNonNull(files, - "files directory must not be null – check GenericReaderStrategy.readContent()"); - JsonNode context = metadataJson.get(PROP_CONTEXT); - - CrateMetadataContext crateContext = new RoCrateMetadataContext(context); - RoCrateUnsafe crate = new RoCrateUnsafe(); - crate.setMetadataContext(crateContext); - JsonNode graph = metadataJson.get(PROP_GRAPH); - - if (graph.isArray()) { - moveRootEntitiesFromGraphToCrate(crate, (ArrayNode) graph); - } - RootDataEntity root = crate.getRootDataEntity(); - boolean rootExtractionSuccessful = root != null; - - if (rootExtractionSuccessful) { - Set dataEntityIds = getDataEntityIds(root, graph); - for (JsonNode entityJson : graph) { - String eId = unpackId(entityJson); - ObjectNode properties = entityJson.deepCopy(); - boolean isDataEntity = dataEntityIds.contains(eId); - - if (isDataEntity) { - DataEntity data = null; - boolean isDataSet = properties.path("@type").asText().equals("Dataset") - || properties.path("@type").valueStream() - .anyMatch(typeString -> typeString.asText().equals("Dataset")); - if (isDataSet) { - data = new DataSetEntity.DataSetBuilder() - .setAllUnsafe(properties) - .build(); - } else { - // data entity - DataEntity.DataEntityBuilder builder = new DataEntity.DataEntityBuilder() - .setAllUnsafe(properties); - - // Handle data entities with corresponding file - checkFolderHasFile(entityJson.get(PROP_ID).asText(), files).ifPresent(file -> { - usedFiles.add(file.getPath()); - builder.setLocationWithExceptions(file.toPath()) - .setId(file.getName()); - }); - data = builder.build(); - } - crate.addDataEntityWithoutRootHasPart(data); - - } else { - // contextual entity - crate.addContextualEntity( - new ContextualEntity.ContextualEntityBuilder() - .setAllUnsafe(properties) - .build()); - } - } - } - - Collection untrackedFiles = Arrays.stream( - Optional.ofNullable(files.listFiles()).orElse(new File[0])) - .filter(f -> !usedFiles.contains(f.getPath())) - .collect(Collectors.toSet()); - - crate.setUntrackedFiles(untrackedFiles); - Validator defaultValidation = new Validator(new JsonSchemaValidation()); - defaultValidation.validate(crate); - return crate; - } - - /** - * Extracts graph connections from top to bottom. - *

- * Example: (connections.get(parent) -> children) - * - * @param graph the ArrayNode with all Entities. - * @return the graph connections. - */ - protected Map> makeEntityGraph(JsonNode graph) { - Map> connections = new HashMap<>(); - - Map idToNodes = new HashMap<>(); - StreamSupport.stream(graph.spliterator(), false) - .forEach(jsonNode -> idToNodes.put(unpackId(jsonNode), jsonNode)); - - for (JsonNode entityNode : graph) { - String currentId = unpackId(entityNode); - StreamSupport.stream(entityNode.path("hasPart").spliterator(), false) - .map(this::unpackId) - .map(s -> idToNodes.getOrDefault(s, null)) - .filter(Objects::nonNull) - .forEach(child -> connections.computeIfAbsent(currentId, key -> new HashSet<>()) - .add(unpackId(child))); - StreamSupport.stream(entityNode.path("isPartOf").spliterator(), false) - .map(this::unpackId) - .map(s -> idToNodes.getOrDefault(s, null)) - .filter(Objects::nonNull) - .forEach(parent -> connections.computeIfAbsent(unpackId(parent), key -> new HashSet<>()) - .add(currentId)); - } - return connections; - } - - protected Set getDataEntityIds(RootDataEntity root, JsonNode graph) { - if (root == null) { - return Set.of(); - } - Map> network = makeEntityGraph(graph); - Set directDataEntities = new HashSet<>(root.hasPart); - - Stack processingQueue = new Stack<>(); - processingQueue.addAll(directDataEntities); - Set result = new HashSet<>(); - - while (!processingQueue.empty()) { - String currentId = processingQueue.pop(); - result.add(currentId); - network.getOrDefault(currentId, new HashSet<>()).stream() - .filter(subId -> !result.contains(subId)) // avoid loops! - .forEach(subId -> { - result.add(subId); - processingQueue.add(subId); - }); - } - return result; - } - - protected String unpackId(JsonNode node) { - if (node.isTextual()) { - return node.asText(); - } else /*if (node.isObject())*/ { - return node.path(PROP_ID).asText(); - } - } - - protected Optional checkFolderHasFile(String filepathOrId, File folder) { - if (IdentifierUtils.isUrl(filepathOrId)) { - return Optional.empty(); - } - return Stream.of(IdentifierUtils.decode(filepathOrId).orElse(filepathOrId), filepathOrId) - .map(filename -> folder.toPath().resolve(filename).normalize().toAbsolutePath()) - // defence-in-depth: ensure we are still inside the crate folder - .filter(resolved -> resolved.startsWith(folder.toPath())) - .map(Path::toFile) - .filter(File::exists) - .findFirst(); - } - - /** - * Moves the descriptor and the root entity from the graph to the crate. - *

- * Extracts the root data entity and the Metadata File Descriptor from the - * graph and inserts them into the crate object. It also deletes it from the - * graph. We will need the root dataset to distinguish between data entities - * and contextual entities. - * - * @param crate the crate, which will receive the entities, if available in - * the graph. - * @param graph the graph of the Metadata JSON file, where the entities are - * extracted and removed from. - */ - protected void moveRootEntitiesFromGraphToCrate(RoCrate crate, ArrayNode graph) { - Optional maybeDescriptor = getMetadataDescriptor(graph); - - maybeDescriptor.ifPresent(descriptor -> { - setCrateDescriptor(crate, descriptor); - JsonUtilFunctions.removeJsonNodeFromArrayNode(graph, descriptor); - - Optional maybeRoot = extractRoot(graph, descriptor); - - maybeRoot.ifPresent(root -> { - Set hasPartIds = extractHasPartIds(root); - - crate.setRootDataEntity( - new RootDataEntity.RootDataEntityBuilder() - .setAllUnsafe(root.deepCopy()) - .setHasPart(hasPartIds) - .build()); - - JsonUtilFunctions.removeJsonNodeFromArrayNode(graph, root); - }); - }); - } - - /** - * Find the metadata descriptor. - *

- * Currently prefers algorithm of version 1.1 over the one of 1.2-DRAFT. - * - * @param graph the graph to search the descriptor in. - * @return the metadata descriptor of the crate. - */ - protected Optional getMetadataDescriptor(ArrayNode graph) { - boolean isParallel = graph.size() > PARALLELIZATION_THRESHOLD; - // use the algorithm described here: - // https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity - Optional maybeDescriptor = StreamSupport.stream(graph.spliterator(), isParallel) - // "2. if the conformsTo property is a URI that starts with - // https://w3id.org/ro/crate/" - .filter(node -> node.path(PROP_CONFORMS_TO).path(PROP_ID).asText().startsWith(SPECIFICATION_PREFIX)) - // "3. from this entity’s about object keep the @id URI as variable root" - .filter(node -> node.path(PROP_ABOUT).path(PROP_ID).isTextual()) - // There should be only one descriptor. If multiple exist, we take the first - // one. - .findFirst(); - return maybeDescriptor.or(() - -> // from https://www.researchobject.org/ro-crate/1.2-DRAFT/root-data-entity.html#finding-the-root-data-entity - StreamSupport.stream(graph.spliterator(), isParallel) - .filter(node -> node.path(PROP_ID).asText().equals(FILE_METADATA_JSON)) - .findFirst() - ); - } - - /** - * Extracts the root entity from the graph, using the information from the - * descriptor. - *

- * Basically implements step 5 of the algorithm described here: - * - * https://www.researchobject.org/ro-crate/1.1/root-data-entity.html#finding-the-root-data-entity - * - * - * @param graph the graph from the metadata JSON-LD file - * @param descriptor the RO-Crate descriptor - * @return the root entity, if found - */ - private Optional extractRoot(ArrayNode graph, JsonNode descriptor) { - String rootId = descriptor.get(PROP_ABOUT).get(PROP_ID).asText(); - boolean isParallel = graph.size() > PARALLELIZATION_THRESHOLD; - return StreamSupport.stream(graph.spliterator(), isParallel) - // root is an object (filter + conversion) - .filter(JsonNode::isObject) - .map(JsonNode::deepCopy) - // "5. if the entity has an @id URI that matches root return it" - .filter(node -> node.path(PROP_ID).asText().equals(rootId)) - .findFirst(); - } - - private Set extractHasPartIds(ObjectNode root) { - JsonNode hasPartNode = root.path(PROP_HAS_PART); - boolean isParallel = hasPartNode.isArray() && hasPartNode.size() > PARALLELIZATION_THRESHOLD; - Set hasPartIds = StreamSupport.stream(hasPartNode.spliterator(), isParallel) - .map(hasPart -> hasPart.path(PROP_ID).asText()) - .filter(text -> !text.isBlank()) - .collect(Collectors.toSet()); - if (hasPartIds.isEmpty() && hasPartNode.path(PROP_ID).isTextual()) { - hasPartIds.add(hasPartNode.path(PROP_ID).asText()); - } - return hasPartIds; - } - - private void setCrateDescriptor(RoCrate crate, JsonNode descriptor) { - ContextualEntity descriptorEntity = new ContextualEntity.ContextualEntityBuilder() - .setAllUnsafe(descriptor.deepCopy()) - .build(); - crate.setJsonDescriptor(descriptorEntity); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java deleted file mode 100644 index 6a9f4bd4..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/GenericReaderStrategy.java +++ /dev/null @@ -1,29 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import com.fasterxml.jackson.databind.node.ObjectNode; -import java.io.File; -import java.io.IOException; - -/** - * Generic interface for the strategy of the reader class. - * This allows for flexible input types when implementing different reading strategies. - * - * @param the type which determines the source of the crate - */ -public interface GenericReaderStrategy { - /** - * Read the metadata.json file from the given location. - * - * @param location the location to read from - * @return the parsed metadata.json as ObjectNode - */ - ObjectNode readMetadataJson(SOURCE_TYPE location) throws IOException; - - /** - * Read the content from the given location. - * - * @param location the location to read from - * @return the content as a File - */ - File readContent(SOURCE_TYPE location) throws IOException; -} \ No newline at end of file diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java deleted file mode 100644 index 927d77de..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadFolderStrategy.java +++ /dev/null @@ -1,32 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Path; - -/** - * A class for reading a crate from a folder. - * - * @author Nikola Tzotchev on 9.2.2022 г. - * @version 1 - */ -public class ReadFolderStrategy implements GenericReaderStrategy { - - @Override - public ObjectNode readMetadataJson(String location) throws IOException { - Path metadata = new File(location).toPath().resolve("ro-crate-metadata.json"); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode objectNode = objectMapper.createObjectNode(); - objectNode = objectMapper.readTree(metadata.toFile()).deepCopy(); - return objectNode; - } - - @Override - public File readContent(String location) { - return new File(location); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java deleted file mode 100644 index 3cc41086..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/ReadZipStreamStrategy.java +++ /dev/null @@ -1,176 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.entities.contextual.JsonDescriptor; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import java.io.File; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.nio.file.Path; -import java.util.UUID; - -import edu.kit.datamanager.ro_crate.util.FileSystemUtil; -import net.lingala.zip4j.io.inputstream.ZipInputStream; -import net.lingala.zip4j.model.LocalFileHeader; -import org.apache.commons.io.FileUtils; -import org.apache.commons.io.filefilter.FileFilterUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Reads a crate from a streamed ZIP archive. - *

- * This class handles reading and extraction of RO-Crate content from ZIP archives - * into a temporary directory structure on the file system, - * which allows accessing the contained files. - *

- * Supports ELN-Style crates, - * meaning the crate may be either in the zip archive directly or in a single, - * direct subfolder beneath the root folder (/folder). - *

- * Note: This implementation checks for up to 50 subdirectories if multiple are present. - * This is to avoid zip bombs, which may contain a lot of subdirectories, - * and at the same time gracefully handle valid crated with hidden subdirectories - * (for example, thumbnails). - *

- * NOTE: The resulting crate may refer to these temporary files. Therefore, - * these files are only being deleted before the JVM exits. If you need to free - * space because your application is long-running or creates a lot of - * crates, you may use the getters to retrieve information which will help - * you to clean up manually. Keep in mind that crates may refer to this - * folder after extraction. Use RoCrateWriter to export it so some - * persistent location and possibly read it from there, if required. Or use - * the ZipWriter to write it back to its source. - * - * @author jejkal - */ -public class ReadZipStreamStrategy implements GenericReaderStrategy { - - private static final Logger logger = LoggerFactory.getLogger(ReadZipStreamStrategy.class); - protected final String ID = UUID.randomUUID().toString(); - protected Path temporaryFolder = Path.of(String.format("./.tmp/ro-crate-java/zipStreamReader/%s/", ID)); - protected boolean isExtracted = false; - - /** - * Crates an instance with the default configuration. - *

- * The default configuration is to extract the ZipFile to - * `./.tmp/ro-crate-java/zipStreamReader/%UUID/`. - */ - public ReadZipStreamStrategy() {} - - /** - * Creates a ZipStreamReader which will extract the contents temporary to - * the given location instead of the default location. - * - * @param folderPath the custom directory to extract content to for - * temporary access. - * @param shallAddUuidSubfolder if true, the reader will extract into - * subdirectories of the given directory. These subdirectories will have - * UUIDs as their names. - */ - public ReadZipStreamStrategy(Path folderPath, boolean shallAddUuidSubfolder) { - if (shallAddUuidSubfolder) { - this.temporaryFolder = folderPath.resolve(ID); - } else { - this.temporaryFolder = folderPath; - } - } - - /** - * @return the identifier which may be used as the name for a subfolder in - * the temporary directory. - */ - public String getID() { - return ID; - } - - /** - * @return the folder (considered temporary) where the zipped crate will be - * or has been extracted to. - */ - public Path getTemporaryFolder() { - return temporaryFolder; - } - - /** - * @return whether the crate has already been extracted into the temporary - * folder. - */ - public boolean isExtracted() { - return isExtracted; - } - - /**Read the crate metadata and content from the provided input stream. - * - * @param stream The input stream. - */ - private void readCrate(InputStream stream) throws IOException { - File folder = temporaryFolder.toFile(); - FileSystemUtil.mkdirOrDeleteContent(folder); - - LocalFileHeader localFileHeader; - int readLen; - byte[] readBuffer = new byte[4096]; - - try (ZipInputStream zipInputStream = new ZipInputStream(stream)) { - while ((localFileHeader = zipInputStream.getNextEntry()) != null) { - String fileName = localFileHeader.getFileName(); - File extractedFile = new File(folder, fileName).getCanonicalFile(); - Path targetRoot = folder.toPath().toRealPath(); - if (!extractedFile.toPath().startsWith(targetRoot)) { - throw new IOException("Entry is outside of target directory: " + fileName); - } - if (localFileHeader.isDirectory()) { - FileUtils.forceMkdir(extractedFile); - continue; - } - FileUtils.forceMkdir(extractedFile.getParentFile()); - try (OutputStream outputStream = new FileOutputStream(extractedFile)) { - while ((readLen = zipInputStream.read(readBuffer)) != -1) { - outputStream.write(readBuffer, 0, readLen); - } - } - } - } - this.isExtracted = true; - // register deletion on exit - FileUtils.forceDeleteOnExit(folder); - } - - @Override - public ObjectNode readMetadataJson(InputStream stream) throws IOException { - if (!isExtracted) { - this.readCrate(stream); - } - - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - File jsonMetadata = temporaryFolder.resolve(JsonDescriptor.ID).toFile(); - if (!jsonMetadata.isFile()) { - // Try to find the metadata file in subdirectories - File firstSubdir = FileUtils.listFilesAndDirs( - temporaryFolder.toFile(), - FileFilterUtils.directoryFileFilter(), - null - ) - .stream() - .limit(50) - .filter(file -> file.toPath().toAbsolutePath().resolve(JsonDescriptor.ID).toFile().isFile()) - .findFirst() - .orElseThrow(() -> new IllegalStateException("No %s found in zip file".formatted(JsonDescriptor.ID))); - jsonMetadata = firstSubdir.toPath().resolve(JsonDescriptor.ID).toFile(); - } - return objectMapper.readTree(jsonMetadata).deepCopy(); - } - - @Override - public File readContent(InputStream stream) throws IOException { - if (!isExtracted) { - this.readCrate(stream); - } - return temporaryFolder.toFile(); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java b/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java deleted file mode 100644 index 83a43701..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/reader/Readers.java +++ /dev/null @@ -1,77 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import java.io.InputStream; -import java.nio.file.Path; - -/** - * Factory for creating common RO-Crate reader instances. - * Provides convenient static methods to instantiate readers with pre-configured strategies. - */ -public class Readers { - - /** - * Private constructor to prevent instantiation of this utility class. - */ - private Readers() {} - - /** - * Creates a reader that reads from ZIP files using input streams. - * - * @return A reader configured for ZIP files - * - * @see ReadZipStreamStrategy#ReadZipStreamStrategy() - */ - public static CrateReader newZipStreamReader() { - return new CrateReader<>(new ReadZipStreamStrategy()); - } - - /** - * Creates a reader that reads from ZIP files using input streams, - * extracting to a custom temporary location. - * - * @param extractPath Path where ZIP contents should be extracted - * @param useUuidSubfolder Whether to create a UUID subfolder under extractPath - * @return A reader configured for ZIP files with custom extraction - * - * @see ReadZipStreamStrategy#ReadZipStreamStrategy(Path, boolean) - */ - public static CrateReader newZipStreamReader(Path extractPath, boolean useUuidSubfolder) { - return new CrateReader<>(new ReadZipStreamStrategy(extractPath, useUuidSubfolder)); - } - - /** - * Creates a reader that reads from a folder using a string path. - * - * @return A reader configured for folders - * - * @see ReadFolderStrategy - */ - public static CrateReader newFolderReader() { - return new CrateReader<>(new ReadFolderStrategy()); - } - - /** - * Creates a reader that reads from a ZIP file using a string path. - * - * @return A reader configured for ZIP files - * - * @see ReadZipStrategy#ReadZipStrategy() - */ - public static CrateReader newZipPathReader() { - return new CrateReader<>(new ReadZipStrategy()); - } - - /** - * Creates a reader that reads from a ZIP file using a string path, - * extracting to a custom temporary location. - * - * @param extractPath Path where ZIP contents should be extracted - * @param useUuidSubfolder Whether to create a UUID subfolder under extractPath - * @return A reader configured for ZIP files with custom extraction - * - * @see ReadZipStrategy#ReadZipStrategy(Path, boolean) - */ - public static CrateReader newZipPathReader(Path extractPath, boolean useUuidSubfolder) { - return new CrateReader<>(new ReadZipStrategy(extractPath, useUuidSubfolder)); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java b/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java deleted file mode 100644 index 74d8ca1c..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/special/CrateVersion.java +++ /dev/null @@ -1,111 +0,0 @@ -package edu.kit.datamanager.ro_crate.special; - -import java.net.URI; -import java.net.URISyntaxException; -import java.util.Optional; - -/** - * Represents a crate version and has information for each version available. - * - * It offers also convenience functionality like version comparison similar to - * numbers. - */ -public enum CrateVersion { - // NOTE: Java defines compareTo for enums to work in the order of the defined - // elements. This means higher versions have to be defined below the lower - // versions. Consider this when adding a new version. - // - // NOTE: To add a new version, simply append a new variant with the correct - // data and read the comment below the versions. - V1P1("https://w3id.org/ro/crate/1.1"), - V1P2_DRAFT("https://w3id.org/ro/crate/1.2-DRAFT"); - - // NOTE: Do not forget to adjust the following when adding a version: - public static final CrateVersion LATEST_STABLE = CrateVersion.V1P1; - public static final CrateVersion LATEST_UNSTABLE = CrateVersion.V1P2_DRAFT; - - /** - * The String which is referred to by the crates conformsTo value. - * Should lead to the specification when resolved as a URL. - */ - public final String conformsTo; - - /** - * The String representation of the version. - * - * Example: assertEquals("1.2-DRAFT", CrateVersion.V1P2_DRAFT); - */ - public final String version; - - /** - * Basically a constructor of a version, if it needs to be created from the spec - * URI. - * - * @param conformsTo the specification URI. Example: - * https://w3id.org/ro/crate/1.1 - * @return the matching CrateVersion enum, if the URI matches any. Empty if not. - */ - public static Optional fromSpecUri(String conformsTo) { - return Optional.ofNullable(crateVersionOfConformsTo(conformsTo)); - } - - /** - * Private constructor which is being used for the internally given information - * above. - * - * @param spec the specification URI / conformsTo value - */ - private CrateVersion(String spec) { - this.conformsTo = spec; - this.version = getVersionFromConformsToString(spec); - } - - public boolean isStable() { - return !this.version.endsWith("-DRAFT"); - } - - public URI getConformsToUri() { - try { - return new URI(this.conformsTo); - } catch (URISyntaxException e) { - // can not happen as the user can not set this string - return null; - } - } - - /** - * Extracts the version from the spec uri. - * - * @param specUri the uri of the spec - * @return the version of the spec - */ - private static String getVersionFromConformsToString(String specUri) { - String[] parts = specUri.split("/"); - return parts[parts.length - 1]; - } - - private static CrateVersion crateVersionOfConformsTo(String conformsTo) { - for (CrateVersion e : values()) { - if (e.conformsTo.equals(conformsTo)) { - return e; - } - } - return null; - } - - public boolean isGreaterThan(CrateVersion other) { - return this.compareTo(other) > 0; - } - - public boolean isGreaterOrEqualThan(CrateVersion other) { - return this.compareTo(other) >= 0; - } - - public boolean isLowerThan(CrateVersion other) { - return this.compareTo(other) < 0; - } - - public boolean isLowerOrEqualThan(CrateVersion other) { - return this.compareTo(other) <= 0; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java b/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java deleted file mode 100644 index 4fec8e58..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java +++ /dev/null @@ -1,158 +0,0 @@ -package edu.kit.datamanager.ro_crate.special; - -import java.net.MalformedURLException; -import java.net.URL; -import java.net.URLDecoder; -import java.net.URLEncoder; -import java.nio.charset.StandardCharsets; -import java.nio.file.InvalidPathException; -import java.nio.file.Path; -import java.util.Optional; - -import com.apicatalog.jsonld.uri.UriUtils; -import java.net.URI; -import java.net.URISyntaxException; - -/** - * This class defines methods regarding URIs in general, which in RO-Crate - * context means usually a valid, resolvable URL or a relative file path. - *

- * The purpose is to have a simple abstraction where the way e.g. a URL is - * checked can be changed and tested easily for the whole library. - */ -public class IdentifierUtils { - - /** Static class */ - private IdentifierUtils() {} - - /** - * Returns true, if the given String is encoded and can be used as an - * identifier in RO-Crate. - *

- * Possible identifiers include: - * - a uri - * - a url - * - a valid LD identifier (including blank node identifiers) - * - relative identifiers - * - * @param uri the given URI. Usually a URL or relative file path. - * @return true if the url is encoded, false if it is not. - */ - public static boolean isValidUri(String uri) { - return UriUtils.isURI(uri) || isLdBlankNode(uri); - } - - /** - * Returns true, if the given string is a url. - * - * @param uri the given string - * @return true if it is a url, false otherwise. - */ - public static boolean isUrl(String uri) { - try { - return encode(uri) - .map(encodedUri -> asUrl(encodedUri).isPresent()) - .orElse(false); - } catch (Exception e) { - return false; - } - } - - /** - * Tests if the given String is a URL, and if so, returns it. - * - * @param uriAsString the given String which will be tested. - * @return the url, if it is one. - */ - public static Optional asUrl(String uriAsString) { - try { - URI uri = new URI(uriAsString); - if (uri.isAbsolute()) { - return Optional.of(uri.toURL()); - } - } catch (URISyntaxException | MalformedURLException | NullPointerException ex) { - return Optional.empty(); - } - return Optional.empty(); - } - - /** - * Returns true, if the given string is a file path. - * - * @param uri the given string - * @return true if it is a path, false otherwise. - */ - public static boolean isPath(String uri) { - return asPath(uri).isPresent(); - } - - /** - * Tests if the given String is a file path, and if so, returns it. - * - * @param uri the given String which will be tested. - * @return the path, if it is one. - */ - public static Optional asPath(String uri) { - try { - Path u = Path.of(uri); - if (!isUrl(uri)) { - return Optional.of(u); - } - } catch (InvalidPathException e) { - return Optional.empty(); - } - return Optional.empty(); - } - - /** - * Encodes a string using the description if the ro-crate-specification. - * - * @param uri the string to encode. - * @return the encoded version of the given string, if possible. - */ - public static Optional encode(String uri) { - String result = uri; - // according to - // https://www.researchobject.org/ro-crate/1.1/data-entities.html#encoding-file-paths - // a file path may not be fully encoded and may contain international unicode - // characters. So we try a "soft"-encoding first, and if this is not yet valid, - // we really fully encode it. - - result = result.replace("\\", "/"); // "...express any relative paths using / separator..." - result = result.replace("%", "%25"); // "...escape special characters like space (%25)..." - result = result.replace(" ", "%20"); // "...and percent (%25)..." - if (isValidUri(result)) { - return Optional.of(result); - } - // from here on, our soft-encoding failed and we will fully encode the url or - // path. - result = URLEncoder.encode(uri, StandardCharsets.UTF_8); - result = result.replace("+", "%20"); // UrlEncoder encodes spaces with "+" - result = result.replace("%3A", ":"); // Convert colons back - result = result.replace("%2F", "/"); // Convert slashes back - - if (isValidUri(result)) { - return Optional.of(result); - } else { - return Optional.empty(); - } - } - - public static Optional decode(String uri) { - if (!isValidUri(uri) || isLdBlankNode(uri)) { - return Optional.of(uri); - } - return Optional.of(URLDecoder.decode(uri, StandardCharsets.UTF_8)); - } - - /** - * Returns true if the given string is a blank node identifier in the Linked - * Data world. - * - * @param uri the given String - * @return true if the string is a blank node. False if not. - */ - private static boolean isLdBlankNode(String uri) { - return uri.startsWith("_:") && !uri.contains(" "); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java b/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java deleted file mode 100644 index 812772cd..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java +++ /dev/null @@ -1,42 +0,0 @@ -package edu.kit.datamanager.ro_crate.util; - -import java.io.IOException; -import java.io.InputStream; -import java.net.URL; -import java.util.Properties; - -public class ClasspathPropertiesVersionProvider implements VersionProvider { - public static final String VERSION_PROPERTIES = "version.properties"; - - /** - * Cached version to avoid repeated file/resource reads. - */ - private String cachedVersion = null; - - /** - * Constructs a ClasspathPropertiesVersionProvider that reads the version from a properties file in the classpath. - */ - public ClasspathPropertiesVersionProvider() { - // Lazy initialization - version loaded on first access - } - - @Override - public String getVersion() { - if (cachedVersion != null) { - return cachedVersion; - } - - URL resource = this.getClass().getResource("/" + VERSION_PROPERTIES); - assert resource != null : VERSION_PROPERTIES + " not found in classpath"; - - try (InputStream input = resource.openStream()) { - Properties properties = new Properties(); - properties.load(input); - String version = properties.getProperty("version"); - assert version != null : "Version property not found in " + VERSION_PROPERTIES; - return version.trim(); - } catch (IOException e) { - throw new IllegalStateException("Failed to read version from properties file", e); - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java b/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java deleted file mode 100644 index 82c39529..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/util/FileSystemUtil.java +++ /dev/null @@ -1,122 +0,0 @@ -package edu.kit.datamanager.ro_crate.util; - -import org.apache.commons.io.FileUtils; - -import java.io.File; -import java.io.IOException; -import java.util.Collection; -import java.util.regex.Matcher; - -public class FileSystemUtil { - private FileSystemUtil() { - // Utility class, no instantiation - } - - /** - * Checks if the given ID appears to be a file path. - *

- * Specifically excludes IDs starting with "doi:", "http", or "https". - * - * @param id the ID to check - * @return true if it looks like a file path, false otherwise - */ - public static boolean isFilePath(String id) { - return id != null && !( - id.startsWith("doi:") || - id.startsWith("http://") || - id.startsWith("https://") - ); - } - - /** - * Gets the parent path of a given path. - * @param path the path to evaluate. - * @return the parent path, or null if no parent exists. - */ - public static String getParentPath(String path) { - if (path == null || path.equals("./") || path.isEmpty()) { - return null; - } - - // Normalize path - remove trailing slash for consistency - String normalizedPath = path.endsWith("/") - ? path.substring(0, path.length() - 1) - : path; - - int lastSlash = normalizedPath.lastIndexOf('/'); - if (lastSlash == -1) { - return "./"; // Root directory - } - - String parentPath = normalizedPath.substring(0, lastSlash); - - // If parent is empty, it's root - if (parentPath.isEmpty()) { - return "./"; - } - - // For validation, we need to check both with and without trailing slash - // since files don't have trailing slash but folders do - return parentPath; - } - - /** - * Removes a specific set of given file extensions from a file name, if present. - * The extensions are case-insensitive. Given "ELN", "eln" or "Eln" will also match. - * The dot (.) before the extension is also assumed and removed implicitly: - *

- * Example: - * filterExtensionsFromFileName("test.eln", Set.of("ELN")) -> "test" - * - * @param filename the file name to filter (must not be null) - * @param extensionsToRemove the extensions to remove (must not be null) - * @return the filtered file name - * @throws NullPointerException if any parameter is null - */ - public static String filterExtensionsFromFileName(String filename, Collection extensionsToRemove) { - String dot = Matcher.quoteReplacement("."); - String end = Matcher.quoteReplacement("$"); - for (String extension : extensionsToRemove) { - // (?i) removes case sensitivity - filename = filename.replaceFirst("(?i)" + dot + extension + end, ""); - } - return filename; - } - - /** - * Ensures that a given path ends with a trailing slash. - * - * @param path the path to check - * @return the path with a trailing slash if it didn't have one, or the original path - */ - public static String ensureTrailingSlash(String path) { - if (path == null || path.isEmpty()) { - return path; - } - if (!path.endsWith("/")) { - return path + "/"; - } - return path; - } - - /** - * Creates a directory or deletes its content if it already exists. - * - * @param folder the folder to create or delete content from - * @throws IOException if an I/O error occurs - */ - public static void mkdirOrDeleteContent(File folder) throws IOException { - File[] files = folder.listFiles(); - boolean isNonEmptyDir = folder.exists() - && folder.isDirectory() - && files != null - && files.length > 0; - boolean isFile = folder.exists() - && !folder.isDirectory(); - - if (isNonEmptyDir || isFile) { - FileUtils.forceDelete(folder); - } - FileUtils.forceMkdir(folder); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java b/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java deleted file mode 100644 index 45161f16..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java +++ /dev/null @@ -1,61 +0,0 @@ -package edu.kit.datamanager.ro_crate.util; - -import com.fasterxml.jackson.databind.JsonNode; - -import java.util.stream.StreamSupport; - -/** - * Utility class for handling operations on RO-Crate graphs. - * Provides methods to find entities by ID or type within a graph. - *

- * {@see JsonUtilFunctions}. - */ -public class Graph { - - private Graph() { - // Private constructor to prevent instantiation - } - - /** - * Finds an entity in the graph by its ID. - * - * @param graph The JSON node representing the graph. - * @param id The ID of the entity to find. - * @return The entity as a JsonNode if found, null otherwise. - */ - public static JsonNode findEntityById(JsonNode graph, String id) { - for (JsonNode entity : graph) { - if (entity.has("@id") && entity.get("@id").asText().equals(id)) { - return entity; - } - } - return null; - } - - /** - * Finds an entity in the graph by its type. - * - * @param graph The JSON node representing the graph. - * @param type The type of the entity to find. - * @return The entity as a JsonNode if found, null otherwise. - */ - public static JsonNode findEntityByType(JsonNode graph, String type) { - return StreamSupport.stream(graph.spliterator(), false) - .filter(entity -> entity.path("@type").asText().equals(type)) - .findFirst() - .orElse(null); - } - - /** - * Finds all entities in the graph by their type. - * - * @param graph The JSON node representing the graph. - * @param type The type of the entities to find. - * @return An array of JsonNode containing all entities of the specified type. - */ - public static JsonNode[] findEntitiesByType(JsonNode graph, String type) { - return StreamSupport.stream(graph.spliterator(), false) - .filter(entity -> entity.path("@type").asText().equals(type)) - .toArray(JsonNode[]::new); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java b/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java deleted file mode 100644 index cd5c4ad2..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java +++ /dev/null @@ -1,10 +0,0 @@ -package edu.kit.datamanager.ro_crate.util; - -public interface VersionProvider { - /** - * Returns the version of the ro-crate-java library. - * - * @return The version string. - */ - String getVersion(); -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java b/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java deleted file mode 100644 index b8eb2ef1..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/util/ZipStreamUtil.java +++ /dev/null @@ -1,93 +0,0 @@ -package edu.kit.datamanager.ro_crate.util; - -import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import net.lingala.zip4j.model.ZipParameters; - -/** - * - * @author jejkal - */ -public class ZipStreamUtil { - - /** - * Adds a folder and its contents to a ZipOutputStream. - * - * @param zipOutputStream The ZipOutputStream to which the folder will be added. - * @param folder The folder to be added. - * @param parentPath The path in the zip file where the folder will be added. - * @throws IOException If an I/O error occurs. - */ - public static void addFolderToZipStream( - ZipOutputStream zipOutputStream, - File folder, - String parentPath - ) throws IOException { - if (!folder.exists() || !folder.isDirectory()) { - throw new IllegalArgumentException( - "The provided folder path is not a valid directory: %s" - .formatted(folder.getAbsolutePath()) - ); - } - - File[] files = folder.listFiles(); - if (files == null) { - return; - } - - for (File file : files) { - String zipEntryPath = parentPath.isEmpty() ? file.getName() : parentPath + "/" + file.getName(); - if (file.isDirectory()) { - addFolderToZipStream(zipOutputStream, file.getAbsolutePath(), zipEntryPath); - } else { - addFileToZipStream(zipOutputStream, file, zipEntryPath); - } - } - } - - /** - * Adds a folder and its contents to a ZipOutputStream. - * @param zipOutputStream The ZipOutputStream to which the folder will be added. - * @param folderPath The path of the folder to be added. - * @param parentPath The path in the zip file where the folder will be added. - * @throws IOException If an I/O error occurs. - */ - public static void addFolderToZipStream( - ZipOutputStream zipOutputStream, - String folderPath, - String parentPath - ) throws IOException { - addFolderToZipStream(zipOutputStream, new File(folderPath), parentPath); - } - - /** - * Adds a file to a ZipOutputStream. - * - * @param zipOutputStream The ZipOutputStream to which the file will be added. - * @param file The file to be added. - * @param zipEntryPath The path in the zip file where the file will be added. - * @throws IOException If an I/O error occurs. - */ - public static void addFileToZipStream( - ZipOutputStream zipOutputStream, - File file, - String zipEntryPath - ) throws IOException { - ZipParameters zipParameters = new ZipParameters(); - zipParameters.setFileNameInZip(zipEntryPath); - zipOutputStream.putNextEntry(zipParameters); - - try (InputStream inputStream = new FileInputStream(file)) { - byte[] buffer = new byte[4096]; - int len; - while ((len = inputStream.read(buffer)) != -1) { - zipOutputStream.write(buffer, 0, len); - } - } - - zipOutputStream.closeEntry(); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java deleted file mode 100644 index d708ddd7..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java +++ /dev/null @@ -1,55 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.validation.Validator; - -import java.io.IOException; - -/** - * The class used for writing (exporting) crates. The class uses a strategy - * pattern for writing crates as different formats. (zip, folders, etc.) - * - * @param the type which determines the destination of the result - */ -public class CrateWriter { - - private final GenericWriterStrategy strategy; - protected ProvenanceManager provenanceManager = new ProvenanceManager(); - - /** - * Constructs a CrateWriter with a specified strategy for writing crates. - * - * @param strategy the strategy to use for writing crates. - */ - public CrateWriter(GenericWriterStrategy strategy) { - this.strategy = strategy; - } - - /** - * Sets the ProvenanceManager to be used for automatic provenance information - * generation when saving the crate. - * - * @param provenanceManager the ProvenanceManager to use. Using null will disable provenance management. - * @return this CrateWriter instance for method chaining. - */ - public CrateWriter withAutomaticProvenance(ProvenanceManager provenanceManager) { - this.provenanceManager = provenanceManager; - return this; - } - - /** - * This method saves the crate to a destination provided. - * - * @param crate the crate to write. - * @param destination the location where the crate should be written. - */ - public void save(Crate crate, DESTINATION_TYPE destination) throws IOException { - Validator defaultValidation = new Validator(new JsonSchemaValidation()); - defaultValidation.validate(crate); - if (this.provenanceManager != null) { - this.provenanceManager.addProvenanceInformation(crate); - } - this.strategy.save(crate, destination); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java deleted file mode 100644 index bd6310cd..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/ElnFormatWriter.java +++ /dev/null @@ -1,27 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -/** - * An Interface for {@link GenericWriterStrategy} implementations which support writing - * ELN-Style crates. - * - * @param the type which determines the destination of the result - */ -public interface ElnFormatWriter extends GenericWriterStrategy { - - /** - * Write in ELN format style, meaning with a root subfolder in the zip file. - * Same as {@link #withRootSubdirectory()}. - * - * @return this writer - */ - ElnFormatWriter usingElnStyle(); - - /** - * Alias with more generic name for {@link #usingElnStyle()}. - * - * @return this writer - */ - default ElnFormatWriter withRootSubdirectory() { - return this.usingElnStyle(); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java deleted file mode 100644 index fd4a2c50..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java +++ /dev/null @@ -1,138 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; -import edu.kit.datamanager.ro_crate.util.ClasspathPropertiesVersionProvider; -import edu.kit.datamanager.ro_crate.util.VersionProvider; - -import java.time.Instant; - -import static edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity.ContextualEntityBuilder; - -/** - * Manages provenance information for RO-Crates. - * Handles the creation and updating of ro-crate-java entity and its actions. - */ -public class ProvenanceManager { - /** - * A record to hold the prefix for the ro-crate-java ID. - * This is used to ensure that the ID is consistent across different versions of the library. - * Having a type for the prefix avoids using it by accident as a full ID. - */ - protected record IdPrefix(String prefix) { - /** - * Constructs a String with the given suffix. - * - * @param suffix The suffix to append to the prefix. - * @return A String combining the prefix and suffix, separated by a hyphen. - * Like this: "$prefix-$suffix". - */ - public String withSuffix(String suffix) { - return prefix + "-" + suffix; - } - - @Override - public String toString() { - return prefix; - } - } - - /** - * The prefix for the ro-crate-java ID. - * This is used to identify the ro-crate-java entity in the crate. - */ - protected static final IdPrefix RO_CRATE_JAVA_ID_PREFIX = new IdPrefix("#ro-crate-java"); - - /** - * The VersionProvider used to retrieve the version of ro-crate-java. - * This allows for flexibility in how the version is determined, e.g., from a properties file. - */ - protected VersionProvider versionProvider; - - /** - * Constructs a ProvenanceManager with the default ClasspathPropertiesVersionProvider. - */ - public ProvenanceManager() { - this(new ClasspathPropertiesVersionProvider()); - } - - /** - * Constructs a ProvenanceManager with a specified VersionProvider. - * - * @param versionProvider The VersionProvider to use for retrieving the version of ro-crate-java. - */ - public ProvenanceManager(VersionProvider versionProvider) { - this.versionProvider = versionProvider; - } - - /** - * Returns the full ID for the ro-crate-java entity of this library version - * to be used for an entity describing it. - *

- * The ID is constructed using the RO_CRATE_JAVA_ID_PREFIX and the version from the VersionProvider. - * - * @return The ID for the ro-crate-java entity. - */ - public String getLibraryId() { - return RO_CRATE_JAVA_ID_PREFIX.withSuffix(versionProvider.getVersion().toLowerCase()); - } - - /** - * Adds provenance information to the given crate. - * This includes creating or updating the ro-crate-java entity and its associated action entity. - * - * @param crate The crate to which provenance information will be added. - */ - public void addProvenanceInformation(Crate crate) { - // Determine if this is the first write - boolean isFirstWrite = crate.getAllContextualEntities().stream().noneMatch( - entity -> entity.getId().startsWith(RO_CRATE_JAVA_ID_PREFIX.toString())) - && !crate.isImported(); - - String libraryId = this.getLibraryId(); - - // Create action entity first - ContextualEntity actionEntity = buildNewActionEntity(isFirstWrite, libraryId); - - // Create or update ro-crate-java entity - ContextualEntity roCrateJavaEntity = buildRoCrateJavaEntity(crate, actionEntity.getId(), libraryId); - - // Add entities to crate - crate.addContextualEntity(roCrateJavaEntity); - crate.addContextualEntity(actionEntity); - } - - protected ContextualEntity buildNewActionEntity(boolean isFirstWrite, String libraryId) { - return new ContextualEntityBuilder() - .addType(isFirstWrite ? "CreateAction" : "UpdateAction") - .addIdProperty("result", "./") - .addProperty("startTime", Instant.now().toString()) - .addIdProperty("agent", libraryId) - .build(); - } - - protected ContextualEntity buildRoCrateJavaEntity( - Crate crate, - String newActionId, - String libraryId - ) { - String version = this.versionProvider.getVersion(); - ContextualEntity self = crate.getAllContextualEntities().stream() - .filter(contextualEntity -> libraryId.equals(contextualEntity.getId())) - .findFirst() - .orElseGet(() -> new ContextualEntityBuilder() - .setId(libraryId) - .addType("SoftwareApplication") - .addProperty("name", "ro-crate-java") - .addProperty("url", "https://github.com/kit-data-manager/ro-crate-java") - .addProperty("version", version) - .addProperty("softwareVersion", version) - .addProperty("license", "Apache-2.0") - .addProperty("description", "A Java library for creating and manipulating RO-Crates") - .addIdProperty("Action", newActionId) - .build() - ); - self.addIdProperty("Action", newActionId); - return self; - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java deleted file mode 100644 index 0816cd59..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteFolderStrategy.java +++ /dev/null @@ -1,91 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.special.IdentifierUtils; -import org.apache.commons.io.FileUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.IOException; -import java.io.InputStream; -import java.nio.charset.StandardCharsets; -import java.nio.file.Path; - -/** - * A class for writing a crate to a folder. - * - * @author Nikola Tzotchev on 9.2.2022 г. - * @version 1 - */ -public class WriteFolderStrategy implements GenericWriterStrategy { - - private static final Logger logger = LoggerFactory.getLogger(WriteFolderStrategy.class); - - protected boolean writePreview = true; - - /** - * For internal use. Skips the preview generation when writing the crate. - * - * @return this instance of WriteFolderStrategy - * - * @deprecated May be removed in future versions. Not intended for public use. - */ - @Deprecated(since = "2.1.0", forRemoval = true) - public WriteFolderStrategy disablePreview() { - this.writePreview = false; - return this; - } - - @Override - public void save(Crate crate, String destination) throws IOException { - File file = new File(destination); - FileUtils.forceMkdir(file); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node = objectMapper.readTree(crate.getJsonMetadata()); - String str = objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(node); - InputStream inputStream = new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8)); - - File json = new File(destination, "ro-crate-metadata.json"); - FileUtils.copyInputStreamToFile(inputStream, json); - inputStream.close(); - // save also the preview files to the crate destination - if (crate.getPreview() != null && this.writePreview) { - crate.getPreview().saveAllToFolder(file); - } - for (var e : crate.getUntrackedFiles()) { - if (e.isDirectory()) { - FileUtils.copyDirectoryToDirectory(e, file); - } else { - FileUtils.copyFileToDirectory(e, file); - } - } - for (DataEntity dataEntity : crate.getAllDataEntities()) { - saveToFile(dataEntity, file); - } - } - - private void saveToFile(DataEntity entity, File file) throws IOException { - if (entity.getPath() != null) { - String id = entity.getId(); - String filename = IdentifierUtils.decode(id).orElse(id); - Path baseFolder = file.toPath().toAbsolutePath().normalize(); - Path destination = baseFolder.resolve(filename).normalize(); - // defence-in-depth: ensure the resolved path remains inside the crate folder - if (!destination.startsWith(baseFolder)) { - logger.warn("Skipping entity '{}': resolved path '{}' escapes destination folder '{}'", id, destination, file); - return; - } - if (entity.getPath().toFile().isDirectory()) { - FileUtils.copyDirectory(entity.getPath().toFile(), destination.toFile()); - } else { - FileUtils.copyFile(entity.getPath().toFile(), destination.toFile()); - } - } - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java deleted file mode 100644 index 003f7973..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStrategy.java +++ /dev/null @@ -1,33 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import edu.kit.datamanager.ro_crate.Crate; - -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStream; - -/** - * Implementation of the writing strategy to provide a way of writing crates to - * a zip archive. - */ -public class WriteZipStrategy implements - GenericWriterStrategy, - ElnFormatWriter -{ - private static final Logger logger = LoggerFactory.getLogger(WriteZipStrategy.class); - protected ElnFormatWriter delegate = new WriteZipStreamStrategy(); - - @Override - public ElnFormatWriter usingElnStyle() { - this.delegate = this.delegate.withRootSubdirectory(); - return this; - } - - @Override - public void save(Crate crate, String destination) throws IOException { - this.delegate.save(crate, new FileOutputStream(destination)); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java deleted file mode 100644 index 8dfb6adf..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/WriteZipStreamStrategy.java +++ /dev/null @@ -1,223 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; - -import java.io.*; -import java.nio.charset.StandardCharsets; -import java.nio.file.Path; -import java.util.ArrayList; -import java.util.List; -import java.util.Optional; -import java.util.Set; -import java.util.UUID; - -import edu.kit.datamanager.ro_crate.preview.CratePreview; -import edu.kit.datamanager.ro_crate.special.IdentifierUtils; -import edu.kit.datamanager.ro_crate.util.FileSystemUtil; -import edu.kit.datamanager.ro_crate.util.ZipStreamUtil; -import net.lingala.zip4j.io.outputstream.ZipOutputStream; -import net.lingala.zip4j.model.ZipParameters; -import org.apache.commons.io.FileUtils; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -/** - * Implementation of the writing strategy to provide a way of writing crates to - * a zip archive. - */ -public class WriteZipStreamStrategy implements - GenericWriterStrategy, - ElnFormatWriter { - - private static final Logger logger = LoggerFactory.getLogger(WriteZipStreamStrategy.class); - public static final String TMP_DIR = "./.tmp/ro-crate-java/writer-zip-stream-strategy/"; - - /** - * Defines if the zip file will directly contain the crate, - * or if it will contain a subdirectory with the crate. - */ - protected boolean createRootSubdir = false; - - /** - * In streams, we do not have a file name yet (or do not know it), - * so we need to set a default name for the root subdirectory. - */ - protected String rootSubdirName = "content"; - - @Override - public ElnFormatWriter usingElnStyle() { - this.createRootSubdir = true; - return this; - } - - /** - * Sets the name of a root subdirectory in the zip file. - * Implicitly also enables the creation of a root subdirectory. - * If used for ELN files, note the subdirectory name should be the same as the zip - * files name. - * - * @param name the name of the subdirectory - * @return this instance of ReadZipStreamStrategy - */ - public WriteZipStreamStrategy setSubdirectoryName(String name) { - this.rootSubdirName = name; - this.createRootSubdir = true; - return this; - } - - @Override - public void save(Crate crate, OutputStream destination) throws IOException { - String innerFolderName = ""; - if (this.createRootSubdir) { - innerFolderName = FileSystemUtil.filterExtensionsFromFileName( - this.rootSubdirName, - Set.of("ELN", "ZIP")); - innerFolderName = FileSystemUtil.ensureTrailingSlash(innerFolderName); - } - try (ZipOutputStream zipFile = new ZipOutputStream(destination)) { - saveMetadataJson(crate, zipFile, innerFolderName); - saveDataEntities(crate, zipFile, innerFolderName); - savePreview(crate, zipFile, innerFolderName); - } - } - - private void saveDataEntities(Crate crate, ZipOutputStream zipStream, String prefix) throws IOException { - for (DataEntity dataEntity : crate.getAllDataEntities()) { - this.saveToStream(dataEntity, zipStream, prefix); - } - } - - private void saveMetadataJson(Crate crate, ZipOutputStream zipStream, String prefix) throws IOException { - // write the metadata.json file - ZipParameters zipParameters = new ZipParameters(); - zipParameters.setFileNameInZip(prefix + "ro-crate-metadata.json"); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - // we create an JsonNode only to have the file written pretty - JsonNode node = objectMapper.readTree(crate.getJsonMetadata()); - String str = objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(node); - // write the ro-crate-metadata - - byte[] buff = new byte[4096]; - int readLen; - zipStream.putNextEntry(zipParameters); - try (InputStream inputStream = new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8))) { - while ((readLen = inputStream.read(buff)) != -1) { - zipStream.write(buff, 0, readLen); - } - } - zipStream.closeEntry(); - } - - private void savePreview(Crate crate, ZipOutputStream zipStream, String prefix) throws IOException { - Optional preview = Optional.ofNullable(crate.getPreview()); - if (preview.isEmpty()) { - return; - } - final String ID = UUID.randomUUID().toString(); - File tmpPreviewFolder = Path.of(TMP_DIR) - .resolve(ID) - .toFile(); - FileUtils.forceMkdir(tmpPreviewFolder); - FileUtils.forceDeleteOnExit(tmpPreviewFolder); - - preview.get().generate(crate, tmpPreviewFolder); - String[] paths = tmpPreviewFolder.list(); - if (paths == null) { - throw new IOException("No preview files found in temporary folder. Preview generation failed."); - } - for (String path : paths) { - File file = tmpPreviewFolder.toPath().resolve(path).toFile(); - if (file.isDirectory()) { - ZipStreamUtil.addFolderToZipStream( - zipStream, - file, - prefix + path); - } else { - ZipStreamUtil.addFileToZipStream( - zipStream, - file, - prefix + path); - } - } - try { - FileUtils.forceDelete(tmpPreviewFolder); - } catch (IOException e) { - logger.error("Could not delete temporary preview folder: {}", tmpPreviewFolder); - } - } - - private void saveToStream(DataEntity entity, ZipOutputStream zipStream, String prefix) throws IOException { - if (entity == null) { - return; - } - - boolean isDirectory = entity.getPath().toFile().isDirectory(); - String id = entity.getId(); - String filename = IdentifierUtils.decode(id).orElse(id); - String safeName = sanitizeZipEntryName(filename); - if (safeName.isEmpty()) { - logger.warn("Skipping entity '{}': decoded name resolves outside the crate root", id); - return; - } - String entryName = prefix + safeName; - if (isDirectory) { - ZipStreamUtil.addFolderToZipStream( - zipStream, - entity.getPath().toFile(), - entryName); - } else { - ZipStreamUtil.addFileToZipStream( - zipStream, - entity.getPath().toFile(), - entryName); - } - } - - /** - * Normalizes a decoded entry name into a safe relative path, consistent - * with the containment check in {@link WriteFolderStrategy#saveToFile}. - *

- * Absolute paths (leading {@code /}) and Windows drive-qualified paths - * (e.g. {@code C:/}) are rejected. Internal {@code .} and {@code ..} - * segments are resolved; if the result escapes the virtual crate root - * the name is rejected. - * - * @param name the raw decoded entry name - * @return a canonical relative entry name, or an empty string if the name - * is absolute, drive-qualified, or escapes the crate root - */ - private static String sanitizeZipEntryName(String name) { - // zip entries always use forward slashes as separators - String normalized = name.replace('\\', '/'); - - // Reject absolute paths and Windows drive-qualified paths (e.g. C:/) - if (normalized.startsWith("/") - || (normalized.length() >= 2 && normalized.charAt(1) == ':' - && Character.isLetter(normalized.charAt(0)))) { - return ""; - } - - // Normalize "." and ".." segments, rejecting paths that escape the root - String[] segments = normalized.split("/"); - List stack = new ArrayList<>(); - for (String segment : segments) { - if (segment.isEmpty() || segment.equals(".")) { - continue; - } - if (segment.equals("..")) { - if (stack.isEmpty()) { - return ""; - } - stack.remove(stack.size() - 1); - } else { - stack.add(segment); - } - } - return String.join("/", stack); - } -} diff --git a/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java b/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java deleted file mode 100644 index d1a41d66..00000000 --- a/src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java +++ /dev/null @@ -1,42 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import java.io.OutputStream; - -/** - * Utility class for creating instances of different crate writers. - * This class is not meant to be instantiated. - */ -public class Writers { - - /** - * Prevents instantiation of this utility class. - */ - private Writers() {} - - /** - * Creates a new instance of a crate writer that writes to a folder. - * - * @return a new instance of {@link CrateWriter} for writing to a folder - */ - public static CrateWriter newFolderWriter() { - return new CrateWriter<>(new WriteFolderStrategy()); - } - - /** - * Creates a new instance of a crate writer that writes to a zip stream. - * - * @return a new instance of {@link CrateWriter} for writing to a zip stream - */ - public static CrateWriter newZipStreamWriter() { - return new CrateWriter<>(new WriteZipStreamStrategy()); - } - - /** - * Creates a new instance of a crate writer that writes to a zip file. - * - * @return a new instance of {@link CrateWriter} for writing to a zip file - */ - public static CrateWriter newZipPathWriter() { - return new CrateWriter<>(new WriteZipStrategy()); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java b/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java deleted file mode 100644 index 24a57a07..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java +++ /dev/null @@ -1,178 +0,0 @@ -package edu.kit.datamanager.ro_crate; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; - -import com.fasterxml.jackson.databind.SerializationFeature; -import edu.kit.datamanager.ro_crate.entities.AbstractEntity; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; - -import org.apache.commons.io.FileUtils; -import io.json.compare.JSONCompare; -import io.json.compare.JsonComparator; -import org.opentest4j.AssertionFailedError; - -import java.io.File; -import java.io.IOException; -import java.io.InputStream; -import java.nio.file.Files; -import java.nio.file.Path; -import java.util.Map; -import java.util.function.Function; -import java.util.stream.Collectors; -import static org.junit.jupiter.api.Assertions.assertEquals; - -public class HelpFunctions { - - public static void compareEntityWithFile(AbstractEntity entity, String string) throws IOException { - InputStream inputStream - = HelpFunctions.class.getResourceAsStream(string); - JsonNode expectedJson = MyObjectMapper.getMapper().readTree(inputStream); - JsonNode node = MyObjectMapper.getMapper().convertValue(entity, JsonNode.class); - //compare the size of the expected and actual node. Both nodes should have the same number of properties. - assertEquals(expectedJson.size(), node.size()); - compare(expectedJson, node, true); - } - - public static void compare(JsonNode node1, JsonNode node2, Boolean equals) { - var comparator = new JsonComparator() { - public boolean compareValues(Object expected, Object actual) { - return expected.equals(actual); - } - - public boolean compareFields(String expected, String actual) { - return expected.equals(actual); - } - }; - - if (equals) { - JSONCompare.assertMatches(node1, node2, comparator); - } else { - JSONCompare.assertNotMatches(node1, node2, comparator); - } - } - - public static void compareTwoMetadataJsonNotEqual(Crate crate1, Crate crate2) throws JsonProcessingException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata()); - JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata()); - compare(node1, node2, false); - } - - public static void compareTwoMetadataJsonNotEqual(Crate crate1, String jsonFileString) throws IOException { - InputStream inputStream = HelpFunctions.class.getResourceAsStream( - jsonFileString); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata()); - JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream)); - compare(node1, node2, false); - } - - public static void compareTwoCrateJson(Crate crate1, Crate crate2) throws JsonProcessingException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata()); - JsonNode node2 = objectMapper.readTree(crate2.getJsonMetadata()); - compare(node1, node2, true); - } - - public static void prettyPrintJsonString(String minimalJsonMetadata) { - try { - ObjectMapper objectMapper = new ObjectMapper(); - JsonNode jsonNode = objectMapper.readTree(minimalJsonMetadata); - // Enable pretty printing - String prettyJson = objectMapper - .enable(SerializationFeature.INDENT_OUTPUT) - .writeValueAsString(jsonNode); - // Print the pretty JSON - System.out.println(prettyJson); - } catch (JsonProcessingException e) { - throw new AssertionFailedError("Not able to process string as JSON!", e); - } - } - - public static void printAndAssertEquals(RoCrate crate, String pathToResource) { - // So you get something to see - prettyPrintJsonString(crate.getJsonMetadata()); - // Compare with the example from the specification - try { - HelpFunctions.compareCrateJsonToFileInResources(crate, pathToResource); - } catch (IOException e) { - throw new AssertionFailedError("Missing resources file!", e); - } - } - - public static void compareCrateJsonToFileInResources(File file1, File file2) throws IOException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node1 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file1)); - JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(file2)); - compare(node1, node2, true); - } - - /** - * Compares the JSON metadata of a Crate object with a JSON file in the resources directory. - * - * @param crate1 The Crate object to compare. - * @param jsonFileString The path to the JSON file in the resources directory. - * @throws IOException If an error occurs while reading the JSON file. - */ - public static void compareCrateJsonToFileInResources(Crate crate1, String jsonFileString) throws IOException { - InputStream inputStream = HelpFunctions.class.getResourceAsStream( - jsonFileString); - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - JsonNode node1 = objectMapper.readTree(crate1.getJsonMetadata()); - JsonNode node2 = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(inputStream)); - compare(node1, node2, true); - } - - public static boolean compareTwoDir(File dir1, File dir2) throws IOException { - // compare the content of the two directories - Map compareWithMe = FileUtils.listFiles(dir1, null, true) - .stream() - .collect(Collectors.toMap(java.io.File::getName, Function.identity())); - - Map testMe = FileUtils.listFiles(dir2, null, true) - .stream() - .collect(Collectors.toMap(java.io.File::getName, Function.identity())); - - - if (compareWithMe.size() != testMe.size()) { - return false; - } - for (String filename : testMe.keySet()) { - // we do that because the ro-crate-metadata.json can be differently formatted, - // or the order of the entities may be different - // the same holds for the html file - if (filename.equals("ro-crate-preview.html") || filename.equals("ro-crate-metadata.json")) { - if (!compareWithMe.containsKey(filename)) { - return false; - } - } else if (!FileUtils.contentEqualsIgnoreEOL(testMe.get(filename), compareWithMe.get(filename), null)) { - return false; - } - } - return true; - } - - /** - * Prints the file tree of the given directory for debugging and understanding - * a test more quickly. - * - * @param directoryToPrint the directory to print - * @throws IOException if an error occurs while printing the file tree - */ - @SuppressWarnings("resource") - public static void printFileTree(Path directoryToPrint) throws IOException { - // Print all files recursively in a tree structure for debugging - System.out.printf("Files in %s:%n", directoryToPrint.getFileName().toString()); - Files.walk(directoryToPrint) - .forEach(path -> { - if (!path.toAbsolutePath().equals(directoryToPrint.toAbsolutePath())) { - int depth = path.relativize(directoryToPrint).getNameCount(); - String prefix = " ".repeat(depth); - System.out.printf("%s%s%s%n", prefix, "└── ", path.getFileName()); - } - }); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java b/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java deleted file mode 100644 index 270127af..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/crate/BuilderSpec12Test.java +++ /dev/null @@ -1,82 +0,0 @@ -package edu.kit.datamanager.ro_crate.crate; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertFalse; -import static org.junit.jupiter.api.Assertions.assertTrue; - -import java.io.IOException; -import java.net.URI; -import java.net.URISyntaxException; -import java.util.Collection; - -import edu.kit.datamanager.ro_crate.reader.Readers; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.JsonNode; - -import edu.kit.datamanager.ro_crate.Crate; -import edu.kit.datamanager.ro_crate.RoCrate; -import edu.kit.datamanager.ro_crate.entities.contextual.ContextualEntity; -import edu.kit.datamanager.ro_crate.special.CrateVersion; -import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.validation.Validator; - -class BuilderSpec12Test { - private URI profile1; - private URI profile2; - - @Test - void testAppendConformsTo() throws URISyntaxException { - Crate crate = new RoCrate.BuilderWithDraftFeatures() - .alsoConformsTo(new URI("https://w3id.org/ro/wfrun/process/0.1")) - .alsoConformsTo(new URI("https://example.com/myprofile/1.0")) - .build(); - JsonNode conformsTo = crate.getJsonDescriptor().getProperty("conformsTo"); - assertTrue(conformsTo.isArray()); - // one version and two profiles - assertEquals(1 + 2, conformsTo.size()); - } - - @Test - void testModificationOfDraftCrate() throws URISyntaxException, IOException { - String path = this.getClass().getResource("/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array").getPath(); - RoCrate crate = Readers.newFolderReader().readCrate(path); - Collection existingProfiles = crate.getProfiles(); - profile1 = new URI("https://example.com/myprofile/1.0"); - profile2 = new URI("https://example.com/myprofile/2.0"); - // the loaded crate has at least one profile - assertFalse(existingProfiles.isEmpty()); - // and the ones we will add later are not part of it - assertFalse(existingProfiles.contains(profile1.toString())); - assertFalse(existingProfiles.contains(profile2.toString())); - - // add profiles - RoCrate modifiedCrate = new RoCrate.BuilderWithDraftFeatures(crate) - .alsoConformsTo(profile1) - .alsoConformsTo(profile2) - .addContextualEntity(new ContextualEntity.ContextualEntityBuilder() - .addType("CreativeWork") - .build()) - .build(); - - // sanity checks - Validator defaultValidation = new Validator(new JsonSchemaValidation()); - assertTrue(defaultValidation.validate(modifiedCrate)); - assertEquals(CrateVersion.LATEST_UNSTABLE, crate.getVersion().get()); - assertEquals(CrateVersion.LATEST_UNSTABLE, modifiedCrate.getVersion().get()); - - // number of profiles increased by 2 - Collection newProfileState = modifiedCrate.getProfiles(); - assertEquals(existingProfiles.size() + 2, newProfileState.size()); - // new profiles are present - assertTrue(newProfileState.contains(profile1.toString())); - assertTrue(newProfileState.contains(profile2.toString())); - // old profiles are present - assertEquals( - 0, - existingProfiles.stream() - .filter(txt -> !newProfileState.contains(txt)) - .count() - ); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java b/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java deleted file mode 100644 index bc959c29..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/crate/TestRemoveAddEntity.java +++ /dev/null @@ -1,178 +0,0 @@ -package edu.kit.datamanager.ro_crate.crate; - -import com.fasterxml.jackson.core.JsonProcessingException; - -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.RoCrate; -import edu.kit.datamanager.ro_crate.entities.contextual.PersonEntity; -import edu.kit.datamanager.ro_crate.entities.contextual.PlaceEntity; -import edu.kit.datamanager.ro_crate.entities.data.FileEntity; - -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.assertEquals; - -import java.io.IOException; - -public class TestRemoveAddEntity { - @Test - void testAddRemoveEntity() throws IOException { - RoCrate roCrate = new RoCrate.RoCrateBuilder("minimal", "minimal RO_crate", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addDataEntity( - new FileEntity.FileEntityBuilder() - .setId("survey-responses-2019.csv") - .addProperty("name", "Survey responses") - .addProperty("contentSize", "26452") - .addProperty("encodingFormat", "text/csv") - .build() - ) - .build(); - HelpFunctions.compareCrateJsonToFileInResources(roCrate, "/json/crate/onlyOneFile.json"); - - assertEquals(0, roCrate.getAllContextualEntities().size()); - assertEquals(1, roCrate.getAllDataEntities().size()); - - // remove entity and check if equals to the basic crate - roCrate.deleteEntityById("survey-responses-2019.csv"); - assertEquals(0, roCrate.getAllDataEntities().size()); - HelpFunctions.compareCrateJsonToFileInResources(roCrate, "/json/crate/simple.json"); - } - - @Test - void withTwoFiles() throws IOException { - PlaceEntity place = new PlaceEntity.PlaceEntityBuilder() - .setId("http://sws.geonames.org/8152662/") - .addProperty("name", "Catalina Park") - .build(); - - PersonEntity person = new PersonEntity.PersonEntityBuilder() - .setId("#alice") - .addProperty("name", "Alice") - .addProperty("description", "One of hopefully many Contextual Entities") - .build(); - - FileEntity file = new FileEntity.FileEntityBuilder() - .setId("data1.txt") - .addProperty("description", "One of hopefully many Data Entities") - .setContentLocation(place.getId()) - .addAuthor(person.getId()) - .build(); - - RoCrate roCrate = new RoCrate.RoCrateBuilder("Example RO-Crate", - "The RO-Crate Root Data Entity", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addContextualEntity(place) - .addContextualEntity(person) - .addDataEntity(file) - .addDataEntity( - new FileEntity.FileEntityBuilder().setId("data2.txt").build() - ) - .build(); - - HelpFunctions.compareCrateJsonToFileInResources(roCrate, "/json/crate/twoFiles.json"); - - assertEquals(2, roCrate.getAllDataEntities().size()); - assertEquals(2, roCrate.getAllContextualEntities().size()); - - roCrate.deleteEntityById("data1.txt"); - assertEquals(1, roCrate.getAllDataEntities().size()); - - roCrate.deleteEntityById("data2.txt"); - assertEquals(0, roCrate.getAllDataEntities().size()); - - roCrate.deleteEntityById("#alice"); - assertEquals(1, roCrate.getAllContextualEntities().size()); - - roCrate.deleteEntityById("http://sws.geonames.org/8152662/"); - assertEquals(0, roCrate.getAllContextualEntities().size()); - - RoCrate roCrate2 = new RoCrate.RoCrateBuilder("Example RO-Crate", - "The RO-Crate Root Data Entity", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/").build(); - HelpFunctions.compareTwoCrateJson(roCrate, roCrate2); - } - - @Test - void removeOtherOccur() throws JsonProcessingException { - PlaceEntity place = new PlaceEntity.PlaceEntityBuilder() - .setId("http://sws.geonames.org/8152662/") - .addProperty("name", "Catalina Park") - .build(); - - PersonEntity person = new PersonEntity.PersonEntityBuilder() - .setId("#alice") - .addProperty("name", "Alice") - .addProperty("description", "One of hopefully many Contextual Entities") - .build(); - - FileEntity file = new FileEntity.FileEntityBuilder() - .setId("data1.txt") - .addProperty("description", "One of hopefully many Data Entities") - .setContentLocation(place.getId()) - .addAuthor(person.getId()) - .addAuthor(person.getId()) - .build(); - - RoCrate roCrate = new RoCrate.RoCrateBuilder("Example RO-Crate", - "The RO-Crate Root Data Entity", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addContextualEntity(place) - .addContextualEntity(person) - .addDataEntity(file) - .build(); - - assertEquals(1, roCrate.getAllDataEntities().size()); - assertEquals(2, roCrate.getAllContextualEntities().size()); - - roCrate.deleteEntityById(person.getId()); - assertEquals(1, roCrate.getAllContextualEntities().size()); - - roCrate.deleteEntityById(place.getId()); - assertEquals(0, roCrate.getAllContextualEntities().size()); - assertEquals(1, roCrate.getAllDataEntities().size()); - - FileEntity file2 = new FileEntity.FileEntityBuilder() - .setId("data1.txt") - .addProperty("description", "One of hopefully many Data Entities") - .build(); - RoCrate second2 = new RoCrate.RoCrateBuilder("Example RO-Crate", "The RO-Crate Root Data Entity", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addDataEntity(file2) - .build(); - - HelpFunctions.compareTwoCrateJson(roCrate, second2); - } - - @Test - void testAddEntitiesWithSameId() { - - PersonEntity person = new PersonEntity.PersonEntityBuilder() - .setId("person") - .addProperty("name", "Alice") - .addProperty("description", "One of hopefully many Contextual Entities") - .build(); - - RoCrate roCrate = new RoCrate.RoCrateBuilder("Example RO-Crate", - "The RO-Crate Root Data Entity", "2024", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addContextualEntity(person) - .build(); - - RoCrate roCrateNew = new RoCrate.RoCrateBuilder("Example RO-Crate", - "The RO-Crate Root Data Entity", "2023", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/") - .addContextualEntity(person) - .build(); - - assertEquals(1, roCrate.getAllContextualEntities().size()); - assertEquals(1, roCrateNew.getAllContextualEntities().size()); - - PersonEntity personNew = new PersonEntity.PersonEntityBuilder() - .setId("person") - .addProperty("name", "Peter Sefton") - .addProperty("email", "peter.sefton@uts.edu.au") - .build(); - - roCrateNew.addContextualEntity(personNew); - - assertEquals(1, roCrate.getAllContextualEntities().size()); - assertEquals(1, roCrateNew.getAllContextualEntities().size()); - - assertEquals(roCrate.getContextualEntityById("person"), person); - assertEquals(roCrateNew.getContextualEntityById("person"), personNew); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java b/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java deleted file mode 100644 index 678642ba..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/entities/AbstractEntityTest.java +++ /dev/null @@ -1,111 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.NullAndEmptySource; -import org.junit.jupiter.params.provider.ValueSource; - -import java.util.Optional; - -import static org.junit.jupiter.api.Assertions.*; - -class AbstractEntityTest { - - @ParameterizedTest - @NullAndEmptySource - @ValueSource(strings = {" ", "\t", "\n"}) - void mergeIdIntoValue_withInvalidId_returnsEmpty(String invalidId) { - Optional result = AbstractEntity.mergeIdIntoValue(invalidId, null); - assertTrue(result.isEmpty(), "Should return empty Optional for invalid ID"); - - Optional result2 = AbstractEntity.mergeIdIntoValue( - invalidId, - MyObjectMapper.getMapper().createObjectNode() - ); - assertTrue(result2.isEmpty(), "Should return empty Optional for invalid ID"); - } - - @Test - void mergeIdIntoValue_withNullCurrentValue_returnsIdObject() { - String id = "test-id"; - Optional result = AbstractEntity.mergeIdIntoValue(id, null); - - // Should return a value for valid ID - JsonNode node = result.orElseThrow(); - assertTrue(node.isObject(), "Should return an object"); - assertEquals(id, node.get("@id").asText(), "Should contain the ID"); - } - - @Test - void mergeIdIntoValue_withExistingIdAsString_returnsEmpty() { - String id = "test-id"; - JsonNode currentValue = MyObjectMapper.getMapper().valueToTree(id); - - Optional result = AbstractEntity.mergeIdIntoValue(id, currentValue); - assertTrue(result.isEmpty(), "Should return empty when ID already exists as string"); - } - - @Test - void mergeIdIntoValue_withExistingIdObject_returnsEmpty() { - String id = "test-id"; - ObjectNode currentValue = MyObjectMapper.getMapper().createObjectNode(); - currentValue.put("@id", id); - - Optional result = AbstractEntity.mergeIdIntoValue(id, currentValue); - assertTrue(result.isEmpty(), "Should return empty when ID already exists as object"); - } - - @Test - void mergeIdIntoValue_withNonArrayValue_createsArray() { - String id = "new-id"; - String existingId = "existing-id"; - ObjectNode existingValue = MyObjectMapper.getMapper().createObjectNode(); - existingValue.put("@id", existingId); - - Optional result = AbstractEntity.mergeIdIntoValue(id, existingValue); - - assertTrue(result.isPresent(), "Should return a value"); - JsonNode node = result.get(); - assertTrue(node.isArray(), "Should be converted to array"); - assertEquals(2, node.size(), "Should contain both values"); - assertEquals(existingId, node.get(0).get("@id").asText(), "Should contain existing ID"); - assertEquals(id, node.get(1).get("@id").asText(), "Should contain new ID"); - } - - @Test - void mergeIdIntoValue_withExistingArray_addsToArray() { - String id = "new-id"; - String existingId = "existing-id"; - - ArrayNode currentValue = MyObjectMapper.getMapper().createArrayNode(); - ObjectNode existingIdObj = MyObjectMapper.getMapper().createObjectNode(); - existingIdObj.put("@id", existingId); - currentValue.add(existingIdObj); - - Optional result = AbstractEntity.mergeIdIntoValue(id, currentValue); - - assertTrue(result.isPresent(), "Should return a value"); - JsonNode node = result.get(); - assertTrue(node.isArray(), "Should remain an array"); - assertEquals(2, node.size(), "Should contain both values"); - assertEquals(existingId, node.get(0).get("@id").asText(), "Should contain existing ID"); - assertEquals(id, node.get(1).get("@id").asText(), "Should contain new ID"); - } - - @Test - void mergeIdIntoValue_withExistingArrayContainingId_returnsEmpty() { - String id = "test-id"; - ArrayNode currentValue = MyObjectMapper.getMapper().createArrayNode(); - ObjectNode existingIdObj = MyObjectMapper.getMapper().createObjectNode(); - existingIdObj.put("@id", id); - currentValue.add(existingIdObj); - - Optional result = AbstractEntity.mergeIdIntoValue(id, currentValue); - assertTrue(result.isEmpty(), "Should return empty when ID already exists in array"); - } -} - diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java b/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java deleted file mode 100644 index 7bc868f3..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/entities/contextual/ContextualEntityTest.java +++ /dev/null @@ -1,149 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.contextual; - -import java.io.IOException; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.node.ObjectNode; -import edu.kit.datamanager.ro_crate.HelpFunctions; - -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.*; - -/** - * @author Nikola Tzotchev on 5.2.2022 г. - * @version 1 - */ -public class ContextualEntityTest { - - /** - * This is exactly the same test as the PlaceEntityTest it shows again (similarly to the - * DataEntityTest) that we can also just use this class for the creation of our Contextual - * Entities - */ - @Test - void testSerialization() throws IOException { - // this does not make any difference for our testcase it just shows how the GeoCoordinates entity will look - ContextualEntity geo = new ContextualEntity.ContextualEntityBuilder() - .setId("#b4168a98-8534-4c6d-a568-64a55157b656") - .addType("GeoCoordinates") - .addProperty("latitude", "-33.7152") - .addProperty("longitude", "150.30119") - .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") - .build(); - - ContextualEntity place = new ContextualEntity.ContextualEntityBuilder() - .addType("Place") - .setId("https://sws.geonames.org/8152662/") - .addProperty("description", - "Catalina Park is a disused motor racing venue, located at Katoomba ...") - .addProperty("identifier", "https://sws.geonames.org/8152662/") - .addProperty("uri", "https://www.geonames.org/8152662/catalina-park.html") - .addProperty("name", "Catalina Park") - // here we can also do .setGeo(geo) - .addIdProperty("geo", geo) - .build(); - - assertTrue(place.getLinkedTo().contains(geo.getId())); - HelpFunctions.compareEntityWithFile(place, "/json/entities/contextual/place.json"); - } - - @Test - void testAddAllValidCase() throws JsonProcessingException { - ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() - .setId("#b4168a98-8534-4c6d-a568-64a55157b656") - .addType("GeoCoordinates") - .addProperty("latitude", "-33.7152") - .addProperty("longitude", "150.30119") - .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") - .build(); - - String allProperties = """ - { - "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", - "@type": "GeoCoordinates", - "latitude": "-33.7152", - "longitude": "150.30119", - "name": "Latitude: -33.7152 Longitude: 150.30119" - } - """; - - ObjectNode properties = MyObjectMapper.getMapper() - .readValue(allProperties, ObjectNode.class); - ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() - .setAllIfValid(properties) - .build(); - assertEquals(second.getProperties(), first.getProperties()); - } - - @Test - void testAddAllInvalidCase() throws JsonProcessingException { - ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() - .setId("#b4168a98-8534-4c6d-a568-64a55157b656") - .addType("GeoCoordinates") - .addProperty("latitude", "-33.7152") - .addProperty("longitude", "150.30119") - .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") - .build(); - - String allProperties = """ - { - "wrong property": {"any": "value"}, - "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", - "@type": "GeoCoordinates", - "latitude": "-33.7152", - "longitude": "150.30119", - "name": "Latitude: -33.7152 Longitude: 150.30119" - } - """; - - ObjectNode properties = MyObjectMapper.getMapper() - .readValue(allProperties, ObjectNode.class); - ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() - .setId("second") - .setAllIfValid(properties) - .build(); - assertNotEquals(second.getProperties(), first.getProperties()); - ObjectNode empty = new ContextualEntity.ContextualEntityBuilder() - .setId("second") - .build() - .getProperties(); - assertEquals(empty, second.getProperties()); - } - - @Test - void testAddAllUnsafeDoesInvalidCase() throws JsonProcessingException { - ContextualEntity first = new ContextualEntity.ContextualEntityBuilder() - .setId("#b4168a98-8534-4c6d-a568-64a55157b656") - .addType("GeoCoordinates") - .addProperty("latitude", "-33.7152") - .addProperty("longitude", "150.30119") - .addProperty("name", "Latitude: -33.7152 Longitude: 150.30119") - .build(); - - String allProperties = """ - { - "wrong property": {"any": "value"}, - "@id": "#b4168a98-8534-4c6d-a568-64a55157b656", - "@type": "GeoCoordinates", - "latitude": "-33.7152", - "longitude": "150.30119", - "name": "Latitude: -33.7152 Longitude: 150.30119" - } - """; - - ObjectNode properties = MyObjectMapper.getMapper() - .readValue(allProperties, ObjectNode.class); - ContextualEntity second = new ContextualEntity.ContextualEntityBuilder() - .setId("second") - .setAllUnsafe(properties) - .build(); - assertNotEquals(second.getProperties(), first.getProperties()); - ObjectNode empty = new ContextualEntity.ContextualEntityBuilder() - .setId("second") - .build() - .getProperties(); - assertNotEquals(empty, second.getProperties()); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java b/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java deleted file mode 100644 index f551c891..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataEntityTest.java +++ /dev/null @@ -1,239 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.data; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - -import java.io.IOException; -import java.net.URL; - -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.entities.data.DataEntity.DataEntityBuilder; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import java.net.URI; - -import java.net.URISyntaxException; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Stream; - -import org.junit.jupiter.api.Test; -import org.junit.jupiter.params.ParameterizedTest; -import org.junit.jupiter.params.provider.MethodSource; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertNotEquals; -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertThrows; -import static org.junit.jupiter.api.Assertions.assertTrue; - -/** - * @author Nikola Tzotchev on 4.2.2022 г. - * @version 1 - */ -class DataEntityTest { - - @Test - void testSerialization() throws IOException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - - ObjectNode bigJson = objectMapper.createObjectNode(); - bigJson.put("onefield", "dalkfa"); - ObjectNode address = objectMapper.createObjectNode(); - address.put("street", "x"); - address.put("city", "other"); - address.put("state", "this"); - address.put("zipCode", 66439); - bigJson.set("nestedObject", address); - - DataEntity file = new DataEntityBuilder() - .addType("File") - .setId("https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf") - .addProperty("name", "RO-Crate specification") - .addProperty("encodingFormat", "application/pdf") - .addProperty("url", "https://zenodo.org/record/3541888") - // this should not be included since it does not follow the json flatten form of the RO-Crate - .addProperty("test", bigJson) - .build(); - assertNull(file.getProperty("test")); - HelpFunctions.compareEntityWithFile(file, "/json/entities/data/fileEntity.json"); - } - - @Test - void testSerializationOutside() throws IOException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode json = objectMapper.createObjectNode(); - json.put("name", "RO-Crate specification"); - json.put("encodingFormat", "application/pdf"); - json.put("url", "https://zenodo.org/record/3541888"); - json.put("@id", "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf"); - json.put("@type", "File"); - - DataEntity data = new DataEntity.DataEntityBuilder().build(); - data.setProperties(json); - HelpFunctions.compareEntityWithFile(data, "/json/entities/data/fileEntity.json"); - - ObjectNode address = objectMapper.createObjectNode(); - address.put("street", "x"); - address.put("city", "other"); - address.put("state", "this"); - address.put("zipCode", 66439); - json.set("nestedObject", address); - // this should not be included into the entity since it does not follow the basic RO-Crate structure - data.setProperties(json); - assertNotEquals("", data.getId()); - HelpFunctions.compareEntityWithFile(data, "/json/entities/data/fileEntity.json"); - } - - @Test - void testUriCheck() { - //this entity id is a valid URL so there should not be any console information - DataEntity dataEntity = new DataEntity.DataEntityBuilder() - .addType("File") - .setLocation(URI.create("https://www.example.com/19")) - .build(); - - assertNotNull(dataEntity); - - Exception exception = assertThrows( - IllegalArgumentException.class, - () -> - new DataEntity.DataEntityBuilder() - .addType("File") - .setLocationWithExceptions(URI.create("zzz://wrong/url")) - .build() - ); - - assertEquals("This Data Entity remote ID does not resolve to a valid URL.", exception.getMessage()); - - assertNotNull(dataEntity); - - } - - @Test - void testPathCheck() throws IOException { - FileEntity dataEntity = new FileEntity.FileEntityBuilder() - .setLocationWithExceptions(Paths.get("example.json")) - .setId("example.json") - .addProperty("name", "RO-Crate specification") - .setEncodingFormat("application/json") - .build(); - assertEquals("example.json", dataEntity.getId()); - HelpFunctions.compareEntityWithFile(dataEntity, "/json/entities/data/localFile.json"); - - String fileName = "cp7glop.ai"; - Path filePath = Paths.get(fileName); - - dataEntity = new FileEntity.FileEntityBuilder() - .setLocationWithExceptions(filePath) - .setId(fileName) - .addProperty("name", "Diagram showing trend to increase") - .setEncodingFormat("application/pdf") - .build(); - assertEquals(fileName, dataEntity.getId()); - assertEquals(dataEntity.getPath(), filePath); - assertEquals("application/pdf", dataEntity.getProperty("encodingFormat").asText()); - } - - @Test - void testEncodedUrl() throws URISyntaxException { - //this entity id is a valid URL so there should not be any console information - DataEntity dataEntity = new DataEntity.DataEntityBuilder() - .addType("File") - .setLocation(URI.create("https://github.com/kit-data-manager/ro-crate-java/issues/5")) - .build(); - - assertEquals("https://github.com/kit-data-manager/ro-crate-java/issues/5", dataEntity.getId()); - - URL url - = HelpFunctions.class.getResource("/json/crate/simple2.json"); - assert url != null; - dataEntity = new DataEntity.DataEntityBuilder() - .addType("File") - .setLocationWithExceptions(Paths.get(url.toURI())) - .setId("simple2.json") - .build(); - - assertNotNull(dataEntity); - - dataEntity = new DataEntity.DataEntityBuilder() - .addType("File") - .setLocationWithExceptions(Paths.get("/json/crate/Results%20and%20Diagrams/almost-50%25.json")) - .setId("almost-50%25.json") - .build(); - - assertTrue(dataEntity.getTypes().contains("File")); - assertEquals("almost-50%25.json", dataEntity.getId()); - - // even if the Path is not correctly encoded, the data entity will be added with an encoded Path. - dataEntity = new DataEntity.DataEntityBuilder() - .addType("File") - .setLocationWithExceptions(Paths.get("/json/crate/Results and Diagrams/almost-50%.json")) - .setId("almost-50%.json") - .build(); - assertEquals("almost-50%25.json", dataEntity.getId()); - - } - - @Test - void testRemoveProperty() { - FileEntity dataEntity = new FileEntity.FileEntityBuilder() - .addProperty("name", "RO-Crate specification") - .setEncodingFormat("application/json") - .addProperty("url", "https://zenodo.org/record/3541888") - .addProperty("@id", "https://zenodo.org/record/3541888/files/ro-crate-1.0.0.pdf") - .build(); - - dataEntity.removeProperty("url"); - assertNull(dataEntity.getProperty("url")); - assertEquals(4, dataEntity.getProperties().size()); - - List keyList = Arrays.asList("encodingFormat", "name"); - dataEntity.removeProperties(keyList); - assertEquals(2, dataEntity.getProperties().size()); - } - - @Test - void testMixedArrayProperties() { - ObjectMapper mapper = new ObjectMapper(); - - ArrayNode propertyValue = mapper.createArrayNode(); - propertyValue - .add(1) - .add("2") - .add(3.14) - .add(true) - .add((JsonNode) null) - .add(mapper.nullNode()); - String propertyName = "mixedArray"; - - DataEntity entity = new DataEntityBuilder() - .addProperty(propertyName, propertyValue) - .build(); - assertEquals(propertyValue, entity.getProperty(propertyName)); - } - - @ParameterizedTest - @MethodSource("provideInvalidPropertyValues") - void testNestedArrayProperties(ArrayNode propertyValue) { - String propertyName = "invalidArray"; - DataEntity entity = new DataEntityBuilder() - .addProperty(propertyName, propertyValue) - .build(); - assertNull(entity.getProperty(propertyName)); - } - - private static Stream provideInvalidPropertyValues() { - ObjectMapper mapper = new ObjectMapper(); - ArrayNode withSubArray = mapper.createArrayNode().add(1).add("2"); - withSubArray.addArray(); - ArrayNode withSubObject = mapper.createArrayNode().add(1).add("2"); - withSubObject.addObject(); - - return Stream.of(withSubArray, withSubObject); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java b/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java deleted file mode 100644 index 5ae4142d..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/DataSetEntityTest.java +++ /dev/null @@ -1,104 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.data; - -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ObjectNode; - -import java.io.IOException; - -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import java.net.URI; -import java.nio.file.Paths; -import java.util.Objects; - -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.*; - -/** - * @author Nikola Tzotchev on 5.2.2022 г. - * @version 1 - */ -public class DataSetEntityTest { - - @Test - void testImpossibleRootId() { - DataSetEntity e = new DataSetEntity.DataSetBuilder() - .setId("./") - .addProperty("not_root", true) - .build(); - assertNotNull(e.getId()); - assertFalse(e.getId().isBlank()); - assertNotEquals(RootDataEntity.ID, e.getId()); - } - - @Test - void testSimpleDirDeserialization() throws IOException { - - String id = "lots_of_little_files/"; - DataSetEntity dir = new DataSetEntity.DataSetBuilder() - // this does not change anything, but it shows that the entity contains a physical file - .setLocationWithExceptions(Paths.get("invalid_file")) - .setId(id) - .addProperty("name", "Too many files") - .addProperty("description", - "This directory contains many small files, that we're not going to describe in detail.") - .build(); - - assertEquals(id, dir.getId()); - HelpFunctions.compareEntityWithFile(dir, "/json/entities/data/directory.json"); - } - - /** - * This is a test with a directory that is located on the web. It is - * recommended that such a dir list all of its files in the hasPart property - * https://www.researchobject.org/ro-crate/1.1/data-entities.html#directories-on-the-web-dataset-distributions - */ - @Test - void testDirWithHasPartDeserialization() throws IOException { - - String id = "second_content"; - DataEntity second_content = new DataEntity.DataEntityBuilder() - .setLocationWithExceptions(Paths.get("does_not_matter")) - .setId(id) - .addProperty("description", "This entity just describes one of the contents in the Dir") - .build(); - - // we can add to hasPart using directly the id, or passing the entity to it - DataSetEntity dir = new DataSetEntity.DataSetBuilder() - .setLocation(URI.create("https://www.example.com/urltodir")) - .addProperty("name", "Directory that is located on the web") - .addToHasPart("first_content") - .addToHasPart(second_content) - .build(); - - assertTrue(dir.hasPart(id)); - HelpFunctions.compareEntityWithFile(dir, "/json/entities/data/directoryWeb.json"); - } - - @Test - void testWebDir() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode propertyValue = objectMapper.createObjectNode(); - propertyValue.put("@id", "http://example.com/downloads/2020/lots_of_little_files.zip"); - - DataSetEntity dir = new DataSetEntity.DataSetBuilder() - .setLocationWithExceptions(Paths.get("lots_of_little_files/")) - .setId("lots_of_little_files/") - .addProperty("name", "Too many files") - .addProperty("description", "This directory contains many small files, that we're not going to describe in detail.") - .addProperty("distribution", propertyValue) - .build(); - - assertEquals(dir.getProperty("distribution"), propertyValue); - - DataEntity webDir = new DataEntity.DataEntityBuilder() - .setLocation(URI.create("http://example.com/downloads/2020/lots_of_little_files.zip")) - .addType("DataDownload") - .addProperty("encodingFormat", "application/zip") - .addProperty("contentSize", "82818928") - .build(); - - assertNotNull(webDir); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java b/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java deleted file mode 100644 index 76033f70..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/entities/data/RootDataEntityTest.java +++ /dev/null @@ -1,66 +0,0 @@ -package edu.kit.datamanager.ro_crate.entities.data; - -import com.fasterxml.jackson.databind.ObjectMapper; -import static org.junit.jupiter.api.Assertions.assertTrue; - -import java.io.IOException; - -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import java.nio.file.Paths; - -import org.junit.jupiter.api.Test; - -/** - * @author Nikola Tzotchev on 5.2.2022 г. - * @version 1 - */ -public class RootDataEntityTest { - - @Test - void testSerialization() throws IOException { - String id1 = "file1_id"; - FileEntity file1 = new FileEntity.FileEntityBuilder() - .setLocationWithExceptions(Paths.get("does_not_matter")) - .setId(id1) - .build(); - - String id2 = "file2_id"; - FileEntity file2 = new FileEntity.FileEntityBuilder() - .addIdProperty("name", "dsklfajs") - .addIdProperty("name", "11111111") - .setLocationWithExceptions(Paths.get("does_not_matter")) - .setId(id2) - .build(); - - RootDataEntity rootDataEntity = new RootDataEntity.RootDataEntityBuilder() - .addProperty("identifier", "https://doi.org/10.4225/59/59672c09f4a4b") - .addProperty("datePublished", "2000-02-01T00:00:00Z") - .addProperty("name", - "Data files associated with the manuscript:Effects of facilitated family case conferencing for ...") - .addProperty("description", - "Palliative care planning for nursing home residents with advanced dementia ...") - .addToHasPart(file1) - .addToHasPart(file2) - .addAuthor("a1") - .addAuthor("a2") - .build(); - - assertTrue(rootDataEntity.hasPart(id1)); - assertTrue(rootDataEntity.hasPart(id2)); - HelpFunctions.compareEntityWithFile(rootDataEntity, "/json/entities/data/root.json"); - } - - @Test - void testSerializationMinimalExample() throws IOException, IllegalArgumentException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - RootDataEntity rootDataEntity = new RootDataEntity.RootDataEntityBuilder() - .addProperty("name", "Data files") - .addProperty("description", "Palliative care planning...") - .addDateTimePropertyWithExceptions("datePublished", "2024-02-09T08:21:41Z") - .addProperty("license", objectMapper.createObjectNode().put("@id", "https://creativecommons.org/licenses/by-nc-sa/3.0/au/")) - .build(); - HelpFunctions.compareEntityWithFile(rootDataEntity, "/json/entities/data/rootMinimalExample.json"); - - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java b/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java deleted file mode 100644 index 9300e157..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/externalproviders/RorProviderTest.java +++ /dev/null @@ -1,43 +0,0 @@ -package edu.kit.datamanager.ro_crate.externalproviders; - -import java.io.IOException; - -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.entities.contextual.OrganizationEntity; -import edu.kit.datamanager.ro_crate.externalproviders.organizationprovider.RorProvider; -import org.junit.jupiter.api.Assertions; - -import org.junit.jupiter.api.Test; - -import static org.junit.jupiter.api.Assertions.assertNotNull; -import static org.junit.jupiter.api.Assertions.assertNull; -import static org.junit.jupiter.api.Assertions.assertThrows; - -/** - * @author Nikola Tzotchev on 11.2.2022 г. - * @version 1 - */ -public class RorProviderTest { - - @Test - void testExternalRorProvider() throws IOException { - OrganizationEntity organizationEntity = RorProvider.getOrganization("https://ror.org/04t3en479"); - assertNotNull(organizationEntity); - Assertions.assertEquals("https://ror.org/04t3en479", organizationEntity.getProperty("@id").asText()); - Assertions.assertEquals("https://ror.org/04t3en479", organizationEntity.getProperty("url").asText()); - Assertions.assertEquals("Karlsruhe Institute of Technology", organizationEntity.getProperty("name").asText()); - } - - @Test - void testInvalidRorUrl() { - assertThrows(IllegalArgumentException.class, () -> { - RorProvider.getOrganization("https://notror.org/04t3en479"); - }); - } - - @Test - void testInvalidRorId() { - OrganizationEntity organizationEntity = RorProvider.getOrganization("https://ror.org/42"); - assertNull(organizationEntity); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java b/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java deleted file mode 100644 index 246aca0f..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/other/UtilFunctionsTest.java +++ /dev/null @@ -1,81 +0,0 @@ -package edu.kit.datamanager.ro_crate.other; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.databind.node.ArrayNode; -import com.fasterxml.jackson.databind.node.ObjectNode; - -import edu.kit.datamanager.ro_crate.objectmapper.MyObjectMapper; -import edu.kit.datamanager.ro_crate.special.JsonUtilFunctions; - -import org.junit.jupiter.api.Test; -import io.json.compare.JSONCompare; - -import java.io.IOException; -import java.io.InputStream; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; - -public class UtilFunctionsTest { - - @Test - void testUnwrapSimple() throws IOException { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - InputStream fileJson = - UtilFunctionsTest.class.getResourceAsStream("/json/unwrap/simple.json"); - - JsonNode node = JsonUtilFunctions.unwrapSingleArray(objectMapper.readTree(fileJson)); - JsonNode expectedResult = objectMapper.readTree( - UtilFunctionsTest.class.getResourceAsStream("/json/unwrap/simpleResult.json") - ); - JSONCompare.assertMatches(node, expectedResult); - } - - @Test - void testGettingIdEntriesFromJsonProperty() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode jsonNode = objectMapper.createObjectNode(); - jsonNode.put("@id", "string1"); - - var result = JsonUtilFunctions.getIdPropertiesFromProperty(jsonNode); - assertEquals(1, result.size()); - assertEquals("string1", result.stream().findFirst().get()); - - - ArrayNode arrayNode = objectMapper.createArrayNode(); - arrayNode.add(objectMapper.createObjectNode().put("@id", "string1")); - arrayNode.add(objectMapper.createObjectNode().put("@id", "string2")); - - result = JsonUtilFunctions.getIdPropertiesFromProperty(arrayNode); - assertEquals(2, result.size()); - assertTrue(result.contains("string1")); - assertTrue(result.contains("string2")); - } - - @Test - void testGettingIdFromObject() { - ObjectMapper objectMapper = MyObjectMapper.getMapper(); - ObjectNode jsonNode = objectMapper.createObjectNode(); - - jsonNode.put("random", "not id"); - jsonNode.set("other", objectMapper.createArrayNode().add("kdfjdlk").add("kdfjalkfj")); - - jsonNode.set("test", objectMapper.createObjectNode().put("@id", "test1")); - - jsonNode.set("another", objectMapper.createObjectNode().put("@id", "test2")); - - jsonNode.set("singleArray", objectMapper.createArrayNode().add(objectMapper.createObjectNode().put("@id", "test3"))); - jsonNode.set("multipleArrayEl", objectMapper.createArrayNode() - .add(objectMapper.createObjectNode().put("@id", "test4")) - .add(objectMapper.createObjectNode().put("@id", "test5"))); - - var set = JsonUtilFunctions.getIdPropertiesFromJsonNode(jsonNode); - - assertEquals(5, set.size()); - - for (int i = 1 ; i <= 5 ; i++) { - assertTrue(set.contains("test"+i)); - } - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java b/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java deleted file mode 100644 index 68094231..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/reader/RoCrateReaderSpec12Test.java +++ /dev/null @@ -1,47 +0,0 @@ -package edu.kit.datamanager.ro_crate.reader; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; - -import java.io.IOException; -import java.util.stream.StreamSupport; - -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.databind.JsonNode; - -import edu.kit.datamanager.ro_crate.Crate; - -/** - * These reading tests are specific for reading 1.2 compliant crates. - * - * They will refer to 1.2-DRAFT as long as the specification is not final. - * Base for these tests are usually examples from the specification, but may - * contain modifications if no example for a certain property is given. - * - * Current specification: https://www.researchobject.org/ro-crate/1.2-DRAFT/ - */ -public class RoCrateReaderSpec12Test { - - /** - * Test reading a minimal crate with multiple conformsTo values, as described in - * https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles.html#declaring-conformance-of-an-ro-crate-profile - */ - @Test - void testReadingCrateWithConformsToArray() throws IOException { - String path = this.getClass().getResource("/crates/spec-1.2-DRAFT/minimal-with-conformsTo-Array").getPath(); - Crate crate = Readers.newFolderReader().readCrate(path); - JsonNode conformsTo = crate.getJsonDescriptor().getProperty("conformsTo"); - assertTrue(conformsTo.isArray()); - assertEquals(2, conformsTo.size()); - // filter the list to only contain the two expected values and expect no changes - long numFiltered = StreamSupport.stream(conformsTo.spliterator(), false) - .filter(node -> { - String asText = node.path("@id").asText(); - return asText.equals("https://w3id.org/ro/crate/1.2-DRAFT") - || asText.equals("https://example.com/my/profile/1.0-TEST"); - }) - .count(); - assertEquals(2, numFiltered); - } -} diff --git a/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java b/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java deleted file mode 100644 index 3c88ef07..00000000 --- a/src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java +++ /dev/null @@ -1,406 +0,0 @@ -package edu.kit.datamanager.ro_crate.writer; - -import com.fasterxml.jackson.databind.JsonNode; -import com.fasterxml.jackson.databind.ObjectMapper; -import edu.kit.datamanager.ro_crate.RoCrate; -import edu.kit.datamanager.ro_crate.HelpFunctions; -import edu.kit.datamanager.ro_crate.reader.Readers; -import edu.kit.datamanager.ro_crate.validation.JsonSchemaValidation; -import edu.kit.datamanager.ro_crate.validation.Validator; -import org.junit.jupiter.api.BeforeEach; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.io.TempDir; - -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -import static edu.kit.datamanager.ro_crate.util.Graph.*; -import static org.junit.jupiter.api.Assertions.*; - -class RoCrateMetadataGenerationTest { - - private final String currentVersionId = new ProvenanceManager().getLibraryId(); - - private final ObjectMapper objectMapper = new ObjectMapper(); - private Validator validator; - - @BeforeEach - void setUp() { - validator = new Validator(new JsonSchemaValidation()); - } - - private void validateCrate(RoCrate crate) { - assertTrue(validator.validate(crate), - "Crate should validate against the JSON schema"); - } - - @Test - void should_ContainRoCrateJavaEntities_When_WritingEmptyCrate(@TempDir Path tempDir) throws IOException { - // Create and write crate - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - - // Re-read the crate to verify it's still valid after writing - RoCrate readCrate = Readers.newFolderReader().readCrate(outputPath.toString()); - validateCrate(readCrate); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode graph = rootNode.get("@graph"); - - // Find ro-crate-java entity - JsonNode roCrateJavaEntity = findEntityById(graph, this.currentVersionId); - assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); - assertEquals("SoftwareApplication", roCrateJavaEntity.get("@type").asText(), - "ro-crate-java should be of type SoftwareApplication"); - - // Find CreateAction entity - JsonNode createActionEntity = findEntityByType(graph, "CreateAction"); - assertNotNull(createActionEntity, "CreateAction entity should exist"); - assertNotNull(createActionEntity.get("startTime"), "CreateAction should have startTime"); - assertEquals(this.currentVersionId, createActionEntity.get("agent").get("@id").asText(), - "CreateAction should reference ro-crate-java as agent"); - } - - @Test - void should_HaveRequiredPropertiesInRoCrateJavaEntity_When_WritingCrate(@TempDir Path tempDir) throws IOException { - // Create and write crate - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - - RoCrate readCrate = Readers.newFolderReader().readCrate(outputPath.toString()); - validateCrate(readCrate); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode roCrateJavaEntity = findEntityById(rootNode.get("@graph"), this.currentVersionId); - - assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); - assertEquals("ro-crate-java", roCrateJavaEntity.get("name").asText(), - "should have correct name"); - assertEquals("https://github.com/kit-data-manager/ro-crate-java", - roCrateJavaEntity.get("url").asText(), - "should have correct repository URL"); - assertNotNull(roCrateJavaEntity.get("version"), - "should have version property"); - } - - @Test - void should_HaveBidirectionalRelation_Between_RoCrateJavaAndItsAction(@TempDir Path tempDir) throws IOException { - // Create and write crate - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - - RoCrate readCrate = Readers.newFolderReader().readCrate(outputPath.toString()); - validateCrate(readCrate); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode graph = rootNode.get("@graph"); - - // Get both entities - JsonNode roCrateJavaEntity = findEntityById(graph, this.currentVersionId); - JsonNode createActionEntity = findEntityByType(graph, "CreateAction"); - - assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); - assertNotNull(createActionEntity, "CreateAction entity should exist"); - - // Test CreateAction -> ro-crate-java reference - JsonNode agentRef = createActionEntity.get("agent"); - assertNotNull(agentRef, "CreateAction should have agent property"); - assertEquals(this.currentVersionId, agentRef.get("@id").asText(), - "CreateAction's agent should reference ro-crate-java"); - - // Test ro-crate-java -> CreateAction reference - JsonNode actionRef = roCrateJavaEntity.get("Action"); - assertNotNull(actionRef, "ro-crate-java should have action property"); - assertEquals(createActionEntity.get("@id").asText(), actionRef.get("@id").asText(), - "ro-crate-java's action should reference the CreateAction"); - } - - @Test - void should_AccumulateActions_When_WritingMultipleTimes(@TempDir Path tempDir) throws IOException, InterruptedException { - // Create and write crate first time - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); - Thread.sleep(10); - - // Write same crate two more times to simulate updates - Writers.newFolderWriter().save(crate, outputPath.toString()); - Thread.sleep(10); - Writers.newFolderWriter().save(crate, outputPath.toString()); - validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); - Thread.sleep(10); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode graph = rootNode.get("@graph"); - - // Get ro-crate-java entity - JsonNode roCrateJavaEntity = findEntityById(graph, this.currentVersionId); - assertNotNull(roCrateJavaEntity, "ro-crate-java entity should exist"); - - // Verify actions array exists and has three entries - assertTrue(roCrateJavaEntity.get("Action").isArray(), - "ro-crate-java should have an array of actions"); - assertEquals(3, roCrateJavaEntity.get("Action").size(), - "should have three actions after three writes"); - - // Find all action entities - JsonNode createAction = findEntityByType(graph, "CreateAction"); - assertNotNull(createAction, "should have one CreateAction"); - - JsonNode[] createActions = findEntitiesByType(graph, "CreateAction"); - assertEquals(1, createActions.length, "should have exactly one CreateAction"); - - JsonNode[] updateActions = findEntitiesByType(graph, "UpdateAction"); - assertEquals(2, updateActions.length, "should have two UpdateActions"); - - // Verify CreateAction properties - assertNotNull(createAction.get("startTime"), "CreateAction should have startTime"); - assertEquals(this.currentVersionId, createAction.get("agent").get("@id").asText(), - "CreateAction should reference ro-crate-java as agent"); - - // Verify UpdateAction properties - for (JsonNode updateAction : updateActions) { - assertNotNull(updateAction.get("startTime"), - "UpdateAction should have startTime"); - assertEquals(this.currentVersionId, updateAction.get("agent").get("@id").asText(), - "UpdateAction should reference ro-crate-java as agent"); - } - - // Verify chronological order of timestamps - String createTime = createAction.get("startTime").asText(); - String updateTime1 = updateActions[0].get("startTime").asText(); - String updateTime2 = updateActions[1].get("startTime").asText(); - // The order of updates is not the order in the graph. - // But we can check that creation happened before the updates: - assertTrue(createTime.compareTo(updateTime1) < 0, - "First update should be after creation"); - assertTrue(createTime.compareTo(updateTime2) < 0, - "Second update should be after creation"); - } - - @Test - void should_HaveValidVersionFormat_When_WritingCrate(@TempDir Path tempDir) throws IOException { - // Create and write crate - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode roCrateJavaEntity = findEntityById(rootNode.get("@graph"), this.currentVersionId); - - // Version format validation - @SuppressWarnings("DataFlowIssue") - String version = roCrateJavaEntity.get("version").asText(); - - // Semantic versioning regex pattern that allows: - // - Required: major.minor.patch (e.g., 1.2.3) - // - Optional: pre-release identifier (e.g., -rc1, -RC1, -beta.1, -SNAPSHOT) - // - Optional: build metadata (e.g., +build.123) - String semverPattern = "(?i)^\\d+\\.\\d+\\.\\d+(?:-(?:rc\\d+|alpha|beta|snapshot)(?:\\.\\d+)?)?(?:\\+[0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*)?$"; - - assertTrue(version.matches(semverPattern), - String.format("Version '%s' should match semantic versioning format: major.minor.patch[-prerelease][+build]%n" + - "Examples: 1.2.3, 1.2.3-rc1, 1.2.3-SNAPSHOT, 1.2.3-beta.1, 1.2.3+build.123", version)); - } - - @SuppressWarnings("DataFlowIssue") - @Test - void should_HaveCompleteMetadata_When_WritingCrate(@TempDir Path tempDir) throws IOException { - // Create and write crate - RoCrate crate = new RoCrate.RoCrateBuilder().build(); - validateCrate(crate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(crate, outputPath.toString()); - validateCrate(Readers.newFolderReader().readCrate(outputPath.toString())); - - // Read and print metadata for debugging - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - // Parse metadata file - JsonNode rootNode = objectMapper.readTree(metadata); - JsonNode roCrateJavaEntity = findEntityById(rootNode.get("@graph"), this.currentVersionId); - - // Required properties with specific values - assertEquals("ro-crate-java", roCrateJavaEntity.get("name").asText(), - "should have correct name"); - assertEquals("https://github.com/kit-data-manager/ro-crate-java", - roCrateJavaEntity.get("url").asText(), - "should have correct repository URL"); - assertEquals("SoftwareApplication", roCrateJavaEntity.get("@type").asText(), - "should have correct type"); - - // Optional but recommended properties - assertNotNull(roCrateJavaEntity.get("description"), - "should have a description"); - assertFalse(roCrateJavaEntity.get("description").asText().isEmpty(), - "description should not be empty"); - - assertNotNull(roCrateJavaEntity.get("license"), - "should have a license"); - assertTrue(roCrateJavaEntity.has("softwareVersion"), - "should have softwareVersion as an alias for version"); - assertEquals(roCrateJavaEntity.get("version").asText(), - roCrateJavaEntity.get("softwareVersion").asText(), - "version and softwareVersion should match"); - } - - @Test - void should_AddProvenanceInfo_When_ModifyingExistingCrateWithoutProvenance(@TempDir Path tempDir) throws IOException { - // First create a crate without provenance information - RoCrate originalCrate = new RoCrate.RoCrateBuilder().build(); - validateCrate(originalCrate); - - Path outputPath = tempDir.resolve("test-crate"); - - // Use writer with disabled provenance (not implemented yet) - Writers.newFolderWriter() - .withAutomaticProvenance(null) - .save(originalCrate, outputPath.toString()); - - // Verify the original crate has no provenance information - String originalMetadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(originalMetadata); - - JsonNode originalRoot = objectMapper.readTree(originalMetadata); - JsonNode originalGraph = originalRoot.get("@graph"); - assertNull(findEntityById(originalGraph, this.currentVersionId), - "Original crate should not have ro-crate-java entity"); - assertNull(findEntityByType(originalGraph, "CreateAction"), - "Original crate should not have CreateAction"); - assertNull(findEntityByType(originalGraph, "UpdateAction"), - "Original crate should not have UpdateAction"); - - // Now read and modify the crate - RoCrate modifiedCrate = Readers.newFolderReader().readCrate(outputPath.toString()); - validateCrate(modifiedCrate); - modifiedCrate.getRootDataEntity().addProperty("description", "Modified crate"); - validateCrate(modifiedCrate); - - // Write the modified crate with provenance enabled (default) - Path modifiedPath = tempDir.resolve("modified-crate"); - Writers.newFolderWriter().save(modifiedCrate, modifiedPath.toString()); - - // Read and verify the modified crate's metadata - String modifiedMetadata = Files.readString(modifiedPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(modifiedMetadata); - - JsonNode modifiedRoot = objectMapper.readTree(modifiedMetadata); - JsonNode modifiedGraph = modifiedRoot.get("@graph"); - - // Verify ro-crate-java entity was added - JsonNode roCrateJavaEntity = findEntityById(modifiedGraph, this.currentVersionId); - assertNotNull(roCrateJavaEntity, "ro-crate-java entity should be added"); - - // Should only have UpdateAction, no CreateAction - assertNull(findEntityByType(modifiedGraph, "CreateAction"), - "Modified crate should not have CreateAction"); - - JsonNode updateAction = findEntityByType(modifiedGraph, "UpdateAction"); - assertNotNull(updateAction, "Should have UpdateAction"); - - // Verify update action properties - assertNotNull(updateAction.get("startTime"), - "UpdateAction should have startTime"); - assertEquals(this.currentVersionId, - updateAction.get("agent").get("@id").asText(), - "UpdateAction should reference ro-crate-java as agent"); - - // Verify ro-crate-java references the action - assertTrue(roCrateJavaEntity.get("Action").isObject(), - "ro-crate-java should have a single reference to an UpdateAction"); - assertEquals(updateAction.get("@id").asText(), - roCrateJavaEntity.get("Action").get("@id").asText(), - "ro-crate-java should reference the UpdateAction"); - } - - @Test - void should_PreserveExistingProvenance_When_ModifyingCrate(@TempDir Path tempDir) throws IOException, InterruptedException { - // First create a crate with normal provenance - RoCrate originalCrate = new RoCrate.RoCrateBuilder().build(); - validateCrate(originalCrate); - - Path outputPath = tempDir.resolve("test-crate"); - Writers.newFolderWriter().save(originalCrate, outputPath.toString()); - Thread.sleep(10); - - // Now read and modify the crate - RoCrate modifiedCrate = Readers.newFolderReader().readCrate(outputPath.toString()); - validateCrate(modifiedCrate); - modifiedCrate.getRootDataEntity().addProperty("description", "Modified crate"); - validateCrate(modifiedCrate); - - // Write the modified crate - Writers.newFolderWriter().save(modifiedCrate, outputPath.toString()); - - // Read and verify the metadata - String metadata = Files.readString(outputPath.resolve("ro-crate-metadata.json")); - HelpFunctions.prettyPrintJsonString(metadata); - - JsonNode root = objectMapper.readTree(metadata); - JsonNode graph = root.get("@graph"); - - // Should have both CreateAction and UpdateAction - JsonNode createAction = findEntityByType(graph, "CreateAction"); - assertNotNull(createAction, "Original CreateAction should be preserved"); - - JsonNode[] updateActions = findEntitiesByType(graph, "UpdateAction"); - assertEquals(1, updateActions.length, "Should have exactly one UpdateAction"); - - // Verify chronological order - String createTime = createAction.get("startTime").asText(); - String updateTime = updateActions[0].get("startTime").asText(); - assertTrue(createTime.compareTo(updateTime) < 0, - "Update should be after creation"); - - // Verify ro-crate-java entity references both actions - JsonNode roCrateJavaEntity = findEntityById(graph, this.currentVersionId); - //noinspection DataFlowIssue - assertTrue(roCrateJavaEntity.get("Action").isArray(), - "ro-crate-java should have an array of actions"); - assertEquals(2, roCrateJavaEntity.get("Action").size(), - "should have both actions"); - } -}