Use operation outcome (#27)

## Summary

- Routine Change

### Details

- returns a FHIR operation outcome
- refactor

Author: anthony-nhs

Makefile

@@ -39,7 +39,10 @@ check-licenses-python:
 	scripts/check_python_licenses.sh
 
 check-licenses-java:
-	mvn validate	
+	mvn validate
+
+show-unused-dependencies:
+	mvn dependency:analyze
 
 # clean targets
 clean-packages:
@@ -101,4 +104,4 @@ aws-configure:
 	aws configure sso --region eu-west-2
 
 aws-login:
-	aws sso login --sso-session sso-session
+	aws sso login --sso-session sso-session

SAMtemplates/main_template.yaml

@@ -56,7 +56,7 @@ Resources:
     Properties:
       FunctionName: !Sub "${AWS::StackName}-FHIRValidator"
       CodeUri: ../
-      Handler: software.nhs.FHIRValidator.HandlerStream::handleRequest
+      Handler: software.nhs.fhirvalidator.handler.HandlerStream::handleRequest
       Role: !GetAtt FHIRValidatorResources.Outputs.LambdaRoleArn
       SnapStart:
         ApplyOn: PublishedVersions

pom.xml

@@ -3,7 +3,7 @@
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
-    <groupId>software.nhs.FHIRValidator</groupId>
+    <groupId>software.nhs.fhirvalidator</groupId>
     <artifactId>FHIRValidator</artifactId>
     <packaging>jar</packaging>
     <version>dev</version>
@@ -13,7 +13,7 @@
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <fhir.version>5.5.0</fhir.version>
+        <fhir.version>7.0.0</fhir.version>
         <log4j.version>2.23.0</log4j.version>
         <fasterxml.version>2.16.1</fasterxml.version>
         <sonar.organization>nhsdigital</sonar.organization>
@@ -31,7 +31,12 @@
         </dependencies>
     </dependencyManagement>
     <dependencies>
-
+        <dependency>
+            <groupId>io.github.hakky54</groupId>
+            <artifactId>logcaptor</artifactId>
+            <version>2.9.2</version>
+            <scope>test</scope>
+        </dependency>
         <!--The
         following runtime dependencies are specific to a FHIR version-->
         <!--Enable
@@ -52,6 +57,26 @@
             <artifactId>hapi-fhir-validation</artifactId>
             <version>${fhir.version}</version>
         </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-caching-caffeine</artifactId>
+            <version>${fhir.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-base</artifactId>
+            <version>${fhir.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.utilities</artifactId>
+            <version>6.1.2.2</version>
+        </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>org.hl7.fhir.r4</artifactId>
+            <version>6.1.2.2</version>
+        </dependency>
         <dependency>
             <groupId>com.amazonaws</groupId>
             <artifactId>aws-lambda-java-core</artifactId>
@@ -84,8 +109,8 @@
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-slf4j18-impl</artifactId>
-            <version>2.18.0</version>
+            <artifactId>log4j-slf4j2-impl</artifactId>
+            <version>${log4j.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
@@ -97,12 +122,6 @@
             <artifactId>powertools-logging</artifactId>
             <version>1.18.0</version>
         </dependency>
-        <dependency>
-            <groupId>org.projectlombok</groupId>
-            <artifactId>lombok</artifactId>
-            <version>1.18.30</version>
-            <scope>provided</scope>
-        </dependency>
         <dependency>
             <groupId>org.aspectj</groupId>
             <artifactId>aspectjrt</artifactId>
@@ -129,7 +148,11 @@
             <artifactId>junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
-
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -186,6 +209,27 @@
                     </execution>
                 </executions>
             </plugin>
+
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.11</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <!-- attached to Maven test phase -->
+                    <execution>
+                        <id>report</id>
+                        <phase>test</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
             <!--
               Using the Apache Maven Shade plugin to package the jar
 

src/main/java/software/nhs/FHIRValidator/Utils.java

@@ -1,13 +1,13 @@
-package software.nhs.FHIRValidator;
+package software.nhs.fhirvalidator.configuration;
 
 import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 
-import com.google.common.collect.ImmutableList;
 import com.google.gson.Gson;
-import com.google.gson.JsonSyntaxException;
 
+import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
 import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
 import org.hl7.fhir.common.hapi.validation.support.NpmPackageValidationSupport;
@@ -18,50 +18,57 @@
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.ElementDefinition;
 import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.utilities.npm.NpmPackage;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.ConceptValidationOptions;
 import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
 import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.context.support.ValidationSupportContext;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.util.ClasspathUtil;
 import ca.uhn.fhir.validation.FhirValidator;
-import ca.uhn.fhir.validation.ValidationResult;
+import software.nhs.fhirvalidator.models.SimplifierPackage;
+import software.nhs.fhirvalidator.util.ResourceUtils;
+
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import software.nhs.FHIRValidator.models.SimplifierPackage;
-import software.amazon.lambda.powertools.logging.Logging;
 
 /**
  * This class is a wrapper around the HAPI FhirValidator.
  * The FhirValidator is built using default settings and the available
  * implementation guides are loaded into it.
  */
 
-public class Validator {
-    private final FhirValidator validator;
+public class ValidatorConfiguration {
+    public final FhirValidator validator;
+    public final FhirContext fhirContext;
+    public final List<NpmPackage> npmPackages = new ArrayList<>();
 
-    private final FhirContext ctx;
-    Logger log = LogManager.getLogger(Validator.class);
+    Logger log = LogManager.getLogger(ValidatorConfiguration.class);
 
-    public Validator() {
-        ctx = FhirContext.forR4();
+    public ValidatorConfiguration() {
+        fhirContext = FhirContext.forR4();
 
         // Create a chain that will hold our modules
         ValidationSupportChain supportChain = new ValidationSupportChain(
-                new DefaultProfileValidationSupport(ctx),
-                new CommonCodeSystemsTerminologyService(ctx),
-                terminologyValidationSupport(ctx),
-                new SnapshotGeneratingValidationSupport(ctx));
+                new DefaultProfileValidationSupport(fhirContext),
+                new CommonCodeSystemsTerminologyService(fhirContext),
+                terminologyValidationSupport(fhirContext),
+                new SnapshotGeneratingValidationSupport(fhirContext));
 
-        NpmPackageValidationSupport npmPackageSupport = new NpmPackageValidationSupport(ctx);
         SimplifierPackage[] packages = getPackages();
+        NpmPackageValidationSupport npmPackageSupport = new NpmPackageValidationSupport(fhirContext);
+
         try {
             for (SimplifierPackage individualPackage : packages) {
                 String packagePath = String.format("classpath:package/%s-%s.tgz", individualPackage.packageName,
                         individualPackage.version);
                 npmPackageSupport.loadPackageFromClasspath(packagePath);
+                try (InputStream is = ClasspathUtil.loadResourceAsStream(packagePath)) {
+                    NpmPackage pkg = NpmPackage.fromPackage(is);
+                    npmPackages.add(pkg);
+                }
             }
         } catch (InternalErrorException | IOException ex) {
             log.error(ex.getMessage(), ex);
@@ -71,40 +78,11 @@ public Validator() {
         generateSnapshots(supportChain);
         supportChain.fetchCodeSystem("http://snomed.info/sct");
 
-        // Create a validator using the FhirInstanceValidator module.
-        FhirInstanceValidator validatorModule = new FhirInstanceValidator(supportChain);
-        validator = ctx.newValidator().registerValidatorModule(validatorModule);
-    }
-
-    @Logging
-    public ValidatorResponse validate(String resourceAsJsonText) {
-        try {
-            ValidationResult result = validator.validateWithResult(resourceAsJsonText);
-            return toValidatorResponse(result);
-        } catch (JsonSyntaxException | NullPointerException | IllegalArgumentException | InvalidRequestException e) {
-            log.error(e.toString());
-            return ValidatorResponse.builder()
-                    .isSuccessful(false)
-                    .errorMessages(ImmutableList.of(ValidatorErrorMessage.builder()
-                            .msg("Invalid JSON")
-                            .severity("error")
-                            .build()))
-                    .build();
-        }
-    }
+        CachingValidationSupport validationSupport = new CachingValidationSupport(supportChain);
 
-    private ValidatorResponse toValidatorResponse(ValidationResult result) {
-        return ValidatorResponse.builder()
-                .isSuccessful(result.isSuccessful())
-                .errorMessages(result.getMessages().stream()
-                        .map(singleValidationMessage -> ValidatorErrorMessage.builder()
-                                .severity(singleValidationMessage.getSeverity().getCode())
-                                .msg(singleValidationMessage.getLocationString() + " - "
-                                        + singleValidationMessage.getMessage())
-                                .build())
-
-                        .collect(Collectors.toList()))
-                .build();
+        // Create a validator using the FhirInstanceValidator module.
+        FhirInstanceValidator validatorModule = new FhirInstanceValidator(validationSupport);
+        validator = fhirContext.newValidator().registerValidatorModule(validatorModule);
     }
 
     private void generateSnapshots(IValidationSupport supportChain) {
@@ -121,7 +99,7 @@ private void generateSnapshots(IValidationSupport supportChain) {
                     try {
                         circularReferenceCheck(it, supportChain);
                     } catch (Exception e) {
-                        log.error("Failed to generate snapshot for " + it, e);
+                        log.error(String.format("Failed to generate snapshot for %s", it), e);
                     }
                 });
 
@@ -131,7 +109,7 @@ private void generateSnapshots(IValidationSupport supportChain) {
                     try {
                         supportChain.generateSnapshot(context, it, it.getUrl(), "https://fhir.nhs.uk/R4", it.getName());
                     } catch (Exception e) {
-                        log.error("Failed to generate snapshot for " + it, e);
+                        log.error(String.format("Failed to generate snapshot for %s", it), e);
                     }
                 });
     }
@@ -144,7 +122,7 @@ private boolean shouldGenerateSnapshot(StructureDefinition structureDefinition)
     private StructureDefinition circularReferenceCheck(StructureDefinition structureDefinition,
             IValidationSupport supportChain) {
         if (structureDefinition.hasSnapshot()) {
-            log.error(structureDefinition.getUrl() + " has snapshot!!");
+            log.error(String.format("%s has snapshot!!", structureDefinition.getUrl()));
         }
 
         for (ElementDefinition element : structureDefinition.getDifferential().getElement()) {
@@ -163,7 +141,8 @@ private StructureDefinition circularReferenceCheck(StructureDefinition structure
                     element.getId().contains("Encounter.reasonReference") ||
                     element.getId().contains("Encounter.appointment")) && element.hasType()) {
 
-                log.warn(structureDefinition.getUrl() + " has circular references (" + element.getId() + ")");
+                log.warn(String.format("%s has circular references (%s)", structureDefinition.getUrl(),
+                        element.getId()));
 
                 for (ElementDefinition.TypeRefComponent typeRef : element.getType()) {
                     if (typeRef.hasTargetProfile()) {
@@ -202,7 +181,7 @@ public IValidationSupport.CodeValidationResult validateCodeInValueSet(
                     String theCode,
                     String theDisplay,
                     IBaseResource theValueSet) {
-                String valueSetUrl = CommonCodeSystemsTerminologyService.getValueSetUrl(theValueSet);
+                String valueSetUrl = CommonCodeSystemsTerminologyService.getValueSetUrl(fhirContext, theValueSet);
 
                 if ("https://fhir.nhs.uk/ValueSet/NHSDigital-MedicationRequest-Code".equals(valueSetUrl)
                         || "https://fhir.nhs.uk/ValueSet/NHSDigital-MedicationDispense-Code".equals(valueSetUrl)
@@ -224,8 +203,7 @@ public IValidationSupport.CodeValidationResult validateCodeInValueSet(
     }
 
     private SimplifierPackage[] getPackages() {
-        String manifestContent = Utils.getResourceContent("manifest.json");
-        SimplifierPackage[] packages = new Gson().fromJson(manifestContent, SimplifierPackage[].class);
-        return packages;
+        String manifestContent = ResourceUtils.getResourceContent("manifest.json");
+        return new Gson().fromJson(manifestContent, SimplifierPackage[].class);
     }
 }