fixes issues with data extraction#245
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tomjemmett merged 3 commits intomainfrom May 1, 2026
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tomjemmett
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Apr 27, 2026
- files were being created as inputs-data/inputs-data/dev, stopped the duplication of the container name
- we were not removing previous files, which could cause issues if the files were not overwritten
- files were being created as inputs-data/inputs-data/dev, stopped the duplication of the container name - we were not removing previous files, which could cause issues if the files were not overwritten
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Pull request overview
Fixes issues in the data extraction upload process to prevent incorrect container path duplication and to ensure old extracted files are removed before uploading new ones.
Changes:
- Switch blob uploads to use a container URL directly (via
ContainerClient.from_container_url) to avoidinputs-data/inputs-data/...style duplication. - Add a pre-upload delete of the target
extract_versiondirectory using the ADLS Gen2 (Data Lake) API. - Add
azure-storage-file-datalakeas a dependency (and lock it inuv.lock).
Reviewed changes
Copilot reviewed 2 out of 3 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
src/nhp/data/extract_data.py |
Refactors upload client creation and adds deletion of prior extracted directories before upload. |
pyproject.toml |
Adds azure-storage-file-datalake dependency needed for directory deletion. |
uv.lock |
Locks the new dependency and associated wheel metadata. |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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yiwen-h
approved these changes
May 1, 2026
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yiwen-h
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Thank you! The update-sas-tokens.ps1 script also very useful - have updated our guidance for running the data pipeline accordingly
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