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@csc-jm csc-jm released this 01 Apr 11:20
· 50 commits to main since this release
2025.4.0
55e9b30

Devs

  • Added: Added mock PID service and PID tests (#839)
  • Added: minimal and full publication test cases for each workflow
  • Added: Use CSC PID service for DOI in FEGA and generic workflows (#827)
  • Added: Implemented support for Bigpicture annotation and observer metadata schemas
  • Added: Included new Bigpicture related schemas
  • Added: Add /ingest endpoint for starting data ingestion
  • Added: Mocked Admin API service #843
  • Added: Instructions on how to use the SD Submit API for BigPicture programmatic dataset submissions #815
  • Added: Defined a discovery service for each workflow 512
  • Added: Total size of files is included in Metax metadata #507
  • Added: Tests for taxonomy search #826
  • Added: Created an endpoint for getting taxonomy names and id based on NCBI database dump files #281
  • Added: Endpoint for flagging file as deleted #824
  • Added: BP metadata gets accession attribute added to the XML content as well before it's stored #818
  • Added: Endpoint to add and remove a linked folder path to a submission #825
  • Added: new format for error responses of /validate endpoint #641
  • Added: Validate files against file schema #823
  • Added: List of Funding references from crossref API and enum values for Funder Names in Submission schema #817
  • Added: Added a POST endpoint for receiving file information #814
  • Added: Added additional 'announce' endpoint for BP workflow and to openapi document #813
  • Added: Added new endpoint /users/{userId}/key for generating a signing key #777
  • Removed: Some XSD files which are perceivably not being utilized at the moment
  • Removed: Previously implemented logic that automatically converted ISO-8601 duration string in incoming metadata to a numeric value
  • Removed: Some schemas that are unnecessary for Generic use case workflow #841
  • Removed: RabbitMQ message broker functionality
  • Fixed: Fixed faulty Datacite unit tests (#859)
  • Fixed: Addressed utcnow deprecation warnings
  • Fixed: Fix pyspelling not ignoring urls (#857)
  • Fixed: Update broken and permanent redirect links in documentation (#856)
  • Fixed: Fixed taxonomy script file permissions and ´docker casing warnings
  • Fixed: Automated changelog generation with CI jobs and github actions recognizes git LFS files
  • Fixed: Add missing schema check that disallowed multiple metadata objects
  • Fixed: Fixed newly posted versions of deleted files still showing up as deleted #828
  • Fixed: Fixed bugs in file version creation #823
  • Changed: Altered and removed some of the Github actions workflows that were either not doing the correct thing or not needed anymore
  • Changed: Updated instructions in the README and the CONTRIBUTING files
  • Changed: Updated OpenAPI specifications
  • Changed: all required schemas are needed before publishing a submission in unit and integration tests
  • Changed: Updated some EGA related XML schemas to be up-to-date
  • Changed: Updated XML to JSON conversion logic to accommodate new metadata schema versions
  • Changed: REMS object is refined and validated when it is added to a submission #532 #649
  • Changed: GET files request returns only latest file versions #840
  • Changed: Removed large taxonomy related names.json file from the repository commit history and brought back as git LFS pointer file
  • Changed: Modify SDSX workflow to be the same as FEGA workflow
  • Changed: Refactored POST files endpoint to address several issues #828
  • Changed: BigPicture workflow no longer requires a study
  • Changed: XML objects are parsed from multipart XML structure into single objects before storing so the content matches with its JSON counterpart #818
  • Changed: Modified workflow for Generic use case #821
  • Changed: Updated middleware to accept user signed tokens #777
  • Changed: Switch to idpyoidc library instead of oidc-rp
  • Changed: Updated dependencies

Users

  • Added: Process information from XML file for bprems schema and add it to the rems key in a BP submission
  • Changed: Submission can no longer have the same name inside the project
  • Changed: Previous functionality behind POST and PUT request for adding/modifying submission files is unified and the endpoint is retitled to PATCH /v1/submissions/{submissionId}/files
  • Changed: Bigpicture related metadata validation process now follows the Bigpicture metadata version 2.0.0
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