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Simplified file-retrieval support using HTSGET and SDA protocols #21

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@mrtamm mrtamm commented Nov 7, 2024

Overview of changes:

  1. Added support for file-retrieval using protocol: sda://<dataset_id>/path/to/file
    • Bearer token is implicitly re-used from the "create-task" request.
    • The "create-task" request without a Bearer token will fail immediately.
    • It is possible to provide explicit Bearer token at the end of the URL after hash-sign; for example: sda://<dataset_id>/file#token-here
    • Supports downloading both Crypt4gh files (over /s3-encrypted/... path; decrypting *.c4gh files locally) and decrypted files (over /s3/... path)
    • Configuration just specifies the ServiceURL for the SDA to be used.
  2. Simplified support for file-retrieval using HTSGET htsget://{reads|variants}/path/to/file-without-extension
    • Bearer token is implicitly re-used from the "create-task" request.
    • The "create-task" request will NOT fail without a Bearer token or credentials. (HTSGET may support non-authenticated requests.)
    • It is possible to provide explicit username:password or Bearer token at the end of the URL after hash-sign; for example: htsget://.../file#user:pass
    • Configuration just specifies the ServiceURL for the HTSGET to be used.
  3. Refactored type names (simpler) in crypt4gh and htsget.
  4. Updated documentation about HTSGET and SDA protocols.

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mrtamm commented Nov 12, 2024

PR has been updated with a fix for retrieving non-encrypted content from SDA.

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