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Add retry for reads prefetch in import-sra #1320

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merged 1 commit into from
Mar 26, 2024

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marcellevstek
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@marcellevstek marcellevstek commented Mar 11, 2024

REID-2233

  • Update CHANGELOG.rst for each commit separately:
    • Pay attention to write entries under the "Unreleased" section.
    • Mark all breaking changes as "BACKWARD INCOMPATIBLE:" and put them
      before non-breaking changes.
    • If a commit modifies a feature listed under "Unreleased" section,
      it might be sufficient to modify the existing CHANGELOG entry from previous
      commit(s).
  • Bump the process version:
    • MAJOR version (first number): Backward incompatible changes (changes
      that break the api/interface). Examples: renaming the input/output, adding
      mandatory input, removing input/output...
    • MINOR version (middle number): add functionality or changes in a
      backwards-compatible manner. Examples: add output field, add non-mandatory
      input parameter, use a different tool that produces same results...
    • PATCH version (last number): changes/bug fixes that do not affect
      the api/interface. Examples: typo fix, change/add warning messages...
  • All inputs are used in process.
  • All output fields have a value assigned to them.

@jkokosar jkokosar requested a review from AnzeLovse March 11, 2024 13:34
resolwe_bio/processes/import_data/sra_file.py Outdated Show resolved Hide resolved
resolwe_bio/processes/import_data/sra_file.py Outdated Show resolved Hide resolved
def prefetch_reads(self, max_size_prefetch, srr, retry_counts=3):
"""Prefetch reads from SRA. Retry if prefetch fails."""
for _ in range(retry_counts):
return_code, _, _ = Cmd["prefetch"][
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When this is deployed make sure to validate that the prefetch messages and errors are getting printed to stdout. The tests do not cover that because it takes too long to fetch data.

@jkokosar jkokosar merged commit 9e5ee37 into genialis:master Mar 26, 2024
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4 participants