ont-artic: repoint consistently-broken NCBI SRA read URL at ENA + test schema regularization#1298
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mvdbeek merged 1 commit intoJul 15, 2026
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…gularization The be-md.ncbi.nlm.nih.gov backend host returns HTTP 200 with an HTML error page instead of the FASTQ, so the upload job has errored in every run. Repoint at ENA and re-derive the SHA-1 (verified against ENA's published md5). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
mvdbeek
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Jul 15, 2026
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Attention: deployment skipped! https://github.com/galaxyproject/iwc/actions/runs/29392483056 |
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Thanks so much @jmchilton for fixing this and all your other cleanup work! |
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Unblocks
ont-artic-variationand carries its share of the test-schema regularization split out of #1286.The read URL is consistently broken, not flaky
The test fetched its ONT reads from:
be-md.ncbi.nlm.nih.govis an NCBI backend host, not a public data endpoint. It no longer serves this accession, and it fails in the nastiest possible way: it returns HTTP 200 with an HTML page titled "NCBI - WWW Error Diagnostic" (3713 bytes) instead of a FASTQ.Because the status code is 200, Galaxy downloads it happily, then the content fails to decompress as
fastqsanger.gzand the declared SHA-1 does not match — so the upload job errors and the workflow is never invoked:This has failed in every run I can find — identical accession, identical error:
It is not a transient SRA outage and no amount of retrying will fix it. It reads like a network flake, which is probably why it has survived this long.
The fix
Repointed at ENA, which serves the same accession from a stable, public, versioned path:
The declared SHA-1 is re-derived from the actual file, since the old hash described whatever the dead endpoint used to serve. The download was verified before hashing:
c68b7c19b4ee19d668a927e55c9e4d78— matches ENA's independently published md5 for this run exactly@SRR12447380.1 1/1)cd93c6dcbcf46b795d7cc2f41a81c9d87f8601d6Test schema
Also adds the
class: Collection/collection_typeannotations for this workflow — same mechanical change as #1290/#1291/#1292, held back from those because this workflow could not run at all.Expectations
planemo workflow_lint --iwcpasses locally. The workflow test has never successfully executed on CI — it has been dying at upload — so this run is the first real signal. If something downstream fails (e.g. the variant-call comparison, which allowslines_diff: 6), that is a pre-existing problem this PR merely reveals, and can be handled separately.