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Fix ENA cart addition when sample metadata is missing - #299

Merged
pansapiens merged 1 commit into
MonashBioinformaticsPlatform:masterfrom
Cateline:fix-ena-missing-sample
Oct 6, 2026
Merged

pansapiens merged 1 commit into
MonashBioinformaticsPlatform:masterfrom
Cateline:fix-ena-missing-sample

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@Cateline

@Cateline Cateline commented Oct 5, 2026 •

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This PR fixes an issue where ENA FASTQ files could not be added to the cart when the associated sample metadata was unavailable on ENA.

What changed?
The ENA species lookup is now handled separately from adding samples to the cart. If the sample metadata lookup fails, the error is caught and the FASTQ samples can still be added to the cart. The species lookup is still used when the sample metadata is available, so automatic reference genome selection continues to work normally.

To test
I ran npm run build:dev successfully.
I verified the working tree and diff before committing.

@pansapiens
pansapiens merged commit edac88e into MonashBioinformaticsPlatform:master Oct 6, 2026
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@pansapiens

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Thanks - it would be useful to know which ENA or SRA accession can reproduce the original issue - it would be worth inspecting in case it can be mocked as a unit test.

@Cateline

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Thank you for merging my request and for the suggestion. I checked the ENA API and found a potential reproducer:

SRR26449549 returns successfully, and the ENA run report links it to sample SAMN37904062 (secondary sample accession SRS19213103). But, a direct request to the ENA XML endpoint for SAMN37904062 returns HTTP 404. The sample accession SAMN44459348 from the original traceback also returned HTTP 404 when I checked it.

I also performed a check on the frontend set-up. It is running Vue 2.7.16 but the npm test command is just a placeholder, and there is no Jest or Vue Test Utils setup yet. I hope I've understood your suggestion correctly, but please let me know if I've missed anything.

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2 participants