[bot] Re-baseline test fixtures after GO pipeline file migration - #171
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The GO pipeline migrated to a new annotation file layout and naming (go-technical-announcements#20). The new MOD-centric GAFs carry smaller gene coverage and lower per-gene annotation counts than the legacy files, and GOlr is a faithful load of the new files -- gene counts match to the digit. The failing tests were baselined on legacy-pipeline data. - Repoint the ZFIN:ZDB-GENE-980526-388 fixtures to ZFIN:ZDB-GENE-990415-72. The old ID is bmp2a, which has no rows in the new DANRE-mod.gaf and so 404s on the bioentity, function and slimmer endpoints. The new ID is the actual fgf8a, which resolves cleanly -- and it corrects a long-standing misnomer, since test_slimmer_endpoint_fgf8a had been querying bmp2a. - Drop the dead ID from test_ribbon.py's gene_ids, which already listed ZFIN:ZDB-GENE-990415-72. - Re-baseline the test_fly_ribbon molecular-function threshold from 4 to 2. DROME-mod.gaf carries 2 MF annotations for FBgn0051155 where the legacy fb.gaf carried 5; GOlr matches the new file exactly. The BP and CC thresholds still hold and are unchanged. Commented in place with the reason so it does not read as arbitrary relaxation. No production code changes. tests/unit: 141 passed, 1 skipped (was 6 failed, 135 passed). Addresses #170. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
ZFIN:ZDB-GENE-050417-357 (twist1b) has no rows in the new DANRE-mod.gaf, so the bioentity function scenario 404s. Repoint to ZFIN:ZDB-GENE-010302-1 (foxc1a), which is present in the new data and carries the same GO:0030500 "regulation of bone mineralization" annotation the scenario asserts on. Only the gene ID changes; the GO term and label assertions are untouched, so the scenario tests exactly what it did before. I had noted this ID in #170 as "not asserted on today" -- that was wrong, it is asserted in the integration suite, which I had not run. tests/integration: 7 passed. tests/unit: 141 passed, 1 skipped. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Re-aligning tests with current reality. |
This was referenced Jul 28, 2026
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[bot] Opened by a Claude Code agent on behalf of @kltm.
What
Re-baselines test fixtures against the new GO annotation files.
tests/unitgoes from 6 failed / 135 passed to 141 passed, 1 skipped. No production code changes —tests/only.Why
The GO pipeline migrated to a new annotation file layout and naming (go-technical-announcements#20). The new MOD-centric GAFs carry smaller gene coverage and lower per-gene annotation counts than the legacy files they replace, and GOlr is a faithful load of the new files:
zfin.gaf.gz— 19,738gaf/DANRE-mod.gaf.gz— 15,163fb.gaf.gz— 13,633gaf/DROME-mod.gaf.gz— 12,392FBgn0051155aspectsCounts match to the digit. The failing tests were baselined on legacy-pipeline data, so this is a re-baseline to current upstream truth — not a defect in go-fastapi or GOlr, and not assertions being relaxed to get green. Background and the full investigation are in #170.
Changes
Repoint
ZFIN:ZDB-GENE-980526-388→ZFIN:ZDB-GENE-990415-72(9 files). The old ID isbmp2a, which has zero rows inDANRE-mod.gafand therefore 404s on the bioentity, function and slimmer endpoints. It is still a live, valid, unmerged ZFIN gene — it is simply not in the new data. The new ID is the actualfgf8a, verified to resolve on all three endpoints with all three slim groups populated.This also fixes a long-standing misnomer:
test_slimmer_endpoint_fgf8ahad been queryingbmp2a, notfgf8a. It now tests what its name claims.Drop the dead ID from
test_ribbon.py'sgene_idsrather than repointing, since that list already containedZFIN:ZDB-GENE-990415-72.Re-baseline
test_fly_ribbon's molecular-function threshold, 4 → 2. This is the one assertion that is genuinely weaker, so it carries an in-place comment explaining thatDROME-mod.gafhas 2 MF annotations forFBgn0051155where the legacy file had 5, and that GOlr matches the new file exactly. The BP (>= 5) and CC (>= 5) thresholds still hold and are untouched, as are the label and taxon assertions.Testing
tests/unit— 141 passed, 1 skipped against live services, versus 6 failed / 135 passed onmain.codespellclean.ruff check tests/is unchanged frommain(andtox -e lint-fixonly coversapp/).Scope note
Two things deliberately left alone:
ZFIN:ZDB-GENE-050417-357, another fixture in the suite, is also absent from the new data. Nothing asserts on it today so it is not failing; noted in [bot] QC failures after GO pipeline file migration: new MOD-centric GAFs have reduced coverage #170 rather than pre-emptively changed here.bmp2adropped out of the MOD-centric file is a pipeline/QC question, not an API one. It does appear ingaf/DANRE-uniprot.gaf.gzunder its symbol but keyed by UniProt accession, which looks like a MOD-ID mapping gap rather than a deliberate exclusion. Recorded in [bot] QC failures after GO pipeline file migration: new MOD-centric GAFs have reduced coverage #170 for whoever owns that; not chased here.— Posted by Claude Code agent on behalf of @kltm.
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