[P1][Usability/Correctness] FASTAとGFFのseqid不一致を解析前に検出して具体例を表示する - #54
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| if gff_contig not in gff_contigs: | ||
| examples = ", ".join(gff_contigs[:5]) or "(no feature rows)" | ||
| raise ValueError(f"Source contig '{payload['contig']}' (GFF name '{gff_contig}') has no features in '{source['name']}'. GFF seqids include: {examples}. FASTA and GFF sequence names must match.") |
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When the selected FASTA contig legitimately has no GFF feature rows, this exception aborts the job before marker mapping or liftover, even though those evidence classes can still produce a valid result without synteny. The existing zero-gene path already represents this uncertainty, so emit an explicit annotation warning and continue rather than recording the entire job as failed.
AGENTS.md reference: AGENTS.md:L11-L12
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| if line.startswith("#") or not line.strip(): | ||
| continue | ||
| seqid = line.split("\t", 1)[0] | ||
| if seqid not in seen: | ||
| seen.append(seqid) |
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For a valid GFF3 containing a ##FASTA section, the directive is skipped as a comment but every following > header and sequence line is treated as a seqid. This produces false GFF-only mismatch warnings and, because distinct values are tracked with linear list membership, a large embedded genome can make this preflight consume enormous memory and quadratic time; stop at ##FASTA or only accept valid tab-delimited feature rows.
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| gff_contigs = gff_seqids(source["gff"]) | ||
| if gff_contig not in gff_contigs: | ||
| examples = ", ".join(gff_contigs[:5]) or "(no feature rows)" | ||
| raise ValueError(f"Source contig '{payload['contig']}' (GFF name '{gff_contig}') has no features in '{source['name']}'. GFF seqids include: {examples}. FASTA and GFF sequence names must match.") |
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When the UI is Japanese, this exception is persisted by JobManager and rendered verbatim as job.error; the new consistency warning is likewise rendered directly from job.warnings. Since neither diagnostic has a Japanese representation or localization key, Japanese users now receive English-only user-facing messages; return structured/localized diagnostics or add both EN and JA variants.
AGENTS.md reference: AGENTS.md:L108-L110
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# Conflicts: # backend/qtlift/pipeline.py # tests/test_pipeline.py
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Fixes #49
実施内容
un_job(): 解析開始前にsource GFFのseqidを走査し
テスト
uff check\ パス