v26 remaining P1s: templates + interval + MCP debug + P0 regression test#44
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lucapinello merged 1 commit intomainfrom Apr 24, 2026
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…egression test Picks up the parts of v26 my PR #43 fixed that didn't land in the parallel 96fc28d commit. 96fc28d landed the track-ID _validate_assay_ids override + INFO→DEBUG demotion (4 files). These 5 files close the remaining items from v26's list. ## P1 #12 — subprocess templates raise bare Exception enformer_source/templates/predict_template.py and borzoi_source/templates/predict_template.py had raise Exception(f"Some assay IDs not found in metadata: {...}") The env-runner wraps subprocess failures in RuntimeError, so the user saw a generic traceback prefix instead of a recognisable exception type. Upgraded to ValueError with a `get_track_info()` pointer and a specific missing-IDs list (vs dumping the whole assay_ids arg). ## P1 #13 — interval.py bare Exception('') CIGAR parser fallback at interval.py:673 raised an empty Exception('') — meaningless if a user ever hit it. Replaced with IntervalException naming the bad symbol + valid set ('=MIDX'). ## P1 #18 — MCP _safe_tool hides traceback The decorator returns {"error", "error_type", "tool"} dicts — MCP clients debugging a failing tool couldn't see which line raised. Opt-in: CHORUS_MCP_DEBUG=1 includes a "traceback" field in the error payload. Default behaviour unchanged. ## P0 #9 regression test tests/test_prediction_methods.py::test_unknown_track_id_gives_actionable_error exercises the EnformerOracle._validate_assay_ids path (96fc28d added this override, but no regression test for it landed). Covers: - unknown ENCFF ID → InvalidAssayError naming list_tracks/search_tracks - bad description → same - None/[] input → no-op (doesn't raise) Stubs enformer_metadata.get_metadata so the test runs in the base chorus env without TF. ## Tests 340 passed / 1 skipped in 9m 17s (+1 regression test from 339). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This was referenced Apr 24, 2026
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Summary
Closes the 4 remaining v26 items (3 P1s + 1 regression test) that didn't land in the parallel
96fc28dcommit. That commit picked up the track-ID_validate_assay_idsoverride + INFO→DEBUG demotion — great. These 5 files are the rest.Answer to "so all good?": not quite — these 4 remaining items are real and worth one more small PR.
P1 #12 — subprocess templates raised bare
ExceptionBoth
predict_template.pyfiles hadraise Exception(f"Some assay IDs not found in metadata: {args['assay_ids']}"). The env-runner wraps subprocess failures inRuntimeError, so users saw a generic traceback instead of a recognisable type. Now raisesValueErrorwith:assay_idsarg)get_track_info()pointer consistent with the direct-load pathP1 #13 —
chorus/core/interval.pybareException('')CIGAR parser fallback at line 673 raised an empty
Exception('')— if a user ever hit it they'd get no information. Replaced withIntervalExceptionnaming the bad CIGAR symbol and the valid set'=MIDX'.P1 #18 — MCP
_safe_toolhides tracebackThe decorator returns
{"error", "error_type", "tool"}dicts on failure. MCP clients debugging a failing tool can't see which line raised. Opt-in viaCHORUS_MCP_DEBUG=1env var now includes a"traceback"field in the error payload. Default behaviour unchanged.P0 regression test
96fc28daddedEnformerOracle._validate_assay_idsbut shipped no regression test. Addedtest_unknown_track_id_gives_actionable_errorthat exercises the override with a stubbed metadata (no TF needed in the basechorusenv). Covers:ENCFF…ID →InvalidAssayErrornaminglist_tracks/search_tracksNone/[]input → no-op, doesn't raiseTest plan
pytest tests/ --ignore=tests/test_smoke_predict.py -q→ 340 passed / 1 skipped (+1 from 339, the new regression test)oracle.predict(..., ['ENCFF999BADID'])via env-runner → error containsget_track_info()+ list of missing IDsgrep "raise Exception('')" chorus/→ 0 matches (was 1)grep "raise Exception(f\"Some assay" chorus/→ 0 matches (was 2)CHORUS_MCP_DEBUG=1includes traceback in MCP error payload; unset omits it🤖 Generated with Claude Code