v26 tail cleanup: CLI preflight + ChorusError hierarchy + MCP guard#46
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lucapinello merged 1 commit intomainfrom Apr 24, 2026
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v26 tail cleanup: CLI preflight + ChorusError hierarchy + MCP guard#46lucapinello merged 1 commit intomainfrom
lucapinello merged 1 commit intomainfrom
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…guard Closes the last v26 backlog items. P1 #1 / #2 (cli/main.py): `chorus setup --oracle <bad>`, `chorus health --oracle <bad>`, `chorus validate --oracle <bad>` now reject unknown names up front with the valid list, instead of dropping into "Environment file not found" or "Environment does not exist" with no recovery hint. Exit codes were already non-zero; this makes the message actionable. P2 #19 (core/exceptions.py, mcp/server.py): `_parse_region` and `_parse_position` raise `InvalidRegionError` (ChorusError subclass) instead of bare `ValueError`. `InvalidSequenceError`, `InvalidAssayError`, and `InvalidRegionError` now inherit from both `ChorusError` and `ValueError` so legacy `except ValueError` handlers still catch them. P2 #20 (mcp/server.py): `list_tracks(oracle_name)` preflight-validates the oracle name against `ORACLE_SPECS` and logs + returns an explicit error dict naming the valid oracles, rather than dropping through to the fall-through "Unknown oracle" branch without context. Tests: 340 passed, 1 skipped on fast suite (6 tests that expected `ValueError` from `_parse_region` pass through the dual-base class). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Closes the last v26 backlog items so v26 is fully landed on main.
cli/main.py):chorus setup --oracle <bad>,chorus health --oracle <bad>, andchorus validate --oracle <bad>now reject unknown names up front with the valid list. Exit codes were already non-zero; this makes the message actionable. (chorus genome download <bad>already did this.)core/exceptions.py,mcp/server.py):_parse_region/_parse_positionraiseInvalidRegionError(aChorusErrorsubclass) instead of bareValueError.InvalidSequenceError,InvalidAssayError,InvalidRegionErrornow multiply inherit fromChorusError+ValueErrorso legacyexcept ValueErrorhandlers still catch them.mcp/server.py):list_tracks(oracle_name)preflight-validates the oracle name againstORACLE_SPECSand logs + returns an explicit error dict naming the valid oracles, rather than falling through.Scope: 3 files, +79/−18.
Test plan
pytest tests/ --ignore=tests/test_smoke_predict.py -q→ 340 passed, 1 skippedchorus setup --oracle fakeoracle→ exit 1, "Valid oracles: alphagenome, borzoi, chrombpnet, enformer, legnet, sei"chorus health --oracle fakeoracle→ exit 1, same valid-list messageRemaining v26
After this: only P2 #5 (inconsistent error style sweep) remains — deferred because it's a diffuse stylistic cleanup, not a correctness issue.
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