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Support OBO edit files: catalog-based imports + generic term_id - #8
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Found while integrating this package into uberon (obophenotype/uberon
issue #3778, PR #3779).
- extract()/robot diff/robot convert now take an optional `catalog`
(ODK-style catalog-v001.xml), passed through as --left-catalog/
--right-catalog/--catalog. This is what makes both real fixes work:
1. `robot diff` failed outright against a real uberon-edit.obo
because one of its owl:imports PURLs currently 404s -- ROBOT
resolves every import over the network by default. With the
repo's own catalog (checked into git, mapping each import IRI to
a locally-committed file), resolution is fully offline and immune
to a moved PURL.
2. definition_refs() silently returned nothing for OBO edit files
(it only parses OWL functional-syntax AnnotationAssertion(...)
lines; extract() fed it raw OBO text unconverted). Fixed by
converting the right file to functional syntax first
(robot convert -f ofn, with the obo:/oboInOwl: prefixes
definition_refs() expects), using the same catalog.
The caller (the GitHub Action) is expected to pass its own
catalog-v001.xml; omitting it falls back to ROBOT's normal
(network) import resolution, unchanged from before.
Verified against real cell-ontology PR 3717: output is byte-
identical to pre-change behavior (labels, axiom text, ref sets all
match) when a catalog is supplied, since CL has its own
catalog-v001.xml too. Also verified against uberon-edit.obo's actual
broken import, both unmodified and with a real definition edit.
- agent_instructions.md dropped the separate underscore-form `cell_id`
concept; everything downstream of the routing payload (including
output paths, `runs/{term_id}/...`) now uses the single CURIE-form
`term_id` already used elsewhere in the same payload. A colon is a
valid POSIX filename character, so this needs no extra encoding.
This changes verdicts.json's schema (drops the `cell_id` field).
Consumers reading it need updating to match -- done for uberon's own
clara-review.yml in PR #3779; cell-ontology's clara-review.yml still
reads `cell_id` and would need the same change before bumping to
this commit.
No changes to parse.py; existing 39 tests pass unmodified.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ubyndr
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Sep 29, 2026
Cellular-Semantics/clara_workflow#8 drops the separate underscore-form cell_id field from verdicts.json in favor of the single CURIE-form term_id already used elsewhere in the routing payload. Updates the summary-comment step here to match, so it doesn't KeyError once the CLARA_WORKFLOW_REF pin is bumped to that commit (not done yet). Signed-off-by: @ai4c-agent Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ubyndr
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to obophenotype/uberon
that referenced
this pull request
Sep 30, 2026
Cellular-Semantics/clara_workflow#8 merged (232e9b4): adds catalog support to the stage-1 extractor and drops the cell_id field (already matched in the previous commit here). - CLARA_WORKFLOW_REF bumped to the merge commit. - Added --catalog src/ontology/catalog-v001.xml to the stage-1 extractor invocation. This is the part that actually matters: without it, the extractor falls back to ROBOT's default network import resolution and hits the same 404 (one of uberon's import PURLs is currently broken) that motivated the catalog fix in the first place. The catalog lets ROBOT resolve every owl:imports from the files it already maps to locally-committed content, with no network call. - Updated the header comment, which described the pre-fix limitations. Signed-off-by: @ai4c-agent Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This was referenced Sep 30, 2026
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Found while integrating this package into uberon (obophenotype/uberon#3778, obophenotype/uberon#3779).
robot diff/robot convertnow accept an optional ODK-stylecatalog-v001.xml(passed by the caller), so imports resolve from locally-committed files instead of the network. Fixes two real problems:robot diff404ing on one of uberon's import PURLs, anddefinition_refs()returning nothing for OBO edit files (it needs functional-syntax input, so the right file is now converted first, using the same catalog). Verified byte-identical output on a real CL PR when a catalog is supplied, and correct behavior against uberon's actual broken import.agent_instructions.md: dropped the separatecell_idconcept; everything now uses the single CURIE-formterm_idalready used elsewhere, including output paths (runs/{term_id}/...). Breaking for consumers:verdicts.jsonno longer has acell_idfield. Already updated in uberon's own workflow (Add CLARA review workflow (issue #3778) obophenotype/uberon#3779); cell-ontology'sclara-review.ymlwould need the same one-line change before bumping to this commit.No changes to
parse.py; existing 39 tests pass unmodified.Co-Authored-By: Claude Sonnet 5 noreply@anthropic.com