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Make pondie's schema checks pass on main - #42
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- Regenerate the extraction YAMLs with pondie.schema.generate: formatting only (quote style, wrapping, key order), plus the header now naming the generator. - extraction-to-storage map: add derivations for CategoryDistribution.category_normalized, CoordinateSet.id/.table/.text_excerpt and Group.age_unit_normalized, the five deterministic fields it did not say how to fill. - storage-parameter-priorities: add the 15 storage fields with no entry. pondie's generate --check, map, priorities, linkml and field_provenance checks pass. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The docs still named gen_extraction_schema.py and the check_*.py scripts, which live in pondie as pondie.schema.generate and pondie.schema.checks.*. Drop the link to test_map_coverage.py, which exists in neither repository. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
review/validate_record.py is pondie.extraction.record.validate (the Validator and its CLI) with the cross-class rules in pondie/extraction/record/rules.py. The tutorial's review/examples/ directory does not exist; point at the example record in this repository. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
jdkent
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October 17, 2026 18:07
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pondie's schema checks (run at pondie #21's head, with PONDIE_SCHEMA_DIR pointed at this branch) flagged three older gaps in main. This closes them.
Extraction YAMLs. Regenerated with
python -m pondie.schema.generate. Quote style, wrapping and key order only, plus the extraction header now saying it is generated bypondie.schema.generaterather thangen_extraction_schema.py.tools/generate_models.py --checkstill passes, so the models and JSON Schemas are unaffected.extraction-to-storage map. Five deterministic fields had no entry. All are
derive(notcopy: the copy contract in test_licensing is the two Study bibliographic fields only):CategoryDistribution.category_normalized: fromcategory, by pondie's sex and handedness normalizers; unset where none runs.Group.age_unit_normalized: fromage_unit, bypondie.normalization.age_unit.CoordinateSet.id: the parse analysis'sParsedAnalysis.key.CoordinateSet.table: the Table whose id isParsedAnalysis.table_id; unset for text and figure sets.CoordinateSet.text_excerpt: the paper text overParsedAnalysis.text_spans; unset for table sets.Priorities. 15 storage fields had no entry. Deterministic ones are
n/a, as for the existing derived fields:Group.age_unit_normalized,Group.other_characteristics,CategoryDistribution.category_normalized,Analysis.mirror_of. Model-extracted ones, 0 = review first:Analysis.outcome(null effects are excluded from pooling, same weight asStudy.result_reporting),Analysis.source_table_analysis(the exact join to the coordinates),Group.sample_source(overlap decides whether a sample is counted twice)Acquisition.brain_coverage,Condition.condition_kind,Condition.stimulus_content(asTask.stimulus_content),Effect.kind(redundant withcells, which is 0),Group.sample_source_reference,Group.sample_overlap_count,InferenceSettings.correction_regions(itscorrection_scopeis 0),Task.referencesOpen question: the priorities for
Group.sample_source*,Analysis.outcomeandEffect.kindare my judgement from how the descriptions weigh them; say if a reviewer would triage them differently.Checks (pondie #21 head 3da9c43, fresh venv):
generate --checkup to date; map: identity, derivations (35), vocabularies, conditional_fields ok; priorities: 365 fields match; linkml andfield_provenancepass. study_schema suite: 210 passed, 1 skipped; each check failed before the change (5 map problems, 15 missing priorities, 10 files out of date).🤖 Generated with Claude Code