feat(organisms): taxonomy enrichment, compound table, and tree of life (#452)#814
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vcnainala wants to merge 7 commits into
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feat(organisms): taxonomy enrichment, compound table, and tree of life (#452)#814vcnainala wants to merge 7 commits into
vcnainala wants to merge 7 commits into
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Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## development #814 +/- ##
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- Coverage 6.13% 6.13% -0.01%
- Complexity 1737 1738 +1
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Files 227 227
Lines 8961 8971 +10
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Hits 550 550
- Misses 8411 8421 +10 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Relax unique-name validation in the request-changes organism repeater so users can link organisms that already exist in the database. Reject names already attached to the target molecule instead. Fixes #772
Align Filament v4 Select option keys with stored state for existing synonyms, CAS, geo locations, organisms, and citations. Resolve the target molecule from form state and report records so options remain valid on Livewire submit requests. Fixes #775
Use explicit null checks for molecule synonyms/CAS options and remove unreachable is_string handling for mol_ids array cast.
Build a rank-only taxonomy tree without per-organism nodes, cache via the file store, and load tree data in render() so Livewire does not dehydrate the full payload on every request.
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Summary
Closes #452
coconut:organisms-map-oggstores exact-match classification JSON on organisms (migrations fortaxonomy,taxonomy_fetched_at,iri,rank). Parallel GNF verifier batching for backfill runs.sp./spp.→ genus, hybrid/infraspecific stripping, author citation removal, and NCBI scientific name from stored IRI.--audit-patternsreports remaining gaps.OrganismResourceedit form embedsOrganismTaxonomyPanelviaFilament\Schemas\Components\Livewirewith taxonomy group/rank table columns./tree-of-lifeexplorer, homepage teaser, and Docs nav link for browsing NP distribution by taxonomy.Test plan
php artisan migratephp artisan coconut:organisms-map-ogg --backfill --taxonomy-only --with-molecules-onlyphp artisan coconut:organisms-map-ogg --audit-patterns --with-molecules-only/tree-of-lifeand homepage teaser kingdom barsphp artisan test tests/Unit/OrganismTaxonomyMapperTest.php tests/Unit/OrganismCurationResolverTest.php tests/Unit/NcbiTaxonomyNameResolverTest.php