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feat(organisms): taxonomy enrichment, compound table, and tree of life (#452) - #814
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## development #814 +/- ##
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+ Coverage 6.14% 21.72% +15.57%
- Complexity 1736 2250 +514
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Files 227 253 +26
Lines 8945 10771 +1826
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+ Hits 550 2340 +1790
- Misses 8395 8431 +36 ☔ 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.
vcnainala
changed the title
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.
Resolve organism-related conflicts by keeping the GNF taxonomy pipeline and compound UI from this branch while adopting development organism form, view page, and report-change validation. Fix PHPStan in taxonomy services.
The needingTaxonomyEnrichment scope uses null-safe SQL only; fuzzy organisms with iri, taxonomy, and fetched_at should be excluded from the scope and filtered in PHP via hasExactTaxonomyEnrichment.
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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