fix(import): prevent placeholder parents from missing in text search#805
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vcnainala wants to merge 5 commits into
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fix(import): prevent placeholder parents from missing in text search#805vcnainala wants to merge 5 commits into
vcnainala wants to merge 5 commits into
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When an entry has stereocenters but no defined stereochemistry, the parent molecule becomes the canonical record but was left flagged as a placeholder. That excluded real compounds from text search (fixes #506). Align ImportEntry and ImportEntryAuto with ImportEntriesAuto, and extend coconut:update-parent-variants-counts to clear is_placeholder on parents that have no variants.
Add unit tests for SearchMolecule text search and UpdateParentVariantsCounts command. Configure Sail-compatible test database via .env.testing and remove hardcoded DB_HOST from phpunit.xml.
Fixes #506
Clear config before migrate so CI env vars take effect, and stop .env.testing from overriding DB_HOST so GitHub Actions can reach Postgres on localhost.
Laravel loads .env.testing when APP_ENV=testing, so the key generated in .env during CI setup was ignored and caused MissingAppKeyException.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## development #805 +/- ##
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+ Coverage 6.13% 7.30% +1.16%
- Complexity 1737 1739 +2
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Files 227 227
Lines 8961 8967 +6
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+ Hits 550 655 +105
+ Misses 8411 8312 -99 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Fixes #506
Summary
is_placeholderwhen import jobs assign a parent molecule as the canonical record without creating a stereo variant, matching the existingImportEntriesAutobehaviourcoconut:update-parent-variants-countsto resetis_placeholderfor parents that have no variants, remediating any already-imported recordsSearchMoleculeandUpdateParentVariantsCounts, plus Sail-compatible test DB configurationProblem
Compounds such as CNP0571280.0 (Mirabilin B) could be reachable on their compound page but absent from text search. This happened when a parent molecule was created for undefined stereochemistry and left with
is_placeholder = trueeven though no variants existed.Changes
ImportEntry/ImportEntryAutois_placeholderwhen stereo is undefined and the parent is the canonical moleculeUpdateParentVariantsCountsis_placeholderfor parents without variants.env.testingfor Sail; remove hardcodedDB_HOSTfromphpunit.xmlTest plan
./vendor/bin/sail artisan test --filter='SearchMoleculeTest|UpdateParentVariantsCountsTest'php artisan coconut:update-parent-variants-countson staging/production to remediate existing mis-flagged parentshttps://coconut.naturalproducts.net/search?q=Mirabilin+Breturns CNP0571280.0 alongside synonym matches