Scope patch psql scripts to a single organism via :ORG_ABBREV#105
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Scope patch psql scripts to a single organism via :ORG_ABBREV#105
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- Fix instantiateSql call to pass organismAbbrev in correct positional slot - Rewrite pseudogenicCDS.psql to filter by organism (GeneFeature->NaSequence->Organism join), prefix all created tables with apidb schema, add DROP TABLE cleanup, and update Oracle implicit-schema references - Add organism scoping to uniprotProductNames.psql Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Prevents table name collisions when the script runs concurrently for multiple organisms. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ev instead of o.public_abbrev
sufenhu
approved these changes
Apr 29, 2026
…leting translated aa sequences Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
instantiateSqlcall inPatchGenomeAndAnnotation.pm—$organismAbbrevwas landing in the$tableNameslot (position 2); now correctly passed as position 4 withundefplaceholderspseudogenicCDS.psql: organism-scoped viaGeneFeature → NaSequence → Organismjoin using:ORG_ABBREVmacro, all created tables prefixed toapidbschema, DROP TABLE cleanup block added, Oracle implicit-schema references removeduniprotProductNames.psqlusing same join patternTest Plan
apidb.pgp_*andapidb.new_pseudo*tables are created and dropped cleanlyuniprotProductNames.psqlonly nullsproductfor the target organism🤖 Generated with Claude Code