Pre-migration fix for SNPRC specimen StorageColumnName mismatches#935
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labkey-martyp wants to merge 6 commits into
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Pre-migration fix for SNPRC specimen StorageColumnName mismatches#935labkey-martyp wants to merge 6 commits into
labkey-martyp wants to merge 6 commits into
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Bumps schema version to 26.001 and registers SNPRC_EHRUpgradeCode, which verifies each PropertyDescriptor in the specimen storage schema points at an actual provisioned column and resets StorageColumnName to Name when it doesn't. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Completes the 26.000 -> 26.001 schema bump by hooking the upgrade SQL to the Java method added in 4c576ca. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Needed by SNPRC_EHRUpgradeCode for SpecimenTablesProvider. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Are you sure this issue affects SNPRC only? They're the only distribution that will receive this fix. |
The existing resolution check used TableInfo.getColumn() which is case-insensitive (CaseInsensitiveHashMap), so a StorageColumnName that differed from the physical column only in case was treated as already correct on the SQL Server source. After migration to a case-sensitive destination database those rows would still fail, defeating the purpose of the pre-migration fix. Resolve the column by StorageColumnName first; consider it correct only when row.storageColumnName().equals(byStorage.getMetaDataIdentifier().getId()). Otherwise rewrite to the physical metadata identifier of either the StorageColumnName-resolved column or, failing that, the column resolved by Name. This catches both entirely-broken StorageColumnName values and case-only mismatches. Also call OntologyManager.clearCaches() after committing the updates so any PropertyDescriptors populated into PROP_DESCRIPTOR_CACHE earlier in startup don't retain pre-update StorageColumnName values. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
labkey-bpatel
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May 20, 2026
…fb_snprc_pg_data_migration_fixes
labkey-martyp
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May 21, 2026
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We can follow up if we need to apply this fix more broadly. Running it multiple times is fine.
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Rationale
The SNPRC SQL Server source has
PropertyDescriptorrows in the specimenstorage schema whose
StorageColumnNamedoes not match any column on theprovisioned table. Left as-is, this prevents the SQL Server -> Postgres
migration from successfully reading/writing the specimen schema. The fix
runs as a SQL Server-only upgrade (26.000 -> 26.001) so the source is
clean before the migration is performed.
Related Pull Requests
Changes
SNPRC_EHRUpgradeCode.fixSpecimenStorageColumnNames: for eachPropertyDescriptorin the specimen storage schema, if itsStorageColumnNamedoesn't resolve on the provisioned table butNamedoes, updateStorageColumnNametoName. Skips and logs when neither name resolves or both already match.snprc_ehrschema version 26.000 -> 26.001 and register the upgrade code.snprc_ehr-26.000-26.001.sqlinvoking the Java upgrade code (no Postgres script -- runs only on the source side prior to migration).platform:studyapiJar dependency required bySNPRC_EHRUpgradeCodeforSpecimenTablesProvider.