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Pre-migration fix for SNPRC specimen StorageColumnName mismatches (#935)
- Add `SNPRC_EHRUpgradeCode.fixSpecimenStorageColumnNames`: for each `PropertyDescriptor` in the specimen storage schema, if its `StorageColumnName` doesn't resolve on the provisioned table but `Name` does, update `StorageColumnName` to `Name`. Skips and logs when neither name resolves or both already match. - Bump `snprc_ehr` schema version 26.000 -> 26.001 and register the upgrade code. - Add SQL Server-only upgrade script `snprc_ehr-26.000-26.001.sql` invoking the Java upgrade code (no Postgres script -- runs only on the source side prior to migration). - Add `platform:study` apiJar dependency required by `SNPRC_EHRUpgradeCode` for `SpecimenTablesProvider`. Co-authored-by: Claude Opus 4.7 (1M context) <[email protected]>
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‎snprc_ehr/build.gradle‎

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@@ -3,6 +3,7 @@ import org.labkey.gradle.util.ExternalDependency
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dependencies
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{
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:platform:study", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:ehrModules:ehr", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:snprcEHRModules:snd", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")

‎snprc_ehr/resources/schemas/dbscripts/sqlserver/snprc_ehr-26.000-26.001.sql‎

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EXEC core.executeJavaUpgradeCode 'fixSpecimenStorageColumnNames';
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‎snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRModule.java‎

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import org.labkey.api.data.Container;
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import org.labkey.api.data.DbSchema;
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import org.labkey.api.data.ObjectFactory;
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import org.labkey.api.data.UpgradeCode;
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import org.labkey.api.ehr.EHRService;
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import org.labkey.api.ehr.dataentry.DefaultDataEntryFormFactory;
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import org.labkey.api.ehr.history.DefaultArrivalDataSource;
@@ -119,7 +120,14 @@ public String getName()
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@Override
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public @Nullable Double getSchemaVersion()
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{
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return 26.000;
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return 26.001;
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}
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@Nullable
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@Override
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public UpgradeCode getUpgradeCode()
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{
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return new SNPRC_EHRUpgradeCode();
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}
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@Override

‎snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRUpgradeCode.java‎

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/*
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* Copyright (c) 2026 LabKey Corporation
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.labkey.snprc_ehr;
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import org.apache.logging.log4j.Logger;
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import org.labkey.api.data.ColumnInfo;
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import org.labkey.api.data.DbSchema;
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import org.labkey.api.data.DbSchemaType;
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import org.labkey.api.data.DbScope;
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import org.labkey.api.data.DbScope.Transaction;
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import org.labkey.api.data.SQLFragment;
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import org.labkey.api.data.SchemaTableInfo;
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import org.labkey.api.data.SqlSelector;
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import org.labkey.api.data.Table;
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import org.labkey.api.data.TableInfo;
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import org.labkey.api.data.UpgradeCode;
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import org.labkey.api.exp.OntologyManager;
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import org.labkey.api.module.ModuleContext;
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import org.labkey.api.specimen.model.SpecimenTablesProvider;
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import org.labkey.api.util.PageFlowUtil;
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import org.labkey.api.util.logging.LogHelper;
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import java.util.List;
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public class SNPRC_EHRUpgradeCode implements UpgradeCode
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{
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private static final Logger LOG = LogHelper.getLogger(SNPRC_EHRUpgradeCode.class, "SNPRC_EHR upgrade status");
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/**
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* Called from snprc_ehr-26.000-26.001.sql
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*
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* For every PropertyDescriptor in the specimen storage schema, verify that its StorageColumnName
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* exactly matches (case-sensitively) the physical metadata identifier of a column on the provisioned
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* table. If not, rewrite it to the physical identifier of the column resolved either by the existing
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* (case-insensitive) StorageColumnName lookup or, failing that, by the descriptor's Name. This makes
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* the value still match after migration to a case-sensitive database.
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*/
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@SuppressWarnings("unused")
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public static void fixSpecimenStorageColumnNames(ModuleContext context)
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{
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if (context.isNewInstall())
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return;
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TableInfo tinfoDomainDescriptor = OntologyManager.getTinfoDomainDescriptor();
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TableInfo tinfoPropertyDomain = OntologyManager.getTinfoPropertyDomain();
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TableInfo tinfoPropertyDescriptor = OntologyManager.getTinfoPropertyDescriptor();
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DbScope scope = tinfoPropertyDescriptor.getSchema().getScope();
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DbSchema specimenSchema = DbSchema.get(SpecimenTablesProvider.SCHEMA_NAME, DbSchemaType.Provisioned);
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SQLFragment sql = new SQLFragment("SELECT px.PropertyId, dd.StorageSchemaName, dd.StorageTableName, px.StorageColumnName, px.Name FROM ")
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.append(tinfoDomainDescriptor, "dd")
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.append(" INNER JOIN ")
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.append(tinfoPropertyDomain, "pd")
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.append(" ON dd.DomainId = pd.DomainId INNER JOIN ")
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.append(tinfoPropertyDescriptor, "px")
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.append(" ON pd.PropertyId = px.PropertyId ")
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.append("WHERE dd.StorageSchemaName = ?").add(SpecimenTablesProvider.SCHEMA_NAME)
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.append(" AND dd.StorageTableName IS NOT NULL AND px.StorageColumnName IS NOT NULL");
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List<PropertyRow> properties = new SqlSelector(scope, sql).getArrayList(PropertyRow.class);
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LOG.info("Checking {} PropertyDescriptors in specimen storage schema '{}'", properties.size(), SpecimenTablesProvider.SCHEMA_NAME);
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int updated = 0;
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int skipped = 0;
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int alreadyCorrect = 0;
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try (Transaction tx = scope.ensureTransaction())
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{
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for (PropertyRow row : properties)
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{
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SchemaTableInfo provisioned = specimenSchema.getTable(row.storageTableName());
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if (provisioned == null)
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{
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LOG.warn("Provisioned table '{}.{}' does not exist; skipping property '{}'",
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row.storageSchemaName(), row.storageTableName(), row.name());
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skipped++;
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continue;
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}
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// getColumn() is case-insensitive, so a case-mismatched StorageColumnName still resolves
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// on SQL Server but will break after migration to a case-sensitive DB. Compare to the
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// physical metadata identifier to decide whether a rewrite is needed.
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ColumnInfo byStorage = provisioned.getColumn(row.storageColumnName());
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if (byStorage != null && row.storageColumnName().equals(byStorage.getMetaDataIdentifier().getId()))
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{
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LOG.debug("Property '{}' in '{}.{}': StorageColumnName '{}' already matches physical column case; nothing to update",
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row.name(), row.storageSchemaName(), row.storageTableName(), row.storageColumnName());
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alreadyCorrect++;
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continue;
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}
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ColumnInfo target = byStorage != null ? byStorage : provisioned.getColumn(row.name());
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if (target == null)
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{
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LOG.warn("Property '{}' in '{}.{}': neither StorageColumnName '{}' nor Name '{}' exists in provisioned table; skipping",
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row.name(), row.storageSchemaName(), row.storageTableName(), row.storageColumnName(), row.name());
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skipped++;
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continue;
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}
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String newStorageColumnName = target.getMetaDataIdentifier().getId();
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LOG.info("Updating StorageColumnName from '{}' to '{}' for property '{}' in table '{}.{}'",
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row.storageColumnName(), newStorageColumnName, row.name(), row.storageSchemaName(), row.storageTableName());
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Table.update(null, tinfoPropertyDescriptor, PageFlowUtil.map("StorageColumnName", newStorageColumnName), row.propertyId());
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updated++;
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}
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tx.commit();
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}
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// Drop any cached PropertyDescriptors that may have been populated earlier in startup with the
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// pre-update StorageColumnName.
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OntologyManager.clearCaches();
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LOG.info("Specimen StorageColumnName fix complete: {} updated, {} skipped, {} already correct",
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updated, skipped, alreadyCorrect);
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}
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public record PropertyRow(int propertyId, String storageSchemaName, String storageTableName, String storageColumnName, String name) {}
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}

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