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Ensure FKs and indices in targetedms schema #1187

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Ensure FKs and indices in targetedms schema
ankurjuneja Mar 25, 2026
e15f981
Merge branch 'release26.3-SNAPSHOT' into 26.3_fb_Issue894_ensureFK
ankurjuneja Mar 26, 2026
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13 changes: 13 additions & 0 deletions resources/schemas/dbscripts/postgresql/targetedms-26.003-26.004.sql
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@@ -0,0 +1,13 @@
-- Adding missing foreign keys to core.Containers(EntityId)
ALTER TABLE targetedms.Runs ADD CONSTRAINT FK_Runs_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
ALTER TABLE targetedms.QCAnnotation ADD CONSTRAINT FK_QCAnnotation_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
ALTER TABLE targetedms.GuideSet ADD CONSTRAINT FK_GuideSet_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
ALTER TABLE targetedms.AutoQCPing ADD CONSTRAINT FK_AutoQCPing_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
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@labkey-jeckels labkey-jeckels Mar 26, 2026

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These three could easily be deleted as part of the upgrade in case there are orphaned rows.

The other three would be harder because they have many more FKs pointed at them. Maybe we should do what I helped the MacCoss lab do - reparent any orphaned rows in Runs, PrecursorChromInfo, or SampleFileChromInfo to the /Shared project before doing the delete.

ALTER TABLE targetedms.PrecursorChromInfo ADD CONSTRAINT FK_PrecursorChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);
ALTER TABLE targetedms.SampleFileChromInfo ADD CONSTRAINT FK_SampleFileChromInfo_Container FOREIGN KEY (Container) REFERENCES core.Containers(EntityId);

-- Adding missing indices on Container
CREATE INDEX IX_QCAnnotationType_Container ON targetedms.QCAnnotationType(Container);
CREATE INDEX IX_QCAnnotation_Container ON targetedms.QCAnnotation(Container);
CREATE INDEX IX_GuideSet_Container ON targetedms.GuideSet(Container);
CREATE INDEX IX_QCMetricConfiguration_Container ON targetedms.QCMetricConfiguration(Container);
1 change: 1 addition & 0 deletions src/org/labkey/targetedms/TargetedMSListener.java
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Expand Up @@ -71,5 +71,6 @@ public void containerDeleted(Container c, User user)
new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoMSInstrument() + " WHERE Container = ?", c);
new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoPaymentMethod() + " WHERE Container = ?", c);
new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoRateType() + " WHERE Container = ?", c);
new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoSampleFileChromInfo() + " WHERE Container = ?", c);
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@labkey-jeckels labkey-jeckels Mar 26, 2026

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If this is needed, it means that the call to deleteSampleFileDependent(getTableInfoSampleFileChromInfo()) in TargetedMSManager.purgeDeletedRuns() isn't doing what it should, or there's another codepath that should be doing the same thing.

Were there test failures or other repros that inspired adding it?

}
}
2 changes: 1 addition & 1 deletion src/org/labkey/targetedms/TargetedMSModule.java
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Expand Up @@ -231,7 +231,7 @@ public String getName()
@Override
public Double getSchemaVersion()
{
return 26.003;
return 26.004;
}

@Override
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