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Issue 53446: misconfigured plate assay design, plate validation query optimization #6839

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Merged
merged 2 commits into from
Jul 14, 2025
+33 −22
Merged

Issue 53446: misconfigured plate assay design, plate validation query optimization #6839

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8803af8
Query optimization for plate set unique samples
labkey-nicka Jul 11, 2025
8b6d408
Issue 53446: A misconfigured assay design could be missing required f…
labkey-nicka Jul 11, 2025
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55 changes: 33 additions & 22 deletions assay/src/org/labkey/assay/plate/PlateManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -609,29 +609,39 @@ private int getRunCountUsingPlateInResults(@NotNull Container c, @NotNull User u

// get the runIds for each protocol, query against its assay results table
List<SQLFragment> fragments = new ArrayList<>();
Set<FieldKey> requiredFields = Set.of(FieldKey.fromParts("DataId"), FieldKey.fromParts("Plate"));

protocolLoop:
for (ExpProtocol protocol : protocols)
{
AssayProtocolSchema assayProtocolSchema = provider.createProtocolSchema(user, protocol.getContainer(), protocol, null);
TableInfo assayDataTable = assayProtocolSchema.createDataTable(ContainerFilter.getUnsafeEverythingFilter(), false);
if (assayDataTable != null)
{
ColumnInfo dataIdCol = assayDataTable.getColumn("DataId");
if (dataIdCol != null)
// Issue 53446: A misconfigured assay design could be missing required fields.
// This is not expected. Don't let that stop the run counting but do log an error with more context.
for (FieldKey requiredFieldKey : requiredFields)
{
SQLFragment subSelectSql = new SQLFragment("SELECT DISTINCT AD.DataId FROM ")
.append(assayDataTable.getFromSQL("AD", Set.of(FieldKey.fromParts("DataId"), FieldKey.fromParts("Plate"))))
.append(" WHERE AD.Plate = ?")
.add(plate.getRowId());

SQLFragment sql = new SQLFragment("SELECT COUNT(DISTINCT D.RunId) AS RunCount FROM\n")
.append(ExperimentService.get().getTinfoData(), "D")
.append(" INNER JOIN ")
.append(ExperimentService.get().getTinfoExperimentRun(), "R")
.append(" ON D.RunId = R.RowId\n")
.append(" WHERE R.ReplacedByRunId IS NULL AND D.RowId IN (").append(subSelectSql).append(")\n");

fragments.add(sql);
if (assayDataTable.getColumn(requiredFieldKey) == null)
{
LOG.error("Required field \"{}\" not found in plate-based assay results domain for protocol \"{}\" in {}.", requiredFieldKey.getName(), protocol.getName(), protocol.getContainer().getPath());
continue protocolLoop;
}
}

SQLFragment subSelectSql = new SQLFragment("SELECT DISTINCT AD.DataId FROM ")
.append(assayDataTable.getFromSQL("AD", requiredFields))
.append(" WHERE AD.Plate = ?")
.add(plate.getRowId());

SQLFragment sql = new SQLFragment("SELECT COUNT(DISTINCT D.RunId) AS RunCount FROM\n")
.append(ExperimentService.get().getTinfoData(), "D")
.append(" INNER JOIN ")
.append(ExperimentService.get().getTinfoExperimentRun(), "R")
.append(" ON D.RunId = R.RowId\n")
.append(" WHERE R.ReplacedByRunId IS NULL AND D.RowId IN (").append(subSelectSql).append(")\n");

fragments.add(sql);
}
}

Expand Down Expand Up @@ -3387,17 +3397,18 @@ public void validatePrimaryPlateSetUniqueSamples(Set<Integer> wellRowIds, BatchV
TableInfo wellTable = dbSchema.getTableInfoWell();

// Determines the set of primary plate sets that are being touched from the collection of well rowIds
SQLFragment primaryPlateSetsFromWellRowIdsSQL = new SQLFragment("SELECT PS.RowId FROM ").append(wellTable, "W")
// From the set of primary plate sets determine if any sample exists in more than one well within the entire plate set
SQLFragment nonUniqueSamplesPerPrimaryPlateSetSQL = new SQLFragment("WITH PlateSetFilter AS (")
.append("SELECT DISTINCT PS.RowId FROM ").append(wellTable, "W")
.append(" INNER JOIN ").append(plateTable, "P").append(" ON P.RowId = W.PlateId")
.append(" INNER JOIN ").append(plateSetTable, "PS").append(" ON PS.RowId = P.PlateSet")
.append(" WHERE PS.Type = ?").add("primary").append(" AND W.RowId ").appendInClause(wellRowIds, dialect);

// From the set of primary plate sets determine if any sample exists in more than one well within the entire plate set
SQLFragment nonUniqueSamplesPerPrimaryPlateSetSQL = new SQLFragment("SELECT PS.Name AS PlateSetName, W.SampleId FROM ")
.append(wellTable, "W")
.append(" WHERE PS.Type = ?").add("primary").append(" AND W.RowId ").appendInClause(wellRowIds, dialect)
.append(" )")
.append(" SELECT PS.Name AS PlateSetName, W.SampleId FROM ").append(wellTable, "W")
.append(" INNER JOIN ").append(plateTable, "P").append(" ON P.RowId = W.PlateId")
.append(" INNER JOIN ").append(plateSetTable, "PS").append(" ON PS.RowId = P.PlateSet")
.append(" WHERE W.SampleId IS NOT NULL AND PS.RowId IN (").append(primaryPlateSetsFromWellRowIdsSQL).append(")")
.append(" INNER JOIN PlateSetFilter PSF ON PSF.RowId = PS.RowId")
.append(" WHERE W.SampleId IS NOT NULL")
.append(" GROUP BY PS.RowId, W.SampleId, PS.Name HAVING COUNT(W.SampleId) > 1");

var duplicates = new SqlSelector(dbSchema.getSchema(), nonUniqueSamplesPerPrimaryPlateSetSQL).getMapCollection();
Expand Down