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Merged
labkey-jeckels merged 2 commits into from
Mar 26, 2026
Merged

Minor code cleanup and correctness improvements #1186

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b9020e7
Minor code cleanup
labkey-jeckels Mar 25, 2026
fbaa1c4
Followup fixes
labkey-jeckels Mar 26, 2026
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21 changes: 21 additions & 0 deletions api-src/org/labkey/api/targetedms/model/QCMetricConfiguration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,16 @@
package org.labkey.api.targetedms.model;

import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.json.JSONObject;

public class QCMetricConfiguration implements Comparable<QCMetricConfiguration>
{
public enum TimeValueOption
{
First, Last, Min, Max
}

private int _id;
private String _name;
private String _queryName;
Expand Down Expand Up @@ -124,6 +130,21 @@ public void setTimeValueOption(String timeValueOption)
_timeValueOption = timeValueOption;
}

@Nullable
public TimeValueOption getParsedTimeValueOption()
{
if (_timeValueOption == null)
return null;
try
{
return TimeValueOption.valueOf(_timeValueOption);
}
catch (IllegalArgumentException e)
{
return null;
}
}

public Double getTraceValue()
{
return _traceValue;
Expand Down
79 changes: 40 additions & 39 deletions src/org/labkey/targetedms/TargetedMSManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ private TargetedMSManager()
* client rendering the overview, all of which need to know the enabled configs.
*/
private static final Cache<Container, List<QCMetricConfiguration>> _metricCache = CacheManager.getBlockingCache(1000, TimeUnit.HOURS.toMillis(1), "Enabled QC metric configs",
(c, argument) ->
(_, argument) ->
{
try
{
Expand Down Expand Up @@ -1048,7 +1048,7 @@ public static TargetedMSRun getRunByFileName(String fileName, Container containe
List<TargetedMSRun> matches = new TableSelector(TargetedMSManager.getTableInfoRuns(), filter, null).getArrayList(TargetedMSRun.class);
if (matches.size() == 1)
{
return matches.get(0);
return matches.getFirst();
}
return null;
}
Expand Down Expand Up @@ -1084,7 +1084,7 @@ else if(representativeState == RunRepresentativeDataState.Representative_Peptide
// for the documents not yet imported.
updateSql.append(" AND StatusId = ? ");
updateSql.add(SkylineDocImporter.STATUS_SUCCESS);
updateSql.append(" AND Id NOT IN ("+StringUtils.join(representativeRunIds, ",")+")");
updateSql.append(" AND Id NOT IN (").append(StringUtils.join(representativeRunIds, ",")).append(")");

new SqlExecutor(TargetedMSManager.getSchema()).execute(updateSql);
}
Expand Down Expand Up @@ -1125,7 +1125,7 @@ private static List<Long> getProteinRepresentativeRunIds(Container container, in
reprRunIdSql.append(TargetedMSManager.getTableInfoRuns(), "runs");
String states = StringUtils.join(stateArray, ',');

reprRunIdSql.append(" WHERE pepgrp.RepresentativeDataState IN (" + states + ")");
reprRunIdSql.append(" WHERE pepgrp.RepresentativeDataState IN (").append(states).append(")");
reprRunIdSql.append(" AND runs.Container = ?");
reprRunIdSql.add(container);
reprRunIdSql.append(" AND runs.Id = pepgrp.RunId");
Expand Down Expand Up @@ -1160,7 +1160,7 @@ private static List<Long> getPeptideRepresentativeRunIds(Container container, in

String states = StringUtils.join(stateArray, ',');

reprRunIdSql.append(" WHERE gp.RepresentativeDataState IN (" + states + ")");
reprRunIdSql.append(" WHERE gp.RepresentativeDataState IN (").append(states).append(")");
reprRunIdSql.append(" AND gp.GeneralMoleculeId = gm.Id");
reprRunIdSql.append(" AND gm.PeptideGroupId = pepgrp.Id");
reprRunIdSql.append(" AND Container = ?");
Expand Down Expand Up @@ -1918,19 +1918,15 @@ private static void purgeDeletedRuns()
// Delete from all list-related tables
deleteListDependent();

// Get a list of runs to be deleted so that we can flush them from the cache
SQLFragment sql = new SQLFragment("SELECT Id FROM " + getTableInfoRuns() + " WHERE Deleted = ?", true);
List<Long> deletedRunIds = new SqlSelector(getSchema(), sql).getArrayList(Long.class);

// Delete from runs
execute("DELETE FROM " + getTableInfoRuns() + " WHERE Deleted = ?", true);

// Remove any cached results for the deleted runs
removeCachedResults();
}

private static void removeCachedResults()
{
// Get a list of deleted runs
SQLFragment sql = new SQLFragment("SELECT Id FROM " + getTableInfoRuns() + " WHERE Deleted = ?", true);
List<Long> deletedRunIds = new SqlSelector(getSchema(), sql).getArrayList(Long.class);
if(!deletedRunIds.isEmpty())
if (!deletedRunIds.isEmpty())
{
ModificationManager.removeRunCachedResults(deletedRunIds);
PeptideManager.removeRunCachedResults(deletedRunIds);
Expand Down Expand Up @@ -2155,18 +2151,22 @@ public static void renameRun(long runId, String newDescription, User user) throw
if (newDescription == null || newDescription.isEmpty())
return;

new SqlExecutor(getSchema()).execute("UPDATE " + getTableInfoRuns() + " SET Description=? WHERE Id = ?",
newDescription, runId);
TargetedMSRun run = getRun(runId);
if (run != null)
try (DbScope.Transaction t = getSchema().getScope().ensureTransaction())
{
// Keep the experiment run wrapper in sync
ExpRun expRun = ExperimentService.get().getExpRun(run.getExperimentRunLSID());
if (expRun != null)
new SqlExecutor(getSchema()).execute("UPDATE " + getTableInfoRuns() + " SET Description=? WHERE Id = ?",
newDescription, runId);
TargetedMSRun run = getRun(runId);
if (run != null)
{
expRun.setName(newDescription);
expRun.save(user);
// Keep the experiment run wrapper in sync
ExpRun expRun = ExperimentService.get().getExpRun(run.getExperimentRunLSID());
if (expRun != null)
{
expRun.setName(newDescription);
expRun.save(user);
}
}
t.commit();
}
}

Expand Down Expand Up @@ -2199,7 +2199,7 @@ public static SampleFile getSampleFile(long id, Container container)
{
throw new IllegalStateException("More than one SampleFile for Id " + id);
}
return matches.isEmpty() ? null : matches.get(0);
return matches.isEmpty() ? null : matches.getFirst();
}

public static List<SampleFile> getSampleFiles(Container container, @Nullable SQLFragment whereClause)
Expand Down Expand Up @@ -2813,13 +2813,6 @@ public static TransitionSettings.FullScanSettings getTransitionFullScanSettings(
.getObject(TransitionSettings.FullScanSettings.class);
}

public static TransitionSettings.Predictor getReplicatePredictor(long predictorId)
{
return new TableSelector(TargetedMSManager.getTableInfoTransitionFullScanSettings(),
new SimpleFilter(FieldKey.fromParts("Id"), predictorId), null)
.getObject(TransitionSettings.Predictor.class);
}

private static List<Long> getPredictorsToDelete()
{
SQLFragment sql = new SQLFragment("Select Id FROM " + getTableInfoPredictor() + " WHERE " +
Expand Down Expand Up @@ -2871,12 +2864,12 @@ public static List<QCTraceMetricValues> calculateTraceMetricValues(List<QCMetric
Double minTimeValue = qcMetricConfiguration.getMinTimeValue();
Double maxTimeValue = qcMetricConfiguration.getMaxTimeValue();
Double traceValue = qcMetricConfiguration.getTraceValue();
String timeValueOption = qcMetricConfiguration.getTimeValueOption();
QCMetricConfiguration.TimeValueOption timeValueOption = qcMetricConfiguration.getParsedTimeValueOption();
float minValue = Float.MAX_VALUE;
float maxValue = Float.MIN_VALUE;
float maxValue = -Float.MAX_VALUE;
for (int i = 0; i < times.length; i++)
{
if (timeValueOption != null && timeValueOption.equals("First"))
if (timeValueOption == QCMetricConfiguration.TimeValueOption.First)
{
// first value after the minTimeValue
if (minTimeValue != null && times[i] > minTimeValue)
Expand All @@ -2891,7 +2884,7 @@ else if (minTimeValue == null)
break;
}
}
else if (timeValueOption != null && timeValueOption.equals("Last"))
else if (timeValueOption == QCMetricConfiguration.TimeValueOption.Last)
{
// last value before the maxTimeValue
if (maxTimeValue != null && times[i] < maxTimeValue)
Expand All @@ -2904,7 +2897,7 @@ else if (maxTimeValue == null)
valuesToStore.put(sampleFileChromInfo, values[i]);
}
}
else if (timeValueOption != null && timeValueOption.equals("Min"))
else if (timeValueOption == QCMetricConfiguration.TimeValueOption.Min)
{
// minValue between minTimeValue and maxTimeValue
if (minTimeValue != null && maxTimeValue != null && times[i] >= minTimeValue && times[i] <= maxTimeValue)
Expand All @@ -2929,9 +2922,8 @@ else if (minTimeValue == null && maxTimeValue == null && values[i] < minValue)
{
minValue = values[i];
}
valuesToStore.put(sampleFileChromInfo, minValue);
}
else if (timeValueOption != null && timeValueOption.equals("Max"))
else if (timeValueOption == QCMetricConfiguration.TimeValueOption.Max)
{
// maxValue between minTimeValue and maxTimeValue
if (minTimeValue != null && maxTimeValue != null && times[i] >= minTimeValue && times[i] <= maxTimeValue)
Expand All @@ -2956,7 +2948,6 @@ else if (minTimeValue == null && maxTimeValue == null && values[i] > maxValue)
{
maxValue = values[i];
}
valuesToStore.put(sampleFileChromInfo, maxValue);
}

else if (traceValue != null && values[i] >= traceValue)
Expand All @@ -2965,6 +2956,16 @@ else if (traceValue != null && values[i] >= traceValue)
break;
}
}

// Store Min/Max only if at least one data point matched the time filter
if (timeValueOption == QCMetricConfiguration.TimeValueOption.Min && minValue != Float.MAX_VALUE)
{
valuesToStore.put(sampleFileChromInfo, minValue);
}
else if (timeValueOption == QCMetricConfiguration.TimeValueOption.Max && maxValue != -Float.MAX_VALUE)
{
valuesToStore.put(sampleFileChromInfo, maxValue);
}
}
}

Expand Down
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