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Auto-refactor assorted Java lint #1009

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a61fb69
Auto-refactor lint cleanup
labkey-jeckels May 9, 2026
ac95844
Fix test logging trickery
labkey-jeckels May 9, 2026
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3 changes: 1 addition & 2 deletions elisa/src/org/labkey/elisa/ElisaDataHandler.java
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Expand Up @@ -61,7 +61,6 @@
import org.labkey.elisa.query.ElisaManager;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
Expand Down Expand Up @@ -349,7 +348,7 @@ private CurveFit<?> calculateStandardCurve(ExpRun run, Plate plate, @Nullable Si
regression.addData(concentration, mean);
}
else
LOG.info("Unable to find a standard concentration for the replicate well group : " + key);
LOG.info("Unable to find a standard concentration for the replicate well group : {}", key);
}

if (!points.isEmpty())
Expand Down
13 changes: 5 additions & 8 deletions elisa/src/org/labkey/elisa/HighThroughputImportHelper.java
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Expand Up @@ -80,7 +80,7 @@ private void ensureData() throws ExperimentException
}
}
else
LOG.warn("No well location and plate name for row : " + row);
LOG.warn("No well location and plate name for row : {}", row);
}
}
catch (IOException e)
Expand Down Expand Up @@ -140,7 +140,7 @@ public Set<String> getPlates()
}

@Override
public Map<Integer, Plate> getAnalyteToPlate(String plateName) throws ExperimentException
public Map<Integer, Plate> getAnalyteToPlate(String plateName)
{
Map<Integer, Plate> analyteToPlate = new IntHashMap<>();
for (Map.Entry<Integer, double[][]> entry : _plateMap.get(plateName).getDataMap().entrySet())
Expand All @@ -152,7 +152,7 @@ public Map<Integer, Plate> getAnalyteToPlate(String plateName) throws Experiment
}

@Override
public Map<String, Double> getStandardConcentrations(String plateName, int analyteNum) throws ExperimentException
public Map<String, Double> getStandardConcentrations(String plateName, int analyteNum)
{
return _plateMap.get(plateName).getStdConcentrations(analyteNum);
}
Expand Down Expand Up @@ -190,10 +190,7 @@ public AnalytePlate(String plateName, Plate plateTemplate)

public Map<String, Double> getStdConcentrations(int analyteNum)
{
if (_stdConcentrations.containsKey(analyteNum))
return _stdConcentrations.get(analyteNum);
else
return Collections.emptyMap();
return _stdConcentrations.getOrDefault(analyteNum, Collections.emptyMap());
}

public Map<Integer, double[][]> getDataMap()
Expand Down Expand Up @@ -224,7 +221,7 @@ public void setRawSignal(Position position, Integer spot, Integer signal) throws
{
if (position != null && spot != null && signal != null)
{
double[][] data = _dataMap.computeIfAbsent(spot, s -> new double[_plateTemplate.getRows()][_plateTemplate.getColumns()]);
double[][] data = _dataMap.computeIfAbsent(spot, _ -> new double[_plateTemplate.getRows()][_plateTemplate.getColumns()]);

if (position.getRow() >= _plateTemplate.getRows() || position.getColumn()-1 >= _plateTemplate.getColumns())
{
Expand Down
1 change: 0 additions & 1 deletion elisa/src/org/labkey/elisa/ManualImportHelper.java
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Expand Up @@ -22,7 +22,6 @@
import org.labkey.elisa.plate.BioTekPlateReader;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Expand Down
6 changes: 3 additions & 3 deletions elisa/src/org/labkey/elisa/actions/ElisaUploadWizardAction.java
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Expand Up @@ -48,7 +48,7 @@
import org.springframework.web.servlet.ModelAndView;

import jakarta.servlet.ServletException;
import java.sql.SQLException;

import java.util.Collections;
import java.util.Map;

Expand Down Expand Up @@ -93,7 +93,7 @@ public void validateStep(ElisaRunUploadForm form, Errors errors)
}

@Override
public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws ServletException, ExperimentException
{
form.setSampleProperties(_postedSampleProperties);
for (Map.Entry<String, Map<DomainProperty, String>> entry : _postedSampleProperties.entrySet())
Expand Down Expand Up @@ -227,7 +227,7 @@ public void validateStep(ElisaRunUploadForm form, Errors errors)
}

@Override
public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public boolean executeStep(ElisaRunUploadForm form, BindException errors)
{
try
{
Expand Down
2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java
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Expand Up @@ -107,7 +107,7 @@ protected void importData(ExpRun run, DataIteratorBuilder dataRows) throws Exper

int rowPos = ConvertHelper.convert(row.get(WELL_ROW_PROPERTY), Integer.class);
int colPos = ConvertHelper.convert(row.get(WELL_COLUMN_PROPERTY), Integer.class);
String dataRowLsid = ElispotDataHandler.getDataRowLsid(runData.get(0).getLSID(), rowPos, colPos).toString();
String dataRowLsid = ElispotDataHandler.getDataRowLsid(runData.getFirst().getLSID(), rowPos, colPos).toString();

Map<String, Object> runDataFields = new HashMap<>();
runDataFields.put("ObjectUri", dataRowLsid);
Expand Down
8 changes: 1 addition & 7 deletions elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java
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Expand Up @@ -21,7 +21,6 @@
import org.labkey.api.assay.plate.AbstractPlateBasedAssayProvider;
import org.labkey.api.data.Container;
import org.labkey.api.data.PropertyStorageSpec;
import org.labkey.api.exp.Lsid;
import org.labkey.api.exp.ObjectProperty;
import org.labkey.api.exp.PropertyType;
import org.labkey.api.exp.api.ExpData;
Expand Down Expand Up @@ -321,12 +320,7 @@ protected Pair<Domain,Map<DomainProperty,Object>> createRunDomain(Container c, U
protected Map<String, Set<String>> getRequiredDomainProperties()
{
Map<String, Set<String>> domainMap = super.getRequiredDomainProperties();
Set<String> runProperties = domainMap.get(ExpProtocol.ASSAY_DOMAIN_RUN);
if (runProperties == null)
{
runProperties = new HashSet<>();
domainMap.put(ExpProtocol.ASSAY_DOMAIN_RUN, runProperties);
}
Set<String> runProperties = domainMap.computeIfAbsent(ExpProtocol.ASSAY_DOMAIN_RUN, _ -> new HashSet<>());
runProperties.add(BACKGROUND_WELL_PROPERTY_NAME);
runProperties.add(READER_PROPERTY_NAME);

Expand Down
2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/ElispotController.java
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Expand Up @@ -225,7 +225,7 @@ private List<WellInfo> createWellInfoList(ExpRun run, ExpProtocol protocol, Abst
{
Position position = template.getPosition(row, col);

Lsid dataRowLsid = ElispotDataHandler.getDataRowLsid(data.get(0).getLSID(), position);
Lsid dataRowLsid = ElispotDataHandler.getDataRowLsid(data.getFirst().getLSID(), position);
for (RunDataRow dataRow : ElispotManager.get().getRunDataRows(dataRowLsid.toString(), run.getContainer()))
{
WellInfo wellInfo = new WellInfo(dataRow, position);
Expand Down
5 changes: 2 additions & 3 deletions elispotassay/src/org/labkey/elispot/ElispotDataHandler.java
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Expand Up @@ -59,7 +59,6 @@
import org.labkey.elispot.plate.PlateInfo;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
Expand Down Expand Up @@ -272,7 +271,7 @@ public static void populateAntigenDataProperties(ExpRun run, Plate plate, PlateR
if (data.size() != 1)
throw new ExperimentException("Elispot should only upload a single file per run.");

String dataLsid = data.get(0).getLSID();
String dataLsid = data.getFirst().getLSID();

// for each antigen well group, we want to flatten that information to the well level
for (WellGroup group : plate.getWellGroups(WellGroup.Type.ANTIGEN))
Expand Down Expand Up @@ -332,7 +331,7 @@ public static void populateAntigenRunProperties(ExpRun run, Plate plate, PlateRe
if (data.size() != 1)
throw new ExperimentException("Elispot should only upload a single file per run.");

String dataLsid = data.get(0).getLSID();
String dataLsid = data.getFirst().getLSID();

// calculate antigen statistics on a per sample basis
Map<String, ExpMaterial> materialMap = new HashMap<>();
Expand Down
2 changes: 1 addition & 1 deletion elispotassay/src/org/labkey/elispot/ElispotManager.java
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Expand Up @@ -116,7 +116,7 @@ private RunDataRow getRunDataRow(Filter filter)
{
List<RunDataRow> runDataRows = new TableSelector(getTableInfoElispotRunData(), filter, null).getArrayList(RunDataRow.class);
if (!runDataRows.isEmpty())
return runDataRows.get(0);
return runDataRows.getFirst();
return null;
}

Expand Down
4 changes: 2 additions & 2 deletions elispotassay/src/org/labkey/elispot/ElispotProtocolSchema.java
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Expand Up @@ -16,8 +16,8 @@

package org.labkey.elispot;

import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.ActionButton;
import org.labkey.api.data.ButtonBar;
import org.labkey.api.data.Container;
Expand Down Expand Up @@ -162,7 +162,7 @@ protected void populateButtonBar(DataView view, ButtonBar bar)
}

@Override
public QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
public @NotNull QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
{
String name = settings.getQueryName();
if (null != name && name.equalsIgnoreCase(ANTIGEN_STATS_TABLE_NAME))
Expand Down
18 changes: 9 additions & 9 deletions elispotassay/src/org/labkey/elispot/ElispotUploadWizardAction.java
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Expand Up @@ -55,7 +55,7 @@
import org.springframework.web.servlet.ModelAndView;

import jakarta.servlet.ServletException;
import java.sql.SQLException;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
Expand Down Expand Up @@ -327,7 +327,7 @@ public void validateStep(ElispotRunUploadForm form, Errors errors)
}

@Override
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, ExperimentException
{
form.setSampleProperties(_postedSampleProperties);
for (Map.Entry<String, Map<DomainProperty, String>> entry : _postedSampleProperties.entrySet())
Expand All @@ -352,7 +352,7 @@ public boolean executeStep(ElispotRunUploadForm form, BindException errors) thro
}

@Override
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ExperimentException
{
if (form.isResetDefaultValues() || errors.hasErrors())
return getRunPropertiesView(form, !form.isResetDefaultValues(), false, errors);
Expand Down Expand Up @@ -392,7 +392,7 @@ public void validateStep(ElispotRunUploadForm form, Errors errors)
}

@Override
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, ExperimentException
{
form.setAntigenProperties(_postedAntigenProperties);

Expand All @@ -413,7 +413,7 @@ public boolean executeStep(ElispotRunUploadForm form, BindException errors) thro
}

@Override
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ExperimentException
{
String detectionMethod = form.getProvider().getSelectedDetectionMethod(form.getContainer(), form.getProtocol());
boolean isLastStep = (detectionMethod == null || detectionMethod.equals(ElispotAssayProvider.DetectionMethodType.COLORIMETRIC.getLabel()));
Expand Down Expand Up @@ -459,7 +459,7 @@ public void validateStep(ElispotRunUploadForm form, Errors errors)
}

@Override
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public boolean executeStep(ElispotRunUploadForm form, BindException errors) throws ServletException, ExperimentException
{
PlateSamplePropertyHelper helper = form.getProvider().getSamplePropertyHelper(form,
getSelectedParticipantVisitResolverType(form.getProvider(), form));
Expand All @@ -479,7 +479,7 @@ public boolean executeStep(ElispotRunUploadForm form, BindException errors) thro
}

@Override
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
public ModelAndView getNextStep(ElispotRunUploadForm form, BindException errors) throws ExperimentException
{
if (form.isResetDefaultValues() || errors.hasErrors())
return getAnalyteView(form, true, errors);
Expand Down Expand Up @@ -508,7 +508,7 @@ protected ExpRun finishPost(ElispotRunUploadForm form, BindException errors)
throw new ExperimentException("Elispot should only upload a single file per run.");

Plate template = provider.getPlate(form.getContainer(), form.getProtocol());
Map<PlateInfo, Plate> plates = Collections.EMPTY_MAP;
Map<PlateInfo, Plate> plates = Collections.emptyMap();
PlateReader reader = null;

// populate property name to value map
Expand All @@ -519,7 +519,7 @@ protected ExpRun finishPost(ElispotRunUploadForm form, BindException errors)
if (runPropMap.containsKey(ElispotAssayProvider.READER_PROPERTY_NAME))
{
reader = provider.getPlateReader(runPropMap.get(ElispotAssayProvider.READER_PROPERTY_NAME));
plates = ElispotDataHandler.initializePlates(form.getProtocol(), data.get(0).getFileLike(), template, reader);
plates = ElispotDataHandler.initializePlates(form.getProtocol(), data.getFirst().getFileLike(), template, reader);
}

boolean subtractBackground = NumberUtils.toInt(runPropMap.get(ElispotAssayProvider.BACKGROUND_WELL_PROPERTY_NAME), 0) > 0;
Expand Down
6 changes: 3 additions & 3 deletions elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java
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Expand Up @@ -122,7 +122,7 @@ public void run()

if (plate != null)
{
String dataLsid = data.get(0).getLSID();
String dataLsid = data.getFirst().getLSID();
Map<String, Object> propMap = new HashMap<>();
Domain antigenDomain = AbstractAssayProvider.getDomainByPrefix(run.getProtocol(), ElispotAssayProvider.ASSAY_DOMAIN_ANTIGEN_WELLGROUP, false);

Expand All @@ -132,7 +132,7 @@ public void run()
// populate the property maps with cells per well and antigen name information (to simulate data upload)
for (WellGroup group : plate.getWellGroups(WellGroup.Type.ANTIGEN))
{
Position groupPos = group.getPositions().get(0);
Position groupPos = group.getPositions().getFirst();
Lsid dataRowLsid = ElispotDataHandler.getDataRowLsid(dataLsid, groupPos);
RunDataRow runDataRow = ElispotManager.get().getRunDataRow(dataRowLsid.toString(), run.getContainer());
if (null != runDataRow && null != cellWellProp && null != antigenNameProp)
Expand Down Expand Up @@ -185,7 +185,7 @@ private Plate initializePlate(PlateBasedAssayProvider provider, ExpRun run, Plat

if (reader != null)
{
FileLike dataFile = data.get(0).getFileLike();
FileLike dataFile = data.getFirst().getFileLike();

if (dataFile.exists())
{
Expand Down
10 changes: 3 additions & 7 deletions flow/enginesrc/org/labkey/flow/Main.java
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Expand Up @@ -162,15 +162,11 @@ private static void executeListSamples(File workspaceFile, Set<PopulationName> g
for (Workspace.SampleInfo sample : workspace.getSamplesComplete())
{
Analysis analysis = workspace.getSampleAnalysis(sample);
List<Workspace.SampleInfo> samples = analysisToSamples.get(analysis);
if (samples == null)
analysisToSamples.put(analysis, samples = new ArrayList<>());
List<Workspace.SampleInfo> samples = analysisToSamples.computeIfAbsent(analysis, _ -> new ArrayList<>());

samples.add(sample);

List<Workspace.SampleInfo> dups = sampleLabels.get(sample.getLabel());
if (dups == null)
sampleLabels.put(sample.getLabel(), dups = new ArrayList<>());
List<Workspace.SampleInfo> dups = sampleLabels.computeIfAbsent(sample.getLabel(), _ -> new ArrayList<>());
dups.add(sample);
}

Expand Down Expand Up @@ -225,7 +221,7 @@ private static void executeListSamples(File workspaceFile, Set<PopulationName> g
{
Analysis analysis = entry.getKey();
List<Workspace.SampleInfo> samples = entry.getValue();
String header = String.format(" %s: ", samples.get(0));
String header = String.format(" %s: ", samples.getFirst());
String indent = StringUtils.repeat(" ", header.length());
System.out.print(header);
printWrapped(System.out, indent, samples);
Expand Down
3 changes: 1 addition & 2 deletions flow/enginesrc/org/labkey/flow/analysis/chart/DensityPlot.java
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Expand Up @@ -29,7 +29,6 @@

import org.labkey.flow.analysis.model.Polygon;
import java.awt.*;
import java.util.Iterator;
import java.util.List;
import java.util.ArrayList;

Expand Down Expand Up @@ -119,7 +118,7 @@ protected void drawLine(Graphics2D g2, Rectangle2D dataArea, double x1, double y
xValues.sort(Double::compareTo);

// now draw the segments
double x = xValues.get(0);
double x = xValues.getFirst();
double y = m*x + b;
int prevX = (int)getDomainAxis().valueToJava2D(x, dataArea, RectangleEdge.BOTTOM);
int prevY = (int)getRangeAxis().valueToJava2D(y, dataArea, RectangleEdge.LEFT);
Expand Down
2 changes: 1 addition & 1 deletion flow/enginesrc/org/labkey/flow/analysis/chart/HistPlot.java
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Expand Up @@ -116,7 +116,7 @@ public boolean render(Graphics2D g2, Rectangle2D dataArea, int series, PlotRende

if (_gates.size() == 1)
{
Range gate = _gates.get(0);
Range gate = _gates.getFirst();
int min = (int) getDomainAxis().valueToJava2D(gate.getLowerBound(), dataArea, getDomainAxisEdge());
int max = (int) getDomainAxis().valueToJava2D(gate.getUpperBound(), dataArea, getDomainAxisEdge());
g2.drawLine(min, (int) dataArea.getMinY(), min + 1, (int) dataArea.getMaxY());
Expand Down
2 changes: 1 addition & 1 deletion flow/enginesrc/org/labkey/flow/analysis/model/Analysis.java
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Expand Up @@ -156,7 +156,7 @@ private void materializeGraphs(Set<GraphSpec> graphs, Population population, Sub
{
if (population.getGates().size() == 1)
{
Gate gate = population.getGates().get(0);
Gate gate = population.getGates().getFirst();
if (gate instanceof PolygonGate poly)
{
GraphSpec graph = new GraphSpec(parent, poly.getXAxis(), poly.getYAxis());
Expand Down
1 change: 0 additions & 1 deletion flow/enginesrc/org/labkey/flow/analysis/model/CompensationMatrix.java
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Expand Up @@ -18,7 +18,6 @@

import Jama.Matrix;
import org.apache.commons.lang3.StringUtils;
import org.apache.xerces.impl.Constants;
import org.junit.Assert;
import org.junit.Test;
import org.labkey.api.util.DateUtil;
Expand Down
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