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Merged
labkey-jeckels merged 1 commit into from
May 12, 2026
Merged

Auto-refactor lint cleanup #633

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37 changes: 1 addition & 36 deletions SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreContainerListener.java
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Expand Up @@ -16,52 +16,17 @@

package org.labkey.skylinetoolsstore;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager.ContainerListener;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.security.User;

import java.sql.SQLException;

import java.beans.PropertyChangeEvent;
import java.util.Collection;
import java.util.Collections;

public class SkylineToolsStoreContainerListener implements ContainerListener
{
@Override
public void containerCreated(Container c, User user)
{
}

@Override
public void containerDeleted(Container c, User user)
{
try
{
SkylineToolsStoreManager.get().deleteAllData(c);
}
catch (SQLException e)
{
throw new RuntimeSQLException(e);
}
}

@Override
public void propertyChange(PropertyChangeEvent evt)
{
}

@Override
public void containerMoved(Container c, Container oldParent, User user)
{
SkylineToolsStoreManager.get().deleteAllData(c);
}

@NotNull
@Override
public Collection<String> canMove(Container c, Container newParent, User user)
{
return Collections.emptyList();
}
}
17 changes: 9 additions & 8 deletions SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java
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Expand Up @@ -24,6 +24,7 @@
import org.apache.commons.lang3.math.NumberUtils;
import org.json.JSONArray;
import org.json.JSONObject;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.action.FormHandlerAction;
import org.labkey.api.action.NavTrailAction;
import org.labkey.api.action.PermissionCheckable;
Expand Down Expand Up @@ -468,7 +469,7 @@ public InsertAction()
}

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final String sender = httpServletRequest.getParameter("sender");
final String updateTargetString = StringUtils.trimToNull(httpServletRequest.getParameter("updatetarget"));
Expand Down Expand Up @@ -703,7 +704,7 @@ public InsertSupplementAction()
}

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final String suppTargetString = httpServletRequest.getParameter("supptarget");
int suppTarget = NumberUtils.toInt(suppTargetString, -1);
Expand Down Expand Up @@ -765,7 +766,7 @@ public DeleteSupplementAction()
}

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final int suppTarget = Integer.parseInt(httpServletRequest.getParameter("supptarget"));

Expand Down Expand Up @@ -896,7 +897,7 @@ public class DeleteLatestAction extends AbstractController implements Permission
private final Class REQ_PERMS = DeletePermission.class;

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(@NotNull HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
int id;
try {
Expand Down Expand Up @@ -961,7 +962,7 @@ public class DownloadToolAction extends AbstractController implements Permission
public static final String DOWNLOADED_COOKIE_PREFIX = "downloadtool";

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final int id = NumberUtils.toInt(httpServletRequest.getParameter("id"), -1);
final String toolName = httpServletRequest.getParameter("name");
Expand Down Expand Up @@ -1239,7 +1240,7 @@ public SetOwnersAction()
}

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final String sender = httpServletRequest.getParameter("sender");
final String updateTargetString = httpServletRequest.getParameter("updatetarget");
Expand Down Expand Up @@ -1312,7 +1313,7 @@ public class UpdatePropertyAction extends AbstractController implements Permissi
private final Class REQ_PERMS = InsertPermission.class;

@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws Exception
{
final int id = Integer.parseInt(httpServletRequest.getParameter("id"));

Expand Down Expand Up @@ -1420,7 +1421,7 @@ public void checkPermissions() throws UnauthorizedException
public class GetToolsApiAction extends AbstractController implements PermissionCheckable
{
@Override
public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws IOException
public ModelAndView handleRequestInternal(@NotNull HttpServletRequest httpServletRequest, @NotNull HttpServletResponse httpServletResponse) throws IOException
{
StringBuilder sb = new StringBuilder();

Expand Down
12 changes: 5 additions & 7 deletions SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreManager.java
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Expand Up @@ -26,8 +26,6 @@
import org.labkey.api.security.User;
import org.labkey.skylinetoolsstore.model.SkylineTool;

import java.sql.SQLException;

public class SkylineToolsStoreManager
{
private static final SkylineToolsStoreManager _instance = new SkylineToolsStoreManager();
Expand All @@ -42,7 +40,7 @@ public static SkylineToolsStoreManager get()
return _instance;
}

public void deleteAllData(Container c) throws SQLException
public void deleteAllData(Container c)
{
// delete all tools when the container is deleted
Filter containerFilter = SimpleFilter.createContainerFilter(c);
Expand Down Expand Up @@ -124,18 +122,18 @@ public SkylineTool getToolByNameAndVersion(String name, String version)
return (tools != null && tools.length > 0) ? tools[0] : null;
}

public void deleteTool(int rowId) throws SQLException
public void deleteTool(int rowId)
{
Table.delete(SkylineToolsStoreSchema.getInstance().getTableInfoSkylineTool(), rowId);
}

public SkylineTool insertTool(Container c, User user, SkylineTool tool) throws SQLException
public SkylineTool insertTool(Container c, User user, SkylineTool tool)
{
tool.setContainer(c.getId());
return Table.insert(user, SkylineToolsStoreSchema.getInstance().getTableInfoSkylineTool(), tool);
}

public SkylineTool updateTool(Container c, User user, SkylineTool tool) throws SQLException
public SkylineTool updateTool(Container c, User user, SkylineTool tool)
{
if (tool.getContainerId() == null)
tool.setContainerId(c.getId());
Expand All @@ -153,7 +151,7 @@ public SkylineTool updateTool(Container c, User user, SkylineTool tool) throws S
tool, tool.getRowId());
}

public SkylineTool recordToolDownload(SkylineTool tool) throws SQLException
public SkylineTool recordToolDownload(SkylineTool tool)
{
tool.setDownloads(tool.getDownloads() + 1);
return Table.update(null, SkylineToolsStoreSchema.getInstance().getTableInfoSkylineTool(),
Expand Down
3 changes: 1 addition & 2 deletions SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java
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Expand Up @@ -26,7 +26,6 @@
import org.labkey.api.view.BaseWebPartFactory;
import org.labkey.api.view.Portal;
import org.labkey.api.view.ViewContext;
import org.labkey.api.view.WebPartConfigurationException;
import org.labkey.api.view.WebPartFactory;
import org.labkey.api.view.WebPartView;
import org.labkey.skylinetoolsstore.model.SkylineTool;
Expand Down Expand Up @@ -74,7 +73,7 @@ protected Collection<WebPartFactory> createWebPartFactories()
}

@Override
public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) throws WebPartConfigurationException
public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart)
{
return new SkylineToolsStoreWebPart();
}
Expand Down
6 changes: 3 additions & 3 deletions lincs/src/org/labkey/lincs/CustomGctBuilder.java
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Expand Up @@ -44,7 +44,7 @@ public Gct build(List<Path> files, List<LincsController.SelectedAnnotation> sele

for(Path file: files)
{
_log.info("LINCS custom GCT: reading file: " + file);
_log.info("LINCS custom GCT: reading file: {}", file);
Gct gct;
try
{
Expand Down Expand Up @@ -87,10 +87,10 @@ private void updateMultiValueProbeAnnotations(Gct gct, Gct customGct)
{
// All replicates in a single GCT file should have the same value for the "det_plate" replicate annotation.
// TODO: This is not true for GCP plate 16 file.
String detPlateAnnotationVal = gct.getReplicates().get(0).getAnnotationValue(LincsAnnotation.PLATE_ANNOTATION);
String detPlateAnnotationVal = gct.getReplicates().getFirst().getAnnotationValue(LincsAnnotation.PLATE_ANNOTATION);

// All replicates in a single GCT file should have the same value for the "provenance_code" replicate annotation
String expType = gct.getExperimentType(gct.getReplicates().get(0).getAnnotationValue(LincsAnnotation.PROVENANCE_CODE));
String expType = gct.getExperimentType(gct.getReplicates().getFirst().getAnnotationValue(LincsAnnotation.PROVENANCE_CODE));

// Append experiment type to plate annotation since we can have same plate (e.g. plate 18) analyzed by both DIA and PRM.
String expTypeAndPlate = expType + "_" + detPlateAnnotationVal;
Expand Down
10 changes: 5 additions & 5 deletions lincs/src/org/labkey/lincs/DocImportListener.java
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Expand Up @@ -70,7 +70,7 @@ public void beforeRunDelete(ExpProtocol protocol, ExpRun run, User user)
}
catch (IOException e)
{
_log.warn("LINCS: Error listing files in folder " + FileUtil.getAbsolutePath(gctDir), e);
_log.warn("LINCS: Error listing files in folder {}", FileUtil.getAbsolutePath(gctDir), e);
return;
}

Expand All @@ -81,7 +81,7 @@ public void beforeRunDelete(ExpProtocol protocol, ExpRun run, User user)
}
catch (IOException e)
{
_log.warn("LINCS: Error deleting file " + FileUtil.getAbsolutePath(path), e);
_log.warn("LINCS: Error deleting file {}", FileUtil.getAbsolutePath(path), e);
}
});
}
Expand Down Expand Up @@ -115,7 +115,7 @@ public void onDocumentImport(Container container, User user, ITargetedMSRun skyl
PipeRoot root = PipelineService.get().findPipelineRoot(container);
if (root == null || !root.isValid())
{
_log.error("LINCS: No valid pipeline root found for " + container.getPath());
_log.error("LINCS: No valid pipeline root found for {}", container.getPath());
return;
}

Expand All @@ -129,7 +129,7 @@ public void onDocumentImport(Container container, User user, ITargetedMSRun skyl
}
catch (PipelineValidationException e)
{
_log.error("Error adding LINCS pipeline job to queue. Message: " + e.getMessage(), e);
_log.error("Error adding LINCS pipeline job to queue. Message: {}", e.getMessage(), e);
if(pspJob != null)
{
LincsManager.get().deleteLincsPspJob(pspJob);
Expand All @@ -138,7 +138,7 @@ public void onDocumentImport(Container container, User user, ITargetedMSRun skyl
}

long jobId = PipelineService.get().getJobId(user, container, job.getJobGUID());
_log.info("LINCS: Queued job Id " + jobId +" for creating GCT files for " + skylineRun.getFileName() + ". Container: " + container.getPath());
_log.info("LINCS: Queued job Id {} for creating GCT files for {}. Container: {}", jobId, skylineRun.getFileName(), container.getPath());

pspJob.setPipelineJobId(jobId);
LincsManager.get().updatePipelineJobId(pspJob);
Expand Down
7 changes: 1 addition & 6 deletions lincs/src/org/labkey/lincs/Gct.java
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Expand Up @@ -126,12 +126,7 @@ public void addMultiValueProbeAnnotation(String annotationName, ProbeExpTypePlat
{
_multiValueProbeAnnotations = new HashMap<>();
}
GctTable<ProbeExpTypePlate> probePlateValues = _multiValueProbeAnnotations.get(annotationName);
if(probePlateValues == null)
{
probePlateValues = new GctTable<>();
_multiValueProbeAnnotations.put(annotationName, probePlateValues);
}
GctTable<ProbeExpTypePlate> probePlateValues = _multiValueProbeAnnotations.computeIfAbsent(annotationName, _ -> new GctTable<>());
probePlateValues.addValue(key, value);
}

Expand Down
55 changes: 0 additions & 55 deletions lincs/src/org/labkey/lincs/LincsContainerListener.java
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This file was deleted.

2 changes: 0 additions & 2 deletions lincs/src/org/labkey/lincs/LincsController.java
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Expand Up @@ -93,8 +93,6 @@
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;

import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
Expand Down
14 changes: 7 additions & 7 deletions lincs/src/org/labkey/lincs/LincsManager.java
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Expand Up @@ -83,7 +83,7 @@ public List<LincsAnnotation> getReplicateAnnotations(User user, Container contai
else
{
// Otherwise, read from the lincs_replicate_annotations.txt file in the module's resources directory
_log.info("Could not find table " + listName + " in schema 'lists'. Trying to read from file.");
_log.info("Could not find table {} in schema 'lists'. Trying to read from file.", listName);
return readFromFile("lincs_replicate_annotations.txt");
}
}
Expand All @@ -100,7 +100,7 @@ public List<LincsAnnotation> getPeptideAnnotations(User user, Container containe
else
{
// Otherwise, read from the lincs_peptide_annotations.txt file in the module's resources directory
_log.info("Could not find table " + listName + " in schema 'lists'. Trying to read from file.");
_log.info("Could not find table {} in schema 'lists'. Trying to read from file.", listName);
return readFromFile("lincs_peptide_annotations.txt");
}
}
Expand All @@ -120,10 +120,10 @@ private List<LincsAnnotation> readFromFile(String filename)
String[] headers = line.split("\\t");
for(int i = 0; i < headers.length; i++)
{
if(headers[i].toLowerCase().equals("name")) {nameCol = i;}
else if(headers[i].toLowerCase().equals("displayname")) {displayNameCol = i;}
else if(headers[i].toLowerCase().equals("advanced")) {advancedCol = i;}
else if(headers[i].toLowerCase().equals("ignored")) {ignoredCol = i;}
if(headers[i].equalsIgnoreCase("name")) {nameCol = i;}
else if(headers[i].equalsIgnoreCase("displayname")) {displayNameCol = i;}
else if(headers[i].equalsIgnoreCase("advanced")) {advancedCol = i;}
else if(headers[i].equalsIgnoreCase("ignored")) {ignoredCol = i;}
}

List<LincsAnnotation> annotations = new ArrayList<>();
Expand All @@ -142,7 +142,7 @@ private List<LincsAnnotation> readFromFile(String filename)
}
catch (IOException e)
{
_log.error("Could not read file " + txt.getPath(), e);
_log.error("Could not read file {}", txt.getPath(), e);
return Collections.emptyList();
}
}
Expand Down
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