Tomcat 10 - Update namespace of Jakarta EE packages (#727)

Co-authored-by: Adam Rauch <adam@labkey.com>
LabKey · Feb 1, 2024 · 5322bcf · 5322bcf
1 parent 5d714fc
commit 5322bcf
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Showing 44 changed files with 50 additions and 110 deletions.
diff --git a/elisa/src/org/labkey/elisa/ElisaSampleFilePropertyHelper.java b/elisa/src/org/labkey/elisa/ElisaSampleFilePropertyHelper.java
@@ -15,7 +15,7 @@
 import org.labkey.api.reader.DataLoaderService;
 import org.labkey.api.study.assay.SampleMetadataInputFormat;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;

diff --git a/elisa/src/org/labkey/elisa/actions/ElisaUploadWizardAction.java b/elisa/src/org/labkey/elisa/actions/ElisaUploadWizardAction.java
@@ -48,7 +48,7 @@
 import org.springframework.validation.ObjectError;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletException;
 import java.sql.SQLException;
 import java.util.Collections;
 import java.util.Map;

diff --git a/elispotassay/src/org/labkey/elispot/ElispotUploadWizardAction.java b/elispotassay/src/org/labkey/elispot/ElispotUploadWizardAction.java
@@ -52,7 +52,7 @@
 import org.springframework.validation.ObjectError;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletException;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collections;

diff --git a/flow/src/org/labkey/flow/FlowPreference.java b/flow/src/org/labkey/flow/FlowPreference.java
@@ -20,8 +20,8 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.controllers.FlowController;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpSession;
 
 public enum FlowPreference
 {
@@ -37,7 +37,7 @@ public enum FlowPreference
     {
         _defValue = defValue;
     }
-    String _defValue;
+    final String _defValue;
 
     public String getValue(HttpServletRequest request)
     {

diff --git a/flow/src/org/labkey/flow/controllers/BaseFlowController.java b/flow/src/org/labkey/flow/controllers/BaseFlowController.java
@@ -41,7 +41,7 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.mvc.Controller;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
 
 

diff --git a/flow/src/org/labkey/flow/controllers/ReportsController.java b/flow/src/org/labkey/flow/controllers/ReportsController.java
@@ -69,7 +69,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.LinkedHashSet;

diff --git a/flow/src/org/labkey/flow/controllers/WorkspaceData.java b/flow/src/org/labkey/flow/controllers/WorkspaceData.java
@@ -16,6 +16,7 @@
 
 package org.labkey.flow.controllers;
 
+import jakarta.servlet.http.HttpServletRequest;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
@@ -43,7 +44,6 @@
 import org.labkey.flow.persist.AttributeCache;
 import org.springframework.validation.Errors;
 
-import javax.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;
@@ -55,7 +55,6 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.TimeUnit;
-import java.util.stream.Collectors;
 
 import static org.labkey.api.action.SpringActionController.ERROR_MSG;
 

diff --git a/flow/src/org/labkey/flow/controllers/compensation/CompensationController.java b/flow/src/org/labkey/flow/controllers/compensation/CompensationController.java
@@ -53,7 +53,7 @@
 import org.springframework.web.multipart.MultipartFile;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.util.List;
 
 public class CompensationController extends BaseFlowController

diff --git a/flow/src/org/labkey/flow/controllers/run/RunController.java b/flow/src/org/labkey/flow/controllers/run/RunController.java
@@ -90,7 +90,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;

diff --git a/flow/src/org/labkey/flow/controllers/well/WellController.java b/flow/src/org/labkey/flow/controllers/well/WellController.java
@@ -77,7 +77,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;

diff --git a/flow/src/org/labkey/flow/data/FlowCompensationMatrix.java b/flow/src/org/labkey/flow/data/FlowCompensationMatrix.java
@@ -37,7 +37,7 @@
 import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.query.FlowTableType;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.io.Serializable;
 import java.util.ArrayList;

diff --git a/flow/src/org/labkey/flow/data/FlowExperiment.java b/flow/src/org/labkey/flow/data/FlowExperiment.java
@@ -32,7 +32,7 @@
 import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.query.FlowTableType;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;

diff --git a/flow/src/org/labkey/flow/data/FlowObject.java b/flow/src/org/labkey/flow/data/FlowObject.java
@@ -39,7 +39,7 @@
 import org.labkey.flow.controllers.FlowParam;
 import org.springframework.web.servlet.mvc.Controller;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.Serializable;
 import java.sql.SQLException;
 import java.util.Collection;

diff --git a/flow/src/org/labkey/flow/data/FlowProtocol.java b/flow/src/org/labkey/flow/data/FlowProtocol.java
@@ -79,7 +79,7 @@
 import org.labkey.flow.query.FlowTableType;
 import org.labkey.flow.script.KeywordsJob;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.sql.ResultSet;
 import java.sql.SQLException;

diff --git a/flow/src/org/labkey/flow/data/FlowProtocolStep.java b/flow/src/org/labkey/flow/data/FlowProtocolStep.java
@@ -26,7 +26,7 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.controllers.FlowParam;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Map;

diff --git a/flow/src/org/labkey/flow/data/FlowRun.java b/flow/src/org/labkey/flow/data/FlowRun.java
@@ -45,7 +45,7 @@
 import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.query.FlowTableType;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.net.URI;
 import java.sql.ResultSet;

diff --git a/flow/src/org/labkey/flow/data/FlowScript.java b/flow/src/org/labkey/flow/data/FlowScript.java
@@ -45,7 +45,7 @@
 import org.labkey.flow.script.FlowAnalyzer;
 import org.springframework.web.servlet.mvc.Controller;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;

diff --git a/flow/src/org/labkey/flow/data/FlowWell.java b/flow/src/org/labkey/flow/data/FlowWell.java
@@ -41,7 +41,7 @@
 import org.labkey.flow.controllers.well.WellController;
 import org.labkey.flow.persist.FlowManager;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collection;

diff --git a/flow/src/org/labkey/flow/data/FlowWorkspace.java b/flow/src/org/labkey/flow/data/FlowWorkspace.java
@@ -26,7 +26,7 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.flow.controllers.FlowParam;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.List;
 import java.util.Map;
 

diff --git a/flow/src/org/labkey/flow/query/FlowSchema.java b/flow/src/org/labkey/flow/query/FlowSchema.java
@@ -99,7 +99,7 @@
 import org.labkey.flow.view.FlowQueryView;
 import org.springframework.validation.BindException;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.beans.PropertyChangeEvent;
 import java.io.IOException;
 import java.io.Writer;
@@ -117,10 +117,6 @@
 import java.util.TreeSet;
 import java.util.function.Supplier;
 
-import static java.lang.Boolean.TRUE;
-import static java.util.Objects.requireNonNull;
-
-
 public class FlowSchema extends UserSchema implements UserSchema.HasContextualRoles
 {
     static public final String SCHEMANAME = "flow";

diff --git a/flow/src/org/labkey/flow/view/FlowQueryView.java b/flow/src/org/labkey/flow/view/FlowQueryView.java
@@ -57,8 +57,8 @@
 import org.labkey.flow.webparts.FlowFolderType;
 import org.springframework.validation.Errors;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Iterator;

diff --git a/luminex/src/org/labkey/luminex/LuminexAssayProvider.java b/luminex/src/org/labkey/luminex/LuminexAssayProvider.java
@@ -71,7 +71,7 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.luminex.query.LuminexProtocolSchema;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -82,8 +82,6 @@
 
 /**
  * Defines the Luminex assay type, creates default batch/run/analyte domains, sets up header links.
- * User: jeckels
- * Date: Jul 13, 2007
  */
 public class LuminexAssayProvider extends AbstractAssayProvider
 {

diff --git a/luminex/src/org/labkey/luminex/LuminexController.java b/luminex/src/org/labkey/luminex/LuminexController.java
@@ -90,8 +90,8 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;

diff --git a/luminex/src/org/labkey/luminex/LuminexRunDatabaseContext.java b/luminex/src/org/labkey/luminex/LuminexRunDatabaseContext.java
@@ -33,7 +33,7 @@
 import org.labkey.luminex.model.Titration;
 import org.labkey.luminex.query.LuminexProtocolSchema;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
@@ -44,12 +44,10 @@
 /**
  * Info source for running transform/validation script over a run that's already been imported into the database
  * (including with exclusions of well groups, analytes, etc.)
- * User: jeckels
- * Date: Oct 7, 2011
  */
 public class LuminexRunDatabaseContext extends AssayRunDatabaseContext<LuminexAssayProvider> implements LuminexRunContext
 {
-    private Map<String, Analyte> _analytes = new LinkedHashMap<>();
+    private final Map<String, Analyte> _analytes = new LinkedHashMap<>();
     private LuminexExcelParser _parser;
 
     public LuminexRunDatabaseContext(ExpRun run, User user, HttpServletRequest request)

diff --git a/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java b/luminex/src/org/labkey/luminex/LuminexUploadWizardAction.java
@@ -68,7 +68,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletException;
 import java.io.File;
 import java.io.IOException;
 import java.io.Writer;
@@ -87,8 +87,6 @@
 /**
  * Adds Analyte Properties as third wizard step, handles analyte and titration definition input view UI and post, saves
  * last entered default values for analyte domain and standard properties
- * User: jeckels
- * Date: Aug 8, 2007
 */
 @RequiresPermission(InsertPermission.class)
 public class LuminexUploadWizardAction extends UploadWizardAction<LuminexRunUploadForm, LuminexAssayProvider>

diff --git a/ms2/src/org/labkey/ms2/AbstractTextSpectrumRenderer.java b/ms2/src/org/labkey/ms2/AbstractTextSpectrumRenderer.java
@@ -18,17 +18,14 @@
 
 import org.labkey.api.util.DateUtil;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.text.DecimalFormat;
 import java.util.Date;
 
 /**
  * A renderer of spectrum information that ends up as some type of text file
- * User: adam
- * Date: May 8, 2006
- * Time: 5:23:26 PM
  */
 public abstract class AbstractTextSpectrumRenderer implements SpectrumRenderer
 {

diff --git a/ms2/src/org/labkey/ms2/ErrorImageRenderer.java b/ms2/src/org/labkey/ms2/ErrorImageRenderer.java
@@ -16,8 +16,9 @@
 
 package org.labkey.ms2;
 
+import jakarta.servlet.http.HttpServletResponse;
+
 import javax.imageio.ImageIO;
-import javax.servlet.http.HttpServletResponse;
 import java.awt.*;
 import java.awt.image.BufferedImage;
 import java.io.IOException;

diff --git a/ms2/src/org/labkey/ms2/MS2Controller.java b/ms2/src/org/labkey/ms2/MS2Controller.java
@@ -176,8 +176,8 @@
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.awt.*;
 import java.io.File;
 import java.io.IOException;

diff --git a/ms2/src/org/labkey/ms2/MS2ExportType.java b/ms2/src/org/labkey/ms2/MS2ExportType.java
@@ -24,7 +24,7 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.ms2.peptideview.AbstractMS2RunView;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.Writer;
 import java.util.List;

diff --git a/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java b/ms2/src/org/labkey/ms2/PeptideProphetGraphs.java
@@ -30,7 +30,7 @@
 import org.labkey.ms2.reader.PeptideProphetSummary;
 import org.labkey.ms2.reader.SensitivitySummary;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.awt.*;
 import java.io.IOException;
 import java.sql.ResultSet;

diff --git a/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java b/ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java
@@ -67,7 +67,7 @@
 import org.labkey.ms2.protein.tools.GoLoader;
 import org.labkey.ms2.protein.tools.ProteinDictionaryHelpers;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;

diff --git a/ms2/src/org/labkey/ms2/protein/tools/FTPUtil.java b/ms2/src/org/labkey/ms2/protein/tools/FTPUtil.java
@@ -22,7 +22,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.util.FileUtil;
 
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletException;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;

diff --git a/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java b/ms2/src/org/labkey/ms2/protein/tools/GoLoader.java
@@ -34,7 +34,7 @@
 import org.labkey.api.view.WebPartView;
 import org.labkey.ms2.protein.ProteinManager;
 
-import javax.servlet.ServletException;
+import jakarta.servlet.ServletException;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;

diff --git a/ms2/src/org/labkey/ms2/query/ComparePeptideTableInfo.java b/ms2/src/org/labkey/ms2/query/ComparePeptideTableInfo.java
@@ -28,7 +28,7 @@
 import org.labkey.ms2.MS2Manager;
 import org.labkey.ms2.MS2Run;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;