Tomcat 10 - Update namespace for Jakarta EE packages

SequenceAnalysis/build.gradle

@@ -20,7 +20,7 @@ repositories {
 
 configurations.all {
     resolutionStrategy {
-        force "com.sun.activation:jakarta.activation:${activationVersion}"
+        force "jakarta.activation:jakarta.activation-api:${activationVersion}"
         // NOTE: this should be kept in sync with mcc module:
         force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbVersion}"
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java

@@ -37,8 +37,8 @@
 import org.springframework.mock.web.MockHttpServletResponse;
 import org.springframework.web.bind.annotation.RequestMethod;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.util.Arrays;
 import java.util.Collections;

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -172,8 +172,8 @@
 import org.springframework.web.bind.ServletRequestParameterPropertyValues;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java

@@ -70,8 +70,8 @@
 import org.springframework.mock.web.MockHttpServletResponse;
 import org.springframework.web.bind.annotation.RequestMethod;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeConcordanceStep.java

@@ -7,6 +7,7 @@
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -22,7 +23,6 @@
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 import org.labkey.sequenceanalysis.run.util.VariantAnnotatorWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GenotypeFiltrationStep.java

@@ -1,6 +1,7 @@
 package org.labkey.sequenceanalysis.run.variant;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -16,7 +17,6 @@
 import org.labkey.api.sequenceanalysis.run.VariantFiltrationWrapper;
 import org.labkey.sequenceanalysis.pipeline.SequenceTaskHelper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -8,6 +8,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -22,11 +23,9 @@
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 public class KingInferenceStep extends AbstractCommandPipelineStep<KingInferenceStep.KingWrapper> implements VariantProcessingStep

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MendelianViolationReportStep.java

@@ -1,6 +1,7 @@
 package org.labkey.sequenceanalysis.run.variant;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep;
@@ -14,7 +15,6 @@
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
 import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/OutputVariantsStartingInIntervalsStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStep;
@@ -14,12 +15,10 @@
 import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
 import org.labkey.api.writer.PrintWriters;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**

blast/src/org/labkey/blast/BLASTController.java

@@ -63,8 +63,8 @@
 import org.springframework.web.multipart.MultipartHttpServletRequest;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStreamWriter;

blast/src/org/labkey/blast/model/BlastJob.java

@@ -1,5 +1,6 @@
 package org.labkey.blast.model;
 
+import jakarta.servlet.jsp.JspWriter;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -24,7 +25,6 @@
 import org.labkey.blast.BLASTSchema;
 import org.labkey.blast.BLASTWrapper;
 
-import javax.servlet.jsp.JspWriter;
 import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;

cluster/resources/web/cluster/htcondor/pipelineConfig.xml

@@ -3,7 +3,7 @@
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd">
 
-    <!--NOTE: if you plan to use ActiveMQ for status updates, you will need to configure this in labkey.xml-->
+    <!--NOTE: if you plan to use ActiveMQ for status updates, you will need to configure this in application.properties-->
 
     <bean id="pipelineJobService" class="org.labkey.pipeline.api.PipelineServiceImpl">
         <!--You will list all remote execution engines.  You will most likely only have one engine to register, but this example contains multiples to show different configurations-->

cluster/resources/web/cluster/slurm/pipelineConfig.xml

@@ -3,7 +3,7 @@
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd">
 
-    <!--NOTE: if you plan to use ActiveMQ for status updates, you will need to configure this in labkey.xml-->
+    <!--NOTE: if you plan to use ActiveMQ for status updates, you will need to configure this in application.properties-->
 
     <bean id="pipelineJobService" class="org.labkey.pipeline.api.PipelineServiceImpl">
         <!--You will list all remote execution engines.  You will most likely only have one engine to register, but this example contains multiples to show different configurations-->

cluster/src/org/labkey/cluster/ClusterManager.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.module.Module;
@@ -36,7 +37,6 @@
 import org.quartz.TriggerBuilder;
 import org.quartz.impl.StdSchedulerFactory;
 
-import javax.annotation.Nullable;
 import java.util.Arrays;
 import java.util.List;
 

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -12,6 +12,7 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -56,7 +57,6 @@
 import org.labkey.jbrowse.pipeline.JBrowseLucenePipelineJob;
 import org.labkey.sequenceanalysis.run.util.TabixRunner;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;

jbrowse/src/org/labkey/jbrowse/pipeline/IndexVariantsStep.java

@@ -1,9 +1,8 @@
 package org.labkey.jbrowse.pipeline;
 
 import htsjdk.samtools.util.Interval;
-import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.SystemUtils;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
@@ -14,12 +13,8 @@
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStepOutputImpl;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
-import org.labkey.api.writer.PrintWriters;
 
-import javax.annotation.Nullable;
 import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
 import java.util.Arrays;
 import java.util.List;
 

singlecell/src/org/labkey/singlecell/SingleCellController.java

@@ -63,7 +63,7 @@
 import org.springframework.validation.BindException;
 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.IOException;

singlecell/src/org/labkey/singlecell/analysis/SingleCellReadsetListener.java

@@ -2,6 +2,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
@@ -22,7 +23,6 @@
 import org.labkey.singlecell.SingleCellModule;
 import org.labkey.singlecell.SingleCellSchema;
 
-import javax.annotation.Nullable;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;

singlecell/src/org/labkey/singlecell/run/NimbleHelper.java

@@ -5,6 +5,7 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.output.StringBuilderWriter;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.data.ColumnInfo;
@@ -31,7 +32,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.writer.PrintWriters;
 
-import javax.annotation.Nullable;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;