Migrate ONPRC repos (#257)

Author: labkey-adam

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;

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/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;