Tomcat 10 - Update namespace of Jakarta EE packages (#190)

Co-authored-by: Adam Rauch <adam@labkey.com>

Author: labkey-tchad

LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingTriggerHelper.java

@@ -16,7 +16,7 @@
 import org.labkey.api.util.MailHelper;
 import org.labkey.api.util.PageFlowUtil;
 
-import javax.mail.Message;
+import jakarta.mail.Message;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

mGAP/src/org/labkey/mgap/mGAPController.java

@@ -98,10 +98,10 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.mail.Address;
-import javax.mail.Message;
-import javax.mail.internet.InternetAddress;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.mail.Address;
+import jakarta.mail.Message;
+import jakarta.mail.internet.InternetAddress;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileInputStream;

mGAP/src/org/labkey/mgap/pipeline/GroupCompareStep.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.util.Interval;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJob;
@@ -23,7 +24,6 @@
 import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
 import org.labkey.api.writer.PrintWriters;
 
-import javax.annotation.Nullable;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;

mGAP/src/org/labkey/mgap/pipeline/IndexVariantsForMgapStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
@@ -26,7 +27,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.mgap.mGAPSchema;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.Arrays;
 import java.util.List;

mGAP/src/org/labkey/mgap/pipeline/SampleSpecificGenotypeFiltrationStep.java

@@ -4,6 +4,7 @@
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -23,7 +24,6 @@
 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;

mGAP/src/org/labkey/mgap/pipeline/VcfComparisonStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 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;
@@ -15,7 +16,6 @@
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAlleleFreqStep.java

@@ -2,6 +2,7 @@
 
 import htsjdk.samtools.util.Interval;
 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;
@@ -16,7 +17,6 @@
 import org.labkey.api.sequenceanalysis.run.AbstractDiscvrSeqWrapper;
 import org.labkey.api.util.PageFlowUtil;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAnnotateNovelSitesStep.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.util.Interval;
 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.data.SimpleFilter;
 import org.labkey.api.data.TableSelector;
@@ -24,7 +25,6 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.mgap.mGAPSchema;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java

@@ -1,6 +1,7 @@
 package org.labkey.mgap.pipeline;
 
 import htsjdk.samtools.util.Interval;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
@@ -18,10 +19,8 @@
 import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep;
 import org.labkey.api.util.PageFlowUtil;
 
-import javax.annotation.Nullable;
 import java.io.File;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 /**

mcc/src/org/labkey/mcc/MccController.java

@@ -76,8 +76,8 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.mail.Address;
-import javax.mail.Message;
+import jakarta.mail.Address;
+import jakarta.mail.Message;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;