Merge branch 'discvr-23.7' into 23.3_fb_ux_tweaks

Sebastian Benjamin · Sebastian Benjamin · commit 2e95098616a9 · 2023-08-14T10:55:34.000-07:00
diff --git a/.github/workflows/branch_release.yml b/.github/workflows/branch_release.yml
@@ -15,7 +15,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Create branches and PRs
         uses: LabKey/gitHubActions/branch-release@develop
diff --git a/.github/workflows/merge_release.yml b/.github/workflows/merge_release.yml
@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Merge PR
         uses: LabKey/gitHubActions/merge-release@develop
diff --git a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapConnectionWrapper.java b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapConnectionWrapper.java
@@ -95,7 +95,7 @@ private LdapConnection getConnection() throws LdapException
     {
         try
         {
-            LdapConnection connection = _pool.makeObject();
+            LdapConnection connection = _pool.makeObject().getObject();
             connection.bind();
 
             if (!connection.isConnected())
diff --git a/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java b/OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java
@@ -1,6 +1,6 @@
 package org.labkey.openldapsync.ldap;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.directory.api.ldap.model.exception.LdapException;
 import org.apache.directory.api.ldap.model.exception.LdapInvalidDnException;
 import org.apache.directory.api.ldap.model.name.Dn;
@@ -347,7 +347,7 @@ private String getNameForGroup(LdapEntry group) throws LdapException
         //concatenate to the group name if the field is not empty
         if (StringUtils.trimToNull(_settings.getGroupNameSuffix()) != null)
         {
-            //Note: do not trim the suffix, as this allows the admin to provide leading whitespace.  for example: the suffix " (LDAP)" would result in "MyGroup (LDAP)"
+//            Note: do not trim the suffix, as this allows the admin to provide leading whitespace.  for example: the suffix " (LDAP)" would result in "MyGroup (LDAP)"
             groupName = groupName.concat(_settings.getGroupNameSuffix());
         }
 
diff --git a/SequenceAnalysis/build.gradle b/SequenceAnalysis/build.gradle
@@ -23,7 +23,6 @@ repositories {
 configurations.all {
     resolutionStrategy {
         force "com.sun.activation:jakarta.activation:${activationVersion}"
-        force "javax.xml.bind:jaxb-api:2.3.0"  // CONSIDER: Exclude jaxb-api? It's essentially the same jar as jakarta.xml.bind-api (below)
         // NOTE: this should be kept in sync with mcc module:
         force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbVersion}"
     }
@@ -61,8 +60,8 @@ dependencies {
             ),
             {
                 // Exclude activation jars from webapp to avoid classloader conflicts with <tomcat>/lib/javax.activation.jar
-                exclude group: 'jakarta.activation', module: 'jakarta.activation-api'
                 exclude group: 'com.sun.activation', module: 'jakarta.activation'
+                exclude group: 'javax.activation', module: 'javax.activation-api'
             }
     )
 
@@ -79,8 +78,8 @@ dependencies {
             ),
             {
                 // Exclude activation jars from webapp to avoid classloader conflicts with <tomcat>/lib/javax.activation.jar
-                exclude group: 'jakarta.activation', module: 'jakarta.activation-api'
                 exclude group: 'com.sun.activation', module: 'jakarta.activation'
+                exclude group: 'javax.activation', module: 'javax.activation-api'
             }
     )
 
@@ -116,7 +115,7 @@ dependencies {
     BuildUtils.addExternalDependency(
             project,
             new ExternalDependency(
-                    "com.github.broadinstitute:picard:2.27.4",
+                    "com.github.broadinstitute:picard:3.0.0",
                     "Picard Tools Lib",
                     "PicardTools",
                     "https://github.com/broadinstitute/picard",
@@ -189,19 +188,18 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
     }
 }
 
-project.task("copyJars",
-        type: Copy,
-        group: "Build",
-        description: "Copy commons-math3 JAR to module's lib directory",
+project.tasks.register("copyJars", Copy)
         { CopySpec copy ->
+            copy.group = "Build"
+            copy.description = "Copy commons-math3 JAR to module's lib directory"
+
             copy.setDuplicatesStrategy(DuplicatesStrategy.EXCLUDE)
             copy.from(project.configurations.external)
             copy.into new File("${project.labkey.explodedModuleLibDir}")
             copy.include {
                 "**commons-math3-**.jar"
             }
         }
-)
 
-project.tasks.module.dependsOn(project.tasks.copyJars)
-project.tasks.copyJars.mustRunAfter(project.tasks.populateExplodedLib)
+project.tasks.named('module').configure { dependsOn(project.tasks.copyJars) }
+project.tasks.named('copyJars').configure { mustRunAfter(project.tasks.populateExplodedLib) }
diff --git a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh
@@ -865,12 +865,13 @@ then
       install ./cutadapt-1.8.1/bin/_preamble.py ${LKTOOLS_DIR}/_preamble.py
       cp -R ./cutadapt-1.8.1/cutadapt ${LKTOOLS_DIR}/cutadapt
     else
-      $PIP_EXE install --user cutadapt
+      $PIP_EXE install --user cutadapt==4.2
       $PIP_EXE show cutadapt
       $PIP_EXE install --user pyinstaller
       $PIP_EXE show pyinstaller
       ~/.local/bin/pyinstaller --onefile --clean ~/.local/bin/cutadapt
       cp ./dist/cutadapt ${LKTOOLS_DIR}/cutadapt
+      ${LKTOOLS_DIR}/cutadapt -h
     fi
 else
     echo "Already installed"
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java
@@ -1952,23 +1952,23 @@ public enum TYPE
 
         public String getJobName()
         {
-            return getNewJsonObject().optString("jobName");
+            return getJsonObject().optString("jobName");
         }
 
         public String getDescription()
         {
-            return getNewJsonObject().optString("description");
+            return getJsonObject().optString("description");
         }
 
         public TYPE getType()
         {
-            return !getNewJsonObject().has("type") ? null : TYPE.valueOf(getNewJsonObject().getString("type"));
+            return !getJsonObject().has("type") ? null : TYPE.valueOf(getJsonObject().getString("type"));
         }
 
         public JSONObject getJobParameters()
         {
-            // Return clone so we dont mutate it:
-            return new JSONObject(getNewJsonObject().optJSONObject("jobParameters").toMap());
+            // Return clone so we don't mutate it:
+            return new JSONObject(getJsonObject().optJSONObject("jobParameters").toMap());
         }
 
         public JSONArray getReadsetIds()
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java
@@ -85,7 +85,7 @@ private void addFileSetCol(AbstractTableInfo ti)
         String name = "fileSets";
         if (ti.getColumn(name) == null)
         {
-            SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, "','")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
+            SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, ",")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
             ExprColumn newCol = new ExprColumn(ti, name, sql, JdbcType.VARCHAR, ti.getColumn("rowId"));
             newCol.setLabel("File Sets");
             newCol.setDisplayColumnFactory(new FileSetDisplayColumnFactory());
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java
@@ -134,7 +134,7 @@ private TableInfo createAnalysesTable(TableInfo sourceTable, ContainerFilter cf)
         {
             String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
             SQLFragment sql = new SQLFragment("(SELECT ").
-                    append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, chr + "(10)")).
+                    append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, new SQLFragment(chr + "(10)"))).
                     append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " rd WHERE rd.analysis_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
             ExprColumn newCol = new ExprColumn(ret, "outputFileTypes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setLabel("Output File Types");
@@ -189,7 +189,7 @@ private TableInfo createOutputFiles(TableInfo sourceTable, ContainerFilter cf)
         if (ret.getColumn("analysisSets") == null)
         {
             String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("a.name"), true, true, chr + "(10)")).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SET_MEMBERS + " asm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SETS + " a ON (asm.analysisSet = a.rowid) WHERE asm.dataid = " + ExprColumn.STR_TABLE_ALIAS + ".dataid)");
+            SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("a.name"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SET_MEMBERS + " asm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SETS + " a ON (asm.analysisSet = a.rowid) WHERE asm.dataid = " + ExprColumn.STR_TABLE_ALIAS + ".dataid)");
             ExprColumn newCol = new ExprColumn(ret, "analysisSets", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=analysisSetMembers&query.dataid~eq=${dataid}", ret.getContainer().isWorkbook() ? ret.getContainer().getParent() : ret.getContainer()));
             newCol.setLabel("Analyses Using This File");
@@ -283,14 +283,14 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
             newCol.setLabel("Total Files");
             ret.addColumn(newCol);
 
-            SQLFragment sql2 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("d.Name"), true, true, "','")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.data d ON (d.RowId = rd.fileId1 OR d.RowId = rd.fileId2) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
+            SQLFragment sql2 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("d.Name"), true, true, ",")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.data d ON (d.RowId = rd.fileId1 OR d.RowId = rd.fileId2) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
             ExprColumn newCol2 = new ExprColumn(ret, "fileNames", sql2, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol2.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=readData&query.readset~eq=${rowid}"));
             newCol2.setLabel("File Names");
             newCol2.setDescription("This will display a comma-separated list of all file names with reads.  This can be useful for SRA submissions.");
             ret.addColumn(newCol2);
 
-            SQLFragment sql3 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.sra_accession"), true, true, "','")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
+            SQLFragment sql3 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.sra_accession"), true, true, ",")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
             ExprColumn newCol3 = new ExprColumn(ret, "sraRuns", sql3, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol3.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=readData&query.readset~eq=${rowid}"));
             newCol3.setLabel("SRA Runs");
@@ -327,7 +327,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
         if (ret.getColumn("distinctGenomes") == null)
         {
             String chr = ret.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("l.name"), true, true, (chr + "(10)"))).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a JOIN " + SequenceAnalysisSchema.SCHEMA_NAME  + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " l ON (a.library_id = l.rowid) WHERE a.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
+            SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("l.name"), true, true,  new SQLFragment(chr + "(10)"))).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a JOIN " + SequenceAnalysisSchema.SCHEMA_NAME  + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " l ON (a.library_id = l.rowid) WHERE a.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
             ExprColumn newCol = new ExprColumn(ret, "distinctGenomes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setLabel("Genomes With Alignments For Readset");
             newCol.setWidth("200");
@@ -351,7 +351,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
         {
             String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
             SQLFragment sql = new SQLFragment("(SELECT ").
-                    append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, chr + "(10)")).
+                    append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, new SQLFragment(chr + "(10)"))).
                     append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
             ExprColumn newCol = new ExprColumn(ret, "outputFileTypes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setLabel("Output File Types");
@@ -390,7 +390,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
 
         if (ret.getColumn("runIds") == null)
         {
-            SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.runId"), true, true, "','")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
+            SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.runId"), true, true, ",")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
             ExprColumn newCol = new ExprColumn(ret, "runIds", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setLabel("Run(s)");
 
@@ -400,7 +400,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
 
         if (ret.getColumn("jobIds") == null)
         {
-            SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("runs.jobId"), true, true, "','")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.experimentrun runs ON (rd.runId = runs.rowId) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
+            SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("runs.jobId"), true, true, ",")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.experimentrun runs ON (rd.runId = runs.rowId) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
             ExprColumn newCol = new ExprColumn(ret, "jobIds", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
             newCol.setLabel("Job(s)");
 
@@ -453,7 +453,7 @@ private TableInfo createRefSequencesTable(TableInfo sourceTable)
     {
         SharedDataTable<?> ret = new SharedDataTable<>(this, sourceTable);
         String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-        SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("r.name"), true, true, chr + "(10)")).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS + " rm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " r ON (rm.library_id = r.rowid) WHERE rm.ref_nt_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
+        SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("r.name"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS + " rm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " r ON (rm.library_id = r.rowid) WHERE rm.ref_nt_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
         ExprColumn newCol = new ExprColumn(ret, "genomes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
         newCol.setLabel("Genome(s) Using Sequence");
         newCol.setWidth("200");
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByCodonAggregator.java
@@ -18,7 +18,6 @@
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.reference.ReferenceSequence;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.SimpleFilter;
@@ -31,7 +30,6 @@
 import org.labkey.api.sequenceanalysis.model.AnalysisModel;
 import org.labkey.api.util.Pair;
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
-import org.labkey.sequenceanalysis.api.picard.CigarPositionIterable;
 import org.labkey.sequenceanalysis.run.util.AASnp;
 import org.labkey.sequenceanalysis.run.util.NTSnp;
 
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/AASnpByReadAggregator.java
@@ -3,13 +3,11 @@
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.reference.ReferenceSequence;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.security.User;
 import org.labkey.api.sequenceanalysis.model.AnalysisModel;
 import org.labkey.api.util.Pair;
-import org.labkey.sequenceanalysis.api.picard.CigarPositionIterable;
 import org.labkey.sequenceanalysis.run.util.AASnp;
 import org.labkey.sequenceanalysis.run.util.NTSnp;
 
diff --git a/jbrowse/build.gradle b/jbrowse/build.gradle
@@ -40,6 +40,10 @@ jbPkgTask.configure {
     outputs.dir(project.file("./resources/external/jb-cli"))
 }
 
+project.tasks.named('processModuleResources').configure {
+    dependsOn jbPkgTask
+}
+
 project.tasks.named("npm_run_build-prod").configure {
     finalizedBy jbPkgTask.get()
 }
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -213,7 +213,6 @@ const VariantTableWidget = observer(props => {
     }
 
     // Contains all features from the API call once the useEffect finished
-    //const [features, setFeatures] = useState<ExtendedVcfFeature[]>([])
     const [features, setFeatures] = useState<any[]>([])
     const [columns, setColumns] = useState<GridColDef[]>([])
 
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java

Original file line number	Diff line number	Diff line change
`@@ -95,7 +95,7 @@ private LdapConnection getConnection() throws LdapException`
`95`	`95`	`{`
`96`	`96`	`try`
`97`	`97`	`{`
`98`		`- LdapConnection connection = _pool.makeObject();`
	`98`	`+ LdapConnection connection = _pool.makeObject().getObject();`
`99`	`99`	`connection.bind();`
`100`	`100`
`101`	`101`	`if (!connection.isConnected())`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`package org.labkey.openldapsync.ldap;`
`2`	`2`
`3`		`-import org.apache.commons.lang.StringUtils;`
	`3`	`+import org.apache.commons.lang3.StringUtils;`
`4`	`4`	`import org.apache.directory.api.ldap.model.exception.LdapException;`
`5`	`5`	`import org.apache.directory.api.ldap.model.exception.LdapInvalidDnException;`
`6`	`6`	`import org.apache.directory.api.ldap.model.name.Dn;`
`@@ -347,7 +347,7 @@ private String getNameForGroup(LdapEntry group) throws LdapException`
`347`	`347`	`//concatenate to the group name if the field is not empty`
`348`	`348`	`if (StringUtils.trimToNull(_settings.getGroupNameSuffix()) != null)`
`349`	`349`	`{`
`350`		`- //Note: do not trim the suffix, as this allows the admin to provide leading whitespace. for example: the suffix " (LDAP)" would result in "MyGroup (LDAP)"`
	`350`	`+// Note: do not trim the suffix, as this allows the admin to provide leading whitespace. for example: the suffix " (LDAP)" would result in "MyGroup (LDAP)"`
`351`	`351`	`groupName = groupName.concat(_settings.getGroupNameSuffix());`
`352`	`352`	`}`
`353`	`353`
Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,6 @@ repositories {`
`23`	`23`	`configurations.all {`
`24`	`24`	`resolutionStrategy {`
`25`	`25`	`force "com.sun.activation:jakarta.activation:${activationVersion}"`
`26`		`- force "javax.xml.bind:jaxb-api:2.3.0" // CONSIDER: Exclude jaxb-api? It's essentially the same jar as jakarta.xml.bind-api (below)`
`27`	`26`	`// NOTE: this should be kept in sync with mcc module:`
`28`	`27`	`force "jakarta.xml.bind:jakarta.xml.bind-api:${jaxbVersion}"`
`29`	`28`	`}`
`@@ -61,8 +60,8 @@ dependencies {`
`61`	`60`	`),`
`62`	`61`	`{`
`63`	`62`	`// Exclude activation jars from webapp to avoid classloader conflicts with <tomcat>/lib/javax.activation.jar`
`64`		`- exclude group: 'jakarta.activation', module: 'jakarta.activation-api'`
`65`	`63`	`exclude group: 'com.sun.activation', module: 'jakarta.activation'`
	`64`	`+ exclude group: 'javax.activation', module: 'javax.activation-api'`
`66`	`65`	`}`
`67`	`66`	`)`
`68`	`67`
`@@ -79,8 +78,8 @@ dependencies {`
`79`	`78`	`),`
`80`	`79`	`{`
`81`	`80`	`// Exclude activation jars from webapp to avoid classloader conflicts with <tomcat>/lib/javax.activation.jar`
`82`		`- exclude group: 'jakarta.activation', module: 'jakarta.activation-api'`
`83`	`81`	`exclude group: 'com.sun.activation', module: 'jakarta.activation'`
	`82`	`+ exclude group: 'javax.activation', module: 'javax.activation-api'`
`84`	`83`	`}`
`85`	`84`	`)`
`86`	`85`
`@@ -116,7 +115,7 @@ dependencies {`
`116`	`115`	`BuildUtils.addExternalDependency(`
`117`	`116`	`project,`
`118`	`117`	`new ExternalDependency(`
`119`		`- "com.github.broadinstitute:picard:2.27.4",`
	`118`	`+ "com.github.broadinstitute:picard:3.0.0",`
`120`	`119`	`"Picard Tools Lib",`
`121`	`120`	`"PicardTools",`
`122`	`121`	`"https://github.com/broadinstitute/picard",`
`@@ -189,19 +188,18 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &`
`189`	`188`	`}`
`190`	`189`	`}`
`191`	`190`
`192`		`-project.task("copyJars",`
`193`		`- type: Copy,`
`194`		`- group: "Build",`
`195`		`- description: "Copy commons-math3 JAR to module's lib directory",`
	`191`	`+project.tasks.register("copyJars", Copy)`
`196`	`192`	`{ CopySpec copy ->`
	`193`	`+ copy.group = "Build"`
	`194`	`+ copy.description = "Copy commons-math3 JAR to module's lib directory"`
	`195`	`+`
`197`	`196`	`copy.setDuplicatesStrategy(DuplicatesStrategy.EXCLUDE)`
`198`	`197`	`copy.from(project.configurations.external)`
`199`	`198`	`copy.into new File("${project.labkey.explodedModuleLibDir}")`
`200`	`199`	`copy.include {`
`201`	`200`	`"commons-math3-.jar"`
`202`	`201`	`}`
`203`	`202`	`}`
`204`		`-)`
`205`	`203`
`206`		`-project.tasks.module.dependsOn(project.tasks.copyJars)`
`207`		`-project.tasks.copyJars.mustRunAfter(project.tasks.populateExplodedLib)`
	`204`	`+project.tasks.named('module').configure { dependsOn(project.tasks.copyJars) }`
	`205`	`+project.tasks.named('copyJars').configure { mustRunAfter(project.tasks.populateExplodedLib) }`
Original file line number	Diff line number	Diff line change
`@@ -1952,23 +1952,23 @@ public enum TYPE`
`1952`	`1952`
`1953`	`1953`	`public String getJobName()`
`1954`	`1954`	`{`
`1955`		`- return getNewJsonObject().optString("jobName");`
	`1955`	`+ return getJsonObject().optString("jobName");`
`1956`	`1956`	`}`
`1957`	`1957`
`1958`	`1958`	`public String getDescription()`
`1959`	`1959`	`{`
`1960`		`- return getNewJsonObject().optString("description");`
	`1960`	`+ return getJsonObject().optString("description");`
`1961`	`1961`	`}`
`1962`	`1962`
`1963`	`1963`	`public TYPE getType()`
`1964`	`1964`	`{`
`1965`		`- return !getNewJsonObject().has("type") ? null : TYPE.valueOf(getNewJsonObject().getString("type"));`
	`1965`	`+ return !getJsonObject().has("type") ? null : TYPE.valueOf(getJsonObject().getString("type"));`
`1966`	`1966`	`}`
`1967`	`1967`
`1968`	`1968`	`public JSONObject getJobParameters()`
`1969`	`1969`	`{`
`1970`		`- // Return clone so we dont mutate it:`
`1971`		`- return new JSONObject(getNewJsonObject().optJSONObject("jobParameters").toMap());`
	`1970`	`+ // Return clone so we don't mutate it:`
	`1971`	`+ return new JSONObject(getJsonObject().optJSONObject("jobParameters").toMap());`
`1972`	`1972`	`}`
`1973`	`1973`
`1974`	`1974`	`public JSONArray getReadsetIds()`
Original file line number	Diff line number	Diff line change
`@@ -85,7 +85,7 @@ private void addFileSetCol(AbstractTableInfo ti)`
`85`	`85`	`String name = "fileSets";`
`86`	`86`	`if (ti.getColumn(name) == null)`
`87`	`87`	`{`
`88`		`- SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, "','")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");`
	`88`	`+ SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, ",")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");`
`89`	`89`	`ExprColumn newCol = new ExprColumn(ti, name, sql, JdbcType.VARCHAR, ti.getColumn("rowId"));`
`90`	`90`	`newCol.setLabel("File Sets");`
`91`	`91`	`newCol.setDisplayColumnFactory(new FileSetDisplayColumnFactory());`