Merge pull request #1 from BimberLab/discvr-21.3

Updating branch from BimberLab repo

Author: jctrotter

.github/workflows/build.yml

@@ -3,7 +3,9 @@ on:
   workflow_dispatch:
   push:
     branches:
-      - !latest
+      - "*"
+    tags-ignore:
+      - latest
   pull_request:
 jobs:
   build-modules:
@@ -12,20 +14,42 @@ jobs:
     if: github.repository == 'BimberLab/DiscvrLabKeyModules'
     runs-on: ubuntu-latest
     steps:
+      - name: "Find default branch"
+        uses: octokit/request-action@v2.x
+        id: get_default_branch
+        with:
+          route: GET /repos/${{ github.repository }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.PAT }}
+
+      - name: "Print default branch"
+        run: |
+          echo 'Default branch: ${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}'
+          echo "##[set-output name=branch;]$(echo '${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}')"
+        id: default-branch
+
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract-branch
+
       - name: "Build DISCVR"
         uses: bimberlabinternal/DevOps/githubActions/discvr-build@master
         with:
           artifactory_user: ${{secrets.artifactory_user}}
           artifactory_password: ${{secrets.artifactory_password}}
           # NOTE: permissions are limited on the default secrets.GITHUB_TOKEN, including updating workflows, so use a personal access token
           github_token: ${{ secrets.PAT }}
+        env:
+          # Only generate the distribution if this is the default branch
+          GENERATE_DIST: ${{ steps.default-branch.branch == steps.extract-branch.branch && '1' || '0' }}
 
       - name: Publish Release
-
+        if: github.ref == '/refs/heads/${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}'
         uses: "marvinpinto/action-automatic-releases@latest"
         with:
           repo_token: "${{ secrets.PAT }}"
+          automatic_release_tag: "latest"
           prerelease: true
-          title: "Release "
-          files: |
-            /home/runner/work/_temp/_github_home/lkDist/discvr/DISCVR-*
+          title: "Development Build: ${{ fromJson(steps.get_default_branch.outputs.data).default_branch }}"
+          files: /home/runner/work/_temp/_github_home/lkDist/discvr/DISCVR-*

SequenceAnalysis/build.gradle

@@ -67,3 +67,20 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
       dependsOn(createPipelineConfigTask)
    }
 }
+
+project.task("copyJars",
+        type: Copy,
+        group: "Build",
+        description: "Copy commons-math3 JAR to module's lib directory",
+        { CopySpec copy ->
+           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.processModuleResources)

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics_analyses_pivoted.sql

@@ -5,9 +5,10 @@ select
   max(category) as category,
   count(*) as records,
   metricName,
-  avg(metricValue) as metricValue
+  avg(metricValue) as metricValue,
+  group_concat(distinct qualValue, chr(10)) as qualValue
 
 from sequenceanalysis.quality_metrics q
 where (category is null or category not in ('FIRST_OF_PAIR', 'SECOND_OF_PAIR'))
 group by analysis_id, metricName
-pivot metricValue by metricName
+pivot metricValue, qualValue by metricName

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics_pivoted.sql

@@ -6,9 +6,10 @@ select
   max(category) as category,
   count(*) as records,
   metricName,
-  avg(metricValue) as metricValue
+  avg(metricValue) as metricValue,
+  group_concat(distinct qualValue, chr(10)) as qualValue
 
 from sequenceanalysis.quality_metrics q
 where (category is null or category not in ('FIRST_OF_PAIR', 'SECOND_OF_PAIR'))
 group by dataId, metricName
-pivot metricValue by metricName
+pivot metricValue, qualValue by metricName

SequenceAnalysis/resources/queries/sequenceanalysis/ref_aa_sequences.js

@@ -28,7 +28,7 @@ function beforeUpsert(row, errors) {
 
     if (row.name){
         //trim name
-        row.name = row.name.replace(/^\s+|\s+$/g, '')
+        row.name = row.name.replace(/^\s+|\s+$/g, '');
 
         //enforce no pipe character in name
         if (row.name.match(/\|/)){
@@ -47,7 +47,7 @@ function beforeUpsert(row, errors) {
         exonArray = row.exons.split(';');
         for (var i = 0;i<exonArray.length; i++) {
             var exon = exonArray[i].split('-');
-            if (exon.length != 2 || isNaN(exon[0]) || isNaN(exon[1])){
+            if (exon.length !== 2 || isNaN(exon[0]) || isNaN(exon[1])){
                 addError(errors, 'exons', 'Improper exons: ' + row.exons);
                 return;
             }
@@ -59,25 +59,25 @@ function beforeUpsert(row, errors) {
     }
 
     //infer from coordinates:
-    if (row.ref_nt_id && exonArray.length){
+    if (!row.sequence && row.ref_nt_id && exonArray.length){
         row.isComplement = !!row.isComplement;
         var sequence = triggerHelper.extractAASequence(row.ref_nt_id, exonArray, row.isComplement);
-        if (sequence && lengthFromExons != sequence.length){
+        if (sequence && lengthFromExons !== sequence.length){
             addError(errors, 'sequence', 'The length of the sequence (' + sequence.length + ') does not match the exon boundaries (' + lengthFromExons + ')');
             return;
         }
 
         row.sequence = sequence;
     }
 
-    if (row.exons && row.sequence && lengthFromExons != row.sequence.length){
+    if (row.exons && row.sequence && lengthFromExons !== row.sequence.length){
         addError(errors, 'sequence', 'The length of the sequence (' + row.sequence.length + ') does not match the exon boundaries (' + lengthFromExons + ')');
     }
 
     if (row.exons && row.exons.length){
         var exonArray = row.exons.split(';');
         var coordinates = exonArray[0].split('-');
-        if(coordinates.length == 2)
+        if(coordinates.length === 2)
             row.start_location = coordinates[0];
     }
 }

SequenceAnalysis/resources/web/SequenceAnalysis/field/TrimmingTextArea.js

@@ -19,6 +19,16 @@ Ext4.define('SequenceAnalysis.field.TrimmingTextArea', {
         this.callParent();
     },
 
+    getErrors: function(value){
+        var errors = this.callParent(arguments);
+
+        if (!this.allowBlank && Ext4.isEmpty(this.getSubmitValue())) {
+            errors = errors.concat('Must enter a value');
+        }
+
+        return errors;
+    },
+
     setValue: function(val){
         if (Ext4.isString(val)) {
             val = val.split(this.delimiter);

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AnalysisSectionPanel.js

@@ -59,8 +59,14 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                 }
 
                 //force checkboxes to submit true instead of 'on'
-                if (o.xtype == 'checkbox' && !Ext4.isDefined(o.inputValue)){
-                    o.inputValue = true;
+                if (o.xtype === 'checkbox'){
+                    if (!Ext4.isDefined(o.inputValue)){
+                        o.inputValue = true;
+                    }
+
+                    if (o.value){
+                        o.checked = true;
+                    }
                 }
 
                 paramCfg.push(o);

SequenceAnalysis/resources/web/SequenceAnalysis/window/OutputHandlerWindow.js

@@ -170,7 +170,7 @@ Ext4.define('SequenceAnalysis.window.OutputHandlerWindow', {
                 }
 
                 //force checkboxes to submit true instead of 'on'
-                if (o.xtype == 'checkbox'){
+                if (o.xtype === 'checkbox'){
                     if (!Ext4.isDefined(o.inputValue)){
                         o.inputValue = true;
                     }

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

@@ -131,6 +131,7 @@
 import org.labkey.sequenceanalysis.run.reference.SavedReferenceLibraryStep;
 import org.labkey.sequenceanalysis.run.reference.VirusReferenceLibraryStep;
 import org.labkey.sequenceanalysis.run.util.CombineGVCFsHandler;
+import org.labkey.sequenceanalysis.run.util.FastqcRunner;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBAppendHandler;
 import org.labkey.sequenceanalysis.run.util.GenomicsDBImportHandler;
 import org.labkey.sequenceanalysis.run.variant.CombineVariantsHandler;
@@ -476,7 +477,8 @@ public Set<Class> getUnitTests()
                 ProcessVariantsHandler.TestCase.class,
                 VariantProcessingJob.TestCase.class,
                 ScatterGatherUtils.TestCase.class,
-                ChainFileValidator.TestCase.class
+                ChainFileValidator.TestCase.class,
+                FastqcRunner.TestCase.class
         );
     }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java

@@ -26,6 +26,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.HasJobParams;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputTracker;
 import org.labkey.api.assay.AssayFileWriter;
+import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
@@ -103,14 +104,23 @@ public SequenceJob(String providerName, Container c, User u, @Nullable String jo
         _taskPipelineId = taskPipelineId;
         _folderPrefix = folderPrefix;
         _webserverJobDir = createLocalDirectory(pipeRoot);
+
+        addCustomParams(params);
         _params = params;
+
         writeParameters(params);
 
         _folderFileRoot = c.isWorkbook()? PipelineService.get().findPipelineRoot(c.getParent()) : pipeRoot;
 
         setLogFile(_getLogFile());
     }
 
+    protected void addCustomParams(JSONObject params)
+    {
+        params.put("serverBaseUrl", AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath());
+        params.put("labkeyFolderPath", getContainer().isWorkbook() ? getContainer().getParent().getPath() : getContainer().getPath());
+    }
+
     private File _getLogFile() throws IOException
     {
         return AssayFileWriter.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectory());