Merge branch 'discvr-21.3-jbrowse2' into 21.4-jbrowse2-2.1.0

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/api-src/org/labkey/api/sequenceanalysis/pipeline/DefaultPipelineStepOutput.java

@@ -105,9 +105,24 @@ public List<SequenceOutput> getSequenceOutputs()
     @Override
     public void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description)
     {
+        _intermediateFiles.remove(file);
+
         _sequenceOutputs.add(new SequenceOutput(file, label, category, readsetId, analysisId, genomeId, description));
     }
 
+    private boolean existsAsOutput(File f)
+    {
+        for (SequenceOutput so  : _sequenceOutputs)
+        {
+            if (so.getFile() != null && so.getFile().equals(f))
+            {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
     @Override
     public void addInput(File input, String role)
     {
@@ -132,13 +147,16 @@ public void addIntermediateFile(File file, String role)
         if (role != null)
             addOutput(file, role);
 
-        _intermediateFiles.add(file);
+        if (!existsAsOutput(file))
+        {
+            _intermediateFiles.add(file);
+        }
     }
 
     @Override
     public void addIntermediateFiles(Collection<File> files)
     {
-        _intermediateFiles.addAll(files);
+        files.forEach(this::addIntermediateFile);
     }
 
     public void addPicardMetricsFile(Readset rs, File metricFile, File inputFile)

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/.qview.xml

@@ -9,6 +9,7 @@
        <column name="readset" />
        <column name="analysis_id" />
        <column name="runid" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="dataid/Name"/>

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/readData/.qview.xml

@@ -19,7 +19,7 @@
            </properties>
        </column>
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

SequenceAnalysis/resources/queries/sequenceanalysis/readData/File Details.qview.xml

@@ -15,7 +15,7 @@
        <column name="archived" />
 
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

SequenceAnalysis/resources/queries/sequenceanalysis/readData/With Filepath.qview.xml

@@ -15,7 +15,7 @@
        <column name="archived" />
 
        <column name="created" />
-       <column name="readset/workbook" />
+       <column name="workbook" />
    </columns>
    <sorts>
        <sort column="readset" />

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];
     }
 }