Merge pull request #25 from LabKey/fb_merge_discvr-19.3

Merge discvr19.3 to develop

Author: bbimber

.github/workflows/sync-repos.yml

@@ -4,25 +4,25 @@ on:
     - cron:  "10 */3 * * *"
 jobs:
   sync-release-branches:
-    if: github.repository == 'BimberLab/DiscvrLabkeyModules'
+    if: github.repository == 'BimberLab/DiscvrLabKeyModules'
     runs-on: ubuntu-latest
     steps:
       - name: "Sync Release Branches"
         uses: bimberlabinternal/DevOps/githubActions/branch-create@master
         with:
-          source_repo: "labkey/DiscvrLabkeyModules"
+          source_repo: "labkey/DiscvrLabKeyModules"
           source_branch_prefix: "release"
-          destination_repo: "BimberLab/DiscvrLabkeyModules"
+          destination_repo: "BimberLab/DiscvrLabKeyModules"
           destination_branch_prefix: "discvr-"
           github_token: ${{ secrets.GITHUB_TOKEN }}
   sync-develop:
-    if: github.repository == 'BimberLab/DiscvrLabkeyModules'
+    if: github.repository == 'BimberLab/DiscvrLabKeyModules'
     runs-on: ubuntu-latest
     steps:
       - name: "Sync Develop Branch"
         uses: bimberlabinternal/DevOps/githubActions/git-sync@master
         with:
-          source_repo: "labkey/DiscvrLabkeyModules"
+          source_repo: "labkey/DiscvrLabKeyModules"
           source_branch: "develop"
           destination_branch: "develop"
           github_token: ${{ secrets.GITHUB_TOKEN }}

.travis.yml

@@ -14,7 +14,6 @@ cache:
     - $HOME/.gradle/caches/
     - $HOME/.gradle/wrapper/
     - $HOME/.m2
-    - $HOME/labkey_build/
     - $HOME/site-library
 
 install: skip

SequenceAnalysis/build.gradle

@@ -29,6 +29,9 @@ dependencies {
    external("com.github.broadinstitute:picard:2.18.4") {
       exclude group: "javax.servlet", module: "servlet-api"
    }
+
+   BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
+   BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
 }
 
 if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null && project.hasProperty("teamcity"))

SequenceAnalysis/module.properties

@@ -1,4 +1,3 @@
 ModuleClass: org.labkey.sequenceanalysis.SequenceAnalysisModule
-ModuleDependencies: Pipeline, FileContent, Experiment, LDK, Laboratory
 ConsolidateScripts: false
 ManageVersion: false

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

@@ -143,6 +143,7 @@
 import org.labkey.sequenceanalysis.pipeline.ImportGenomeTrackPipelineJob;
 import org.labkey.sequenceanalysis.pipeline.OrphanFilePipelineJob;
 import org.labkey.sequenceanalysis.pipeline.ReadsetImportJob;
+import org.labkey.sequenceanalysis.pipeline.ReferenceGenomeImpl;
 import org.labkey.sequenceanalysis.pipeline.ReferenceLibraryPipelineJob;
 import org.labkey.sequenceanalysis.pipeline.SequenceAlignmentJob;
 import org.labkey.sequenceanalysis.pipeline.SequenceConcatPipelineJob;
@@ -2807,6 +2808,22 @@ protected File getTargetFile(String filename) throws IOException
             }
         }
 
+        @Override
+        public void validateCommand(ImportTrackForm form, Errors errors)
+        {
+            super.validateCommand(form, errors);
+
+            //ensure has write access in genome container
+            if (form.getLibraryId() != null)
+            {
+                Container genomeFolder = ReferenceGenomeImpl.getFolderForGenome(form.getLibraryId());
+                if (genomeFolder != null && !genomeFolder.hasPermission(getUser(), UpdatePermission.class))
+                {
+                    throw new UnauthorizedException("The current user does not have permission to update genome " + form.getLibraryId() + " which is saved in the folder: " + genomeFolder.getPath());
+                }
+            }
+        }
+
         @Override
         public String getResponse(ImportTrackForm form, Map<String, Pair<File, String>> files) throws UploadException
         {
@@ -2827,7 +2844,7 @@ public String getResponse(ImportTrackForm form, Map<String, Pair<File, String>>
                         Container target = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
                         PipeRoot root = PipelineService.get().getPipelineRootSetting(target);
 
-                        //TODO: permissions on source container (shared)?
+                        //note: permissions on source container should be checked in validate()
                         ImportGenomeTrackPipelineJob job = new ImportGenomeTrackPipelineJob(target, getUser(), null, root, form.getLibraryId(), form.getTrackName(), file, entry.getValue().getValue(), form.getTrackDescription(), form.getDoChrTranslation() == null ? true : form.getDoChrTranslation());
                         PipelineService.get().queueJob(job);
 
@@ -4967,6 +4984,12 @@ public ApiResponse execute(ImportTracksForm form, BindException errors) throws E
                 try
                 {
                     Container target = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
+                    Container genomeFolder = ReferenceGenomeImpl.getFolderForGenome(o.getInt("libraryId"));
+                    if (!genomeFolder.hasPermission(getUser(), UpdatePermission.class))
+                    {
+                        throw new UnauthorizedException("You do not have permission to update genome " + o.get("libraryId") + ", which is saved in the folder: " + genomeFolder.getPath());
+                    }
+
                     ImportGenomeTrackPipelineJob job = new ImportGenomeTrackPipelineJob(target, getUser(), null, root, o.getInt("libraryId"), o.getString("name"), file, file.getName(), o.getString("description"), form.getDoChrTranslation() == null ? true : form.getDoChrTranslation());
                     toCreate.add(job);
                 }

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

@@ -3,11 +3,18 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.sequenceanalysis.pipeline.AlignerIndexUtil;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 
 import java.io.File;
 
@@ -142,4 +149,11 @@ public File getAlignerIndexDir(String name)
             }
         }
     }
+
+    public static Container getFolderForGenome(int libraryId)
+    {
+        String containerId = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("container"), new SimpleFilter(FieldKey.fromString("rowid"), libraryId), null).getObject(String.class);
+
+        return containerId == null ? null : ContainerManager.getForId(containerId);
+    }
 }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CombineGVCFsHandler.java

@@ -45,8 +45,8 @@ public CombineGVCFsHandler()
         super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), NAME, "This will run GATK\'s CombineGVCFs on a set of GVCF files.  Note: this cannot work against any VCF file - these are primarily VCFs created using GATK\'s HaplotypeCaller.", new LinkedHashSet<>(Arrays.asList("sequenceanalysis/panel/VariantScatterGatherPanel.js")), Arrays.asList(
                 ToolParameterDescriptor.create("fileBaseName", "Filename", "This is the basename that will be used for the output gzipped VCF", "textfield", null, "CombinedGenotypes"),
                 ToolParameterDescriptor.create("doCopyLocal", "Copy gVCFs To Working Directory", "If selected, the gVCFs will be copied to the working directory first, which can improve performance when working with a large set of files.", "checkbox", new JSONObject(){{
-                    put("checked", true);
-                }}, true),
+                    put("checked", false);
+                }}, false),
                 ToolParameterDescriptor.create("scatterGather", "Scatter/Gather Options", "If selected, this job will be divided to run job per chromosome.  The final step will take the VCF from each intermediate step and combined to make a final VCF file.", "sequenceanalysis-variantscattergatherpanel", null, false)
         ));
     }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenomicsDBImportHandler.java

@@ -40,7 +40,7 @@ public GenomicsDBImportHandler()
         super(ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class), NAME, "This will run GATK\'s GenomicsDBImport on a set of GVCF files.  Note: this cannot work against any VCF file - these are primarily VCFs created using GATK\'s HaplotypeCaller.", null, Arrays.asList(
                 ToolParameterDescriptor.create("fileBaseName", "Filename", "This is the basename that will be used for the output gzipped VCF", "textfield", null, "CombinedGenotypes"),
                 ToolParameterDescriptor.create("doCopyLocal", "Copy gVCFs To Working Directory", "If selected, the gVCFs will be copied to the working directory first, which can improve performance when working with a large set of files.", "checkbox", new JSONObject(){{
-                    put("checked", true);
+                    put("checked", false);
                 }}, false),
                 ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--batch-size"), "batchSize", "Batch Size", "Batch size controls the number of samples for which readers are open at once and therefore provides a way to minimize memory consumption. However, it can take longer to complete. Use the consolidate flag if more than a hundred batches were used. This will improve feature read time. batchSize=0 means no batching (i.e. readers for all samples will be opened at once) Defaults to 0.", "ldk-integerfield", null, null),
                 ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--reader-threads"), "readerThreads", "Reader Threads", "How many simultaneous threads to use when opening VCFs in batches; higher values may improve performance when network latency is an issue", "ldk-integerfield", null, null)

blast/build.gradle

@@ -5,4 +5,8 @@ dependencies
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "apiJarFile")
+
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:SequenceAnalysis", depProjectConfig: "published", depExtension: "module")
 }

blast/module.properties

@@ -1,4 +1,3 @@
 ModuleClass: org.labkey.blast.BLASTModule
-ModuleDependencies: FileContent, Experiment, LDK, Laboratory, SequenceAnalysis
 ConsolidateScripts: false
 ManageVersion: false