Merge discvr-23.11 to develop

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BcftoolsRunner.java

@@ -18,7 +18,7 @@ public BcftoolsRunner(@Nullable Logger logger)
         super(logger);
     }
 
-    public File getBcfToolsPath()
+    public static File getBcfToolsPath()
     {
         return SequencePipelineService.get().getExeForPackage("BCFTOOLSPATH", "bcftools");
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/TaskFileManager.java

@@ -56,6 +56,8 @@ public interface TaskFileManager extends PipelineOutputTracker
 
     boolean isDeleteIntermediateFiles();
 
+    public boolean performCleanupAfterEachStep();
+
     boolean isCopyInputsLocally();
 
     void addPicardMetricsFiles(List<PipelineStepOutput.PicardMetricsOutput> files) throws PipelineJobException;

SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml

@@ -17,6 +17,8 @@
        <column name="workbook" />
        <column name="sraRuns" />
        <column name="isArchived" />
+       <column name="totalFiles" />
+       <column name="readdataWithoutSra" />
        <column name="files" />
    </columns>
    <sorts>

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentImportPanel.js

@@ -94,6 +94,14 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
                 inputValue: true,
                 checked: true,
                 xtype: 'checkbox'
+            },{
+                fieldLabel: 'Perform Cleanup After Each Step',
+                helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+                name: 'performCleanupAfterEachStep',
+                inputValue: true,
+                uncheckedValue: false,
+                checked: true,
+                xtype: 'checkbox'
             },{
                 fieldLabel: 'Treatment of Input Files',
                 xtype: 'combo',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceAnalysisPanel.js

@@ -309,6 +309,14 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 uncheckedValue: false,
                 checked: true,
                 xtype: 'checkbox'
+            },{
+                fieldLabel: 'Perform Cleanup After Each Step',
+                helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+                name: 'performCleanupAfterEachStep',
+                inputValue: true,
+                uncheckedValue: false,
+                checked: true,
+                xtype: 'checkbox'
             },{
                 fieldLabel: 'Copy Inputs To Working Directory?',
                 helpPopup: 'Check to copy the input files to the working directory.  Depending on your environment, this may or may not help performance.',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -74,6 +74,14 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 				inputValue: true,
 				checked: true,
 				xtype: 'checkbox'
+			},{
+				fieldLabel: 'Perform Cleanup After Each Step',
+				helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+				name: 'performCleanupAfterEachStep',
+				inputValue: true,
+				uncheckedValue: false,
+				checked: true,
+				xtype: 'checkbox'
 			}, this.getSaveTemplateCfg()]
 		};
 	},

SequenceAnalysis/resources/web/SequenceAnalysis/window/ArchiveReadsetsWindow.js

@@ -0,0 +1,69 @@
+Ext4.define('SequenceAnalysis.window.ArchiveReadsetsWindow', {
+    extend: 'Ext.window.Window',
+
+    statics: {
+        buttonHandler: function(dataRegionName){
+            Ext4.create('SequenceAnalysis.window.ArchiveReadsetsWindow', {
+                dataRegionName: dataRegionName,
+                readsetIds: LABKEY.DataRegions[dataRegionName].getChecked()
+            }).show();
+        }
+    },
+
+    initComponent: function() {
+        Ext4.apply(this, {
+            modal: true,
+            title: 'Archive Readsets',
+            width: 600,
+            bodyStyle: 'padding: 5px;',
+            defaults: {
+                border: false
+            },
+            items: [{
+                html: 'This helper will delete the actual FASTQ files associated with the selected readsets. It will error unless each readdata row has an SRA accession listed. You selected ' + this.readsetIds.length + ' readsets.',
+                style: 'padding-bottom: 10px;'
+            }],
+            buttons: [{
+                text: 'Submit',
+                scope: this,
+                handler: this.onSubmit
+            },{
+                text: 'Cancel',
+                handler: function(btn){
+                    btn.up('window').close();
+                }
+            }]
+        });
+
+        this.callParent(arguments);
+    },
+
+    onSubmit: function(btn){
+        if (!this.readsetIds.length) {
+            Ext4.Msg.alert('Error', 'No readsets selected!');
+            return;
+        }
+
+        Ext4.Msg.wait('Saving...');
+        LABKEY.Ajax.request({
+            url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'archiveReadsets', null),
+            method: 'POST',
+            jsonData: {
+                readsetIds: this.readsetIds
+            },
+            scope: this,
+            success: function(){
+                Ext4.Msg.hide();
+                this.close();
+                Ext4.Msg.alert('Success', 'Readsets archived!', function(){
+                    if (this.dataRegionName){
+                        LABKEY.DataRegions[this.dataRegionName].clearSelected();
+                    }
+
+                    LABKEY.DataRegions[this.dataRegionName].refresh();
+                }, this);
+            },
+            failure: LABKEY.Utils.getCallbackWrapper(LDK.Utils.getErrorCallback())
+        });
+    }
+});

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

@@ -77,6 +77,7 @@
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.files.FileContentService;
 import org.labkey.api.laboratory.NavItem;
+import org.labkey.api.laboratory.security.LaboratoryAdminPermission;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleHtmlView;
 import org.labkey.api.module.ModuleLoader;
@@ -3297,6 +3298,15 @@ public ApiResponse execute(CheckFileStatusForm form, BindException errors)
 
             toolArr.put(intermediateFiles);
 
+            JSONObject performCleanupAfterEachStep = new JSONObject();
+            performCleanupAfterEachStep.put("name", "performCleanupAfterEachStep");
+            performCleanupAfterEachStep.put("defaultValue", true);
+            performCleanupAfterEachStep.put("label", "Perform Cleanup After Each Step");
+            performCleanupAfterEachStep.put("description", "Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.");
+            performCleanupAfterEachStep.put("fieldXtype", "checkbox");
+
+            toolArr.put(performCleanupAfterEachStep);
+
             ret.put("toolParameters", toolArr);
 
             ret.put("description", handler.getDescription());
@@ -5128,4 +5138,157 @@ public void setDataFileUrl(String dataFileUrl)
             _dataFileUrl = dataFileUrl;
         }
     }
+
+    @RequiresPermission(UpdatePermission.class)
+    public static class ArchiveReadsetsAction extends MutatingApiAction<ArchiveReadsetsForm>
+    {
+        @Override
+        public ApiResponse execute(ArchiveReadsetsForm form, BindException errors) throws Exception
+        {
+            if (form.getReadsetIds() == null || form.getReadsetIds().length == 0)
+            {
+                errors.reject(ERROR_MSG, "No readset Ids provided");
+                return null;
+            }
+
+            TableInfo readData = QueryService.get().getUserSchema(getUser(), getContainer(), SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_READ_DATA);
+            for (int readsetId : form.getReadsetIds())
+            {
+                Readset rs = SequenceAnalysisService.get().getReadset(readsetId, getUser());
+                Container c = ContainerManager.getForId(rs.getContainer());
+                if (!getContainer().equals(c))
+                {
+                    Container toTest = c.isWorkbook() ? c.getParent() : c;
+                    if (!getContainer().equals(toTest))
+                    {
+                        errors.reject(ERROR_MSG, "Readset is not from this container: " + readsetId);
+                        return null;
+                    }
+                }
+
+                if (!c.hasPermission(getUser(), LaboratoryAdminPermission.class))
+                {
+                    errors.reject(ERROR_MSG, "Insufficient permissions to archive readsets in the folder: " + c.getPath());
+                    return null;
+                }
+
+                Set<File> toDelete = new HashSet<>();
+                List<Map<String, Object>> toUpdate = new ArrayList<>();
+                for (ReadData rd : rs.getReadData())
+                {
+                    if (rd.getSra_accession() == null)
+                    {
+                        errors.reject(ERROR_MSG, "Cannot mark a readdata as archived that does not have an SRA accession: " + readsetId + " / " + rd.getRowid());
+                        return null;
+                    }
+
+                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", rd.getRowid(), "archived", true, "container", rd.getContainer())));
+
+                    // File 1:
+                    ExpData d1 = ExperimentService.get().getExpData(rd.getFileId1());
+                    if (d1 != null)
+                    {
+                        File file1 = d1.getFile();
+                        if (file1 != null && file1.exists())
+                        {
+                            toDelete.add(file1);
+                        }
+
+                        // find matching readdata:
+                        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("fileid1/dataFileUrl"), d1.getDataFileUrl()).addCondition(FieldKey.fromString("rowid"), rd.getRowid(), CompareType.NEQ);
+                        TableSelector ts = new TableSelector(readData, PageFlowUtil.set("rowid", "container"), filter, null);
+                        if (ts.exists())
+                        {
+                            ts.forEachResults(r -> {
+                                toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", r.getInt(FieldKey.fromString("rowid")), "archived", true, "container", r.getString(FieldKey.fromString("container")))));
+                            });
+                        }
+                    }
+
+                    if (rd.getFileId2() != null)
+                    {
+                        ExpData d2 = ExperimentService.get().getExpData(rd.getFileId2());
+                        if (d2 != null)
+                        {
+                            File file2 = d2.getFile();
+                            if (file2 != null)
+                            {
+                                if (file2.exists())
+                                {
+                                    toDelete.add(file2);
+                                }
+
+                                // find matching readdata:
+                                SimpleFilter filter = new SimpleFilter(FieldKey.fromString("fileid2/dataFileUrl"), d2.getDataFileUrl()).addCondition(FieldKey.fromString("rowid"), rd.getRowid(), CompareType.NEQ);
+                                TableSelector ts = new TableSelector(readData, PageFlowUtil.set("rowid", "container"), filter, null);
+                                if (ts.exists())
+                                {
+                                    ts.forEachResults(r -> {
+                                        toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", r.getInt(FieldKey.fromString("rowid")), "archived", true, "container", r.getString(FieldKey.fromString("container")))));
+                                    });
+                                }
+                            }
+                        }
+                    }
+                }
+
+                if (!toUpdate.isEmpty())
+                {
+                    List<Map<String, Object>> keys = new ArrayList<>();
+                    toUpdate.forEach(row -> {
+
+                        keys.add(new CaseInsensitiveHashMap<>(Map.of("rowid", row.get("rowid"))));
+                    });
+
+                    try
+                    {
+                        readData.getUpdateService().updateRows(getUser(), getContainer(), toUpdate, keys, null, null);
+                    }
+                    catch (Exception e)
+                    {
+                        _log.error(e);
+                        errors.reject(ERROR_MSG, "Error archiving readset: " + readsetId + ", " + e.getMessage());
+                        return null;
+                    }
+                }
+
+                if (!toDelete.isEmpty())
+                {
+                    for (File f : toDelete)
+                    {
+                        _log.info("Deleting archived file: " + f.getPath());
+                        f.delete();
+                    }
+                }
+            }
+
+            return new ApiSimpleResponse("Success", true);
+        }
+    }
+
+    public static class ArchiveReadsetsForm
+    {
+        private int[] _readsetIds;
+        private boolean _doNotRequireSra;
+
+        public int[] getReadsetIds()
+        {
+            return _readsetIds;
+        }
+
+        public void setReadsetIds(int... readsetIds)
+        {
+            _readsetIds = readsetIds;
+        }
+
+        public boolean isDoNotRequireSra()
+        {
+            return _doNotRequireSra;
+        }
+
+        public void setDoNotRequireSra(boolean doNotRequireSra)
+        {
+            _doNotRequireSra = doNotRequireSra;
+        }
+    }
 }

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

@@ -45,6 +45,8 @@
 import org.labkey.sequenceanalysis.analysis.BamHaplotypeHandler;
 import org.labkey.sequenceanalysis.analysis.CombineStarGeneCountsHandler;
 import org.labkey.sequenceanalysis.analysis.CombineSubreadGeneCountsHandler;
+import org.labkey.sequenceanalysis.analysis.DeepVariantHandler;
+import org.labkey.sequenceanalysis.analysis.GLNexusHandler;
 import org.labkey.sequenceanalysis.analysis.GenotypeGVCFHandler;
 import org.labkey.sequenceanalysis.analysis.HaplotypeCallerHandler;
 import org.labkey.sequenceanalysis.analysis.LiftoverHandler;
@@ -58,6 +60,7 @@
 import org.labkey.sequenceanalysis.analysis.SbtGeneCountHandler;
 import org.labkey.sequenceanalysis.analysis.UnmappedSequenceBasedGenotypeHandler;
 import org.labkey.sequenceanalysis.button.AddSraRunButton;
+import org.labkey.sequenceanalysis.button.ArchiveReadsetsButton;
 import org.labkey.sequenceanalysis.button.ChangeReadsetStatusButton;
 import org.labkey.sequenceanalysis.button.ChangeReadsetStatusForAnalysesButton;
 import org.labkey.sequenceanalysis.button.DownloadSraButton;
@@ -77,25 +80,7 @@
 import org.labkey.sequenceanalysis.run.alignment.Pbmm2Wrapper;
 import org.labkey.sequenceanalysis.run.alignment.StarWrapper;
 import org.labkey.sequenceanalysis.run.alignment.VulcanWrapper;
-import org.labkey.sequenceanalysis.run.analysis.BamIterator;
-import org.labkey.sequenceanalysis.run.analysis.BcftoolsFillTagsStep;
-import org.labkey.sequenceanalysis.run.analysis.ExportOverlappingReadsAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.GenrichStep;
-import org.labkey.sequenceanalysis.run.analysis.HaplotypeCallerAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.ImmunoGenotypingAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.LofreqAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.MergeLoFreqVcfHandler;
-import org.labkey.sequenceanalysis.run.analysis.NextCladeHandler;
-import org.labkey.sequenceanalysis.run.analysis.PARalyzerAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.PangolinHandler;
-import org.labkey.sequenceanalysis.run.analysis.PbsvAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.PbsvJointCallingHandler;
-import org.labkey.sequenceanalysis.run.analysis.PindelAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.SequenceBasedTypingAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.SnpCountAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.SubreadAnalysis;
-import org.labkey.sequenceanalysis.run.analysis.UnmappedReadExportHandler;
-import org.labkey.sequenceanalysis.run.analysis.ViralAnalysis;
+import org.labkey.sequenceanalysis.run.analysis.*;
 import org.labkey.sequenceanalysis.run.assembly.TrinityRunner;
 import org.labkey.sequenceanalysis.run.bampostprocessing.AddOrReplaceReadGroupsStep;
 import org.labkey.sequenceanalysis.run.bampostprocessing.BaseQualityScoreRecalibrator;
@@ -280,6 +265,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new ImmunoGenotypingAnalysis.Provider());
         SequencePipelineService.get().registerPipelineStep(new ViralAnalysis.Provider());
         SequencePipelineService.get().registerPipelineStep(new HaplotypeCallerAnalysis.Provider());
+        SequencePipelineService.get().registerPipelineStep(new DeepVariantAnalysis.Provider());
         SequencePipelineService.get().registerPipelineStep(new SnpCountAnalysis.Provider());
         SequencePipelineService.get().registerPipelineStep(new ExportOverlappingReadsAnalysis.Provider());
         SequencePipelineService.get().registerPipelineStep(new SubreadAnalysis.Provider());
@@ -346,6 +332,8 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new NextCladeHandler());
         SequenceAnalysisService.get().registerFileHandler(new ConvertToCramHandler());
         SequenceAnalysisService.get().registerFileHandler(new PbsvJointCallingHandler());
+        SequenceAnalysisService.get().registerFileHandler(new DeepVariantHandler());
+        SequenceAnalysisService.get().registerFileHandler(new GLNexusHandler());
 
         SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());
         SequenceAnalysisService.get().registerReadsetHandler(new RestoreSraDataHandler());
@@ -396,9 +384,10 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
         LDKService.get().registerQueryButton(new AddSraRunButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS);
         LDKService.get().registerQueryButton(new RunMultiQCButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS);
         LDKService.get().registerQueryButton(new DownloadSraButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS);
+        LDKService.get().registerQueryButton(new ArchiveReadsetsButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS);
 
-        LDKService.get().registerQueryButton(new ChangeReadsetStatusForAnalysesButton(), "sequenceanalysis", "sequence_analyses");
-        LDKService.get().registerQueryButton(new ChangeReadsetStatusButton(), "sequenceanalysis", "sequence_readsets");
+        LDKService.get().registerQueryButton(new ChangeReadsetStatusForAnalysesButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_ANALYSES);
+        LDKService.get().registerQueryButton(new ChangeReadsetStatusButton(), SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS);
 
         ExperimentService.get().registerExperimentRunTypeSource(new ExperimentRunTypeSource()
         {