Add action to remove job checkpoints

Author: bbimber

mGAP/resources/views/releaseNotes.html

@@ -2,6 +2,7 @@ <h4>Release 2.5:</h4>
 <ul>
     <li>This release includes a major change in how we perform variant annotation, <a href="mgap-annotation.view">described in more detail here.</a></li>
     <li>This release includes 107 additional datasets. The total number of variants dropped relative to release 2.4 due to a change in our filtering. Previously, certain conditions would allow a variant to remain in the dataset, even if no subjects had this genotype. After this correction, ~4m sites were removed, although no genotype calls should be changed.</li>
+    <li>We introduced an entirely new search feature! The new 'Variant Search' page allows you to perform genome-wide queries based on variant annotations (e.g. predicted coding impact or overlap with databases of human pathogenic variants)</li>
 </ul>
 
 <h4>Release 2.4:</h4>

mGAP/resources/web/mGAP/Utils.js

@@ -142,7 +142,7 @@ mGAP.Utils = (function($){
                         "name": "# Variants",
                         "mode": "markers",
                         "x": annotationData,
-                        "y": ["GWAS Associations<br>(GRASP)", "Enhancer Region<br>(FANTOM5)", "Predicted Enhancer<br>(ENCODE)", "Transcription Factor<br>Binding (ENCODE)", "Predicted High<br>Impact (SnpEff)", "Damaging<br>(Polyphen2)", "ClinVar Overlap"],
+                        "y": ["Enhancer Region<br>(FANTOM5)", "Predicted Enhancer<br>(ENCODE)", "Transcription Factor<br>Binding (ENCODE)", "Predicted High<br>Impact (SnpEff)", "Damaging<br>(Polyphen2)", "ClinVar Overlap"],
                         "type": "bar",
                         "orientation": "h",
                         "autobiny": true

primeseq/resources/web/primeseq/window/DeleteJobCheckpointWindow.js

@@ -0,0 +1,81 @@
+Ext4.define('Primeseq.window.DeleteJobCheckpointWindow', {
+    extend: 'Ext.window.Window',
+
+    statics: {
+        buttonHandler: function(dataRegionName){
+            const checked = LABKEY.DataRegions[dataRegionName].getChecked();
+            if (!checked.length){
+                Ext4.Msg.alert('Error', 'No rows selected');
+                return;
+            }
+
+            Ext4.create('Primeseq.window.DeleteJobCheckpointWindow', {
+                jobIds: checked,
+                dataRegionName: dataRegionName,
+                autoShow: true
+            });
+        }
+    },
+
+    initComponent: function(){
+        Ext4.QuickTips.init();
+        Ext4.apply(this, {
+            title: 'Update Job Resources',
+            width: 600,
+            bodyStyle: 'padding: 5px;',
+            items: [{
+                html: 'This will delete the checkpoint JSON file for the selected pipeline jobs, which will cause them to completely restart, instead of attempting to resume at the last checkpoint. This will only delete a checkpoint file for jobs with a status of error or cancelled.',
+                border: false,
+                style: 'padding-bottom: 20px;'
+            },{
+                xtype: 'checkbox',
+                itemId: 'restartJobs',
+                fieldLabel: 'Restart Jobs',
+                checked: true
+            }],
+            buttons: [{
+                text: 'Submit',
+                handler: this.onSubmit,
+                scope: this
+            },{
+                text: 'Cancel',
+                handler: function (btn) {
+                    btn.up('window').close();
+                }
+            }]
+        });
+
+        this.callParent(arguments);
+    },
+
+    onSubmit: function(btn){
+        Ext4.Msg.wait('Loading...');
+        var restartJobs = btn.up('window').down('#restartJobs');
+
+        LABKEY.Ajax.request({
+            method: 'POST',
+            url: LABKEY.ActionURL.buildURL('primeseq', 'deleteJobCheckpoint'),
+            jsonData: {
+                jobIds: this.jobIds.join(','),
+                restartJobs: !!restartJobs
+            },
+            scope: this,
+            success: function(response){
+                Ext4.Msg.hide();
+
+                var jsonResp = LABKEY.Utils.decode(response.responseText);
+                console.log(jsonResp);
+                var dataRegionName = this.dataRegionName;
+                this.close();
+
+                Ext4.Msg.alert('Success', 'Jobs updated: ' + jsonResp.jobsUpdated + '<br>Jobs restarted: ' + jsonResp.jobsRestarted, function(){
+                    var dataRegion = LABKEY.DataRegions[dataRegionName];
+                    if (dataRegion){
+                        dataRegion.refresh();
+                    }
+                }, this);
+            },
+            failure: LDK.Utils.getErrorCallback()
+        });
+    }
+});

primeseq/src/org/labkey/primeseq/PrimeseqController.java

@@ -65,6 +65,7 @@
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -700,4 +701,98 @@ public void setDeleteMultiLineage(boolean deleteMultiLineage)
             _deleteMultiLineage = deleteMultiLineage;
         }
     }
+
+    @RequiresPermission(UpdatePermission.class)
+    public static class DeleteJobCheckpointAction extends MutatingApiAction<DeleteJobCheckpointForm>
+    {
+        @Override
+        public Object execute(DeleteJobCheckpointForm form, BindException errors) throws Exception
+        {
+            String jobIDs = StringUtils.trimToNull(form.getJobIds());
+            if (jobIDs == null)
+            {
+                errors.reject(ERROR_MSG, "No JobIds provided");
+                return false;
+            }
+
+            int jobsUpdated = 0;
+            int jobsRestarted = 0;
+
+            Set<String> jobs = new HashSet<>(Arrays.asList(jobIDs.split(",")));
+            for (String id : jobs)
+            {
+                int jobId = Integer.parseInt(StringUtils.trimToNull(id));
+                PipelineStatusFile sf = PipelineService.get().getStatusFile(jobId);
+                if (sf == null)
+                {
+                    errors.reject(ERROR_MSG, "Unable to find job: " + id);
+                    return false;
+                }
+
+                if (sf.getFilePath() == null)
+                {
+                    errors.reject(ERROR_MSG, "Unable to find log file: " + sf.getJobId());
+                    return false;
+                }
+
+                File dir = new File(sf.getFilePath()).getParentFile();
+                if (!dir.exists())
+                {
+                    errors.reject(ERROR_MSG, "Unable to find job directory: " + sf.getJobId());
+                    return false;
+                }
+
+                for (String fn : Arrays.asList("processVariantsCheckpoint.json", "alignmentCheckpoint.json", "processSingleCellCheckpoint.json"))
+                {
+                    File checkpoint = new File(dir, fn);
+                    if (checkpoint.exists())
+                    {
+                        jobsUpdated++;
+                        checkpoint.delete();
+
+                        break;
+                    }
+                }
+
+                if (form.isRestartJobs())
+                {
+                    if (PipelineJob.TaskStatus.error.name().equalsIgnoreCase(sf.getStatus()) || PipelineJob.TaskStatus.cancelled.name().equalsIgnoreCase(sf.getStatus()))
+                    {
+                        jobsRestarted++;
+                        PipelineJob job = sf.createJobInstance();
+                        PipelineService.get().queueJob(job);
+                    }
+                }
+            }
+
+            return new ApiSimpleResponse(Map.of("success", true, "jobsUpdated", jobsUpdated, "jobsRestarted", jobsRestarted));
+        }
+    }
+
+    public static class DeleteJobCheckpointForm
+    {
+        private String _jobIds;
+
+        private boolean _restartJobs = false;
+
+        public String getJobIds()
+        {
+            return _jobIds;
+        }
+
+        public void setJobIds(String jobIds)
+        {
+            _jobIds = jobIds;
+        }
+
+        public boolean isRestartJobs()
+        {
+            return _restartJobs;
+        }
+
+        public void setRestartJobs(boolean restartJobs)
+        {
+            _restartJobs = restartJobs;
+        }
+    }
 }

primeseq/src/org/labkey/primeseq/PrimeseqModule.java

@@ -37,6 +37,7 @@
 import org.labkey.primeseq.pipeline.BismarkWrapper;
 import org.labkey.primeseq.pipeline.BlastPipelineJobResourceAllocator;
 import org.labkey.primeseq.pipeline.ClusterMaintenanceTask;
+import org.labkey.primeseq.pipeline.DeleteJobCheckpointButton;
 import org.labkey.primeseq.pipeline.ExacloudResourceSettings;
 import org.labkey.primeseq.pipeline.GeographicOriginStep;
 import org.labkey.primeseq.pipeline.MhcCleanupPipelineJob;
@@ -88,6 +89,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
 
         LDKService.get().registerQueryButton(new UpdateResourcesButton(), "pipeline", "job");
         LDKService.get().registerQueryButton(new PerformMhcCleanupButton(), "sequenceanalysis", "sequence_analyses");
+        LDKService.get().registerQueryButton(new DeleteJobCheckpointButton(), "pipeline", "job");
     }
 
     @Override

primeseq/src/org/labkey/primeseq/pipeline/DeleteJobCheckpointButton.java

@@ -0,0 +1,21 @@
+package org.labkey.primeseq.pipeline;
+
+import org.labkey.api.ldk.table.SimpleButtonConfigFactory;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.view.template.ClientDependency;
+import org.labkey.primeseq.PrimeseqModule;
+
+import java.util.List;
+
+/**
+ * User: bimber
+ * Date: 7/16/2014
+ * Time: 5:37 PM
+ */
+public class DeleteJobCheckpointButton extends SimpleButtonConfigFactory
+{
+    public DeleteJobCheckpointButton()
+    {
+        super(ModuleLoader.getInstance().getModule(PrimeseqModule.class), "Delete Job Checkpoint(s)", "Primeseq.window.DeleteJobCheckpointWindow.buttonHandler(dataRegionName);", List.of(ClientDependency.supplierFromPath("primeseq/window/DeleteJobCheckpointWindow.js")));
+    }
+}