Merge pull request #139 from LabKey/fb_merge_22.3_to_develop

Merge discvr-22.3 to develop

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/ReadData.java

@@ -56,6 +56,8 @@ public interface ReadData extends Serializable
 
     public Integer getModifiedBy();
 
+    public Integer getTotalReads();
+
     public String getSra_accession();
 
     public boolean isArchived();

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

@@ -4,7 +4,6 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
@@ -30,6 +29,11 @@ public SamSorter(@Nullable Logger logger)
     }
 
     public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder sortOrder) throws PipelineJobException
+    {
+        return execute(input, output, sortOrder, null);
+    }
+
+    public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder sortOrder, @Nullable List<String> extraArgs) throws PipelineJobException
     {
         getLogger().info("Sorting SAM/BAM: " + input.getPath());
 
@@ -50,7 +54,7 @@ public File execute(File input, @Nullable File output, SAMFileHeader.SortOrder s
         }
         else if (sortOrder != SAMFileHeader.SortOrder.coordinate)
         {
-            throw new PipelineJobException("Improper sort order: " + sortOrder.name());
+            getLogger().debug("Using sort order: " + sortOrder.name());
         }
 
         Integer threads = SequencePipelineService.get().getMaxThreads(getLogger());
@@ -71,6 +75,11 @@ else if (sortOrder != SAMFileHeader.SortOrder.coordinate)
         params.add("-T");
         params.add(tmpDir);
 
+        if (extraArgs != null)
+        {
+            params.addAll(extraArgs);
+        }
+
         params.add("-o");
         params.add(output.getPath());
 

SequenceAnalysis/resources/queries/sequenceanalysis/outputfiles.js

@@ -14,3 +14,17 @@ function beforeDelete(row, errors){
         errors._form = 'You cannot directly delete analyses.  To delete these records, use the delete button above the analysis grid.';
     }
 }
+
+function beforeInsert(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpdate(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpsert(row, errors) {
+    if (row.dataid && typeof row.dataid == 'string') {
+        row.dataid = triggerHelper.createExpData(row.dataid);
+    }
+}

SequenceAnalysis/resources/web/SequenceAnalysis/field/GenomeField.js

@@ -7,6 +7,8 @@ Ext4.define('SequenceAnalysis.field.GenomeField', {
             forceSelection: true,
             displayField: 'name',
             valueField: 'rowid',
+            queryMode: 'local',
+            triggerAction: 'all',
             store: {
                 type: 'labkey-store',
                 schemaName: 'sequenceanalysis',

SequenceAnalysis/resources/web/SequenceAnalysis/field/SequenceOutputFileSelectorField.js

@@ -49,7 +49,7 @@ Ext4.define('SequenceAnalysis.field.SequenceOutputFileSelectorField', {
                     }
                 }
                 else {
-                    LDK.Utils.logError('unable to find library field in GenomeFileSelectorField');
+                    LDK.Utils.logError('unable to find library field in SequenceOutputFileSelectorField');
                 }
             }
             else if (window && window.libraryId){

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

@@ -128,7 +128,27 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
 
             items.push({
                 xtype: 'ldk-linkbutton',
-                text: 'Add',
+                text: 'Add to Start',
+                linkCls: 'labkey-text-link',
+                step: step,
+                handler: function(btn){
+                    var win = btn.up('window');
+                    var owner = win.ownerPanel;
+                    var target = owner.down('#toolConfgPanel');
+
+                    //check if exists
+                    if (!owner.allowDuplicateSteps && target.down('[stepName=' + btn.step.name + ']')) {
+                        Ext4.Msg.alert('Already Added', 'This step has already been added and cannot be used twice.');
+                    }
+                    else {
+                        target.insert(0, owner.getAbbreviatedConfigForItem(btn.step));
+                    }
+                }
+            });
+
+            items.push({
+                xtype: 'ldk-linkbutton',
+                text: 'Add to End',
                 linkCls: 'labkey-text-link',
                 step: step,
                 handler: function(btn){
@@ -144,7 +164,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                         target.add(owner.getAbbreviatedConfigForItem(btn.step));
                     }
                 }
-            })
+            });
         }, this);
 
         if (items.length){
@@ -161,7 +181,7 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
                 },
                 layout: {
                     type: 'table',
-                    columns: 3
+                    columns: 4
                 },
                 items: items
             }];

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

@@ -1,14 +1,21 @@
 package org.labkey.sequenceanalysis;
 
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.data.Transient;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.pipeline.PipelineJobService;
+import org.labkey.api.query.FieldKey;
 import org.labkey.api.sequenceanalysis.model.ReadData;
+import org.labkey.api.util.PageFlowUtil;
 
 import java.io.File;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -33,13 +40,14 @@ public class ReadDataImpl implements ReadData
     private boolean _archived = false;
     private String sra_accession;
 
-    private Map<Integer, File> _cachedFiles = new HashMap<>();
+    private final Map<Integer, File> _cachedFiles = new HashMap<>();
 
     public ReadDataImpl()
     {
 
     }
 
+    @Override
     public Integer getRowid()
     {
         return _rowid;
@@ -50,6 +58,7 @@ public void setRowid(Integer rowid)
         _rowid = rowid;
     }
 
+    @Override
     public Integer getReadset()
     {
         return _readset;
@@ -60,6 +69,7 @@ public void setReadset(Integer readset)
         _readset = readset;
     }
 
+    @Override
     public String getPlatformUnit()
     {
         return _platformUnit;
@@ -70,6 +80,7 @@ public void setPlatformUnit(String platformUnit)
         _platformUnit = platformUnit;
     }
 
+    @Override
     public String getCenterName()
     {
         return _centerName;
@@ -80,6 +91,7 @@ public void setCenterName(String centerName)
         _centerName = centerName;
     }
 
+    @Override
     public Date getDate()
     {
         return _date;
@@ -90,6 +102,7 @@ public void setDate(Date date)
         _date = date;
     }
 
+    @Override
     public Integer getFileId1()
     {
         return _fileId1;
@@ -100,6 +113,7 @@ public void setFileId1(Integer fileId1)
         _fileId1 = fileId1;
     }
 
+    @Override
     public Integer getFileId2()
     {
         return _fileId2;
@@ -110,11 +124,13 @@ public void setFileId2(Integer fileId2)
         _fileId2 = fileId2;
     }
 
+    @Override
     public String getDescription()
     {
         return _description;
     }
 
+    @Override
     public Integer getRunId()
     {
         return _runId;
@@ -130,6 +146,7 @@ public void setDescription(String description)
         _description = description;
     }
 
+    @Override
     public String getContainer()
     {
         return _container;
@@ -140,6 +157,7 @@ public void setContainer(String container)
         _container = container;
     }
 
+    @Override
     public Date getCreated()
     {
         return _created;
@@ -150,6 +168,7 @@ public void setCreated(Date created)
         _created = created;
     }
 
+    @Override
     public Integer getCreatedBy()
     {
         return _createdBy;
@@ -160,6 +179,7 @@ public void setCreatedBy(Integer createdBy)
         _createdBy = createdBy;
     }
 
+    @Override
     public Date getModified()
     {
         return _modified;
@@ -170,6 +190,7 @@ public void setModified(Date modified)
         _modified = modified;
     }
 
+    @Override
     public Integer getModifiedBy()
     {
         return _modifiedBy;
@@ -180,12 +201,14 @@ public void setModifiedBy(Integer modifiedBy)
         _modifiedBy = modifiedBy;
     }
 
+    @Override
     @Transient
     public File getFile1()
     {
         return getFile(1, _fileId1);
     }
 
+    @Override
     @Transient
     public File getFile2()
     {
@@ -197,6 +220,33 @@ public void setFile(File f, int fileIdx)
         _cachedFiles.put(fileIdx, f);
     }
 
+    @Override
+    @Transient
+    public Integer getTotalReads()
+    {
+        if (getFileId1() == null)
+        {
+            return null;
+        }
+
+        if (PipelineJobService.get().getLocationType() != PipelineJobService.LocationType.WebServer)
+        {
+            throw new IllegalStateException("Cannot call getTotalReads() on the remote server unless this value has been cached");
+        }
+
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("dataid"), getFileId1());
+        filter.addCondition(FieldKey.fromString("readset"), getReadset(), CompareType.EQUAL);
+        filter.addCondition(FieldKey.fromString("metricname"), "Total Reads", CompareType.EQUAL);
+        TableSelector ts = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS), PageFlowUtil.set("metricvalue"), filter, new Sort("-rowid"));
+        List<Double> values = ts.getArrayList(Double.class);
+        if (!values.isEmpty())
+        {
+            return values.get(0).intValue();
+        }
+
+        return 0;
+    }
+
     @Transient
     private File getFile(int fileIdx, Integer fileId)
     {

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

@@ -643,7 +643,14 @@ private static void deleteReferenceLibrary(User user, Container c, Integer rowId
             if (libraryDir.exists())
             {
                 _log.info("deleting reference library dir: " + libraryDir.getPath());
-                FileUtils.deleteDirectory(libraryDir);
+                try
+                {
+                    FileUtils.deleteDirectory(libraryDir);
+                }
+                catch (IOException e)
+                {
+                    _log.error("Unable to delete folder: " + libraryDir.getPath(), e);
+                }
             }
         }
 

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

@@ -547,6 +547,25 @@ private Long getTotalReadsForFile(int fileId, int readsetId)
 
     public static long addQualityMetricsForReadset(Readset rs, int fileId, PipelineJob job) throws PipelineJobException
     {
+        return addQualityMetricsForReadset(rs, fileId, job, false);
+    }
+
+    public static long addQualityMetricsForReadset(Readset rs, int fileId, PipelineJob job, boolean deleteExisting) throws PipelineJobException
+    {
+        if (deleteExisting)
+        {
+            //update metrics. first delete existing:
+            SimpleFilter metricsFilter = new SimpleFilter(FieldKey.fromString("readset"), rs.getRowId());
+            metricsFilter.addCondition(FieldKey.fromString("container"), rs.getContainer());
+            metricsFilter.addCondition(FieldKey.fromString("dataId"), fileId);
+            int deleted = Table.delete(SequenceAnalysisManager.get().getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS), metricsFilter);
+            job.getLogger().debug("existing metrics deleted: " + deleted);
+        }
+        else
+        {
+            job.getLogger().debug("will not attempt to pre-delete existing metrics");
+        }
+
         try
         {
             ExpData d = ExperimentService.get().getExpData(fileId);

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

@@ -115,10 +115,7 @@ public void cacheReadset(SequenceReadsetImpl m, boolean allowReadsetsWithArchive
         }
         else
         {
-            if (_cachedReadsets.contains(m))
-            {
-                _cachedReadsets.remove(m);
-            }
+            _cachedReadsets.remove(m);
         }
 
         _cachedReadsets.add(m);