Merge pull request #112 from LabKey/fb_merge_21.7_to_develop

Merge discvr-21.7 to develop

Author: bbimber

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

@@ -56,5 +56,7 @@ public interface ReadData extends Serializable
 
     public Integer getModifiedBy();
 
+    public String getSra_accession();
+
     public boolean isArchived();
 }

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

@@ -22,6 +22,7 @@
 import org.labkey.api.sequenceanalysis.model.Readset;
 
 import java.io.File;
+import java.util.List;
 
 /**
  * User: bimber
@@ -43,12 +44,27 @@ default public String getIndexCachedDirName(PipelineJob job)
 
     /**
      * Performs a reference guided alignment using the provided files.
-     * @param inputFastq1 The forward FASTQ file
-     * @param inputFastq2 The second FASTQ, if using paired end data
+     * @param inputFastqs1 The forward FASTQ file(s). In most cases this is a single FASTQ. The aligner must return true for canAlignMultiplePairsAtOnce() otherwise.
+     * @param inputFastqs2 The second FASTQ(s), if using paired end data
      * @param basename The basename to use as the output
      * @throws PipelineJobException
      */
-    public AlignmentOutput performAlignment(Readset rs, File inputFastq1, @Nullable File inputFastq2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException;
+    public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException;
+
+    default boolean canAlignMultiplePairsAtOnce()
+    {
+        return false;
+    }
+
+    default File assertSingleFile(List<File> inputs)
+    {
+        if (inputs != null && inputs.size() > 1)
+        {
+            throw new IllegalArgumentException("This aligner only supports a single pair of input FASTQs");
+        }
+
+        return inputs == null ? null : inputs.get(0);
+    }
 
     public boolean doAddReadGroups();
 

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

@@ -0,0 +1,25 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="SRA Info" canOverride="true">
+   <columns>
+       <column name="rowid" />
+       <column name="name" />
+       <column name="subjectid" />
+       <column name="sampledate"/>
+       <column name="platform" />
+       <column name="librarytype" />
+       <column name="application" />
+       <column name="sampletype" />
+       <column name="comments" />
+
+       <column name="runIds"/>
+       <column name="jobIds"/>
+       <column name="created" />
+       <column name="status" />
+       <column name="workbook" />
+       <column name="sraRuns" />
+       <column name="isArchived" />
+       <column name="files" />
+   </columns>
+   <sorts>
+       <sort column="rowid" descending="true"/>
+   </sorts>
+</customView>

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

@@ -610,7 +610,7 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
             },
             scope: this,
             success: this.onFileLoad,
-            failure: LDK.Utils.getErrorCallback
+            failure: LDK.Utils.getErrorCallback()
         });
 
         this.fileNameStore = Ext4.create('Ext.data.Store', {
@@ -860,7 +860,7 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
 
                     var found = false;
                     Ext4.each(cols, function(col, idx){
-                        if (col.name == field || col.text == field || col.dataIndex.toLowerCase() == field.toLowerCase()){
+                        if (col.name === field || col.text === field || col.dataIndex.toLowerCase() === field.toLowerCase()){
                             columns.push(col);
                             found = true;
                             return false;
@@ -918,11 +918,11 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
                                 var recIdx = col.editor.store.find(col.editor.valueField, value, null, false, false);
 
                                 //attempt to resolve by displayField
-                                if (recIdx == -1) {
+                                if (recIdx === -1) {
                                     recIdx = col.editor.store.find(col.editor.displayField, value, null, false, false);
                                 }
 
-                                if (recIdx == -1) {
+                                if (recIdx === -1) {
                                     errors.push('Invalid value for field ' + col.text + ': ' + value);
                                 }
                                 else {
@@ -932,6 +932,10 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
                             }
                         }
 
+                        if (value && col.dataIndex === 'readset' && !Ext4.isNumeric(value)) {
+                            errors.push('Readset Id should be an integer: ' + value);
+                        }
+
                         if (!Ext4.isEmpty(value)){
                             obj[col.dataIndex] = value;
                         }

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js

@@ -36,6 +36,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                     {name: 'fileGroupId', allowBlank: false},
                     {name: 'readset', allowBlank: false},
                     {name: 'readsetname', useNull: true},
+                    {name: 'importType', useNull: true},
                     {name: 'barcode5', useNull: true},
                     {name: 'barcode3', useNull: true},
                     {name: 'platform', allowBlank: false},
@@ -794,6 +795,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 barcode3: r.get('barcode3'),
                 readset: r.get('readset'),
                 readsetname: r.get('readsetname'),
+                importType: r.get('importType'),
                 platform: r.get('platform'),
                 application: r.get('application'),
                 chemistry: r.get('chemistry'),
@@ -1643,6 +1645,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
         Ext4.Msg.wait('Loading...');
         var doDemultiplex = this.down('#doDemultiplex').getValue();
         var showBarcodes = this.down('#showBarcodes').getValue();
+        var allowReadsetMerge = this.down('#allowReadsetMerge').getValue();
 
         LABKEY.Query.selectRows({
             method: 'POST',
@@ -1659,8 +1662,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 if (results && results.rows && results.rows.length){
                     Ext4.Array.forEach(results.rows, function(row) {
                         var records = recordsById[row.rowid];
-                        if (row.totalFiles) {
-                            msgs.push('Readset ' + row.rowid + 'has already been associated with files and cannot be re-used.  If you would like to reanalyze this readset, load the table of readsets and look for the \'Analyze Data\' button.');
+                        if (!allowReadsetMerge && row.totalFiles) {
+                            msgs.push('Readset ' + row.rowid + ' has already been associated with files and cannot be re-used.  If you would like to reanalyze this readset, load the table of readsets and look for the \'Analyze Data\' button.');
                             Ext4.Array.forEach(records, function(record) {
                                 record.data.readset = null;
                             }, this);
@@ -1675,18 +1678,16 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                             return;
                         }
                         else if (!doDemultiplex && !showBarcodes && (row.barcode3 || row.barcode5)) {
-                            msgs.push('Readset ' + row.rowid + ' has barcodes, but you have not selected to either show barcodes or perform demultiplexing');
-                            Ext4.Array.forEach(records, function(record) {
-                                record.data.readset = null;
-                            }, this);
-
-                            return;
+                            this.down('#showBarcodes').setValue(true);
+                            showBarcodes = true;
                         }
 
                         //update row based on saved readset.  avoid firing event
                         Ext4.Array.forEach(records, function(record) {
+                            var importType = !record.data.readset ? null : row.totalFiles ? 'Merge With Existing' : 'New Data';
                             Ext4.apply(record.data, {
                                 readsetname: row.name,
+                                importType: importType,
                                 platform: row.platform,
                                 application: row.application,
                                 chemistry: row.chemistry,
@@ -1716,6 +1717,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                         Ext4.apply(record.data, {
                             readset: null,
                             readsetname: null,
+                            importType: null,
                             platform: null,
                             application: null,
                             chemistry: null,
@@ -1866,7 +1868,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
 
                     var grid = btn.up('panel').down('ldk-gridpanel');
                     Ext4.Array.forEach(grid.columns, function(c){
-                        if (c.dataIndex === 'readset'){
+                        if (c.dataIndex === 'readset' || c.dataIndex === 'importType'){
                             c.setVisible(val);
                         }
                     }, this);
@@ -1881,12 +1883,18 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                 hideMode: 'offsets',
                 width: 'auto',
                 itemId: 'existingReadsetOptions',
+                border: false,
                 fieldDefaults: {
                     width: 350
                 },
                 items: [{
                     html: 'It is possible to import readset information before you import the actual read data.  This is most commonly done when you plan a run upfront (such as the Illumina workflow).  If you did this, just enter the readset Id below and the details will automatically populate.  Note: when this option is selected the readset details are not editable through this form.',
                     border: false
+                },{
+                    itemId: 'allowReadsetMerge',
+                    xtype: 'checkbox',
+                    fieldLabel: 'Allow Merge If Existing Readset Has Data',
+                    helpPopup: 'If there is already data for the selected readset(s), the original readset will be copied (same attrbitues), and a new readset will be creating using these reads and the original data. The original readset will remain.'
                 }]
             },{
                 xtype: 'ldk-gridpanel',
@@ -1964,6 +1972,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                                                 if (records && records.length) {
                                                     records[0].set({
                                                         readset: null,
+                                                        importType: null,
                                                         readsetname: null,
                                                         platform: null,
                                                         application: null,
@@ -1989,6 +1998,18 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                             }
                         }
                     }
+                }, {
+                    text: 'Import Status',
+                    tdCls: 'ldk-wrap-text',
+                    name: 'importType',
+                    hidden: true,
+                    dataIndex: 'importType',
+                    width: 110,
+                    editable: true,
+                    editor: {
+                        xtype: 'displayfield',
+                        allowBlank: true
+                    }
                 },{
                     text: '5\' Barcode',
                     tdCls: 'ldk-wrap-text',
@@ -2615,7 +2636,12 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                     }
 
                     if (obj.readset){
-                        readsetsToUpdate.push(obj.readset);
+                        if (!Ext4.isNumeric(obj.readset)) {
+                            errors.push('Readset Id should be an integer: ' + obj.readset);
+                        }
+                        else {
+                            readsetsToUpdate.push(obj.readset);
+                        }
                     }
                 }, this);
 

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

@@ -31,6 +31,7 @@ public class ReadDataImpl implements ReadData
     private Integer _modifiedBy;
     private Integer _runId;
     private boolean _archived = false;
+    private String sra_accession;
 
     private Map<Integer, File> _cachedFiles = new HashMap<>();
 
@@ -259,4 +260,15 @@ public void setArchived(boolean archived)
     {
         _archived = archived;
     }
+
+    @Override
+    public String getSra_accession()
+    {
+        return sra_accession;
+    }
+
+    public void setSra_accession(String sra_accession)
+    {
+        this.sra_accession = sra_accession;
+    }
 }

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

@@ -72,6 +72,11 @@ public int getRowId()
         return _rowId == null ? 0 : _rowId;
     }
 
+    public void unsetRowId()
+    {
+        _rowId = null;
+    }
+
     public void setRowId(int rowId)
     {
         _rowId = rowId;