Rename instrument run to batch/run

Author: bbimber

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -1177,7 +1177,7 @@
                 <isHidden>true</isHidden>
             </column>
             <column columnName="instrument_run_id">
-                <columnTitle>Instrument Run</columnTitle>
+                <columnTitle>Batch/Run</columnTitle>
                 <fk>
                     <fkDbSchema>sequenceanalysis</fkDbSchema>
                     <fkTable>instrument_runs</fkTable>

SequenceAnalysis/resources/views/sequenceAnalysisDetails.html

@@ -17,6 +17,7 @@
             '<div style="margin-bottom: 10px;"></div>' +
             //'<div id="analysisNav_'+webpart.wrapperDivId+'"></div>' +
             //'<br>' +
+            '<div id="outputs_'+webpart.wrapperDivId+'"></div>' +
             '<div id="qualityMetrics_'+webpart.wrapperDivId+'"></div>' +
             '<div style="margin-bottom: 10px;"></div>' +
             '<div id="readsetDiv_'+webpart.wrapperDivId+'"/>'
@@ -52,6 +53,15 @@
         successCallback: onSuccess
     });
 
+    LDK.Utils.getReadOnlyQWP({
+        title: 'Outputs',
+        schemaName: 'sequenceanalysis',
+        queryName: 'outputfiles',
+        maxRows: 20,
+        containerPath: Laboratory.Utils.getQueryContainerPath(),
+        filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)]
+    }).render('outputs_'+webpart.wrapperDivId);
+
     LDK.Utils.getReadOnlyQWP({
         title: 'Quality Metrics',
         schemaName: 'sequenceanalysis',

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

@@ -2335,8 +2335,8 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                         }).show(btn);
                     }
                 }, {
-                    text: 'Assign To Instrument Run',
-                    tooltip: 'Click to assign the selected rows to an existing or new instrument run',
+                    text: 'Assign To Instrument Run/Batch',
+                    tooltip: 'Click to assign the selected rows to an existing or new instrument run or batch',
                     scope: this,
                     handler: function (btn) {
                         var grid = btn.up('grid');

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

@@ -345,6 +345,8 @@ public RecordedActionSet run() throws PipelineJobException
                             Pair<File, File> p = extractReadGroup(fp.file1, fp.platformUnit, actions, outDir);
                             fp.file1 = p.first;
                             fp.file2 = p.second;
+                            getHelper().getFileManager().addIntermediateFile(fp.file1);
+                            getHelper().getFileManager().addIntermediateFile(fp.file2);
                         }
 
                         //NOTE: continue to normalize sequence, in case the BAM-derived data has non-standard encoding

SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java

@@ -382,7 +382,7 @@ private void readsetFeaturesTest() throws IOException
         dr = new DataRegionTable("query", this);
 
         log("Verifying instrument run and details page");
-        clickAndWait(dr.link(2, "Instrument Run"));
+        clickAndWait(dr.link(2, "Batch/Run"));
 
         waitForText("Instrument Run Details");
         waitForText("Run Id"); //crude proxy for loading of the details panel