automatically set reverse-complement

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/barcodes.js

@@ -0,0 +1,20 @@
+var COMPLEMENT_BASES = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G'};
+
+function beforeUpsert(row, errors) {
+    if (row.sequence){
+        row.sequence = row.sequence.toUpperCase();
+
+        var reverseSeq = row.sequence.split('').reverse().join('');
+        row.reverse_complement = reverseSeq.replace(/[ATCG]/g, function($0){
+            return COMPLEMENT_BASES[$0]
+        });
+    }
+}
+
+function beforeInsert(row, errors) {
+    beforeUpsert(row, errors);
+}
+
+function beforeUpdate(row, oldRow, errors) {
+    beforeUpsert(row, errors);
+}

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -1,4 +1,4 @@
-<tables xmlns="http://labkey.org/data/xml">
+<tables xsi:schemaLocation="http://labkey.org/data/xml ..\..\..\..\schemas\tableInfo.xsd" xmlns="http://labkey.org/data/xml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
     <table tableName="barcodes" tableDbType="TABLE" useColumnOrder="true">
         <auditLogging>DETAILED</auditLogging>
         <tableTitle>DNA Barcodes</tableTitle>
@@ -15,8 +15,9 @@
                 <description>This should be the forward orientation of the sequence, as it appears in the adapter sequence</description>
             </column>
             <column columnName="reverse_complement">
-                <nullable>false</nullable>
+                <nullable>true</nullable>
                 <inputType>textarea</inputType>
+                <isUserEditable>false</isUserEditable>
                 <description>The reverse complement of the sequence</description>
             </column>
             <column columnName="group_name">

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CellHashingHandler.java

@@ -114,8 +114,8 @@ public static List<ToolParameterDescriptor> getDefaultParams(boolean allowScanni
                     put("allowBlank", false);
                 }}, defaultTagGroup),
                 ToolParameterDescriptor.create("useOutputFileContainer", "Submit to Source File Workbook", "If checked, each job will be submitted to the same workbook as the input file, as opposed to submitting all jobs to the same workbook.  This is primarily useful if submitting a large batch of files to process separately. This only applies if 'Run Separately' is selected.", "checkbox", new JSONObject(){{
-                    put("checked", false);
-                }}, false)
+                    put("checked", true);
+                }}, true)
         ));
 
         return ret;