Merge branch 'develop' into fb_fileLike3

Author: labkey-jeckels

SequenceAnalysis/pipeline_code/extra_tools_install.sh

@@ -333,3 +333,20 @@ then
 else
     echo "Already installed"
 fi
+
+
+if [[ ! -e ${LKTOOLS_DIR}/primer3_core || ! -z $FORCE_REINSTALL ]];
+then
+    echo "Cleaning up previous installs"
+    rm -Rf $LKTOOLS_DIR/primer3_core*
+    rm -Rf primer3*
+    rm -Rf v2.6.1.tar.gz
+
+    wget https://github.com/primer3-org/primer3/archive/refs/tags/v2.6.1.tar.gz
+    tar -xf v2.6.1.tar.gz
+    cd primer3-2.6.1/src
+    make
+    install primer3_core $LKTOOLS_DIR/
+else
+    echo "Already installed"
+fi

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java

@@ -45,7 +45,6 @@
 import java.io.StringWriter;
 import java.util.Arrays;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -238,7 +237,7 @@ public void testTranslation() {
             }
         }
     }
-    
+
     public long createExpData(String relPath) {
         PipeRoot pr = PipelineService.get().getPipelineRootSetting(getContainer());
         if (pr == null)
@@ -257,7 +256,7 @@ public long createExpData(String relPath) {
         {
             return d.getRowId();
         }
-        
+
         d = ExperimentService.get().createData(getContainer(), new DataType("Output"));
         d.setDataFileURI(f.toURI());
         d.setName(f.getName());

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java

@@ -72,7 +72,7 @@ public Provider()
                         put("checked", true);
                     }}, true),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--insert-name"), "insertType", "Insert Type", "The type of insert to detect.", "ldk-simplecombo", new JSONObject(){{
-                        put("storeValues", "PiggyBac;Lentivirus;PREDICT");
+                        put("storeValues", "PiggyBac;Lentivirus;PREDICT;BxBI_attP");
                         put("allowBlank", false);
                     }}, null),
                     ToolParameterDescriptor.create(DESIGN_PRIMERS, "Design Primers", "If selected, Primer3 will be used to design primers to flank integration sites", "checkbox", new JSONObject(){{

Studies/resources/queries/studies/studyCohorts/.qview.xml

@@ -0,0 +1,22 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="rowId"/>
+        <column name="studyId"/>
+        <column name="studyId/description">
+            <properties>
+                <property name="columnTitle" value="Study Description"/>
+            </properties>
+        </column>
+        <column name="cohortName"/>
+        <column name="label"/>
+        <column name="category"/>
+        <column name="description"/>
+        <column name="isControlGroup"/>
+        <column name="sortOrder"/>
+    </columns>
+    <sorts>
+        <sort column="studyId/studyName" descending="false"/>
+        <sort column="sortOrder" descending="false"/>
+        <sort column="cohortName" descending="false"/>
+    </sorts>
+</customView>

Studies/resources/schemas/dbscripts/postgresql/studies-23.005-23.006.sql

@@ -0,0 +1 @@
+ALTER TABLE studies.subjectAnchorDates ADD COLUMN sourceRecord varchar(1000);

Studies/resources/schemas/dbscripts/sqlserver/studies-23.005-23.006.sql

@@ -0,0 +1 @@
+ALTER TABLE studies.subjectAnchorDates ADD sourceRecord varchar(1000);

Studies/resources/schemas/studies.xml

@@ -526,6 +526,10 @@
                     <fkDisplayColumnName>label</fkDisplayColumnName>
                 </fk>
             </column>
+            <column columnName="sourceRecord">
+                <columnTitle>Source Record</columnTitle>
+                <isHidden>true</isHidden>
+            </column>
             <column columnName="dataSource">
                 <columnTitle>Data Source</columnTitle>
             </column>

Studies/src/org/labkey/studies/StudiesModule.java

@@ -34,7 +34,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 23.005;
+        return 23.006;
     }
 
     @Override

Studies/src/org/labkey/studies/query/StudiesTriggerFactory.java

@@ -93,6 +93,11 @@ private void possiblyResolveStudyOrCohort(String tableToQuery, @Nullable Map<Str
                 return;
             }
 
+            if (row.get(sourceProperty) instanceof Integer)
+            {
+                return;
+            }
+
             if (row.get(sourceProperty) != null & row.get(sourceProperty) instanceof String & !String.valueOf(row.get(sourceProperty)).isEmpty())
             {
                 if (!NumberUtils.isCreatable(row.get(sourceProperty).toString()))