Add SIV calculated fields

Author: bbimber

SivStudies/resources/queries/study/demographics/Expanded.qview.xml

@@ -9,6 +9,8 @@
         <column name="projects/allStudies"/>
         <column name="projects/categories"/>
         <column name="immunizations/immunizations"/>
+        <column name="sivART/allInfections"/>
+        <column name="sivART/allART"/>
         <column name="outcomes/outcomes"/>
     </columns>
     <sorts>

SivStudies/resources/queries/study/demographicsChallengeAndArt.query.xml

@@ -0,0 +1,22 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="" tableDbType="NOT_IN_DB">
+                <tableTitle>SIV/ART Summary</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="allInfections">
+                        <columnTitle>SIV Infection</columnTitle>
+                    </column>
+                    <column columnName="allART">
+                        <columnTitle>ART</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>allInfections</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

SivStudies/resources/queries/study/demographicsChallengeAndArt.sql

@@ -0,0 +1,13 @@
+SELECT
+  t.Id,
+  group_concat(DISTINCT CASE
+      WHEN t.category = 'SIV Infection' THEN (cast(month(t.date) as varchar) || '-' || cast(dayofmonth(t.date) as varchar) || '-' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
+      ELSE NULL
+  END, char(10)) as allInfections,
+  group_concat(DISTINCT CASE
+      WHEN t.category = 'ART' THEN (cast(month(t.date) as varchar) || '-' || cast(dayofmonth(t.date) as varchar) || '-' || cast(year(t.date) as varchar) || ' (' || t.treatment || ')')
+      ELSE NULL
+  END, char(10)) as allART,
+
+FROM study.treatments t
+GROUP BY t.Id

SivStudies/resources/views/participantView.html

@@ -0,0 +1,7 @@
+<script type="text/javascript" nonce="<%=scriptNonce%>">
+    // NOTE: this is intended to be set as the study participant view through the UI.
+    // Loading ClientDependencies is a pain through that mechanism, so this just redirects
+    Ext4.onReady(function (){
+        window.location = LABKEY.ActionURL.buildURL('laboratory', 'dataBrowser', null, {subjectId: LABKEY.ActionURL.getParameter('participantId')});
+    });
+</script>

SivStudies/src/org/labkey/sivstudies/query/SivStudiesCustomizer.java

@@ -249,6 +249,13 @@ private void appendDemographicsColumns(AbstractTableInfo parentTable)
             colInfo.setLabel("Outcomes");
             parentTable.addColumn(colInfo);
         }
+
+        if (parentTable.getColumn("sivART") == null)
+        {
+            BaseColumnInfo colInfo = getWrappedIdCol(parentTable.getUserSchema(), "demographicsChallengeAndArt", parentTable, "sivART");
+            colInfo.setLabel("SIV/ART Dates");
+            parentTable.addColumn(colInfo);
+        }
     }
 
     private void appendPvlColumns(DatasetTable ds, String subjectColName, String dateColName)