Add calculated column summarizing MCC transfers

Author: bbimber

mcc/resources/etls/mcc.xml

@@ -33,6 +33,7 @@
                     <column>usage_future</column>
                     <column>date_of_observations</column>
                     <column>colony</column>
+                    <column>source</column>
                     <column>dam</column>
                     <column>sire</column>
                     <column>objectid</column>

mcc/resources/queries/study/demographicsLittermates.sql

@@ -3,8 +3,8 @@ SELECT
     d1.Id,
     d1.litterId,
 
-    (SELECT GROUP_CONCAT(distinct d2.Id, ',') as litterMates FROM study.Demographics d2 WHERE d2.qcstate.publicdata = true AND d1.litterId = d2.litterId AND d1.id != d2.id) as litterMates
+    (SELECT GROUP_CONCAT(distinct d2.Id, ',') as litterMates FROM study.Demographics d2 WHERE d2.qcstate.publicdata = true AND d2.litterId IS NOT NULL AND d1.litterId = d2.litterId AND d1.id != d2.id) as litterMates
 
 FROM study.Demographics d1
 
-WHERE d1.qcstate.publicdata = true
+WHERE d1.qcstate.publicdata = true AND d1.litterId IS NOT NULL

mcc/resources/queries/study/demographicsMccTransfer.query.xml

@@ -0,0 +1,29 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsMccTransfer" tableDbType="NOT_IN_DB">
+                <tableTitle>MCC Transfers</tableTitle>
+                <description>Summary of MCC Transfers</description>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="mccRequestId">
+                        <columnTitle>MCC Request ID</columnTitle>
+                    </column>
+                    <column columnName="piLastName">
+                        <columnTitle>PI Last Name</columnTitle>
+                    </column>
+                    <column columnName="piFirstName">
+                        <columnTitle>PI First Name</columnTitle>
+                    </column>
+                    <column columnName="piInstitution">
+                        <columnTitle>PI Institution</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>mccRequestId</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

mcc/resources/queries/study/demographicsMccTransfer.sql

@@ -0,0 +1,9 @@
+SELECT
+    d.Id,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.rowId, ', ') as mccRequestId,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.lastName, char(10)) as piLastName,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.firstName, char(10)) as piFirstName,
+    GROUP_CONCAT(DISTINCT d.mccRequestId.institution, char(10)) as piInstitution
+FROM study.departure d
+WHERE w.qcstate.publicdata = true AND mccRequestId IS NOT NULL
+GROUP BY d.Id

mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java

@@ -16,10 +16,11 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.LookupForeignKey;
 import org.labkey.api.query.QueryForeignKey;
-import org.labkey.api.query.QueryService;
 import org.labkey.api.query.UserSchema;
+import org.labkey.api.security.User;
 import org.labkey.mcc.MccManager;
 import org.labkey.mcc.MccSchema;
+import org.labkey.mcc.security.MccRequestAdminPermission;
 
 public class MccEhrCustomizer extends AbstractTableCustomizer
 {
@@ -141,6 +142,39 @@ private void customizeAnimalTable(AbstractTableInfo ti)
             col.setDescription("Summary of genomic data");
             ti.addColumn(col);
         }
+
+        // Only allow this for authorized users:
+        possiblyAddRequestSummary(ti);
+    }
+
+    private void possiblyAddRequestSummary(AbstractTableInfo ti)
+    {
+        if (ti.getColumn("mccTransfers") != null)
+        {
+            return;
+        }
+
+        Container animalDataContainer = MccManager.get().getMCCContainer(ti.getUserSchema().getContainer());
+        if (animalDataContainer == null)
+        {
+            return;
+        }
+
+        if (!animalDataContainer.equals(ti.getUserSchema().getContainer()))
+        {
+            return;
+        }
+
+        User u = ti.getUserSchema().getUser();
+        if (!animalDataContainer.hasPermission(u, MccRequestAdminPermission.class))
+        {
+            return;
+        }
+
+        var col = getWrappedIdCol(ti.getUserSchema(), ti, "mccTransfers", "demographicsMccTransfer");
+        col.setLabel("MCC Transfers");
+        col.setDescription("Summarizes MCC Transfer Information");
+        ti.addColumn(col);
     }
 
     private BaseColumnInfo getWrappedIdCol(UserSchema us, AbstractTableInfo ds, String name, String queryName)