[bot] Merge 25.7 to 25.10

onprc_ehr/resources/etls/AvailableBlood.xml

@@ -10,6 +10,6 @@
         </transform>
     </transforms>
     	<schedule>
-            <cron expression="0 1,31 5-20 ? * * *"/> <!-- :01 and :31 after the hour for hours 5am through 8pm -->
+            <cron expression="0 5,35 5-20 ? * * *"/> <!-- :05 and :35 after the hour for hours 5am through 8pm -->
         </schedule>
 </etl>

onprc_ehr/resources/schemas/dbscripts/sqlserver/onprc_ehr-24.013-24.014.sql

@@ -0,0 +1,74 @@
+
+
+/*
+**
+** 	Created by
+**      Blasa  		10/8/2025          Process to update birth record;s geogrphic origin data.  The "Genetic Ancestry"
+**                                      geographic_origin information must override the birth's geographic origin values.
+**
+
+**
+**
+**
+**
+*/
+
+CREATE Procedure onprc_ehr.p_BirthGeographicOriginUpdates
+
+    as
+
+
+BEGIN
+
+   ----- Process data
+
+  IF exists (select *  From studydataset.c6d202_birth bir, studydataset.c6d512_geneticancestry b where bir.participantid = b.participantid
+    And b.enddate is null
+    and bir.qcstate = 18
+    and b.qcstate = 18
+    And bir.geographic_origin <> b.result
+    And b.result is not null
+              )
+
+
+
+    BEGIN
+
+   ---- Update birth geographic origin
+
+   Update bir
+   set bir.geographic_origin = b.result,
+       bir.modified = getdate(),
+       bir.modifiedby = b.modifiedby    ---- ancestry staff
+
+    From studydataset.c6d202_birth bir, studydataset.c6d512_geneticancestry b
+    where bir.participantid = b.participantid
+    And b.enddate is null
+    And bir.qcstate = 18
+    And b.qcstate = 18
+    And bir.geographic_origin <> b.result
+    And b.result is not null
+
+
+    If @@Error <> 0
+         GoTo Err_Proc
+
+END  ---- if
+
+
+
+
+
+RETURN 0
+
+
+    Err_Proc:
+                    -------Error Generated, process stopped
+	RETURN 1
+
+
+END
+
+GO
+
+

onprc_ehr/resources/scripts/onprc_ehr/onprc_triggers.js

@@ -1348,12 +1348,6 @@ exports.init = function(EHR){
             }
         });
     });
-    EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'demographics', function (helper, scriptErrors, row, oldRow) {
-        if (row.Id && row.geographic_origin)  {
-            //update birth records
-            triggerHelper.updateBirthGeographics(row.Id, row.geographic_origin);
-        }
-    });
 
     //Added: 10-4-2022  R.Blasa
     EHR.Server.TriggerManager.registerHandler(EHR.Server.TriggerManager.Events.COMPLETE, function(event, errors, helper){

onprc_ehr/resources/views/BSU_BulkEdit.html

@@ -0,0 +1,42 @@
+
+<!--Created 9-25-2025 R.Blasa-->
+
+
+<div id="qwpDiv" />
+
+<script type="text/javascript" nonce="<%=scriptNonce%>">
+
+    var ehrContainer = '/ONPRC/EHR';
+    var wp = new LABKEY.QueryWebPart({
+        containerPath: ehrContainer,
+        schemaName : 'study',
+        queryName : 'pairings',
+        showRecordSelectors : true,
+        renderTo: 'qwpDiv',
+        buttonBar: {
+            includeStandardButtons: true,
+            items:[
+                {text: 'Bulk Edit', requiresSelection : true, handler: function(dataRegion){
+                        if (dataRegion) {
+                            var url = LABKEY.ActionURL.buildURL('query', 'updateQueryRows.view', null, {
+                                schemaName: dataRegion.schemaName,
+                                'query.queryName': dataRegion.queryName,
+                                dataRegionSelectionKey: dataRegion.selectionKey,
+                                returnUrl:window.location
+                            });
+                            var form = dataRegion.form;
+                            if (form && verifySelected.call(this, form, url, 'POST', 'rows')) {
+                                submitForm(form);
+
+                            }
+                            return false;
+                        }
+                    }}
+            ]
+        }
+
+    });
+    wp.render();
+</script>
+
+

onprc_ehr/resources/views/BSU_BulkEdit.view.xml

@@ -0,0 +1,5 @@
+<view xmlns="http://labkey.org/data/xml/view" frame="none" title="BSU Pairings Bulk Edit">
+    <dependencies>
+        <dependency path="ehr.context" />
+    </dependencies>
+</view>

onprc_ehr/resources/web/onprc_ehr/model/sources/ASB_Services.js

@@ -54,8 +54,9 @@ EHR.model.DataModelManager.registerMetadata('ASB_Services', {
                     schemaName: 'onprc_ehr',
                     queryName: 'ASB_SpecialInstructions',
                     displayColumn: 'value',
-                    // columns: 'value'
-                    keyColumn: 'value'
+                    keyColumn: 'value',
+                    filterArray: [
+                        LABKEY.Filter.create('dateDisabled', null, LABKEY.Filter.Types.ISBLANK)]
                 },
                 columnConfig: {
                     width: 300

onprc_ehr/src/org/labkey/onprc_ehr/ONPRC_EHRModule.java

@@ -129,7 +129,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 24.013;
+        return 24.014;
     }
 
     @Override

onprc_ehr/src/org/labkey/onprc_ehr/notification/AvailableBloodVolumeNotification.java

@@ -11,6 +11,7 @@
 import org.labkey.api.query.QueryService;
 import org.labkey.api.security.User;
 
+import java.util.Calendar;
 import java.util.Date;
 
 
@@ -32,9 +33,14 @@ public String getEmailSubject(Container c)
     {
         return "Available Blood Volume Alert: " + getDateTimeFormat(c).format(new Date());
     }
-    /* From Hugh Crank:
+
+    /* Mathematica push:
      * Server mkt7: Runs at :55 from 4:55am to 7:55pm
      * Server mkt8: Runs at :25 from 4:25am to 7:25pm
+     *
+     * ABV ETL:
+     * :05 and :35 after the hour for hours between 05:00 and 20:00
+     * 0 1,31 5-20 ? * * *
      */
     @Override
     public String getCronString()
@@ -45,44 +51,52 @@ public String getCronString()
     @Override
     public String getScheduleDescription()
     {
-        return "15 minutes after every hour between 06:15 and 19:15.";
+        return "15 min past every hour from 06:15 to 19:15.";
     }
 
     @Override
     public String getDescription()
     {
-        return "Sends an alert on status of Available Blood Volume data from Mathematica.";
+        return "Sends status of available blood volume data from Mathematica.";
     }
 
     @Override
     public String getMessageBodyHTML(Container c, User u)
     {
         StringBuilder msg = new StringBuilder();
-
-        AvailableBloodCheck(c, u, msg);
-
+        availableBloodCheck(c, u, msg);
         return msg.toString();
     }
-    /* jonesga 5/8/2024 labkeyPublic.labkeyPublic.ValidateAvailableBloodProcess
-     */
-    protected void AvailableBloodCheck(final Container c, User u, final StringBuilder msg)
+
+    protected void availableBloodCheck(final Container c, User u, final StringBuilder msg)
     {
-        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("date"), new Date(), CompareType.DATE_GTE);
-        TableInfo ti = QueryService.get().getUserSchema(u, c, "onprc_ehr").getTable("ValidateAvailableBloodProcess", ContainerFilter.Type.AllFolders.create(c, u));
-//        ((ContainerFilterable) ti).setContainerFilter(ContainerFilter.Type.AllFolders.create(u);
-        TableSelector ts = new TableSelector(ti, null, null);
+        Calendar cal = Calendar.getInstance();
+        cal.add(Calendar.HOUR, -1);
+        Date staleTime = cal.getTime();
+
+        TableInfo ti = QueryService.get().getUserSchema(u, c, "onprc_ehr").getTable("AvailableBloodVolume", ContainerFilter.Type.AllFolders.create(c, u));
 
+        if (ti == null)
+        {
+            msg.append("<b>ERROR: Unable to access onprc_ehr.AvailableBloodVolume table.</b><br>\n");
+            return;
+        }
+
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("datecreated"), staleTime, CompareType.LTE);
+        TableSelector ts = new TableSelector(ti, filter, null);
         long count = ts.getRowCount();
+
         if (count > 0)
         {
-            msg.append("<b>The available blood volume data from Mathematica is stale.</b><br>\n");
-            msg.append("<p><a href='" + getExecuteQueryUrl(c, "onprc_ehr", "ValidateAvailableBloodProcess", null) + "'>Click here to view labkeyPublic.AvailableBloodVolume.</a><br>\n\n");
-            msg.append("</p><br><hr>");
+            msg.append("<b>WARNING: The available blood volume data from Mathematica is stale (last updated more than 1 hour ago).</b><br>\n");
+            msg.append("<p>View <a href='").append(getExecuteQueryUrl(c, "onprc_ehr", "AvailableBloodVolume", null)).append("'>onprc_ehr.AvailableBloodVolume</a>.</p>\n");
+            msg.append("<br>");
         }
         else
         {
-            msg.append("The available blood volume data from Mathematica is current.<br><hr>");
-            msg.append("<p><a href='" + getExecuteQueryUrl(c, "onprc_ehr", "ValidateAvailableBloodProcess", null) + "'>Click here to view labkeyPublic.AvailableBloodVolume.</a><br>\n\n");
-            msg.append("</p><br><hr>");
+            msg.append("<b>OK:</b> The available blood volume data from Mathematica is current (updated within the last hour).<br>\n");
+            msg.append("<p>View <a href='").append(getExecuteQueryUrl(c, "onprc_ehr", "AvailableBloodVolume", null)).append("'>onprc_ehr.AvailableBloodVolume</a>.</p>\n");
+            msg.append("<br>");
         }
-    }}
+    }
+}

onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java

@@ -2635,54 +2635,6 @@ public void exec(ResultSet object) throws SQLException
     }
 
 
-    public void updateBirthGeographics(String id, String geographic_origin) throws Exception
-    {
-        TableInfo ti = getTableInfo("study", "birth");
-        if (ti == null)
-        {
-            return;
-        }
-
-        Set<FieldKey> keys = new HashSet<>();
-        keys.add(FieldKey.fromString("Id"));
-        keys.add(FieldKey.fromString("geographic_origin"));
-        keys.add(FieldKey.fromString("lsid"));
-        final Map<FieldKey, ColumnInfo> colMap = QueryService.get().getColumns(ti, keys);
-
-
-        final List<Map<String, Object>> toUpdate = new ArrayList<>();
-        final List<Map<String, Object>> oldKeys = new ArrayList<>();
-        TableSelector ts = new TableSelector(ti, colMap.values(), new SimpleFilter(FieldKey.fromString("Id"), id, CompareType.IN), null);
-        ts.forEach(new Selector.ForEachBlock<>()
-        {
-            @Override
-            public void exec(ResultSet object) throws SQLException
-            {
-                ResultsImpl rs = new ResultsImpl(object, colMap);
-                String animalid = rs.getString(FieldKey.fromString("Id"));
-                String origin = rs.getString(FieldKey.fromString("geographic_origin"));
-                String lsid = rs.getString(FieldKey.fromString("lsid"));
-            if (origin != geographic_origin)
-            {
-                Map<String, Object> row = new CaseInsensitiveHashMap<>();
-                row.put("lsid", lsid);
-                row.put("geographic_origin", geographic_origin);
-                Map<String, Object> keyRow = new CaseInsensitiveHashMap<>();
-                keyRow.put("lsid", lsid);
-
-                oldKeys.add(keyRow);
-                toUpdate.add(row);
-
-            }
-            }
-        });
-
-        if (!toUpdate.isEmpty())
-        {
-            TableInfo demographics = getTableInfo("study", "birth");
-            demographics.getUpdateService().updateRows(_user, _container, toUpdate, oldKeys, null, getExtraContext());
-        }
-    }
 
     //Added 9-30-2025
     public String retrieveGeographic_Origin(String Id)

onprc_ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java

@@ -80,6 +80,7 @@ public abstract class AbstractGenericONPRC_EHRTest extends AbstractGenericEHRTes
     protected static String[] ROOMS = {"Room1", "Room2", "Room3"};
     protected static String[] CAGES = {"A1", "B2", "A3"};
     protected static String[] CATEGORY = {"Divider Change", "Event", "STP_Beh"};
+    protected static String[] TINFANT = {"35160", "24456", "36451"};
 
     @Override
     public List<String> getAssociatedModules()

onprc_ehr/test/src/org/labkey/test/tests/onprc_ehr/ONPRC_EHRTest2.java

@@ -818,6 +818,7 @@ public void testPairingObservations() throws Exception
         grid.setGridCell(1, "cage", "A1");
         grid.setGridCellJS(1, "date", TIME_FORMAT.format(today));
         grid.setGridCell(1, "category", CATEGORY[0]);
+        grid.setGridCell(1, "other_infant", TINFANT[0]);
 
         _helper.addRecordToGrid(grid);
         sleep(200);
@@ -827,6 +828,7 @@ public void testPairingObservations() throws Exception
         grid.setGridCell(2, "cage", "A1");
         grid.setGridCellJS(2, "date", TIME_FORMAT.format(today));
         grid.setGridCell(2, "category", CATEGORY[0]);
+        grid.setGridCell(2, "other_infant", TINFANT[0]);
 
         Assert.assertEquals(grid.getFieldValue(1, "pairid"), grid.getFieldValue(2, "pairid"));
 
@@ -843,6 +845,7 @@ public void testPairingObservations() throws Exception
         grid.setGridCell(3, "cage", "A2");
         grid.setGridCellJS(3, "date", TIME_FORMAT.format(today));
         grid.setGridCell(3, "category", CATEGORY[0]);
+        grid.setGridCell(3, "other_infant", TINFANT[0]);
 
         grid.setGridCell(3, "lowestcage", "A1");
         sleep(100);