Tattoo snomed addition

onprc_ehr/resources/queries/study/TattooAlert.sql

@@ -0,0 +1,5 @@
+-- Displays all animals with tattoo procedure missing in the encounters table. Excluding the purchased animals
+Select Id, birth, gender from study.demographics a
+Where a.calculated_status = 'Alive'
+  And a.id not in (Select id from study.arrival where acquisitiontype = 6) --6= Purchase
+  And a.id not in (Select id from study.encounters where procedureid = 760) -- TATTOO procedure

onprc_ehr/resources/scripts/onprc_ehr/onprc_triggers.js

@@ -721,6 +721,15 @@ exports.init = function(EHR){
         }
     });
 
+    //Added: By Kollil on 5/31/2022
+    //When the Tattoo procedure is selected, add snomedcode: P-12090 TATTOOING
+    EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.AFTER_UPSERT, 'study', 'encounters', function(helper, errors, row, oldRow){
+        if (row.procedureid == 760){
+            //Add snomed code.
+            triggerHelper.addTattooSnomedCode(row.Id, row);
+        }
+    });
+
     EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.BEFORE_UPSERT, 'study', 'drug', function(helper, scriptErrors, row, oldRow){
         if (row.outcome && row.outcome != 'Normal' && !row.remark){
             EHR.Server.Utils.addError(scriptErrors, 'remark', 'A remark is required if a non-normal outcome is reported', 'WARN');

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

@@ -62,21 +62,27 @@ public String getEmailSubject(Container c)
     }
 
     @Override
+//    public String getCronString()
+//    {
+//        return "0 0 15 * * ?";
+//    }
+
+    //Kollil 10/13: Changed the daily alert to Tuesdays and Thursdays
     public String getCronString()
     {
-        return "0 0 15 * * ?";
+        return "0 0 15 ? * TUE,THU";
     }
 
     @Override
     public String getScheduleDescription()
     {
-        return "every day at 3PM";
+        return "every Tuesday & Thursday at 3PM";
     }
 
     @Override
     public String getDescription()
     {
-        return "The report is designed alert if there are any animals without rounds observations entered or lacking vet review";
+        return "The report is designed to alert if there are any animals without rounds observations entered or lacking vet review. Also, contains the report to alert for Clinical rounds observations entered today, and not entered recently";
     }
 
     @Override
@@ -86,7 +92,11 @@ public String getMessageBodyHTML(Container c, User u)
 
         duplicateCases(c, u, msg);
         animalsWithoutRounds(c, u, msg);
-        //animalsWithoutVetReview(c, u, msg);
+        animalsWithoutVetReview(c, u, msg);
+
+        //Clinical process alerts : Kollil, 10/13/22
+        animalsWithRounds(c, u, msg);         //Added: 8-22-2016 R.Blasa
+        //animalsWithoutRounds2(c, u, msg);       //Added 8-29-2016
 
         return msg.toString();
     }
@@ -112,7 +122,8 @@ protected void animalsWithoutRounds(final Container c, User u, final StringBuild
         long count = ts.getRowCount();
         if (count > 0)
         {
-            msg.append("<b>WARNING: There are " + count + " active cases that do not have obs entered today.</b><br>");
+            msg.append("<b>Clinical Rounds Alerts: Active cases that do not have observations.</b><br>");
+            msg.append("<b>WARNING:  " + count + " active case(s) found that do not have obs entered today.</b><br>");
             msg.append("<table border=1 style='border-collapse: collapse;'>");
             msg.append("<tr style='font-weight: bold;'><td>Room</td><td>Cage</td><td>Id</td><td>Assigned Vet</td><td>Problem(s)</td><td>Days Since Last Rounds</td></tr>");
 
@@ -163,7 +174,8 @@ protected void animalsWithoutVetReview(final Container c, User u, final StringBu
         long count = ts.getRowCount();
         if (count > 0)
         {
-            msg.append("<b>WARNING: There are " + count + " active cases that have not been vet reviewed in the past 7 days.</b><br>");
+            msg.append("<b>Clinical Rounds Alerts: Active cases with no Vet review.</b><br>");
+            msg.append("<b>WARNING: " + count + " active case(s) found that have not been vet reviewed in the past 7 days.</b><br>");
             msg.append("<table border=1 style='border-collapse: collapse;'>");
             msg.append("<tr style='font-weight: bold;'><td>Room</td><td>Cage</td><td>Id</td><td>Assigned Vet</td><td>Problem(s)</td><td>Days Since last Vet Review</td></tr>");
 
@@ -188,4 +200,108 @@ public void exec(ResultSet object) throws SQLException
             msg.append("<hr>\n");
         }
     }
-}
+
+    //Clinical process alerts
+//
+
+    //Modified: 8-15-2016  R.Blasa     Show Clinical open cases that were entered
+    protected void animalsWithRounds(final Container c, User u, final StringBuilder msg)
+    {
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("daysSinceLastRounds"), 0, CompareType.EQUAL);
+        filter.addCondition(FieldKey.fromString("isActive"), true, CompareType.EQUAL);
+        filter.addCondition(FieldKey.fromString("category"), "Clinical", CompareType.EQUAL);
+        filter.addCondition(FieldKey.fromString("Id/demographics/calculated_status"), "Alive", CompareType.EQUAL);
+
+        TableInfo ti = getStudySchema(c, u).getTable("cases");
+        Set<FieldKey> keys = new HashSet<>();
+        keys.add(FieldKey.fromString("Id"));
+        keys.add(FieldKey.fromString("Id/curLocation/room"));
+        keys.add(FieldKey.fromString("Id/curLocation/cage"));
+        keys.add(FieldKey.fromString("daysSinceLastRounds"));
+        keys.add(FieldKey.fromString("assignedvet/DisplayName"));
+        keys.add(FieldKey.fromString("allProblemCategories"));
+        final Map<FieldKey, ColumnInfo> cols = QueryService.get().getColumns(ti, keys);
+
+        TableSelector ts = new TableSelector(ti, cols.values(), filter, new Sort("Id/curLocation/room_sortValue,Id/curLocation/cage_sortValue"));
+        long count = ts.getRowCount();
+
+        if (count > 0)
+        {
+            msg.append("<b>Clinical Rounds Process Alerts: Active cases that have observations.</b><br>");
+            msg.append("<b>CONFIRMATION: " + count + " active case(s) found that have their obs entered today.</b><br>");
+            msg.append("<table border=1 style='border-collapse: collapse;'>");
+            msg.append("<tr style='font-weight: bold;'><td>Room</td><td>Cage</td><td>Id</td><td>Assigned Vet</td><td>Problem(s)</td></tr>");
+
+            ts.forEach(new Selector.ForEachBlock<ResultSet>()
+            {
+                @Override
+                public void exec(ResultSet object) throws SQLException
+                {
+                    Results rs = new ResultsImpl(object, cols);
+                    msg.append("<tr>");
+                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("Id/curLocation/room")), "None") + "</td>");
+                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("Id/curLocation/cage")), "") + "</td>");
+                    msg.append("<td>" + rs.getString(FieldKey.fromString("Id")) + "</td>");
+                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("assignedvet/DisplayName")), "None") + "</td>");
+                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("allProblemCategories")), "None") + "</td>");
+
+                    msg.append("</tr>");
+                }
+            });
+
+            msg.append("</table>");
+            msg.append("<hr>\n");
+        }
+    }
+
+
+ //   protected void animalsWithoutRounds2(final Container c, User u, final StringBuilder msg)
+//    {
+//        SimpleFilter filter = new SimpleFilter(FieldKey.fromString("daysSinceLastRounds"), 0, CompareType.GT);
+//        filter.addCondition(FieldKey.fromString("isActive"), true, CompareType.EQUAL);
+//        filter.addCondition(FieldKey.fromString("category"), "Clinical", CompareType.EQUAL);
+//        filter.addCondition(FieldKey.fromString("Id/demographics/calculated_status"), "Alive", CompareType.EQUAL);
+//
+//        TableInfo ti = getStudySchema(c, u).getTable("cases");
+//        Set<FieldKey> keys = new HashSet<>();
+//        keys.add(FieldKey.fromString("Id"));
+//        keys.add(FieldKey.fromString("Id/curLocation/room"));
+//        keys.add(FieldKey.fromString("Id/curLocation/cage"));
+//        keys.add(FieldKey.fromString("daysSinceLastRounds"));
+//        keys.add(FieldKey.fromString("assignedvet/DisplayName"));
+//        keys.add(FieldKey.fromString("allProblemCategories"));
+//        final Map<FieldKey, ColumnInfo> cols = QueryService.get().getColumns(ti, keys);
+//
+//        TableSelector ts = new TableSelector(ti, cols.values(), filter, new Sort("Id/curLocation/room_sortValue,Id/curLocation/cage_sortValue"));
+//        long count = ts.getRowCount();
+//
+//        if (count > 0)
+//        {
+//            msg.append("<b>Clinical Rounds Process Alerts: Active cases that do not have observations entered today.</b><br>");
+//            msg.append("<b>WARNING: There are " + count + " active cases that do not have obs entered today.</b><br>");
+//            msg.append("<table border=1 style='border-collapse: collapse;'>");
+//            msg.append("<tr style='font-weight: bold;'><td>Room</td><td>Cage</td><td>Id</td><td>Assigned Vet</td><td>Problem(s)</td><td>Days Since Last Rounds</td></tr>");
+//
+//            ts.forEach(new Selector.ForEachBlock<ResultSet>()
+//            {
+//                @Override
+//                public void exec(ResultSet object) throws SQLException
+//                {
+//                    Results rs = new ResultsImpl(object, cols);
+//                    msg.append("<tr>");
+//                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("Id/curLocation/room")), "None") + "</td>");
+//                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("Id/curLocation/cage")), "") + "</td>");
+//                    msg.append("<td>" + rs.getString(FieldKey.fromString("Id")) + "</td>");
+//                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("assignedvet/DisplayName")), "None") + "</td>");
+//                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("allProblemCategories")), "None") + "</td>");
+//                    msg.append("<td>" + safeAppend(rs.getString(FieldKey.fromString("daysSinceLastRounds")), "") + "</td>");
+//                    msg.append("</tr>");
+//                }
+//            });
+//
+//            msg.append("</table>");
+//            msg.append("<hr>\n");
+//        }
+//    }
+
+    }

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

@@ -18,6 +18,7 @@
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
@@ -92,8 +93,7 @@ public String getMessageBodyHTML(Container c, User u)
         getTbAlerts(sb, c, u);
         getPEAlerts(sb, c, u);
         getAnimalsNotWeightedInPast60Days(sb, c, u);
-
-        //getVirologyAlerts(sb, c, u);
+        getTattooAlerts(sb, c, u);
 
         return sb.toString();
     }
@@ -295,4 +295,47 @@ protected void getAnimalsNotWeightedInPast60Days(StringBuilder msg, Container c,
 
         msg.append("<hr>\n");
     }
+
+    /**
+     * Kollil, 6/01/22 : List the animalIds with missing Tattoos, i.e, Animals with no Tattoo procedure,  ProcedureId = 760
+     */
+    protected void getTattooAlerts(StringBuilder msg, Container c, User u)
+    {
+        msg.append("<b>Animals with missing Tattoo procedure:</b><br><br>\n");
+
+        if (QueryService.get().getUserSchema(u, c, "study") == null) {
+            msg.append("<b>Warning: The study schema has not been enabled in this folder, so the alert cannot run!<p><hr>");
+            return;
+        }
+        //Tattoo query
+        TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("TattooAlert", ContainerFilter.Type.AllFolders.create(c, u));
+        Set<ColumnInfo> cols = appendLocationCols(ti);
+        TableSelector ts = new TableSelector(ti, cols, null, null);
+        long count = ts.getRowCount();
+
+        //Get num of rows
+        if (count > 0)
+        {
+            msg.append("ALERT: " + count + " animals found with no Tattoo procedure recorded in Prime:");
+            //String url = getExecuteQueryUrl(c, "study", "Demographics", "By Location") + "&query.Id/MostRecentWeight/DaysSinceWeight~gt=75&query.calculated_status~eq=Alive&query.Id/curLocation/Room/housingType/value~eq=Cage Location";
+            String url = getExecuteQueryUrl(c, "study", "TattooAlert", null) + "&query.containerFilterName=AllFolders";
+            msg.append("<b><a href='" + url + "'>Click here to view them.</a></b><br><br>\n");
+
+            msg.append("Summary by area:<br>\n");
+            msg.append("<table>");
+            Map<String, Integer> areaMap = getAreaMap(ts, cols);
+            for (String area : areaMap.keySet())
+            {
+                String newUrl = url + "&query.Id/curLocation/area~eq=" + area;
+                msg.append("<tr><td>" + area + ": </td><td><a href='" + newUrl + "'>" + areaMap.get(area) + "</a></td></tr>\n");
+            }
+            msg.append("</table>");
+            msg.append("<br><br>");
+        }
+        else
+        {
+            msg.append("<b> All live animals at the center are tattooed! </b>");
+        }
+        msg.append("<hr>\n");
+    }
 }

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

@@ -63,15 +63,20 @@ public String getEmailSubject(Container c)
     }
 
     @Override
+//    public String getCronString()
+//    {
+//        return "0 0 15 * * ?";
+//    }
+    //Kollil 10/13: Changed the daily alert to once a week, Wednesdays
     public String getCronString()
     {
-        return "0 0 15 * * ?";
+        return "0 0 15 ? * WED";
     }
 
     @Override
     public String getScheduleDescription()
     {
-        return "daily at 3PM";
+        return "every Wednesday at 3PM";
     }
 
     @Override

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

@@ -185,7 +185,8 @@ public Map<String, Object> getExtraContext()
         return map;
     }
 
-    //Added by Kolli 3/3/20
+
+     //Added by Kolli 3/3/20
     //This function automatically sets the study details endDate if previous study details endDate is empty when a new study is created.
     public void closeStudyDetailsRecords(List<Map<String, Object>> records) throws Exception
     {
@@ -1093,6 +1094,7 @@ private Date maxDate(Date d1, Date d2)
         return (d1.after(d2)) ? d1 : d2;
     }
 
+
     public void closeActiveAssignmentRecords(String id, Date deathDate, String causeOfDeath) throws Exception
     {
         try
@@ -1147,6 +1149,45 @@ public void closeActiveAssignmentRecords(String id, Date deathDate, String cause
         }
     }
 
+    /*Added by Kolli 6/3/22
+    When a tattoo procedure is entered into study.encounters table enter a snomed code into ehr.snomed_tags
+    Id - Animalid
+    Date - now()
+    code - TATTOOING
+    code/code - P-12090
+    */
+    public void addTattooSnomedCode(String id, @NotNull Map<String, Object> row) throws QueryUpdateServiceException, DuplicateKeyException, SQLException, BatchValidationException
+    {
+        if (id != null)
+        {
+            //_log.info("Animal Id thats tattooed: " + id);
+            Map<String, Object> snomedProps = new HashMap<String, Object>();
+
+            snomedProps.put("Id", row.get("Id"));
+            snomedProps.put("date", row.get("date"));
+            snomedProps.put("code", "P-12090");
+            snomedProps.put("objectId", new GUID());
+            snomedProps.put("container", _container.getId());
+
+            //_log.info("props: " + snomedProps);
+
+            TableInfo ti = getTableInfo("ehr", "snomed_tags");
+            Map<String, Object> new_row = new CaseInsensitiveHashMap<>();
+            new_row.putAll(snomedProps);
+
+            List<Map<String, Object>> rows = new ArrayList<>();
+            rows.add(new_row);
+
+            BatchValidationException errors = new BatchValidationException();
+            //Insert row into the db table
+            ti.getUpdateService().insertRows(getUser(), getContainer(), rows, errors, null, getExtraContext());
+
+            if (errors.hasErrors())
+                throw errors;
+
+        }
+    }
+
     //Added on 10/5/2016, L.Kolli
     public Map<String, Object> onAnimalArrival_AddDemographics(String id, Map<String, Object> row) throws QueryUpdateServiceException, DuplicateKeyException, SQLException, BatchValidationException
     {
@@ -1228,6 +1269,7 @@ public void createBirthRecord_ONPRC(String id, Map<String, Object> props) throws
         }
 
     }
+
     //    Added: 6-27-2017  F.Blasa  Process when transitioning from Prenatal - Fetus to Live
     public void doBirthConditionAfterPrenatal(String id, Date date, String dam, Date Arrival_Date, String birthCondition, boolean isBecomingPublic) throws Exception
     {
@@ -2119,6 +2161,7 @@ public String validateCaseNo(String caseNo, String type, String objectid)
     {
         SimpleFilter filter = new SimpleFilter(FieldKey.fromString("caseno"), caseNo);
         filter.addCondition(FieldKey.fromString("type"), type);
+
         if (objectid != null)
         {
             filter.addCondition(FieldKey.fromString("objectid"), objectid, CompareType.NEQ_OR_NULL);
@@ -2128,8 +2171,6 @@ public String validateCaseNo(String caseNo, String type, String objectid)
         {
             return "There is already an existing case with the number: " + caseNo;
         }
-
-
         return null;
     }
 
@@ -2337,7 +2378,6 @@ public void exec(ResultSet rs) throws SQLException
 
     }
 
-
     //Added 3-6-2019 Blasa
     public void sendProjectNotifications(Integer projectid)
     {