Pathology assignments alert (#1173)

* Created a new alert to report any animal assignments where projected release condition is terminal in the last 35 days.

* Updated the center project display.

* Updated the display fields on the report
Updated the cron job time

onprc_ehr/resources/queries/study/pathAssignmentData.query.xml

@@ -0,0 +1,9 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="pathAssignmentData" tableDbType="NOT_IN_DB">
+                <tableTitle>Assignments for Pathology</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</query>

onprc_ehr/resources/queries/study/pathAssignmentData.sql

@@ -0,0 +1,21 @@
+SELECT  Id,
+--         Id.demographics.gender as Sex,
+        CASE
+            WHEN Id.demographics.gender = 'F' THEN 'Female'
+            WHEN Id.demographics.gender = 'M' THEN 'Male'
+            ELSE 'Unknown'
+            END AS Sex,
+        Id.Age.ageinyearsrounded as AgeInYearsRounded,
+        project.name as project,
+        project.protocol.investigatorId.lastname as Investigator,
+        project.title as Title,
+        date,
+        enddate,
+        projectedRelease,
+        (Select meaning from ehr_lookups.animal_condition where code = assignment.projectedReleaseCondition) as projectedReleaseCondition,
+        (Select meaning from ehr_lookups.animal_condition where code = assignment.assignCondition) as assignCondition,
+        (Select meaning from ehr_lookups.animal_condition where code = assignment.releaseCondition) as releaseCondition,
+FROM assignment
+Where projectedReleaseCondition = 206 --'Terminal'
+And date <= curdate() and date >= timestampadd(SQL_TSI_DAY, -35, curdate())
+

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

@@ -225,6 +225,9 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         //Added Aug 9th, 2024 Kollil
         ns.registerNotification(new AdminNotifications(this));
 
+        //Added Nov 5th, 2024 Kollil
+        ns.registerNotification(new PathAssignmentNotification(this));
+
         //Added 8-7-2018 R.Blasa
         ns.registerNotification(new BirthHousingMismatchNotification(this));
 

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

@@ -0,0 +1,160 @@
+package org.labkey.onprc_ehr.notification;
+
+import org.apache.commons.lang3.time.DateUtils;
+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.Results;
+import org.labkey.api.data.ResultsImpl;
+import org.labkey.api.data.Selector;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.module.Module;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.security.User;
+import org.labkey.api.util.PageFlowUtil;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+/**
+ * Created by kollil on 10/24/2019.
+ */
+
+public class PathAssignmentNotification extends ColonyAlertsNotification
+{
+    public PathAssignmentNotification(Module owner)
+    {
+        super(owner);
+    }
+
+    @Override
+    public String getName()
+    {
+        return "Pathology Assignemnt Notification";
+    }
+
+    @Override
+    public String getEmailSubject(Container c)
+    {
+        return "Animal assignment alerts for Pathology: " + getDateTimeFormat(c).format(new Date());
+    }
+
+    @Override
+    public String getCronString()
+    {
+        return "0 0 9 ? * MON";
+
+    }
+
+    @Override
+    public String getScheduleDescription()
+    {
+        return "every Monday at 9Am";
+    }
+
+    @Override
+    public String getDescription()
+    {
+        return "The report is designed to send animal assignments data to pathology every Monday!";
+    }
+
+    @Override
+    public String getMessageBodyHTML(Container c, User u)
+    {
+        StringBuilder msg = new StringBuilder();
+
+        pathAssignmentAlert(c, u, msg);
+
+        return msg.toString();
+    }
+
+    /**
+     * Kollil, 11/05/2024 : Ticket # 11319, listing assignments made with release condition as 'terminal' with the anticipated release date. It could look something like this:
+     * a. Query:    Assignment date = within the last 35 days, with 'projected release condition' = Terminal
+     * b. Report:   Table with columns as attached (I created a custom view as an example, but you can include whatever info is relevant)
+     **/
+    private void pathAssignmentAlert(Container c, User u, final StringBuilder msg)
+    {
+        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;
+        }
+        //assignments query
+        TableInfo ti = QueryService.get().getUserSchema(u, c, "study").getTable("pathAssignmentData", ContainerFilter.Type.AllFolders.create(c, u));
+        TableSelector ts = new TableSelector(ti, null, null);
+        long count = ts.getRowCount();
+
+        //Get num of rows
+        if (count > 0)
+        {
+            msg.append("<b>" + count + " assignments found with projected release condition = Terminal in the last 35 days:</b>");
+            msg.append("<p><a href='" + getExecuteQueryUrl(c, "study", "pathAssignmentData", null) + "&query.containerFilterName=AllFolders'>Click here to view the assignments in PRIME</a></p>\n");
+            msg.append("<hr>");
+        }
+        else
+        {
+            msg.append("<b> There are no assignments found with projected release condition = Terminal in the last 35 days </b>");
+            msg.append("<hr>");
+        }
+
+        //Display the daily report in the email
+        if (count > 0)
+        {
+            Set<FieldKey> columns = new HashSet<>();
+            columns.add(FieldKey.fromString("Id"));
+            columns.add(FieldKey.fromString("Sex"));
+            columns.add(FieldKey.fromString("AgeInYearsRounded"));
+            columns.add(FieldKey.fromString("project"));
+            columns.add(FieldKey.fromString("Investigator"));
+            columns.add(FieldKey.fromString("Title"));
+            columns.add(FieldKey.fromString("date"));
+            columns.add(FieldKey.fromString("enddate"));
+            columns.add(FieldKey.fromString("projectedRelease"));
+            columns.add(FieldKey.fromString("projectedReleaseCondition"));
+            columns.add(FieldKey.fromString("assignCondition"));
+            columns.add(FieldKey.fromString("releaseCondition"));
+
+            final Map<FieldKey, ColumnInfo> colMap = QueryService.get().getColumns(ti, columns);
+            TableSelector ts2 = new TableSelector(ti, colMap.values(), null, null);
+
+            msg.append("<hr><b>Assignments:</b><br><br>\n");
+            msg.append("<table border=1 style='border-collapse: collapse;'>");
+            msg.append("<tr bgcolor = " + '"' + "#FFD700" + '"' + "style='font-weight: bold;'>");
+            msg.append("<td>Id </td><td>Sex </td><td>Age (Years, Rounded) </td><td>Center Project </td><td>Investigator </td><td>Title </td><td>Assign Date </td><td>Release Date </td><td>Projected Release Date </td><td>Projected Release Condition </td><td>Condition At Assignment </td><td>Condition At Release </td></tr>");
+
+            ts2.forEach(object -> {
+                Results rs = new ResultsImpl(object, colMap);
+                String url = getParticipantURL(c, rs.getString("Id"));
+
+                msg.append("<tr bgcolor = " + '"' + "#FFFACD" + '"' + ">");
+                msg.append("<td><b> <a href='" + url + "'>" + PageFlowUtil.filter(rs.getString("Id")) + "</a> </b></td>\n");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("Sex")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("AgeInYearsRounded")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("project")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("Investigator")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("Title")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("date")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("enddate")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("projectedRelease")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("projectedReleaseCondition")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("assigncondition")) + "</td>");
+                msg.append("<td>" + PageFlowUtil.filter(rs.getString("releasecondition")) + "</td>");
+                msg.append("</tr>");
+            });
+            msg.append("</table>");
+        }
+    }
+}