Merge 24.11 to develop

WNPRC_EHR/resources/queries/study/ClinpathRefRange.sql

@@ -33,6 +33,7 @@ c.taskid,
 c.qcstate,
 c.alertOnAbnormal,
 c.alertOnAny,
+c.testId.units,
 'Chemistry' as dataset,
 'Chemistry_'||c.testid as test_key,
 from study.chemistryRefRange c
@@ -59,6 +60,7 @@ c.taskid,
 c.qcstate,
 c.alertOnAbnormal,
 c.alertOnAny,
+c.testId.units,
 'Hematology' as dataset,
 'Hematology_'||c.testid as test_key,
 from study.hematologyRefRange c
@@ -85,6 +87,7 @@ c.taskid,
 c.qcstate,
 c.alertOnAbnormal,
 c.alertOnAny,
+c.testId.units,
 'Immunology' as dataset,
 'Immunology_'||c.testid as test_key,
 from study.immunologyRefRange c
@@ -111,6 +114,7 @@ c.taskid,
 c.qcstate,
 c.alertOnAbnormal,
 c.alertOnAny,
+c.testId.units,
 'Urinalysis' as dataset,
 'Urinalysis_'||c.testid as test_key,
 from study.urinalysisRefRange c

WNPRC_EHR/src/org/labkey/wnprc_ehr/WNPRC_EHRModule.java

@@ -393,7 +393,11 @@ public void registerNotifications() {
                 new BloodOverdrawTriggerNotification(this),
                 new EmptyNotificationRevamp(this),
                 new AnimalRequestUpdateNotificationRevamp(this),
-                new TreatmentAlertsNotificationRevamp(this)
+                new TreatmentAlertsNotificationRevamp(this),
+                new ClinpathAbnormalResultsAlertsRevamp(this),
+                new ClinpathAlertsRevamp(this),
+                new ClinpathResultAlertsRevamp(this),
+                new LargeInfantAlertsRevamp(this)
                 );
 
         for (Notification notification : notifications)

WNPRC_EHR/src/org/labkey/wnprc_ehr/notification/ClinpathAbnormalResultsAlertsRevamp.java

@@ -0,0 +1,196 @@
+package org.labkey.wnprc_ehr.notification;
+
+import org.checkerframework.checker.units.qual.A;
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.ldk.notification.NotificationService;
+import org.labkey.api.module.Module;
+import org.labkey.api.security.User;
+
+import java.lang.reflect.Array;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.HashMap;
+
+public class ClinpathAbnormalResultsAlertsRevamp extends AbstractEHRNotification {
+    //Class Variables
+    NotificationToolkit notificationToolkit = new NotificationToolkit();
+    NotificationToolkit.DateToolkit dateToolkit = new NotificationToolkit.DateToolkit();
+    NotificationToolkit.StyleToolkit styleToolkit = new NotificationToolkit.StyleToolkit();
+
+
+
+
+
+    // Constructors
+    /**
+     * This constructor is used to register the notification in WNPRC_EHRModule.java.
+     * @param owner
+     */
+    public ClinpathAbnormalResultsAlertsRevamp(Module owner) {super(owner);}
+
+
+
+
+
+    // Notification Details
+    @Override
+    public String getName() {
+        return "Clinpath Abnormal Results Alerts Notification Revamp";
+    }
+    @Override
+    public String getDescription() {
+        return "This report is designed to identify potential problems related to clinpath.";
+    }
+    @Override
+    public String getEmailSubject(Container c) {
+        return "Abnormal Clinpath Results: " + dateToolkit.getCurrentTime();
+    }
+    @Override
+    public String getScheduleDescription() {
+        return "Daily every hour from 7:05AM - 5:05PM";
+    }
+    @Override
+    public String getCronString() {
+        return notificationToolkit.createCronString("5", "7,8,9,10,11,12,13,14,15,16,17", "*");
+    }
+    @Override
+    public String getCategory() {
+        return "Revamped Notifications";
+    }
+
+
+
+
+
+    // Message Creation
+    @Override
+    public String getMessageBodyHTML(Container c, User u) {
+        // Creates variables & gets data.
+        final StringBuilder messageBody = new StringBuilder();
+
+        // Creates CSS.
+        messageBody.append(styleToolkit.beginStyle());
+        messageBody.append(styleToolkit.setBasicTableStyle());
+        messageBody.append(styleToolkit.setHeaderRowBackgroundColor("#d9d9d9"));
+        messageBody.append(styleToolkit.endStyle());
+
+        // Sets up variables.
+        HashMap<String, HashMap<String, ArrayList<HashMap<String, String>>>> filteredResults = new HashMap<>(); // Areas > Rooms > Results List > Result
+        Date lastRunDate = new Date(NotificationService.get().getLastRun(this));
+        Calendar cal = Calendar.getInstance();
+        cal.setTime(lastRunDate);
+        cal.add(Calendar.DATE, -7);
+        Date lastRunMinusWeek = cal.getTime();
+
+        // Creates filter.
+        SimpleFilter myFilter = new SimpleFilter("qcstate/PublicData", true, CompareType.EQUAL);
+        myFilter.addCondition("taskid/datecompleted", lastRunDate, CompareType.DATE_GTE);
+        myFilter.addCondition("taskid/datecompleted", "", CompareType.NONBLANK);
+        myFilter.addCondition("date", lastRunMinusWeek, CompareType.DATE_GTE);
+        // Creates columns to retrieve.
+        String[] targetColumns = new String[]{"Id", "date", "Id/curLocation/area", "Id/curLocation/room", "Id/curLocation/cage", "alertStatus", "taskid/datecompleted", "testid", "result", "units", "status", "ref_range_min", "ref_range_max", "ageAtTime"};
+        // Runs query.
+        ArrayList<HashMap<String, String>> returnArray = notificationToolkit.getTableMultiRowMultiColumnWithFieldKeys(c, u, "study", "ClinpathRefRange", myFilter, null, targetColumns);
+        // Creates URL.
+        String clinpathTasksUrlView = notificationToolkit.createQueryURL(c, "execute", "study", "ClinpathRefRange", myFilter);
+
+        // Organizes results into a list filtered by [Area > Room > Task].
+        for (HashMap<String, String> result : returnArray) {
+            // Verifies 'alert status' exists before adding results.
+            if (!result.get("alertStatus").isEmpty()) {
+                // Updates current location.
+                if (result.get("Id/curLocation/area").isEmpty()) {
+                    result.put("Id/curLocation/area", "No Active Housing");
+                }
+                // Updates current room.
+                if (result.get("Id/curLocation/room").isEmpty()) {
+                    result.put("Id/curLocation/room", "No Room");
+                }
+
+                // Adds to list if area does not exist yet.
+                if (!filteredResults.containsKey(result.get("Id/curLocation/area"))) {
+                    // Creates new room results list.
+                    ArrayList<HashMap<String, String>> newRoomList = new ArrayList<>();
+                    newRoomList.add(result);
+                    // Creates new room map.
+                    HashMap<String, ArrayList<HashMap<String, String>>> newRoom = new HashMap<>();
+                    newRoom.put(result.get("Id/curLocation/room"), newRoomList);
+                    // Creates new area map and adds to the filtered results.
+                    filteredResults.put(result.get("Id/curLocation/area"), newRoom);
+                }
+                // Adds to list if room does not exist yet.
+                else if (!filteredResults.get(result.get("Id/curLocation/area")).containsKey(result.get("Id/curLocation/room"))) {
+                    // Creates new room results list.
+                    ArrayList<HashMap<String, String>> newRoomList = new ArrayList<>();
+                    newRoomList.add(result);
+                    // Creates new room map and adds to the areas list.
+                    filteredResults.get(result.get("Id/curLocation/area")).put(result.get("Id/curLocation/room"), newRoomList);
+                }
+                // Adds to list if area and room exist already.
+                else {
+                    filteredResults.get(result.get("Id/curLocation/area")).get(result.get("Id/curLocation/room")).add(result);
+                }
+            }
+        }
+
+        // Prints text.
+        messageBody.append("There have been " + returnArray.size() + " clinpath tasks completed since " + lastRunDate + "<br>");
+        messageBody.append(notificationToolkit.createHyperlink("Click here to view them", clinpathTasksUrlView) + "</a><p>\n");
+        messageBody.append("<p>Listed below are the abnormal records.</p>\n");
+
+        // Prints table with all records.
+        String[] tableColumns = new String[]{"Id", "Collect Date", "Date Completed", "Test ID", "Result", "Units", "Status", "Ref Range Min", "Ref Range Max", "Age At Time"};
+        for (String currentArea : notificationToolkit.sortSetWithNulls(filteredResults.keySet())) {
+            messageBody.append("<b>" + currentArea + ":</b><br>\n");
+            for (String currentRoom : notificationToolkit.sortSetWithNulls(filteredResults.get(currentArea).keySet())) {
+                messageBody.append(currentRoom + ":<br>\n");
+                // Reformats the hashmap into a String[] List (to be compatible with the table creation function).
+                ArrayList<String []> currentTableData = new ArrayList<>();
+                ArrayList<String> rowColorsList = new ArrayList<>();
+                for (HashMap<String, String> currentRow : filteredResults.get(currentArea).get(currentRoom)) {
+                    String[] newTableRow = new String[] {
+                            currentRow.get("Id"),
+                            currentRow.get("date"),
+                            currentRow.get("taskid/datecompleted"),
+                            currentRow.get("testid"),
+                            currentRow.get("result"),
+                            currentRow.get("units"),
+                            currentRow.get("status"),
+                            currentRow.get("ref_range_min"),
+                            currentRow.get("ref_range_max"),
+                            currentRow.get("ageAtTime"),
+                    };
+                    currentTableData.add(newTableRow);
+
+                    if (!currentRow.get("ref_range_min").isBlank() && !currentRow.get("result").isBlank()) {
+                        if (Double.parseDouble(currentRow.get("result")) < Double.parseDouble(currentRow.get("ref_range_min"))) {
+                            rowColorsList.add("yellow");
+                        }
+                    }
+                    if (!currentRow.get("ref_range_max").isBlank() && !currentRow.get("result").isBlank()) {
+                        if (Double.parseDouble(currentRow.get("result")) > Double.parseDouble(currentRow.get("ref_range_max"))) {
+                            rowColorsList.add("red");
+                        }
+                    }
+
+                    if (currentTableData.size() > rowColorsList.size()) {
+                        rowColorsList.add("white");
+                    }
+                }
+
+                // Displays table.
+                NotificationToolkit.NotificationRevampTable myTable = new NotificationToolkit.NotificationRevampTable(tableColumns, currentTableData);
+                myTable.rowColors = rowColorsList;
+                messageBody.append(myTable.createBasicHTMLTable());
+            }
+        }
+
+        // Returns message.
+        return messageBody.toString();
+    }
+
+}