Add support for marking table as DEATH table on the client side

app/airflow/dags/libs/queries.py

@@ -24,6 +24,18 @@
 
 
 find_existing_concepts_query = """
+    -- If the date_event is "death_date", mark this as a death table.
+    UPDATE mapping_scanreporttable
+    SET death_table = TRUE
+    WHERE id = %(table_id)s
+      AND date_event_id IS NOT NULL
+      AND EXISTS (
+          SELECT 1
+          FROM mapping_scanreportfield f
+          WHERE f.id = mapping_scanreporttable.date_event_id
+            AND LOWER(TRIM(f.name)) = 'death_date'
+      );
+
     INSERT INTO temp_existing_concepts_%(table_id)s (
         object_id, sr_concept_id, source_concept_id, content_type_id
     )
@@ -139,7 +151,9 @@
 -- Because concepts may or may not have the standard_concept_id, in general. And we prefer to use the standard_concept_id, if it exists.
 WHERE target_concept.concept_id = COALESCE(temp_existing_concepts.standard_concept_id, temp_existing_concepts.source_concept_id);
 
--- When the scan report table is a death table, override dest_table_id to the death OMOP table so rules show destination table: death, field: cause_concept_id
+-- If the scan report table has the "death_table" flag set to TRUE, set the destination table to OMOP's "death" table.
+-- This ensures that mapping rules will use "death" as the destination table and, for example, will select "cause_concept_id" as the mapped field.
+-- Note: The "death_table" flag may have been set automatically if a date_event was mapped to the "death_date" field earlier in the workflow.
 UPDATE temp_existing_concepts_%(table_id)s temp_existing_concepts
 SET dest_table_id = (SELECT id FROM mapping_omoptable WHERE "table" = 'death' LIMIT 1)
 WHERE (SELECT death_table FROM mapping_scanreporttable WHERE id = %(table_id)s) = TRUE;

app/next-client-app/api/scanreports.ts

@@ -149,6 +149,7 @@ export async function getScanReportTable(
       permissions: [],
       jobs: [],
       trigger_reuse: true,
+      death_table: false,
     };
   }
 }

app/next-client-app/app/(protected)/scanreports/[id]/columns.tsx

@@ -3,6 +3,7 @@
 import { ColumnDef } from "@tanstack/react-table";
 import { DataTableColumnHeader } from "@/components/data-table/DataTableColumnHeader";
 import { EditButton } from "@/components/scanreports/EditButton";
+import { Tooltips } from "@/components/core/Tooltips";
 import JobDialog from "@/components/jobs/JobDialog";
 import { FindGeneralStatus, DivideJobs } from "@/components/jobs/JobUtils";
 import Link from "next/link";
@@ -89,6 +90,28 @@ export const columns: ColumnDef<ScanReportTable>[] = [
       );
     }
   },
+  {
+    id: "note",
+    header: ({ column }) => (
+      <DataTableColumnHeader column={column} title="Note" />
+    ),
+    cell: ({ row }) => {
+      const { death_table } = row.original;
+      return (
+        <div>
+          {death_table && (
+            <h3 className="flex">
+              {" "}
+              Death table
+              <Tooltips
+                content="This table is marked as a Death table. In the Carrot data standard, death data is typically provided in a separate file (e.g. death.csv) for mapping to the OMOP Death table."
+              />
+            </h3>
+          )}
+        </div>
+      );
+    }
+  },
   {
     id: "edit",
     header: ({ column }) => <DataTableColumnHeader column={column} title="" />,

app/next-client-app/app/(protected)/scanreports/[id]/tables/[tableId]/fields/[fieldId]/page.tsx

@@ -72,7 +72,9 @@ export default async function ScanReportsValue(props: ScanReportsValueProps) {
           id={id}
           tableId={tableId}
           fieldId={fieldId}
-          tableName={table.name}
+          tableName={
+            table.death_table ? `${table.name} (Death table)` : table.name
+          }
           fieldName={field.name}
           variant="field"
         />

app/next-client-app/app/(protected)/scanreports/[id]/tables/[tableId]/fields/[fieldId]/update/page.tsx

@@ -40,7 +40,9 @@ export default async function ScanReportsEditField(props: ScanReportsEditFieldPr
         id={id}
         tableId={tableId}
         fieldId={fieldId}
-        tableName={table.name}
+        tableName={
+          table.death_table ? `${table.name} (Death table)` : table.name
+        }
         fieldName={field.name}
         variant="fieldUpdate"
       />

app/next-client-app/app/(protected)/scanreports/[id]/tables/[tableId]/page.tsx

@@ -60,7 +60,11 @@ export default async function ScanReportsField(props: ScanReportsFieldProps) {
       <TableBreadcrumbs
         id={id}
         tableId={tableId}
-        tableName={tableName.name}
+        tableName={
+          tableName.death_table
+            ? `${tableName.name} (Death table)`
+            : tableName.name
+        }
         variant="table"
       />
       <div>

app/next-client-app/app/(protected)/scanreports/[id]/tables/[tableId]/update/page.tsx

@@ -74,7 +74,7 @@ export default async function UpdateTable(props: UpdateTableProps) {
     <div>
       <Link href={`/scanreports/${id}/tables/${tableId}`}>
         <Button variant={"secondary"} className="mb-3">
-          Update Table: {table.name}
+          Update Table: {table.name} {table.death_table && "(Death table)"}
         </Button>
       </Link>
       {(table.date_event === null || table.person_id === null) && (

app/next-client-app/components/core/Tooltips.tsx

@@ -48,4 +48,4 @@ export function Tooltips({
       </Tooltip>
     </TooltipProvider>
   );
-}
+}

app/next-client-app/components/scanreports/ScanReportTableUpdateForm.tsx

@@ -1,21 +1,34 @@
 "use client";
 
+import { useState } from "react";
 import { Button } from "@/components/ui/button";
 import { updateScanReportTable } from "@/api/scanreports";
-import { Save } from "lucide-react";
+import { Check, Save, X } from "lucide-react";
 import { toast } from "sonner";
 import { FormDataFilter } from "../form-components/FormikUtils";
 import { Formik } from "formik";
 import { FormField, FormItem, FormLabel, FormControl, FormMessage, FormDescription } from "@/components/ui/form";
 import { FormikSelect } from "../form-components/FormikSelect";
 import { useRouter } from "next/navigation";
 import { Checkbox } from "../ui/checkbox";
+import { Switch } from "@/components/ui/switch";
+import { Label } from "@/components/ui/label";
+import {
+  Dialog,
+  DialogContent,
+  DialogDescription,
+  DialogFooter,
+  DialogHeader,
+  DialogTitle,
+} from "@/components/ui/dialog";
+import { Tooltips } from "@/components/core/Tooltips";
 import { enableReuseTriggerOption } from "@/constants";
 
 interface FormData {
   personId: number | null;
   dateEvent: number | null;
   triggerReuse: boolean;
+  death_table: boolean;
 }
 
 export function ScanReportTableUpdateForm({
@@ -32,6 +45,7 @@ export function ScanReportTableUpdateForm({
   dateEvent: ScanReportField;
 }) {
   const router = useRouter();
+  const [isDialogOpen, setIsDialogOpen] = useState(false);
   const canUpdate =
     permissions.includes("CanEdit") || permissions.includes("CanAdmin");
 
@@ -45,6 +59,7 @@ export function ScanReportTableUpdateForm({
       person_id: data.personId !== 0 ? data.personId : null,
       date_event: data.dateEvent !== 0 ? data.dateEvent : null,
       trigger_reuse: data.triggerReuse,
+      death_table: data.death_table,
     };
 
     const response = await updateScanReportTable(
@@ -68,6 +83,7 @@ export function ScanReportTableUpdateForm({
         dateEvent: initialDateEvent[0].value,
         personId: initialPersonId[0].value,
         triggerReuse: scanreportTable.trigger_reuse,
+        death_table: Boolean(scanreportTable.death_table),
       }}
       onSubmit={(data) => {
         handleSubmit(data);
@@ -109,6 +125,83 @@ export function ScanReportTableUpdateForm({
               </FormControl>
             </FormItem>
 
+            <FormItem>
+              <div className="flex flex-wrap items-center gap-2">
+                <FormLabel className="mb-0">
+                  Does this table contain only death data for the OMOP CDM Death
+                  table?
+                </FormLabel>
+                <Tooltips
+                  content="In the Carrot data standard, death data is provided in a separate file (e.g. death.csv). Mark Yes if this table contains that death data to be mapped to the OMOP Death table."
+                />
+                <Dialog open={isDialogOpen} onOpenChange={setIsDialogOpen}>
+                  <DialogContent>
+                    <DialogHeader>
+                      <DialogTitle>Please Confirm Your Choice</DialogTitle>
+                      <DialogDescription>
+                        Are you sure you want to set this table as a Death table?
+                        Doing so will result in the following:
+                        <ul className="text-gray-500 list-disc pl-4 py-2">
+                          <li>
+                            Mapping Rules that are created either manually or
+                            automatically (built from OMOP vocabulary or Reused)
+                            will have Destination table as{" "}
+                            <span className="font-bold">Death</span>.
+                          </li>
+                          <li>
+                            All concepts in this table will be recognised as{" "}
+                            <span className="font-bold">Cause of Death</span> in
+                            OMOP CDM.
+                          </li>
+                          <li>
+                            Destination of Date Event will be{" "}
+                            <span className="font-bold">Death date</span> field in
+                            OMOP CDM.
+                          </li>
+                        </ul>
+                        <p className="text-muted-foreground text-pretty">
+                          You can turn off this setting later. Mapping rules will
+                          be refreshed when you save.
+                        </p>
+                      </DialogDescription>
+                    </DialogHeader>
+                    <DialogFooter className="flex gap-3">
+                      <Button
+                        type="button"
+                        onClick={() => setIsDialogOpen(false)}
+                        variant="outline"
+                      >
+                        Cancel <X className="size-4 ml-2" />
+                      </Button>
+                      <Button
+                        type="button"
+                        onClick={() => {
+                          setFieldValue("death_table", true);
+                          setIsDialogOpen(false);
+                        }}
+                      >
+                        Confirm <Check className="size-4 ml-2" />
+                      </Button>
+                    </DialogFooter>
+                  </DialogContent>
+                </Dialog>
+                <Switch
+                  checked={values.death_table}
+                  onCheckedChange={(checked) => {
+                    if (checked) {
+                      setIsDialogOpen(true);
+                    } else {
+                      setFieldValue("death_table", false);
+                    }
+                  }}
+                  disabled={!canUpdate}
+                />
+                <Label className="text-lg">
+                  {values.death_table === true ? "YES" : "NO"}
+                </Label>
+              </div>
+            </FormItem>
+
             {enableReuseTriggerOption === "true" && (
               <FormField name="triggerReuse">
                 {({ field }) => (

app/next-client-app/types/scanreport.ts

@@ -29,6 +29,7 @@ interface ScanReportTable {
   permissions: Permission[];
   jobs: Job[];
   trigger_reuse: boolean;
+  death_table?: boolean;
 }
 
 interface ScanReportField {