refactor(frontend): generate administration IDs during stratification (…

…#513) (#533) When a dataset doesn't contain an administration ID column, generate one during the stratification step. Assign a unique administration ID to each group by default.
pkpdapp-team · Oct 2, 2024 · 443ce24 · 443ce24
1 parent cfbf563
commit 443ce24
Show file tree

Hide file tree

Showing 5 changed files with 59 additions and 27 deletions.
diff --git a/frontend-v2/src/features/data/CreateDosingProtocols.tsx b/frontend-v2/src/features/data/CreateDosingProtocols.tsx
@@ -38,11 +38,10 @@ const CreateDosingProtocols: FC<IDosingProtocols> = ({
     (field) =>
       field === "Amount" || state.normalisedFields.get(field) === "Amount",
   );
-  const dosingRows: Row[] =
-    administrationIdField === "Group ID"
-      ? state.data
-      : // ignore rows with no amount and administration ID set to 0.
-        state.data.filter((row) => parseInt(row[administrationIdField]));
+  // ignore rows with no amount and administration ID set to 0.
+  const dosingRows: Row[] = state.data.filter((row) =>
+    parseInt(row[administrationIdField]),
+  );
   if (!amountField) {
     const newNormalisedFields = new Map([
       ...state.normalisedFields.entries(),

diff --git a/frontend-v2/src/features/data/LoadData.tsx b/frontend-v2/src/features/data/LoadData.tsx
@@ -146,14 +146,14 @@ const LoadData: FC<ILoadDataProps> = ({ state, firstTime }) => {
             normalisedFields,
             normalisedHeaders: [...normalisedFields.values()],
           });
-          const primaryCohort =
+          const groupColumn =
             fields.find(
               (field) => normalisedFields.get(field) === "Cat Covariate",
             ) || "Group";
           const errors = csvData.errors
             .map((e) => e.message)
             .concat(fieldValidation.errors);
-          state.setPrimaryCohort(primaryCohort);
+          state.setGroupColumn(groupColumn);
           state.setErrors(errors);
           state.setWarnings(fieldValidation.warnings);
           if (csvData.data.length > 0 && csvData.meta.fields) {

diff --git a/frontend-v2/src/features/data/LoadDataStepper.tsx b/frontend-v2/src/features/data/LoadDataStepper.tsx
@@ -66,8 +66,8 @@ export type StepperState = {
   setWarnings: (warnings: string[]) => void;
   amountUnit?: string;
   setAmountUnit: (amountUnit: string) => void;
-  primaryCohort: string;
-  setPrimaryCohort: (primaryCohort: string) => void;
+  groupColumn: string;
+  setGroupColumn: (primaryCohort: string) => void;
 };
 
 function validateSubjectProtocols(protocols: IProtocol[]) {
@@ -96,7 +96,7 @@ const LoadDataStepper: FC<IStepper> = ({ csv = "", onCancel, onFinish }) => {
   );
   const [timeUnit, setTimeUnit] = useState<string | undefined>(undefined);
   const [amountUnit, setAmountUnit] = useState<string | undefined>(undefined);
-  const [primaryCohort, setPrimaryCohort] = useState("Group");
+  const [groupColumn, setGroupColumn] = useState("Group");
   const selectedProject = useSelector(
     (state: RootState) => state.main.selectedProject,
   );
@@ -121,8 +121,8 @@ const LoadDataStepper: FC<IStepper> = ({ csv = "", onCancel, onFinish }) => {
     setTimeUnit,
     amountUnit,
     setAmountUnit,
-    primaryCohort,
-    setPrimaryCohort,
+    groupColumn,
+    setGroupColumn,
     get fields() {
       return [...normalisedFields.keys()];
     },

diff --git a/frontend-v2/src/features/data/MapDosing.tsx b/frontend-v2/src/features/data/MapDosing.tsx
@@ -82,7 +82,7 @@ const MapDosing: FC<IMapDosing> = ({ state, firstTime }: IMapDosing) => {
     />
   ) : (
     <CreateDosingProtocols
-      administrationIdField={administrationIdField || "Group ID"}
+      administrationIdField={administrationIdField || "Administration ID"}
       amountUnitField={amountUnitField || ""}
       amountUnit={amountUnit}
       state={state}

diff --git a/frontend-v2/src/features/data/Stratification.tsx b/frontend-v2/src/features/data/Stratification.tsx
@@ -37,6 +37,35 @@ function validateGroupProtocols(groups: Group[], protocols: IProtocol[]) {
   return groupedProtocols.every((protocols) => protocols.length <= 1);
 }
 
+/**
+ * Generate a unique administration ID for each group.
+ * @param data
+ * @returns data with administration ID column.
+ */
+function generateAdministrationIds(data: { [key: string]: string }[]) {
+  const newData = data.map((row) => ({ ...row }));
+  const uniqueGroupIds = [...new Set(data.map((row) => row["Group ID"]))];
+  newData.forEach((row) => {
+    const administrationId = uniqueGroupIds.indexOf(row["Group ID"]) + 1;
+    row["Administration ID"] = `${administrationId}`;
+  });
+  return newData;
+}
+
+/**
+ * Assign a group ID to each row based on a categorical covariate column.
+ * @param data
+ * @param columnName
+ * @returns data with group ID and administration ID columns.
+ */
+function groupDataRows(data: { [key: string]: string }[], columnName: string) {
+  const newData = data.map((row) => ({ ...row }));
+  newData.forEach((row) => {
+    row["Group ID"] = row[columnName] || "1";
+  });
+  return newData;
+}
+
 interface IStratification {
   state: StepperState;
   firstTime: boolean;
@@ -55,12 +84,15 @@ const Stratification: FC<IStratification> = ({ state }: IStratification) => {
     const values = state.data.map((row) => row[field]);
     return [...new Set(values)];
   });
+  const administrationIdField = state.fields.find(
+    (field) => state.normalisedFields.get(field) === "Administration ID",
+  );
 
   const [firstRow] = state.data;
   const [tab, setTab] = useState(0);
-  const { primaryCohort, setPrimaryCohort } = state;
+  const { groupColumn, setGroupColumn } = state;
 
-  const groups = groupsFromCatCovariate(state, primaryCohort);
+  const groups = groupsFromCatCovariate(state, groupColumn);
   const isValidGrouping = validateGroupMembers(groups);
   const groupErrorMessage =
     "Invalid group subjects. Each subject ID can only belong to a single cohort.";
@@ -92,10 +124,10 @@ const Stratification: FC<IStratification> = ({ state }: IStratification) => {
   }
 
   if (!firstRow["Group ID"]) {
-    const newData = [...state.data];
-    newData.forEach((row) => {
-      row["Group ID"] = row[primaryCohort] || "1";
-    });
+    let newData = groupDataRows(state.data, groupColumn);
+    if (!administrationIdField) {
+      newData = generateAdministrationIds(newData);
+    }
     state.setData(newData);
     state.setNormalisedFields(
       new Map([...state.normalisedFields.entries(), ["Group ID", "Group ID"]]),
@@ -106,12 +138,13 @@ const Stratification: FC<IStratification> = ({ state }: IStratification) => {
     setTab(newValue);
   };
 
-  const handlePrimaryChange = (event: ChangeEvent<HTMLInputElement>) => {
-    setPrimaryCohort(event.target.value);
-    const newData = [...state.data];
-    newData.forEach((row) => {
-      row["Group ID"] = row[event.target.value];
-    });
+  const handleGroupChange = (event: ChangeEvent<HTMLInputElement>) => {
+    const newGroup = event.target.value;
+    let newData = groupDataRows(state.data, newGroup);
+    if (!administrationIdField) {
+      newData = generateAdministrationIds(newData);
+    }
+    setGroupColumn(newGroup);
     state.setData(newData);
   };
 
@@ -147,7 +180,7 @@ const Stratification: FC<IStratification> = ({ state }: IStratification) => {
             <TableBody>
               {catCovariates.map((field, index) => {
                 const primaryLabel = `heading-primary field-${field}`;
-                const isPrimary = primaryCohort === field;
+                const isPrimary = groupColumn === field;
                 return (
                   <TableRow key={field}>
                     <TableCell id={`field-${field}`}>{field}</TableCell>
@@ -159,7 +192,7 @@ const Stratification: FC<IStratification> = ({ state }: IStratification) => {
                         name="primary"
                         value={field}
                         checked={isPrimary}
-                        onChange={handlePrimaryChange}
+                        onChange={handleGroupChange}
                         inputProps={{ "aria-labelledby": primaryLabel }}
                       />
                     </TableCell>