Allow for a single unit column

- When there's a single unit column, use that column for both dosing and observations. - Split the CSV data into dosing rows and observation rows. - Add administration route to the Map Dosing screen. - Allow for dimensionless observation units. - Filter mapped observation variables for compatibility with the observation unit value.
pkpdapp-team · Mar 4, 2024 · 9574b76 · 9574b76
1 parent 0341d5b
commit 9574b76
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Showing 3 changed files with 49 additions and 43 deletions.
diff --git a/frontend-v2/src/features/data/MapDosing.tsx b/frontend-v2/src/features/data/MapDosing.tsx
@@ -54,21 +54,22 @@ const MapDosing: FC<IMapDosing> = ({ state, firstTime }: IMapDosing) => {
   const amountField = state.fields.find(
     (field, i) => state.normalisedFields[i] === 'Amount'
   );
+  const dosingRows = amountField ? state.data.filter(row => row[amountField] && row[amountField] !== '.') : [];
   const amountValues = amountField ?
-    state.data.map(row => row[amountField]) :
+    dosingRows.map(row => row[amountField]) :
     [];
   const amountUnitField = state.fields.find(
-    (field, i) => state.normalisedFields[i] === 'Amount Unit'
+    (field, i) => ['Amount Unit', 'Unit'].includes(state.normalisedFields[i])
   );
-  const amountUnits = state.data.map(row => row[amountUnitField || 'Amount Unit']);
+  const amountUnits = dosingRows.map(row => row[amountUnitField || 'Amount Unit']);
   const administrationIdField = state.fields.find(
     (field, i) => state.normalisedFields[i] === 'Administration ID'
   );
   const administrationIds = administrationIdField ?
-    state.data.map(row => row[administrationIdField]) :
+    dosingRows.map(row => row[administrationIdField]) :
     [];
   const uniqueAdministrationIds = [...new Set(administrationIds)];
-  const amountVariables = state.data.map(row => row['Dosing Variable']);
+  const amountVariables = dosingRows.map(row => row['Dosing Variable']);
 
   const isAmount = (variable: VariableRead) => {
     const amountUnits = units?.find(
@@ -112,6 +113,16 @@ const MapDosing: FC<IMapDosing> = ({ state, firstTime }: IMapDosing) => {
                   {administrationIdField}
                 </Typography>
               </TableCell>
+              <TableCell>
+                <Typography>
+                  Amount
+                </Typography>
+              </TableCell>
+              <TableCell>
+                <Typography>
+                  Route
+                </Typography>
+              </TableCell>
               <TableCell>
                 <Typography>
                   Unit
@@ -126,15 +137,27 @@ const MapDosing: FC<IMapDosing> = ({ state, firstTime }: IMapDosing) => {
           </TableHead>
           <TableBody>
             {uniqueAdministrationIds.map((adminId, index) => {
-              const currentRow = state.data.find(row => administrationIdField ? row[administrationIdField] === adminId : true);
+              const currentRow = dosingRows.find(row => administrationIdField ? row[administrationIdField] === adminId : true);
               const selectedVariable = variables?.find(variable => variable.qname === currentRow?.['Dosing Variable']);
               const compatibleUnits = units?.find(unit => unit.id === selectedVariable?.unit)?.compatible_units;
               const adminUnit = amountUnitField && currentRow && currentRow[amountUnitField];
+              const amount = amountField && currentRow?.[amountField];
+              const route = currentRow?.['ROUTE'];
               return (
                 <TableRow>
                   <TableCell>
                     {adminId}
                   </TableCell>
+                  <TableCell>
+                    <Typography>
+                      {amount}
+                    </Typography>
+                  </TableCell>
+                  <TableCell>
+                    <Typography>
+                      {route}
+                    </Typography>
+                  </TableCell>
                   <TableCell>
                     {adminUnit ?
                       adminUnit :
@@ -175,36 +198,6 @@ const MapDosing: FC<IMapDosing> = ({ state, firstTime }: IMapDosing) => {
             })}
           </TableBody>
         </Table>
-        <Table>
-          <TableHead>
-            <TableRow>
-              <TableCell>
-                <Typography>
-                  Amount
-                </Typography>
-              </TableCell>
-              <TableCell>
-                <Typography>
-                  Unit
-                </Typography>
-              </TableCell>
-              <TableCell>
-                <Typography>
-                  Mapping
-                </Typography>
-              </TableCell>
-            </TableRow>
-          </TableHead>
-          <TableBody>
-            {amountValues.map((amount, index) => (
-              <TableRow key={index}>
-                <TableCell>{amount}</TableCell>
-                <TableCell>{amountUnits[index]}</TableCell>
-                <TableCell>{amountVariables[index]}</TableCell>
-              </TableRow>
-            ))}
-          </TableBody>
-        </Table>
       </Box>
     </>
   )

diff --git a/frontend-v2/src/features/data/MapObservations.tsx b/frontend-v2/src/features/data/MapObservations.tsx
@@ -43,18 +43,19 @@ const MapObservations: FC<IMapObservations> = ({state}: IMapObservations) => {
   const observationIdField = state.fields.find(
     (field, i) => state.normalisedFields[i] === 'Observation ID'
   );
+  const observationRows = observationField ? state.data.filter(row => row[observationField] !== '.') : [];
   const observationIds = observationIdField ?
-    state.data.map(row => row[observationIdField]) :
+    observationRows.map(row => row[observationIdField]) :
     [observationField];
   const uniqueObservationIds = [...new Set(observationIds)];
   const observationValues = observationField ?
-    state.data.map(row => row[observationField]) :
+    observationRows.map(row => row[observationField]) :
     [];
   const observationUnitField = state.fields.find(
-    (field, i) => state.normalisedFields[i] === 'Observation Unit'
+    (field, i) => ['Observation Unit', 'Unit'].includes(state.normalisedFields[i])
   );
-  const observationUnits = state.data.map(row => row[observationUnitField || 'Observation Unit']);
-  const observationVariables = state.data.map(row => row['Observation Variable']);
+  const observationUnits = observationRows.map(row => row[observationUnitField || 'Observation Unit']);
+  const observationVariables = observationRows.map(row => row['Observation Variable']);
 
   const filterOutputs = model?.is_library_model
     ? ["environment.t", "PDCompartment.C_Drug"]
@@ -114,10 +115,21 @@ const MapObservations: FC<IMapObservations> = ({state}: IMapObservations) => {
           </TableHead>
           <TableBody>
             {uniqueObservationIds.map((obsId) => {
-              const currentRow = state.data.find(row => observationIdField ? row[observationIdField] === obsId : true);
+              const currentRow = observationRows.find(row => observationIdField ? row[observationIdField] === obsId : true);
               const selectedVariable = variables?.find(variable => variable.qname === currentRow?.['Observation Variable']);
               const compatibleUnits = units?.find(unit => unit.id === selectedVariable?.unit)?.compatible_units;
               const obsUnit = observationUnitField && currentRow && currentRow[observationUnitField];
+              let obsUnitSymbol = obsUnit;
+              ['%', 'fraction', 'ratio'].forEach(token => {
+                if (obsUnitSymbol?.toLowerCase().includes(token)) {
+                  obsUnitSymbol = '';
+                }
+              });
+              const compatibleVariables = modelOutputs.filter(variable => {
+                const variableUnit = units?.find(unit => unit.id === variable.unit);
+                const compatibleSymbols = variableUnit?.compatible_units.map(u => u.symbol);
+                return compatibleSymbols?.includes(obsUnitSymbol || '');
+              });
               return (
                 <TableRow>
                   <TableCell>
@@ -152,7 +164,7 @@ const MapObservations: FC<IMapObservations> = ({state}: IMapObservations) => {
                         value={selectedVariable?.qname}
                         onChange={handleObservationChange(obsId)}
                       >
-                        {modelOutputs?.map((variable) => (
+                        {compatibleVariables?.map((variable) => (
                           <MenuItem key={variable.name} value={variable.qname}>{variable.name}</MenuItem>
                         ))}
                       </Select>

diff --git a/frontend-v2/src/features/data/normaliseDataHeaders.ts b/frontend-v2/src/features/data/normaliseDataHeaders.ts
@@ -21,6 +21,7 @@ const normalisation = {
     'Regressor': ['x', 'regressor'],
     'Time': ['time', 't', 'ivar'],
     'Time Unit': ['time_unit', 'time_units', 't_units', 'tunit'],
+    'Unit': ['unit', 'units'],
 }
 
 export const manditoryHeaders = ['ID', 'Time', 'Observation', 'Administration ID', 'Amount']