feat(cohortMiddleWareEndpointUpdate): Initial commit (#1465)

* feat(cohortMiddleWareEndpointUpdate): Initial commit

* feat(cohortMiddleWareEndpointUpdate): Removed unneeded console log

Author: jarvisraymond-uchicago

src/Analysis/GWASApp/Components/Covariates/CustomDichotomousCovariates.jsx

@@ -13,6 +13,7 @@ const CustomDichotomousCovariates = ({
   covariates,
   outcome,
   submitButtonLabel,
+  selectedTeamProject,
 }) => {
   const [firstPopulation, setFirstPopulation] = useState(undefined);
   const [secondPopulation, setSecondPopulation] = useState(undefined);
@@ -86,12 +87,16 @@ const CustomDichotomousCovariates = ({
               </div>
               <div>
                 <h3>Get Value 0</h3>
-                <SelectCohortDropDown handleCohortSelect={setFirstPopulation} />
+                <SelectCohortDropDown
+                  handleCohortSelect={setFirstPopulation}
+                  selectedTeamProject={selectedTeamProject}
+                />
               </div>
               <div>
                 <h3>Get Value 1</h3>
                 <SelectCohortDropDown
                   handleCohortSelect={setSecondPopulation}
+                  selectedTeamProject={selectedTeamProject}
                 />
               </div>
             </div>
@@ -128,6 +133,7 @@ CustomDichotomousCovariates.propTypes = {
   outcome: PropTypes.object,
   submitButtonLabel: PropTypes.string,
   handleClose: PropTypes.func.isRequired,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 
 CustomDichotomousCovariates.defaultProps = {

src/Analysis/GWASApp/Components/Covariates/CustomDichotomousCovariates.stories.jsx

@@ -72,7 +72,7 @@ SuccessAndZeroOverlapCases.parameters = {
         }
       ),
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => {
           const { cohortmiddlewarepath } = req.params;
           const { cohortdefinitionA } = req.params;
@@ -132,7 +132,7 @@ ErrorCase.parameters = {
   msw: {
     handlers: [
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => res(ctx.delay(800), ctx.status(403))
       ),
     ],

src/Analysis/GWASApp/Components/SelectCohort/SelectCohort.jsx

@@ -7,7 +7,7 @@ import CohortDefinitions from './Utils/CohortDefinitions';
 import SearchBar from '../SearchBar/SearchBar';
 import './SelectCohort.css';
 
-const SelectCohort = ({ selectedCohort, handleCohortSelect }) => {
+const SelectCohort = ({ selectedCohort, handleCohortSelect, selectedTeamProject }) => {
   const [cohortSearchTerm, setCohortSearchTerm] = useState('');
 
   const handleCohortSearch = (searchTerm) => {
@@ -36,6 +36,7 @@ const SelectCohort = ({ selectedCohort, handleCohortSelect }) => {
               selectedCohort={selectedCohort}
               handleCohortSelect={handleCohortSelect}
               searchTerm={cohortSearchTerm}
+              selectedTeamProject={selectedTeamProject}
             />
           </div>
         </div>
@@ -47,6 +48,7 @@ const SelectCohort = ({ selectedCohort, handleCohortSelect }) => {
 SelectCohort.propTypes = {
   selectedCohort: PropTypes.any,
   handleCohortSelect: PropTypes.func.isRequired,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 SelectCohort.defaultProps = {
   selectedCohort: null,

src/Analysis/GWASApp/Components/SelectCohort/SelectCohort.stories.jsx

@@ -73,7 +73,7 @@ MockedSuccess.parameters = {
     handlers: [
       ///cohort-middleware/cohortdefinition-stats/by-source-id/1
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => {
           const { cohortmiddlewarepath } = req.params;
           const { sourceid } = req.params;
@@ -247,7 +247,7 @@ MockedError.parameters = {
   msw: {
     handlers: [
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => res(ctx.delay(800), ctx.status(403))
       ),
     ],

src/Analysis/GWASApp/Components/SelectCohort/SelectCohortDropDown.jsx

@@ -7,11 +7,11 @@ import queryConfig from '../../../SharedUtils/QueryConfig';
 import { useFetch } from '../../Utils/formHooks';
 import { useSourceContext } from '../../Utils/Source';
 
-const SelectCohortDropDown = ({ handleCohortSelect }) => {
+const SelectCohortDropDown = ({ handleCohortSelect, selectedTeamProject }) => {
   const { source } = useSourceContext();
   const cohorts = useQuery(
-    ['cohortdefinitions', source],
-    () => fetchCohortDefinitions(source),
+    ['cohortdefinitions', source, selectedTeamProject],
+    () => fetchCohortDefinitions(source, selectedTeamProject),
     queryConfig,
   );
   const fetchedCohorts = useFetch(cohorts, 'cohort_definitions_and_stats');
@@ -53,6 +53,7 @@ const SelectCohortDropDown = ({ handleCohortSelect }) => {
 
 SelectCohortDropDown.propTypes = {
   handleCohortSelect: PropTypes.any.isRequired,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 
 export default SelectCohortDropDown;

src/Analysis/GWASApp/Components/SelectCohort/SelectCohortDropDown.stories.jsx

@@ -40,9 +40,8 @@ export const MockedSuccess = MockTemplate.bind({});
 MockedSuccess.parameters = {
   msw: {
     handlers: [
-      ///cohort-middleware/cohortdefinition-stats/by-source-id/1
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => {
           const { cohortmiddlewarepath } = req.params;
           const { sourceid } = req.params;
@@ -217,7 +216,7 @@ MockedError.parameters = {
   msw: {
     handlers: [
       rest.get(
-        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid',
+        'http://:cohortmiddlewarepath/cohort-middleware/cohortdefinition-stats/by-source-id/:sourceid/by-team-project?team-project=:selectedTeamProject',
         (req, res, ctx) => res(ctx.delay(800), ctx.status(403))
       ),
     ],

src/Analysis/GWASApp/Components/SelectCohort/Utils/CohortDefinitions.jsx

@@ -11,11 +11,12 @@ const CohortDefinitions = ({
   selectedCohort = undefined,
   handleCohortSelect,
   searchTerm,
+  selectedTeamProject,
 }) => {
   const { source } = useSourceContext();
   const cohorts = useQuery(
-    ['cohortdefinitions', source],
-    () => fetchCohortDefinitions(source),
+    ['cohortdefinitions', source, selectedTeamProject],
+    () => fetchCohortDefinitions(source, selectedTeamProject),
     queryConfig,
   );
   const fetchedCohorts = useFetch(cohorts, 'cohort_definitions_and_stats');
@@ -43,6 +44,7 @@ const CohortDefinitions = ({
       key: 'size',
     },
   ];
+  if (cohorts?.status === 'error') return <React.Fragment>Error getting data for table</React.Fragment>;
 
   return cohorts?.status === 'success' ? (
     <Table
@@ -76,6 +78,7 @@ CohortDefinitions.propTypes = {
   selectedCohort: PropTypes.any,
   handleCohortSelect: PropTypes.any.isRequired,
   searchTerm: PropTypes.string.isRequired,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 
 CohortDefinitions.defaultProps = {

src/Analysis/GWASApp/GWASContainer.jsx

@@ -26,6 +26,7 @@ const GWASContainer = () => {
           <SelectStudyPopulation
             selectedCohort={state.selectedStudyPopulationCohort}
             dispatch={dispatch}
+            selectedTeamProject={state.selectedTeamProject}
           />
         </div>
       );
@@ -36,6 +37,7 @@ const GWASContainer = () => {
           outcome={state.outcome}
           covariates={state.covariates}
           dispatch={dispatch}
+          selectedTeamProject={state.selectedTeamProject}
         />
       );
     case 2:
@@ -45,6 +47,7 @@ const GWASContainer = () => {
           outcome={state.outcome}
           covariates={state.covariates}
           dispatch={dispatch}
+          selectedTeamProject={state.selectedTeamProject}
         />
       );
     case 3:

src/Analysis/GWASApp/Steps/SelectCovariates/SelectCovariates.jsx

@@ -13,6 +13,7 @@ const SelectCovariates = ({
   studyPopulationCohort,
   outcome,
   covariates,
+  selectedTeamProject,
 }) => {
   const [selectionMode, setSelectionMode] = useState('');
   useEffect(() => {
@@ -76,6 +77,7 @@ const SelectCovariates = ({
                   });
                 }}
                 submitButtonLabel={'Add'}
+                selectedTeamProject={selectedTeamProject}
               />
             </div>
           )}
@@ -137,6 +139,7 @@ SelectCovariates.propTypes = {
   studyPopulationCohort: PropTypes.object.isRequired,
   outcome: PropTypes.object.isRequired,
   covariates: PropTypes.array.isRequired,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 
 export default SelectCovariates;

src/Analysis/GWASApp/Steps/SelectOutcome/SelectOutcome.jsx

@@ -12,6 +12,7 @@ const SelectOutcome = ({
   studyPopulationCohort,
   outcome,
   covariates,
+  selectedTeamProject,
 }) => {
   const [selectionMode, setSelectionMode] = useState('');
   useEffect(
@@ -67,6 +68,7 @@ const SelectOutcome = ({
                 payload: chosenOutcome,
               });
             }}
+            selectedTeamProject={selectedTeamProject}
           />
         </div>
       );
@@ -131,6 +133,7 @@ SelectOutcome.propTypes = {
   studyPopulationCohort: PropTypes.object.isRequired,
   outcome: PropTypes.object,
   covariates: PropTypes.array,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 
 SelectOutcome.defaultProps = {

src/Analysis/GWASApp/Steps/SelectStudyPopulation/SelectStudyPopulation.jsx

@@ -3,7 +3,7 @@ import PropTypes from 'prop-types';
 import ACTIONS from '../../Utils/StateManagement/Actions';
 import CohortSelect from '../../Components/SelectCohort/SelectCohort';
 
-const SelectStudyPopulation = ({ selectedCohort, dispatch }) => {
+const SelectStudyPopulation = ({ selectedCohort, dispatch, selectedTeamProject }) => {
   const handleStudyPopulationSelect = (selectedRow) => {
     dispatch({
       type: ACTIONS.SET_SELECTED_STUDY_POPULATION_COHORT,
@@ -16,6 +16,7 @@ const SelectStudyPopulation = ({ selectedCohort, dispatch }) => {
       <CohortSelect
         selectedCohort={selectedCohort}
         handleCohortSelect={handleStudyPopulationSelect}
+        selectedTeamProject={selectedTeamProject}
       />
     </div>
   );
@@ -24,6 +25,7 @@ const SelectStudyPopulation = ({ selectedCohort, dispatch }) => {
 SelectStudyPopulation.propTypes = {
   dispatch: PropTypes.func.isRequired,
   selectedCohort: PropTypes.object,
+  selectedTeamProject: PropTypes.string.isRequired,
 };
 SelectStudyPopulation.defaultProps = { selectedCohort: null };
 export default SelectStudyPopulation;

src/Analysis/GWASApp/Utils/cohortMiddlewareApi.js

@@ -153,8 +153,8 @@ export const fetchCovariateStats = async (
   return response.json();
 };
 
-export const fetchCohortDefinitions = async (sourceId) => {
-  const cohortEndPoint = `${cohortMiddlewarePath}cohortdefinition-stats/by-source-id/${sourceId}`;
+export const fetchCohortDefinitions = async (sourceId, selectedTeamProject) => {
+  const cohortEndPoint = `${cohortMiddlewarePath}cohortdefinition-stats/by-source-id/${sourceId}/by-team-project?team-project=${selectedTeamProject}`;
   const response = await fetch(cohortEndPoint);
   if (!response.ok) {
     const message = `An error has occured: ${response.status}`;