CanDIG · CourtneyGosselin · Nov 25, 2024 · Nov 23, 2024
diff --git a/src/store/constant.js b/src/store/constant.js
@@ -37,7 +37,7 @@ export const primarySiteCount = {
     'Tonsil C09': 50
 };
 
-export const cohortByNode = {
+export const programByNode = {
     BCGSC: {
         POG: 50
     },
@@ -84,7 +84,7 @@ export const fullClinicalData = {
 
 export const PRIMARY_SITES = ['Breast', 'Trachea', 'Panceas'];
 
-export const COHORTS = ['POG', 'Inspire', 'Biocan', 'Biodiva', 'Compass', 'Palms', 'IO-Alines'];
+export const PROGRAMS = ['POG', 'Inspire', 'Biocan', 'Biodiva', 'Compass', 'Palms', 'IO-Alines'];
 
 export const CLIN_METADATA = [
     'patients',
@@ -135,8 +135,8 @@ export const DataVisualizationChartInfo = {
         xAxis: 'Primary Site',
         yAxis: 'Number of Primary Sites'
     },
-    patients_per_cohort: {
-        title: 'Distribution of Cohort by Node',
+    patients_per_program: {
+        title: 'Distribution of Program by Node',
         xAxis: 'Site',
         yAxis: 'Number of Patients'
     },
@@ -152,7 +152,7 @@ export const DataVisualizationChartInfo = {
     }
 };
 export const validCharts = ['bar', 'line', 'scatter', 'column'];
-export const validStackedCharts = ['patients_per_cohort', 'full_clinical_data', 'full_genomic_data'];
+export const validStackedCharts = ['patients_per_program', 'full_clinical_data', 'full_genomic_data'];
 
 // Highcharts Map requires a specific set of codes for provinces
 // and territories, as represented by hcProvCodes below.

diff --git a/src/ui-component/ingest/ClinicalIngest.js b/src/ui-component/ingest/ClinicalIngest.js
@@ -45,7 +45,7 @@ const Root = styled('div')({
 function ClinicalIngest({ setTab, fileUpload, clinicalData }) {
     // setTab should be a function that sets the tab to the genomic ingest page
 
-    const [authorizedCohorts, setAuthorizedCohorts] = useState([]);
+    const [authorizedPrograms, setAuthorizedPrograms] = useState([]);
 
     useEffect(() => {
         function fetchPrograms() {
@@ -56,13 +56,13 @@ function ClinicalIngest({ setTab, fileUpload, clinicalData }) {
                         const fields = [];
                         Object.keys(programs).forEach((program) => {
                             const field = [
-                                makeField('Cohort', program),
+                                makeField('Program', program),
                                 makeField('Clinical Patients', programs[program].toString()),
                                 makeField('Read Access', 'Unknown')
                             ];
                             fields.push(field);
                         });
-                        setAuthorizedCohorts(fields);
+                        setAuthorizedPrograms(fields);
                     });
                 })
                 .catch((error) => console.log(error));
@@ -75,26 +75,26 @@ function ClinicalIngest({ setTab, fileUpload, clinicalData }) {
             <Grid container direction="column" spacing={4}>
                 <Grid item>
                     <Typography align="left" className={classes.titleText}>
-                        <b>Your authorized cohorts</b>
+                        <b>Your authorized programs</b>
                     </Typography>
-                    {authorizedCohorts.length > 0 ? (
+                    {authorizedPrograms.length > 0 ? (
                         <Grid direction="row" spacing={3} container>
-                            {authorizedCohorts.map((fields, index) => (
+                            {authorizedPrograms.map((fields, index) => (
                                 <Grid item xs={5} key={index}>
                                     <DataRow rowWidth="100%" itemSize="0.9em" fields={fields} />
                                 </Grid>
                             ))}
                         </Grid>
                     ) : (
                         <Typography align="left" className={classes.bodyText}>
-                            No cohorts found.
+                            No Programs found.
                         </Typography>
                     )}
                 </Grid>
                 <Grid item sx={{ width: '100%' }}>
                     <div>
                         <Typography align="left" className={classes.titleText}>
-                            <b>Choose a cohort for validation</b>
+                            <b>Choose a program for validation</b>
                         </Typography>
                         <Grid container sx={{ marginTop: '0.5em', marginLeft: '1em' }} direction="row" alignItems="center" spacing={2}>
                             <Grid item>
@@ -121,7 +121,7 @@ function ClinicalIngest({ setTab, fileUpload, clinicalData }) {
                             rowWidth="100%"
                             itemSize="0.9em"
                             fields={[
-                                makeField('Cohort', clinicalData.donors[0].program_id),
+                                makeField('Program', clinicalData.donors[0].program_id),
                                 makeField('Clinical Patients', clinicalData.donors.length),
                                 makeField('Read Access', '1')
                             ]}

diff --git a/src/ui-component/ingest/GenomicIngest.js b/src/ui-component/ingest/GenomicIngest.js
@@ -41,8 +41,8 @@ const Root = styled('div')({
 function GenomicIngest({ beginIngest, fileUpload, clinicalData, genomicData }) {
     const [ingestButtonEnabled, setIngestButtonEnabled] = useState(false);
 
-    const cohort = [
-        makeField('Cohort', clinicalData.donors[0].program_id),
+    const program = [
+        makeField('Program', clinicalData.donors[0].program_id),
         makeField('Clinical Patients', clinicalData.donors.length),
         makeField('Read Access', '1')
     ];
@@ -54,9 +54,9 @@ function GenomicIngest({ beginIngest, fileUpload, clinicalData, genomicData }) {
             <Grid container direction="column" sx={{ flexGrow: 1 }} spacing={4}>
                 <Grid item>
                     <Typography align="left" className={classes.titleText}>
-                        <b>Cohort for ingestion</b>
+                        <b>Program for ingestion</b>
                     </Typography>
-                    <DataRow rowWidth="100%" itemSize="0.9em" fields={cohort} />
+                    <DataRow rowWidth="100%" itemSize="0.9em" fields={program} />
                 </Grid>
                 <Grid item width="100%">
                     <Typography align="left" className={classes.titleText}>

diff --git a/src/views/clinicalGenomic/clinicalGenomicSearch.js b/src/views/clinicalGenomic/clinicalGenomicSearch.js
@@ -95,9 +95,9 @@ const StyledMainCard = styled(MainCard)((_) => ({
 
 const sections = [
     {
-        id: 'cohorts summary',
+        id: 'Programs summary',
         header: undefined,
-        component: <AuthorizationSections title="All Cohorts" />
+        component: <AuthorizationSections title="All Programs" />
     },
     {
         id: 'counts',
@@ -110,9 +110,9 @@ const sections = [
         component: <DataVisualization />
     },
     {
-        id: 'authorized cohorts',
+        id: 'authorized programs',
         header: undefined,
-        component: <AuthorizationSections title="Authorized Cohorts" />
+        component: <AuthorizationSections title="Authorized Programs" />
     },
     {
         id: 'clinical',

diff --git a/src/views/clinicalGenomic/search/SearchHandler.js b/src/views/clinicalGenomic/search/SearchHandler.js
@@ -26,7 +26,7 @@ function SearchHandler({ setLoading }) {
                 .then((data) => {
                     writer((old) => ({ ...old, sidebar: data }));
                 })
-                .then(() => fetchFederationStat('/patients_per_cohort'))
+                .then(() => fetchFederationStat('/patients_per_program'))
                 .then((data) => {
                     writer((old) => ({ ...old, federation: data }));
                 })
@@ -88,10 +88,10 @@ function SearchHandler({ setLoading }) {
                         age_at_diagnosis: CollateSummary(data, 'age_at_diagnosis'),
                         treatment_type_count: CollateSummary(data, 'treatment_type_count'),
                         primary_site_count: CollateSummary(data, 'primary_site_count'),
-                        patients_per_cohort: {}
+                        patients_per_program: {}
                     };
                     data.forEach((site) => {
-                        discoveryCounts.patients_per_cohort[site.location.name] = site.results?.patients_per_cohort;
+                        discoveryCounts.patients_per_program[site.location.name] = site.results?.patients_per_program;
                     });
 
                     writer((old) => ({ ...old, counts: discoveryCounts }));
@@ -124,7 +124,7 @@ function SearchHandler({ setLoading }) {
                     if (reader.filter?.node) {
                         data = data.filter((site) => !reader.filter.node.includes(site.location.name));
                     }
-                    // Reorder the data, and fill out the patients per cohort
+                    // Reorder the data, and fill out the patients per program
                     const clinicalData = {};
                     data.forEach((site) => {
                         if ('results' in site) {
@@ -162,12 +162,12 @@ function SearchHandler({ setLoading }) {
 
     // Query 3: when the selected donor changes, re-query the server
     useEffect(() => {
-        if (!reader.donorID || !reader.cohort) {
+        if (!reader.donorID || !reader.program) {
             return;
         }
         setLoading(true);
 
-        const url = `v3/authorized/donor_with_clinical_data/program/${reader.cohort}/donor/${reader.donorID}`;
+        const url = `v3/authorized/donor_with_clinical_data/program/${reader.program}/donor/${reader.donorID}`;
         trackPromise(
             fetchFederation(url, 'katsu')
                 .then((data) => {

diff --git a/src/views/clinicalGenomic/widgets/dataVisualization.js b/src/views/clinicalGenomic/widgets/dataVisualization.js
@@ -75,7 +75,7 @@ function DataVisualization() {
     };
 
     const dataVis = {
-        patients_per_cohort: handleCensoring('patients_per_cohort', (site, _) => site, true) || {},
+        patients_per_program: handleCensoring('patients_per_program', (site, _) => site, true) || {},
         diagnosis_age_count: handleCensoring('age_at_diagnosis', (_, age) => age.replace(/ Years$/, '')) || {},
         treatment_type_count: handleCensoring('treatment_type_count') || {},
         primary_site_count: handleCensoring('primary_site_count') || {}
@@ -93,7 +93,7 @@ function DataVisualization() {
     const [dataValue, setDataValue] = useState(
         localStorage.getItem('dataVisData') && JSON.parse(localStorage.getItem('dataVisData'))?.[0]
             ? JSON.parse(localStorage.getItem('dataVisData'))[0]
-            : 'patients_per_cohort'
+            : 'patients_per_program'
     );
     const [chartType, setChartType] = useState(
         localStorage.getItem('dataVisChartType') && JSON.parse(localStorage.getItem('dataVisChartType'))?.[0]

diff --git a/src/views/clinicalGenomic/widgets/genomicData.js b/src/views/clinicalGenomic/widgets/genomicData.js
@@ -55,7 +55,7 @@ function GenomicData() {
     const columns = [
         { field: 'location', headerName: 'Node', minWidth: 120, sortable: false, filterable: false },
         { field: 'donor_id', headerName: 'Donor ID', minWidth: 150, sortable: false, filterable: false },
-        { field: 'program_id', headerName: 'Cohort ID', minWidth: 150, sortable: false, filterable: false },
+        { field: 'program_id', headerName: 'Program ID', minWidth: 150, sortable: false, filterable: false },
         { field: 'position', headerName: 'Position', minWidth: 150, sortable: false, filterable: false },
         { field: 'tumour_normal_designation', headerName: 'Tumour/Normal', minWidth: 200, sortable: false, filterable: false },
         { field: 'submitter_specimen_id', headerName: 'Sample Registration ID', minWidth: 300, sortable: false, filterable: false },

diff --git a/src/views/clinicalGenomic/widgets/patientCountSingle.js b/src/views/clinicalGenomic/widgets/patientCountSingle.js
@@ -66,18 +66,18 @@ function PatientCountSingle(props) {
 
     const SumCensoredTotals = (countsArray) =>
         countsArray.reduce(
-            (partialSum, cohortTotal) => {
-                if (typeof cohortTotal === 'object') {
-                    if (cohortTotal.patients_count.startsWith('<')) {
-                        return [partialSum[0], partialSum[1] + parseInt(cohortTotal.patients_count.substring(1), 10)];
+            (partialSum, programTotal) => {
+                if (typeof programTotal === 'object') {
+                    if (programTotal.patients_count.startsWith('<')) {
+                        return [partialSum[0], partialSum[1] + parseInt(programTotal.patients_count.substring(1), 10)];
                     }
-                    const toAdd = parseInt(cohortTotal.patients_count, 10);
+                    const toAdd = parseInt(programTotal.patients_count, 10);
                     return [partialSum[0] + toAdd, partialSum[1] + toAdd];
                 }
-                if (typeof cohortTotal === 'string' && cohortTotal.startsWith('<')) {
-                    return [partialSum[0], partialSum[1] + parseInt(cohortTotal.substring(1), 10)];
+                if (typeof programTotal === 'string' && programTotal.startsWith('<')) {
+                    return [partialSum[0], partialSum[1] + parseInt(programTotal.substring(1), 10)];
                 }
-                return [partialSum[0] + parseInt(cohortTotal, 10), partialSum[1] + parseInt(cohortTotal, 10)];
+                return [partialSum[0] + parseInt(programTotal, 10), partialSum[1] + parseInt(programTotal, 10)];
             },
             [0, 0]
         );
@@ -86,7 +86,7 @@ function PatientCountSingle(props) {
 
     const totalPatients = SumCensoredTotals(Object.values(counts.totals)) || [0, 0];
     const patientsInSearch = SumCensoredTotals(Object.values(counts.counts)) || [0, 0];
-    const numCohorts = Object.values(counts.totals)?.length || 0;
+    const numPrograms = Object.values(counts.totals)?.length || 0;
     return (
         <StyledBox pr={2} sx={{ border: 1, borderRadius: 2, boxShadow: 2, borderColor: 'primary.main' }}>
             <Grid container justifyContent="center" alignItems="center" spacing={2} className={classes.container}>
@@ -111,12 +111,12 @@ function PatientCountSingle(props) {
                 <Divider flexItem orientation="vertical" className={classes.divider} />
                 <Grid item xs={2}>
                     <Typography align="center" className={classes.patientEntry}>
-                        {numCohorts}
+                        {numPrograms}
                     </Typography>
                 </Grid>
                 <Divider flexItem orientation="vertical" className={classes.divider} />
                 <Grid item className={classes.button} pr={-2}>
-                    {numCohorts > 1 ? (
+                    {numPrograms > 1 ? (
                         <Button
                             onClick={(_) => setExpanded((old) => !old)}
                             variant="contained"
@@ -134,23 +134,23 @@ function PatientCountSingle(props) {
             </Grid>
 
             {expanded
-                ? counts.totals.map((cohort) => {
-                      const locked = !counts.unlockedPrograms?.some((programID) => programID === cohort.program_id);
+                ? counts.totals.map((program) => {
+                      const locked = !counts.unlockedPrograms?.some((programID) => programID === program.program_id);
                       return (
                           <Grid
                               container
                               justifyContent="center"
                               alignItems="center"
                               spacing={2}
-                              key={cohort.program_id}
+                              key={program.program_id}
                               className={classes.container}
                           >
                               <Grid item xs={2}>
                                   <Typography variant="h5" align="center" className={classes.patientEntry}>
                                       <b className={classes.patientEntry}>
-                                          {cohort.program_id}
+                                          {program.program_id}
                                           {locked && (
-                                              <Tooltip title="Unauthorized Cohort" placement="right">
+                                              <Tooltip title="Unauthorized Program" placement="right">
                                                   <LockOutlinedIcon className={classes.lockIcon} />
                                               </Tooltip>
                                           )}
@@ -160,13 +160,13 @@ function PatientCountSingle(props) {
                               <Divider flexItem orientation="vertical" className={classes.divider} />
                               <Grid item xs={2}>
                                   <Typography align="center" className={classes.patientEntry}>
-                                      {counts.counts?.[cohort.program_id] || 0}
+                                      {counts.counts?.[program.program_id] || 0}
                                   </Typography>
                               </Grid>
                               <Divider flexItem orientation="vertical" className={classes.divider} />
                               <Grid item xs={2}>
                                   <Typography align="center" className={classes.patientEntry}>
-                                      {cohort.patients_count || 0}
+                                      {program.patients_count || 0}
                                   </Typography>
                               </Grid>
                               <Divider flexItem orientation="vertical" className={classes.divider} />

diff --git a/src/views/clinicalGenomic/widgets/patientCounts.js b/src/views/clinicalGenomic/widgets/patientCounts.js
@@ -27,15 +27,15 @@ function PatientCounts() {
     const context = useSearchResultsReaderContext();
     const sites = context?.federation;
     const programs = context?.programs;
-    const discoveryCounts = context?.counts?.patients_per_cohort;
+    const discoveryCounts = context?.counts?.patients_per_program;
     const clinicalCounts = context?.clinical;
 
-    // Generate the map of site->cohort->numbers
+    // Generate the map of site->program->numbers
     let siteData = [];
     if (Array.isArray(sites)) {
         siteData = sites.map((entry) => {
             const counts = discoveryCounts?.[entry.location.name] || {};
-            const realCounts = clinicalCounts?.[entry.location.name]?.summary?.patients_per_cohort || {};
+            const realCounts = clinicalCounts?.[entry.location.name]?.summary?.patients_per_program || {};
             let unlockedPrograms = [];
             // Fill up the programs using the summary counts
             if (Array.isArray(programs)) {
@@ -80,7 +80,7 @@ function PatientCounts() {
                     </Grid>
                     <Grid item xs={2}>
                         <Typography variant="h5" className={`${PREFIX}-header`}>
-                            Total Cohorts
+                            Total Programs
                         </Typography>
                     </Grid>
                     <Grid item xs={1} ml="auto" className={`${PREFIX}-button`}>