Merge pull request #287 from RENCI/489-metrics-additions-changes-for-…

…study-data

489 metrics additions changes for study data

api/templates/study-sites-template.csv

@@ -1,3 +1,3 @@
-Proposal ID,Principal Investigator,Site Number,Site ID,CTSA ID,Site Name, Date Protocol Sent (mm-dd-yyyy),Date Contract Sent (mm-dd-yyyy),Date of IRB Submission (mm-dd-yyyy),Date of IRB Approval (mm-dd-yyyy),Date of Contract Execution (mm-dd-yyyy),Last Patient First Visit (mm-dd-yyyy),Date of Site Activation (mm-dd-yyyy),First Patient First Visit (mm-dd-yyyy),Number of Patients Consented,Number of Patients Enrolled,Number of Patients Withdrawn,Number of Patients Expected,Queries per total data elements,Number of Protocol Deviations,data Element,lost To FollowUp
-ProposalID,principalInvestigator,siteNumber,siteId,ctsaId,siteName,dateRegPacketSent,dateContractSent,dateIrbSubmission,dateIrbApproval,dateContractExecution,lpfv,dateSiteActivated,fpfv,patientsConsentedCount,patientsEnrolledCount,patientsWithdrawnCount,patientsExpectedCount,queriesCount,protocolDeviationsCount,dataElement,lostToFollowUp
+Proposal ID,Principal Investigator,Site Number,Site ID,CTSA ID,Site Name, Date Protocol Sent (mm-dd-yyyy),Date Contract Sent (mm-dd-yyyy),Date of IRB Submission (mm-dd-yyyy),Date of IRB Approval (mm-dd-yyyy),Date of Contract Execution (mm-dd-yyyy),Last Patient First Visit (mm-dd-yyyy),Date of Site Activation (mm-dd-yyyy),First Patient First Visit (mm-dd-yyyy),Number of Patients Consented,Number of Patients Enrolled,Number of Patients Withdrawn,Number of Patients Expected,Number of Queries,Number of Protocol Deviations,lost To FollowUp
+ProposalID,principalInvestigator,siteNumber,siteId,ctsaId,siteName,dateRegPacketSent,dateContractSent,dateIrbSubmission,dateIrbApproval,dateContractExecution,lpfv,dateSiteActivated,fpfv,patientsConsentedCount,patientsEnrolledCount,patientsWithdrawnCount,patientsExpectedCount,queriesCount,protocolDeviationsCount,lostToFollowUp
 ,,,,,,,,,,,,,,,,,,,,,

frontend/src/components/Tables/DetailPanels/SiteDetailPanel.js

@@ -4,33 +4,42 @@ import { DetailPanel } from './DetailPanel'
 import { StarBullet } from '../../Bullets' 
 import { formatDate } from '../../../utils/DateFormat'
 
+const invalidDisplay = 'N/A'
+
 export const dayCount = (startDate, endDate) => {
         if (startDate && endDate) {
             const num = Math.round((new Date(endDate) - new Date(startDate)) / (1000 * 60 * 60 * 24))
             return `${ num } day${ num === 1 ? '' : 's' }`
         } else {
-            return 'N/A'
+            return invalidDisplay
         }
     }
 
 export const displayRatio = (a, b, precision = 2) => {
         a = parseInt(a)
         b = parseInt(b)
         if ( !a || !b ) {
-            return 'N/A'
+            return invalidDisplay
         }
         if (a === 0) {
-            if (b === 0) return `N/A`
+            if (b === 0) return invalidDisplay
             return `0% (${ a }/${ b })`
         }
         return b !== 0
             ? `${ (100 * a/b).toFixed(precision) }% (${ a }/${ b })`
             : `N/A`
     }
 
+const displayRatioAsWholeNumberString = (a, b) => {
+    return b === 0 ? invalidDisplay : `${ Math.round(a / b) } ≈ ${ a } / ${ b }`
+}
+
 export const SiteDetailPanel = props => {
     const {
-        siteName, dateRegPacketSent, dateContractSent, dateIrbSubmission, dateIrbApproval, dateContractExecution, dateSiteActivated, lpfv, fpfv, patientsConsentedCount, patientsEnrolledCount, patientsWithdrawnCount, patientsExpectedCount, queriesCount, protocolDeviationsCount, dataElement
+        siteName, dateRegPacketSent, dateContractSent, dateIrbSubmission, dateIrbApproval,
+        dateContractExecution, dateSiteActivated, lpfv, fpfv, patientsConsentedCount, patientsEnrolledCount,
+        patientsWithdrawnCount, patientsExpectedCount, queriesCount, protocolDeviationsCount, dataElement,
+        queriesPerConsentedPatient,
     } = props
 
     return (
@@ -87,7 +96,7 @@ export const SiteDetailPanel = props => {
                         </ListItem>
                         <ListItem>
                             <ListItemIcon><StarBullet /></ListItemIcon>
-                            <ListItemText primary="Queries per data element:" secondary={ displayRatio(queriesCount, dataElement )} />
+                            <ListItemText primary="Queries per patient:" secondary={ displayRatioAsWholeNumberString(queriesCount, patientsConsentedCount) } />
                         </ListItem>
                     </List>
                 </Grid>

frontend/src/components/Tables/SitesTable.js

@@ -4,6 +4,12 @@ import { StoreContext } from '../../contexts/StoreContext'
 import { SiteDetailPanel, dayCount, displayRatio } from './DetailPanels'
 import { EnrollmentBar } from '../Widgets/EnrollmentBar'
 
+const invalidDisplay = 'N/A'
+
+const ratioAsWholeNumberString = (a, b) => {
+    return b === 0 ? invalidDisplay : Math.round(a / b)
+}
+
 export const SitesTable = props => {
     let { title, sites } = props
     const [store, ] = useContext(StoreContext)
@@ -28,7 +34,7 @@ export const SitesTable = props => {
                 site.actualToExpectedRandomizedPtRatio = displayRatio(site.patientsEnrolledCount, site.patientsExpectedCount)
                 site.ratioRandomizedPtsDropout = displayRatio(site.patientsWithdrawnCount, site.patientsEnrolledCount)
                 site.majorProtocolDeviationsPerRandomizedPt = displayRatio( site.protocolDeviationsCount, site.patientsEnrolledCount)
-                site.queriesPerDataElement = displayRatio(site.queriesCount, site.dataElement )
+                site.queriesPerConsentedPatient = ratioAsWholeNumberString(site.queriesCount, site.patientsConsentedCount )
             })
         }
     }, [sites, store.proposals])
@@ -59,7 +65,7 @@ export const SitesTable = props => {
 
     return (
         <MaterialTable
-            title={ title || null }
+            title={ null }
             components={{ }}
             columns={
                 [
@@ -83,9 +89,7 @@ export const SitesTable = props => {
                     { title: 'Patients Enrolled', field: 'patientsEnrolledCount', hidden: true, },
                     { title: 'Patients Withdrawn', field: 'patientsWithdrawnCount', hidden: true, },
                     { title: 'Patients Expected', field: 'patientsExpectedCount', hidden: true, },
-                    { title: 'Queries Count', field: 'queriesCount', hidden: true, },
                     { title: 'Protocol Deviations', field: 'protocolDeviationsCount', hidden: true, },
-                    { title: 'Data Element', field: 'dataElement', hidden: true, },
                     { title: 'Lost to Follow Up', field: 'lostToFollowUp', hidden: true, },
                     { title: 'Protocol to FPFV', field: 'protocolToFpfv', hidden: true, },
                     { title: 'Contract Execution Time', field: 'contractExecutionTime', hidden: true, },
@@ -96,7 +100,12 @@ export const SitesTable = props => {
                     { title: 'Actual to expected randomized patient ratio', field: 'actualToExpectedRandomizedPtRatio', hidden: true, },
                     { title: 'Ratio of randomized patients that dropout of the study', field: 'ratioRandomizedPtsDropout', hidden: true, },
                     { title: 'Major Protocol deviations per randomized patient', field: 'majorProtocolDeviationsPerRandomizedPt', hidden: true, },
-                    { title: 'Queries per data element', field: 'queriesPerDataElement', hidden: true, }
+                    { title: 'Number of Queries', field: 'queriesCount', hidden: true, },
+                    {
+                        title: 'Queries per patient',
+                        render: row => row.queriesPerConsentedPatient,
+                        hidden: true,
+                    },
                 ]
             }
             data={ sites }

frontend/src/views/Studies/CombinedMetrics.js

@@ -42,35 +42,69 @@ export const CombinedMetrics = ({ study, studyProfile, sites }) => {
     return sites.reduce((sum, site) => sum + site[key], 0)
   }
 
-  const ratioString = (a, b, precision = 2) => {
-    return b === 0 ? invalidDisplay : `${ (100 * a/b).toFixed(precision) }% (${ a }/${ b })`
+  const ratioAsPercentString = (a, b, precision = 2) => {
+    return b === 0 ? invalidDisplay : `${ (100 * a/b).toFixed(precision) }% ≈ ${ a } / ${ b }`
   }
 
-  const item = (label, value) => (
+  const ratioAsWholeNumberString = (a, b) => {
+    return b === 0 ? invalidDisplay : `${ Math.round(a / b) } ≈ ${ a } / ${ b }`
+  }
+
+  const Metric = React.useCallback(({ label, value }) => (
     <ListItem>
       <ListItemIcon><StarBullet /></ListItemIcon>
       <ListItemText primary={ label + ":" } secondary={ value } />
     </ListItem>
-  )
+  ), [])
 
   return (
     <Grid container>
       <Grid item xs={ 12 } md={ 6 }>
         <List>
-          { item('Activation (protocol to FPFV)', dayString(averageDays('dateRegPacketSent', 'fpfv'))) }
-          { item('Contract execution time', dayString(averageDays('dateContractSent', 'dateContractExecution'))) }
-          { item('sIRB approval time', dayString(averageDays('dateIrbSubmission', 'dateIrbApproval'))) }
-          { item('Site open to FPFV', dayString(averageDays('dateSiteActivated', 'fpfv'))) }
-          { item('Site open to LPFV', dayString(averageDays('dateSiteActivated', 'lpfv'))) }
+          <Metric
+            label="Activation (protocol to FPFV)"
+            value={ dayString(averageDays('dateRegPacketSent', 'fpfv')) }
+          />
+          <Metric
+            label="Contract execution time"
+            value={ dayString(averageDays('dateContractSent', 'dateContractExecution')) }
+          />
+          <Metric
+            label="sIRB approval time"
+            value={ dayString(averageDays('dateIrbSubmission', 'dateIrbApproval')) }
+          />
+          <Metric
+            label="Site open to FPFV"
+            value={ dayString(averageDays('dateSiteActivated', 'fpfv')) }
+          />
+          <Metric
+            label="Site open to LPFV"
+            value={ dayString(averageDays('dateSiteActivated', 'lpfv')) }
+          />
         </List>
       </Grid>
       <Grid item xs={ 12 } md={ 6 }>
         <List>
-          { item('Percent of consented patients randomized', ratioString(sum('patientsEnrolledCount'), sum('patientsConsentedCount'))) }
-          { item('Actual to expected randomized patient ratio', ratioString(sum('patientsEnrolledCount'), sum('patientsExpectedCount'))) }
-          { item('Ratio of randomized patients that dropped out of the study', ratioString(sum('patientsWithdrawnCount'), sum('patientsEnrolledCount'))) }
-          { item('Major protocol deviations per randomized patients', ratioString(sum('protocolDeviationsCount'), sum('patientsEnrolledCount'))) }        
-          { item('Queries per data element', ratioString(sum('queriesCount'), sum('dataElement'))) }
+          <Metric
+            label="Percent of consented patients randomized"
+            value={ ratioAsPercentString(sum('patientsEnrolledCount'), sum('patientsConsentedCount')) }
+          />
+          <Metric
+            label="Actual to expected randomized patient ratio"
+            value={ ratioAsPercentString(sum('patientsEnrolledCount'), sum('patientsExpectedCount')) }
+          />
+          <Metric
+            label="Ratio of randomized patients that dropped out of the study"
+            value={ ratioAsPercentString(sum('patientsWithdrawnCount'), sum('patientsEnrolledCount')) }
+          />
+          <Metric
+            label="Major protocol deviations per randomized patients"
+            value={ ratioAsPercentString(sum('protocolDeviationsCount'), sum('patientsEnrolledCount')) }        
+          />
+          <Metric
+            label="Queries per patient"
+            value={ ratioAsWholeNumberString(sum('queriesCount'), sum('patientsConsentedCount')) }
+          />
         </List>
       </Grid>
     </Grid>