Merge pull request #173 from dbmi-bgm/cohort-to-case-edits

Cohort to case edits
dbmi-bgm · Aug 11, 2020 · d161866 · d161866
2 parents 12c43d6 + 2f81ebd
commit d161866
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Showing 25 changed files with 82 additions and 3,092 deletions.
diff --git a/src/encoded/static/components/browse/CaseSearchView.js b/src/encoded/static/components/browse/CaseSearchView.js
diff --git a/src/encoded/static/components/forms/CGAPSubmissionView.js b/src/encoded/static/components/forms/CGAPSubmissionView.js
@@ -3,7 +3,7 @@ import memoize from 'memoize-one';
 import url from 'url';
 
 import SubmissionView from '@hms-dbmi-bgm/shared-portal-components/es/components/forms/SubmissionView';
-import CohortSubmissionView from './../item-pages/CohortView/CohortSubmissionView';
+// import CaseSubmissionView from './../item-pages/CaseView/CaseSubmissionView';
 
 
 export function getSubmissionItemType(context, href){

diff --git a/src/encoded/static/components/index.js b/src/encoded/static/components/index.js
@@ -20,7 +20,6 @@ import ReleaseUpdates           from './static-pages/ReleaseUpdates';
 
 
 import DefaultItemView          from './item-pages/DefaultItemView';
-import CohortView, { CohortSubmissionView } from './item-pages/CohortView';
 import CaseView, { CaseSubmissionView } from './item-pages/CaseView';
 import IndividualView           from './item-pages/IndividualView';
 import FileProcessedView        from './item-pages/FileProcessedView';
@@ -47,7 +46,6 @@ content_views.register(ReleaseUpdates,          'Release-updatesPage');
 
 content_views.register(DefaultItemView,         'Item');
 content_views.register(CaseView,                'Case');
-content_views.register(CohortView,              'Cohort');
 content_views.register(IndividualView,          'Individual');
 content_views.register(FileProcessedView,       'FileProcessed');
 content_views.register(SampleView,              'Sample');
@@ -62,7 +60,7 @@ content_views.register(CGAPSubmissionView,      'Item', 'edit');
 content_views.register(CGAPSubmissionView,      'Item', 'create');
 content_views.register(CGAPSubmissionView,      'Item', 'clone');
 content_views.register(CGAPSubmissionView,      'Search', 'add');
-content_views.register(CohortSubmissionView,    'CohortSearchResults', 'add');
+// content_views.register(CaseSubmissionView,      'CaseSearchResults', 'add');
 
 content_views.register(SearchView,              'Search');
 content_views.register(SearchView,              'Search', 'selection');

diff --git a/src/encoded/static/components/item-pages/CaseView/CaseStats.js b/src/encoded/static/components/item-pages/CaseView/CaseStats.js
@@ -1,8 +1,7 @@
 'use strict';
 
-import React, { useState, useMemo } from 'react';
+import React from 'react';
 import _ from 'underscore';
-import { Collapse } from '@hms-dbmi-bgm/shared-portal-components/es/components/ui/Collapse';
 import { LocalizedTime, formatPublicationDate } from '@hms-dbmi-bgm/shared-portal-components/es/components/ui/LocalizedTime';
 
 
@@ -26,12 +25,9 @@ function mapFeaturesToBadges(features = []) {
     });
 }
 
-/** @param {Object} props - Contents of a family sub-embedded object. */
+/** @param {Object} props - Contents of a caseItem */
 export const CaseStats = React.memo(function CaseStats(props){
     const {
-        numFamilies = 0,
-        numIndividuals = 0,
-        numWithSamples = 0,
         className = '',
         caseItem = null
     } = props;
@@ -53,7 +49,7 @@ export const CaseStats = React.memo(function CaseStats(props){
                     <PhenotypicFeatures caseItem={caseItem} />
                 </StatCard>
                 <StatCard title="Family Info:" subtitle={famAccession} className="flex-fill">
-                    <FamilyInfo {...{ numFamilies, numIndividuals, numWithSamples, family }} />
+                    <FamilyInfo {...{ family, caseItem }} />
                 </StatCard>
             </div>
         </div>
@@ -80,7 +76,6 @@ export const PatientInfo = React.memo(function PatientInfo(props) {
     const {
         caseItem = null
     } = props || {};
-    console.log("patientinfo props", props);
 
     const { '@id': atId, case_title = null, individual = null } = caseItem || {};
     const {
@@ -103,7 +98,7 @@ export const PatientInfo = React.memo(function PatientInfo(props) {
                 <label className="mb-0">Sex:</label> { sex || 'N/A'}
             </div>
             <div className="card-text mb-1">
-                <label className="mb-0">Age: </label> { age && age_units ? `${age} age_units` : "N/A" }
+                <label className="mb-0">Age: </label> { age && age_units ? `${age} ${age_units}(s)` : "N/A" }
             </div>
             <div className="card-text mb-1">
                 <label className="mb-0">Life Status:</label> { life_status || 'N/A' }
@@ -130,28 +125,31 @@ export const PhenotypicFeatures = React.memo(function PhenotypicFeatures({ caseI
 });
 
 
-export const FamilyInfo = React.memo(function FamilyInfo({ family }) {
+export const FamilyInfo = React.memo(function FamilyInfo({ family, caseItem }) {
     const {
-        display_title : family_display_title = null,
-        title: family_title= null,
+        display_title : familyDisplayTitle = null,
+        title: familyTitle= null,
         family_phenotypic_features: familyFeatures = [],
-        cohort = null,
         project = null
     } = family || {};
-    const { display_title: project_title } = project || {};
+    const { display_title: projectTitle } = project || {};
+    const {
+        cohort = null
+    } = caseItem || {};
+    const { display_title: cohortTitle = null } = cohort || {};
 
     const renderedPhenotypicFeatures = mapFeaturesToBadges(familyFeatures);
 
     return (
         <>
             <div className="card-text mb-1">
-                <label className="mb-0">Family:</label> { family_title || family_display_title || "N/A" }
+                <label className="mb-0">Family:</label> { familyTitle || familyDisplayTitle || "N/A" }
             </div>
             <div className="card-text mb-1">
-                <label className="mb-0">Cohort:</label> { cohort || "N/A" }
+                <label className="mb-0">Cohort:</label> { cohortTitle || "N/A" }
             </div>
             <div className="card-text mb-1">
-                <label className="mb-0">Project:</label> { project_title || "N/A" }
+                <label className="mb-0">Project:</label> { projectTitle || "N/A" }
             </div>
             <div className="card-text">
                 <label className="mb-03">Family Phenotypic Features: </label>

diff --git a/src/encoded/static/components/item-pages/CaseView/CaseSubmissionView.js b/src/encoded/static/components/item-pages/CaseView/CaseSubmissionView.js
@@ -378,7 +378,7 @@ class PanelOne extends React.PureComponent {
             });
         };
 
-        const postData = { title, institution, project };
+        const postData = { case_id: title, institution, project };
 
         this.setState({ isCreating: true }, ()=>{
             this.request = ajax.load(

diff --git a/src/encoded/static/components/item-pages/CaseView/CaseSummaryTable.js b/src/encoded/static/components/item-pages/CaseView/CaseSummaryTable.js
@@ -527,25 +527,9 @@ export const CaseSummaryTable = React.memo(function CaseSummaryTable(props){
     const renderedSummary = (membersWithoutSamplesLen + membersWithoutViewPermissionsLen) > 0 ? (
         <div className="processing-summary">
             { membersWithoutSamplesLen > 0 ?
-                <p className="pl-2 mb-0">
+                <p className="pl-1 mb-0">
                     <span className="text-600">{ membersWithoutSamplesLen }</span> members without samples.
                 </p>
-                /*
-                <React.Fragment>
-                    <p className="mb-0">{ (membersWithoutSamplesLen + " members without samples: ") }</p>
-                    {
-                        membersWithoutSamples.map(function(member, idx){
-                            const { '@id' : id, display_title } = member;
-                            return (
-                                <React.Fragment key={id}>
-                                    { idx !== 0 ? ", " : null }
-                                    <a href={id}>{ display_title }</a>
-                                </React.Fragment>
-                            );
-                        })
-                    }
-                </React.Fragment>
-                */
                 : null }
             { membersWithoutViewPermissionsLen > 0 ?
                 <p className="mb-0">

diff --git a/src/encoded/static/components/item-pages/CaseView/CurrentFamilyController.js b/src/encoded/static/components/item-pages/CaseView/CurrentFamilyController.js
@@ -19,6 +19,7 @@ import { idToGraphIdentifier } from './PedigreeTabViewBody';
 export class CurrentFamilyController extends React.PureComponent {
 
     static haveFullViewPermissionForFamily(family){
+        if (!family) { return false; }
         const { original_pedigree = null, proband = null, members = [] } = family;
         // if (original_pedigree && !object.isAnItem(original_pedigree)){
         //     // Tests for presence of display_title and @id, lack of which indicates lack of view permission.