Merge pull request #536 from opentargets/cc-rename-phenodigm

LucaFumis · web-flow · commit b2343b2b1762 · 2022-04-22T14:27:46.000+01:00
[Evidence]: Rename Phenodigm
diff --git a/src/dataSources.js b/src/dataSources.js
@@ -94,9 +94,9 @@ const dataSources = [
     isPrivate: isPrivateDataSource('expression_atlas'),
   },
   {
-    id: 'phenodigm',
-    label: 'PhenoDigm',
-    isPrivate: isPrivateDataSource('phenodigm'),
+    id: 'impc',
+    label: 'IMPC',
+    isPrivate: isPrivateDataSource('impc'),
   },
   {
     id: 'uniprot_variants',
diff --git a/src/pages/EvidencePage/sections.js b/src/pages/EvidencePage/sections.js
@@ -11,7 +11,7 @@ import * as Gene2Phenotype from '../../sections/evidence/Gene2Phenotype';
 import * as GenomicsEngland from '../../sections/evidence/GenomicsEngland';
 import * as IntOgen from '../../sections/evidence/IntOgen';
 import * as OTGenetics from '../../sections/evidence/OTGenetics';
-import * as Phenodigm from '../../sections/evidence/Phenodigm';
+import * as Impc from '../../sections/evidence/Impc';
 import * as PheWASCatalog from '../../sections/evidence/PheWASCatalog';
 import * as Progeny from '../../sections/evidence/Progeny';
 import * as Reactome from '../../sections/evidence/Reactome';
@@ -49,7 +49,7 @@ const sections = [
   SysBio,
   EuropePmc,
   ExpressionAtlas,
-  Phenodigm,
+  Impc,
   OTCRISPR,
   OTEncore,
   OTValidation,
diff --git a/src/sections/evidence/Impc/Body.js b/src/sections/evidence/Impc/Body.js
@@ -118,7 +118,7 @@ const columns = [
 function Body({ definition, id: { ensgId, efoId }, label: { symbol, name } }) {
   const {
     data: {
-      phenodigm: { count: size },
+      impc: { count: size },
     },
   } = usePlatformApi(Summary.fragments.PhenodigmSummaryFragment);
 
diff --git a/src/sections/evidence/Impc/Description.js b/src/sections/evidence/Impc/Description.js
@@ -6,8 +6,8 @@ function Description({ symbol, name }) {
     <>
       Mapping of phenotypes in <strong>{symbol}</strong> animal model mutants
       similar to <strong>{name}</strong>. Source:{' '}
-      <Link to="https://www.sanger.ac.uk/tool/phenodigm/" external>
-        Phenodigm
+      <Link to="https://www.mousephenotype.org" external>
+        IMPC
       </Link>
     </>
   );
diff --git a/src/sections/evidence/Impc/IMCPSummaryFragment.gql b/src/sections/evidence/Impc/IMCPSummaryFragment.gql
@@ -0,0 +1,10 @@
+fragment IMCPSummaryFragment on Disease {
+  impc: evidences(
+    ensemblIds: [$ensgId]
+    enableIndirect: true
+    datasourceIds: ["impc"]
+    size: 0
+  ) {
+    count
+  }
+}
diff --git a/src/sections/evidence/Impc/Summary.js b/src/sections/evidence/Impc/Summary.js
@@ -4,27 +4,25 @@ import SummaryItem from '../../../components/Summary/SummaryItem';
 import usePlatformApi from '../../../hooks/usePlatformApi';
 import { dataTypesMap } from '../../../dataTypes';
 
-const PHENODIGM_SUMMARY_FRAGMENT = loader('./PhenodigmSummaryFragment.gql');
+const IMCP_SUMMARY_FRAGMENT = loader('./IMCPSummaryFragment.gql');
 
 function Summary({ definition }) {
-  const request = usePlatformApi(PHENODIGM_SUMMARY_FRAGMENT);
+  const request = usePlatformApi(IMCP_SUMMARY_FRAGMENT);
 
   return (
     <SummaryItem
       definition={definition}
       request={request}
       renderSummary={data =>
-        `${data.phenodigm.count} entr${
-          data.phenodigm.count === 1 ? 'y' : 'ies'
-        }`
+        `${data.imcp.count} entr${data.imcp.count === 1 ? 'y' : 'ies'}`
       }
       subText={dataTypesMap.animal_model}
     />
   );
 }
 
 Summary.fragments = {
-  PhenodigmSummaryFragment: PHENODIGM_SUMMARY_FRAGMENT,
+  IMCPSummaryFragment: IMCP_SUMMARY_FRAGMENT,
 };
 
 export default Summary;
diff --git a/src/sections/evidence/Impc/index.js b/src/sections/evidence/Impc/index.js
@@ -1,8 +1,8 @@
 export const definition = {
-  id: 'phenodigm',
-  name: 'PhenoDigm',
-  shortName: 'PH',
-  hasData: data => data.phenodigm.count > 0,
+  id: 'impc',
+  name: 'IMPC',
+  shortName: 'IM',
+  hasData: data => data.impc.count > 0,
 };
 
 export { default as Summary } from './Summary';
diff --git a/src/sections/evidence/Impc/sectionQuery.gql b/src/sections/evidence/Impc/sectionQuery.gql
@@ -1,11 +1,11 @@
-query IntOgenQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
+query impcQuery($ensemblId: String!, $efoId: String!, $size: Int!) {
   disease(efoId: $efoId) {
     id
     evidences(
       ensemblIds: [$ensemblId]
       enableIndirect: true
       size: $size
-      datasourceIds: ["phenodigm"]
+      datasourceIds: ["impc"]
     ) {
       rows {
         disease {
diff --git a/src/sections/evidence/Phenodigm/PhenodigmSummaryFragment.gql b/src/sections/evidence/Phenodigm/PhenodigmSummaryFragment.gql

Original file line number	Diff line number	Diff line change
`@@ -94,9 +94,9 @@ const dataSources = [`
`94`	`94`	`isPrivate: isPrivateDataSource('expression_atlas'),`
`95`	`95`	`},`
`96`	`96`	`{`
`97`		`- id: 'phenodigm',`
`98`		`- label: 'PhenoDigm',`
`99`		`- isPrivate: isPrivateDataSource('phenodigm'),`
	`97`	`+ id: 'impc',`
	`98`	`+ label: 'IMPC',`
	`99`	`+ isPrivate: isPrivateDataSource('impc'),`
`100`	`100`	`},`
`101`	`101`	`{`
`102`	`102`	`id: 'uniprot_variants',`