Merge pull request #783 from q4wen/databaseLabels

Database labels

Author: jvwong

src/client/features/interactions/index.js

@@ -89,7 +89,7 @@ class Interactions extends React.Component {
         : source.replace(/\//g,' ')
     );
     Promise.all(geneIds).then(geneIds=>{
-      ServerAPI.geneQuery({genes:geneIds.join(' '),target: 'NCBIGENE'}).then(result=>{
+      ServerAPI.geneQuery({genes:geneIds,target: 'NCBIGENE'}).then(result=>{
         const ncbiIds=result.geneInfo.map(gene=> gene.convertedAlias);
         ServerAPI.getGeneInformation(ncbiIds).then(result=>{
           const geneResults=result.result;

src/client/features/search/landing-box.js

@@ -6,6 +6,7 @@ const { ServerAPI } = require('../../services');
 const databases = require('../../common/config').databases;
 const Loader = require('react-loader');
 const _ = require('lodash');
+
 //usedDatabases=[['Uniprot lookup name',{configName:,gProfiler:}]]
 const usedDatabases=new Map ([
   ['GeneCards',{configName:'Gene Cards',gProfiler:'HGNCSYMBOL',displayName:'Gene Cards'}],
@@ -14,7 +15,13 @@ const usedDatabases=new Map ([
   ['Uniprot',{configName:'Uniprot',gProfiler:'Uniprot',displayName:'Uniprot'}]
 ]);
 
-const linkBuilder= (source,geneQuery)=>{
+/**
+ * Get database link and display name based on gene ids
+ * @param {string} source Database name
+ * @param {JSON} geneQuery User input string and matching gene id.
+ * @return {string: {string: string}} e.g.{MDM2: {Uiprot: Q00978}}
+ */
+const idFormatter= (source,geneQuery)=>{
   let genes={};
   const geneArray=geneQuery.geneInfo;
   genes.unrecognized=geneQuery.unrecognized;
@@ -28,27 +35,16 @@ const linkBuilder= (source,geneQuery)=>{
   return genes;
 };
 
-const pcFallback = (unrecognized,genes) => {
- return unrecognized.map(entry=>{
-    if(!genes[entry]){
-     return ServerAPI.pcQuery('search', {q:entry,type:'entityreference'}).then((search)=>{
-        const ids = _.compact(search.searchHit.map(hit=>{
-          hit =_.reverse(hit.uri.split('/'));
-          return hit[1]==='uniprot' ? hit[0] : false;
-        }));
-        const duplicateCheck = _.compact(ids.map(id=>_.findKey(genes,{'Uniprot':id})));
-        if(!_.isEmpty(ids) && _.isEmpty(duplicateCheck)){
-          genes[entry]={'Uniprot': ids[0]};
-        }
-      });
-    }
-  });
-};
-
+/**
+ * Get database link and display name based on gene ids
+ * @param {{string:string}} ids NCBI id to search, e.g.{GENE CARD:MDM2}
+ * @return {[{string:string,string,string}]} Array of database containing link and display name, e.g.{link: URI, displayName: MDM2}
+ */
 const idToLinkConverter = (ids)  =>{
   const dbSet = databases.filter(databaseValue => ids[databaseValue.database]);
-  let dbs =  _.assign({},
-    ...dbSet.map(database=>({[database.database]:database.url+database.search+ids[database.database].replace(/[^a-zA-Z0-9:]/g)}))
+  let dbs =  _.assign({}, ...dbSet.map(database=>({
+      [database.database]: database.url+database.search+ids[database.database].replace(/[^a-zA-Z0-9:]/g)
+  }))
   );
 
   let links = [];
@@ -61,6 +57,12 @@ const idToLinkConverter = (ids)  =>{
   return links;
 };
 
+/**
+ * Get gene information from NCBI
+ * @param {string:string} ids NCBI id to search, e.g.{4193:MDM2}
+ * @param {} genes Validated gene id from databse, e.g.{gene:{db1:id,db2:id}}
+ * @return {json} JSON of gene information.
+ */
 const getNcbiInfo = (ids,genes) => {
   const ncbiIds=_.map(ids,(search,id)=>id);
   return ServerAPI.getGeneInformation(ncbiIds).then(result=>{
@@ -81,7 +83,12 @@ const getNcbiInfo = (ids,genes) => {
   });
 };
 
-const getUniprotInfo= (ids,genes) => {
+/**
+ * Get gene information from Uniprot
+ * @param {string:string} ids Uniprot accessions to search, e.g.{4193:MDM2}
+ * @return {json} JSON of gene information.
+ */
+const getUniprotInfo= (ids) => {
   const uniprotIds=_.map(ids,(search,id)=>id);
   return ServerAPI.getUniprotnformation(uniprotIds).then(result=>{
     return result.map(gene=>{
@@ -92,24 +99,19 @@ const getUniprotInfo= (ids,genes) => {
         }
       });
       const hgncSymbol = links['Gene Cards'];
-      const duplicateCheck = _.findKey(genes,{'Gene Cards':hgncSymbol});
-      if(!duplicateCheck || genes[duplicateCheck]['Uniprot']===gene.accession){
       links=idToLinkConverter(links);
-        return {
-          databaseID:gene.accession,
-          name:gene.gene[0].name.value,
-          function: gene.comments && gene.comments[0].type==='FUNCTION' ? gene.comments[0].text[0].value:'',
-          hgncSymbol:hgncSymbol,
-          showMore:{full:true,function:false,synonyms:false},
-          links:links
-        };
-      }
-      else{
-        return;
-      }
+      return {
+        databaseID:gene.accession,
+        name:gene.gene[0].name.value,
+        function: gene.comments && gene.comments[0].type==='FUNCTION' ? gene.comments[0].text[0].value:'',
+        hgncSymbol:hgncSymbol,
+        showMore:{full:true,function:false,synonyms:false},
+        links:links
+      };
     });
   });
 };
+
 /*Gets info for a landing box
 input: 'TP53'
 output: [{
@@ -122,37 +124,59 @@ synonyms:"TP53, BCC7, LFS1, P53, TRP53"
 }]
 */
 const getLandingResult= (query)=> {
-  const q=query.trim();
+  let q=query.trim().split(' ');
+  let ncbiIds={},uniprotIds={},labeledId={};
+  const genesToSearch = [];
+  q.forEach ((id)=> {
+    const splitId=id.split(':');
+
+    //Parse the query based on the format
+    if(/uniprot:\w+$/i.test(id)) {
+      uniprotIds[splitId[1]]=splitId[1];
+    } else if(/(ncbi:[0-9]+|hgnc:\w+)$/i.test(id)) {
+      labeledId[splitId[1]]=splitId[1];
+      genesToSearch.push(splitId[1]);
+    } else {
+      genesToSearch.push(splitId[0]);
+    }
+  });
+
+  //Get gene IDs from each database
   const promises= [];
   usedDatabases.forEach((database)=>promises.push(
-    ServerAPI.geneQuery({genes: q,target: database.gProfiler}).then(result=>linkBuilder(database.configName,result))
+    ServerAPI.geneQuery({
+      genes: genesToSearch,
+      target: database.gProfiler
+    }).then(result=>idFormatter(database.configName,result))
   ));
-  return Promise.all(promises).then(values=>{
-    let genes=values[0];
-    _.tail(values).forEach(gene=>_.mergeWith(genes,gene,(objValue, srcValue)=>_.assign(objValue,srcValue)));
+
+  return Promise.all(promises).then(databaseResults=>{
+    let genes={};
+    databaseResults.forEach(databaseResult=>_.merge(genes,databaseResult)); //Merge the array of result into one json
     return genes;
-  }).then(genes=>{
-      let ncbiIds={},uniprotIds={};
-      _.forEach(genes,(gene,search)=>{
-        if(gene['NCBI Gene']){
-          ncbiIds[gene['NCBI Gene']]=search;
-        }
-        else if(gene['Uniprot']){
-          uniprotIds[gene['Uniprot']]=search;
-        }
-      });
-      let landingBoxes=[];
-       if(!_.isEmpty(ncbiIds)){
-        landingBoxes.push(getNcbiInfo(ncbiIds,genes));
-       }
-       if(!_.isEmpty(uniprotIds)){
-        landingBoxes.push(getUniprotInfo(uniprotIds,genes));
-       }
-      return Promise.all(landingBoxes).then(landingBoxes=> {
-        landingBoxes=_.compact(_.flatten(landingBoxes));
-        if(landingBoxes.length>1){landingBoxes.forEach(box=>box.showMore.full=false);}
-        return landingBoxes;
-      });
+  }).then(genes=> {
+    _.forEach(genes,(gene,search)=>{
+      if(gene['NCBI Gene']){
+        ncbiIds[gene['NCBI Gene']]=search;
+      }
+      else if(gene['Uniprot']){
+        uniprotIds[gene['Uniprot']]=search;
+      }
+    });
+    let landingBoxes=[];
+     if(!_.isEmpty(ncbiIds)){
+      landingBoxes.push(getNcbiInfo(ncbiIds,genes));
+     }
+     if(!_.isEmpty(uniprotIds)){
+      landingBoxes.push(getUniprotInfo(uniprotIds));
+     }
+    return Promise.all(landingBoxes).then(landingBoxes=> {
+      landingBoxes=_.uniqWith(_.flatten(landingBoxes),(arrVal, othVal)=>
+        _.intersectionWith(_.values(arrVal.links),_.values(othVal.links),_.isEqual).length
+      );
+      if(landingBoxes.length>1){landingBoxes.forEach(box=>box.showMore.full=false);}
+      return landingBoxes;
+    });
   });
 };
 
@@ -243,7 +267,7 @@ const landingBox = (props) => {
         h('div.search-landing-section',{key: 'ids'},[hgncSymbol,otherNames]),
         h('div.search-landing-section',{key: 'functions'},[functions]),
         h('div.search-landing-section',{key: 'links'},[links]),
-        interactionsLink(box.databaseID,'View Interactions')
+        interactionsLink(box.hgncSymbol,'View Interactions')
       ])
     ];
   });

src/client/services/server-api/index.js

@@ -25,19 +25,24 @@ const ServerAPI = {
   },
 
   querySearch(query){
-    return fetch(`/pc-client/querySearch?${qs.stringify(query)}`, defaultFetchOpts).then(res => res.json());
+    const queryClone=_.assign({},query);
+    if(/(uniprot:\w+|ncbi:[0-9]+|hgnc:\w+)$/.test(queryClone.q)){queryClone.q=queryClone.q.split(':')[1];}
+    return fetch(`/pc-client/querySearch?${qs.stringify(queryClone)}`, defaultFetchOpts).then(res => res.json());
   },
 
   geneQuery(query){
-    query.genes=query.genes.split(' ');
-    return fetch('/api/validation', {
-      method:'POST',
-      headers: {
-        'Accept': 'application/json',
-        'Content-Type': 'application/json'
-      },
-      body:JSON.stringify(query)
-    }).then(res => res.json()).then(ids=> _.assign(ids,{unrecognized:_.tail(ids.unrecognized)}));//remove padding
+    if(query.genes.length>=1){
+      return fetch('/api/validation', {
+        method:'POST',
+        headers: {
+          'Accept': 'application/json',
+          'Content-Type': 'application/json'
+        },
+        body:JSON.stringify(query)
+      }).then(res => res.json());
+    }else{
+      return Promise.resolve({geneInfo:[],unrecognized:[]});
+    }
   },
 
   getGeneInformation(ids){