Merge remote-tracking branch 'origin/development' into v.2.1.0

Author: d2fong

src/client/features/pathways/pathway-node-metadata.js

@@ -3,18 +3,18 @@ const h = require('react-hyperscript');
 const _ = require('lodash');
 
 const { ServerAPI } = require('../../services');
+const { NS_CHEBI, NS_ENSEMBL, NS_HGNC, NS_HGNC_SYMBOL, NS_NCBI_GENE, NS_PUBMED, NS_REACTOME, NS_UNIPROT } = require('../../../config');
 
 const DEFAULT_NUM_NAMES = 3;
-// TODO - collection names (keys) should be accessed from config https://github.com/PathwayCommons/app-ui/issues/1131
 const SUPPORTED_COLLECTIONS = new Map([
-  ['Reactome'.toLowerCase(), 'Reactome'],
-  ['UniProt Knowledgebase'.toLowerCase(), 'UniProt'],
-  ['NCBI Gene'.toLowerCase(), 'NCBI'],
-  ['HGNC Symbol'.toLowerCase(), 'HGNC'],
-  ['ChEBI'.toLowerCase(), 'ChEBI'],
-  ['Ensembl'.toLowerCase(), 'Ensembl']
+  [NS_CHEBI, 'ChEBI'],
+  [NS_ENSEMBL, 'Ensembl'],
+  [NS_HGNC, 'HGNC'],
+  [NS_HGNC_SYMBOL, 'HGNC'],
+  [NS_NCBI_GENE, 'NCBI Gene'],
+  [NS_REACTOME, 'Reactome'],
+  [NS_UNIPROT, 'UniProt']
 ]);
-const PUBMED_DB_KEY = 'pubmed';
 
 const getUriIds = uris => uris.map( uri => _.last( uri.split( '/' ) ) );
 
@@ -33,7 +33,7 @@ class PathwayNodeMetadataView extends React.Component {
   componentDidMount(){
     let { node } = this.props;
     let metadata = node.data('metadata');
-    let pubmedUris = _.get(metadata, `xrefLinks.${PUBMED_DB_KEY}`, null);
+    let pubmedUris = _.get(metadata, `xrefLinks.${NS_PUBMED}`, null);
 
     if( pubmedUris != null ){
       const pubmedIds = getUriIds( pubmedUris );
@@ -61,10 +61,10 @@ class PathwayNodeMetadataView extends React.Component {
       ]);
     }
 
-    let dbLinks = _.keys( xrefLinks ).map( db => {
+    let dbLinks = _.keys( xrefLinks ).map( collection => {
       let link = null;
-      const displayName = SUPPORTED_COLLECTIONS.get( db.toLowerCase() );
-      const uri = _.get( xrefLinks, `${db}[0]` );
+      const displayName = SUPPORTED_COLLECTIONS.get( collection );
+      const uri = _.get( xrefLinks, `${collection}[0]` );
       if ( displayName && uri ) link = h('a.plain-link', { href: uri, target: '_blank' }, displayName );
       return link;
     });

src/client/features/search/entity-summary-box.js

@@ -6,30 +6,23 @@ const _ = require('lodash');
 const classNames = require('classnames');
 
 const { fetch } = require('../../../util');
-const config = require('../../../config');
-let { DATASOURCES } = require('../../../models/entity/summary');
+const { MAX_SIF_NODES, NS_HGNC_SYMBOL, NS_GENECARDS, NS_NCBI_GENE, NS_UNIPROT } = require('../../../config');
 
 const ENTITY_OTHER_NAMES_LIMIT = 4;
 const ENTITY_SUMMARY_DISPLAY_LIMIT = 6;
 
-//Temporary - to be dealt with in #1116 (https://github.com/PathwayCommons/app-ui/issues/1116)
-const DATASOURCE_NAMES = {
-  [DATASOURCES.NCBIGENE]: {
-    displayName: 'NCBI Gene',
-    linkUrl: DATASOURCES.NCBIGENE
-  },
-  [DATASOURCES.HGNC]: {
-    displayName: 'HGNC',
-    linkUrl: 'http://identifiers.org/hgnc.symbol/'
-  },
-  [DATASOURCES.UNIPROT]: {
-    displayName: 'UniProt',
-    linkUrl: DATASOURCES.UNIPROT
-  },
-  [DATASOURCES.GENECARDS]: {
-    displayName: 'GeneCards',
-    linkUrl: 'https://www.genecards.org/cgi-bin/carddisp.pl?gene='
-  },
+const SUPPORTED_COLLECTIONS = new Map([
+  [NS_GENECARDS, 'GeneCards'],
+  [NS_HGNC_SYMBOL, 'HGNC'],
+  [NS_NCBI_GENE, 'NCBI Gene'],
+  [NS_UNIPROT, 'UniProt']
+]);
+
+const getHgncFromXref = xrefLinks => {
+  let symbol;
+  const hgncXrefLink = _.find( xrefLinks, link  => link.namespace === NS_HGNC_SYMBOL );
+  if( hgncXrefLink ) symbol = _.last( _.compact( hgncXrefLink.uri.split('/') ) );
+  return symbol;
 };
 
 class EntitySummaryBox extends React.Component {
@@ -43,12 +36,11 @@ class EntitySummaryBox extends React.Component {
   }
   render(){
     let { summary } = this.props;
-    let { dataSource, displayName, localID, description, aliasIds, xref } = summary;
-    // Retrieve the HGNC symbol (http://www.pathwaycommons.org/sifgraph/swagger-ui.html)
-    let hgncSymbol = summary.xref[ DATASOURCES.HGNC ] || localID; // Prefix is hgnc
-    let sortedLinks = _.toPairs( xref ).concat([[ dataSource, localID ]])
-        .sort( (p1, p2) => p1[0] > p2[0] ? 1: -1 )
-        .map( pair => h('a.plain-link', { href: (DATASOURCE_NAMES[pair[0]]).linkUrl + pair[1], target:'_blank' }, (DATASOURCE_NAMES[pair[0]]).displayName));
+    let { displayName, description, aliasIds, xrefLinks } = summary;
+    const hgncSymbol = getHgncFromXref( xrefLinks );
+
+    let sortedLinks = xrefLinks.sort( (p1, p2) => p1.namespace > p2.namespace ? 1: -1 )
+        .map( link => h( 'a.plain-link', { href: link.uri, target:'_blank' }, SUPPORTED_COLLECTIONS.get( link.namespace ) ) );
 
     let moreInfo = h('div.entity-more-info',[
       h('div.entity-names', [
@@ -109,9 +101,7 @@ class EntitySummaryBoxList extends React.Component {
 
   componentDidMount(){
     let { entitySummaryResults } = this.props;
-    let hgncSymbols = _.values( entitySummaryResults )
-        .map( summary => summary.xref[ DATASOURCES.HGNC ] || summary.xref[ 'localID' ] ); // Prefix is hgnc
-
+    let hgncSymbols = entitySummaryResults.map( summaryResult => getHgncFromXref( _.get( summaryResult, ['summary', 'xrefLinks'] ) ) );
 
     fetch('/api/interactions/image?' + queryString.stringify({ sources: hgncSymbols })).then( r => r.json() ).then( res => {
       let { img } = res;
@@ -121,21 +111,15 @@ class EntitySummaryBoxList extends React.Component {
 
   render(){
     let { entitySummaryResults } = this.props;
-    const entitySummaryKeys = _.keys( entitySummaryResults );
-
-    // Retrieve the HGNC symbol (http://www.pathwaycommons.org/sifgraph/swagger-ui.html)
-    let sources = _.values( entitySummaryResults )
-        .map( summary => summary.xref[ DATASOURCES.HGNC ] || summary.xref[ 'localID' ] ); // Prefix is hgnc
-
-    let singleSrcLabel = `View interactions between ${sources[0]} and top ${config.MAX_SIF_NODES} genes`;
+    let sources = entitySummaryResults.map( summaryResult => getHgncFromXref( _.get( summaryResult, ['summary', 'xrefLinks'] ) ) );
+    let singleSrcLabel = `View interactions between ${sources[0]} and top ${MAX_SIF_NODES} genes`;
     let multiSrcLabel = `View iteractions between ${sources.slice(0, sources.length - 1).join(', ')} and ${sources.slice(-1)}`;
-
     let interactionsLinkLabel = sources.length === 1 ? singleSrcLabel : multiSrcLabel;
 
-    let entitySummaryBoxes = entitySummaryKeys
+    let entitySummaryBoxes = entitySummaryResults
        .slice( 0, ENTITY_SUMMARY_DISPLAY_LIMIT )
-       .map( key => {
-         const summary = _.get( entitySummaryResults, key );
+       .map( summaryResult => {
+         const summary = _.get( summaryResult, 'summary' );
          let props = { summary };
          return h(EntitySummaryBox, props);
        });

src/config.js

@@ -24,11 +24,15 @@ let defaults = {
   // factoid specific urls
   FACTOID_URL: 'http://unstable.factoid.baderlab.org/',
   BIOPAX_CONVERTERS_URL: 'http://biopax.baderlab.org/',
+  NS_CHEBI: 'chebi',
+  NS_ENSEMBL: 'ensembl',
+  NS_GENECARDS: 'genecards',
   NS_HGNC: 'hgnc',
   NS_HGNC_SYMBOL: 'hgnc.symbol',
-  NS_UNIPROT: 'uniprot',
   NS_NCBI_GENE: 'ncbigene',
-  NS_ENSEMBL: 'ensembl'
+  NS_PUBMED: 'pubmed',
+  NS_REACTOME: 'reactome',
+  NS_UNIPROT: 'uniprot'
 };
 
 let envVars = _.pick( process.env, Object.keys( defaults ) );

src/models/entity/summary.js

@@ -1,22 +1,14 @@
 // Entity summary
 const _ = require('lodash');
 
-//To be moved and integrated with all the other 'datasource'
-const DATASOURCES = {
-  NCBIGENE: 'http://identifiers.org/ncbigene/',
-  HGNC: 'http://identifiers.org/hgnc/',
-  UNIPROT: 'http://identifiers.org/uniprot/',
-  GENECARDS: 'http://identifiers.org/genecards/'
-};
-
 const DEFAULTS = {
-  dataSource: '',
+  namespace: '',
   displayName: '',
-  localID: '',
+  localId: '',
   description: '',
   aliases: [],
   aliasIds: [],
-  xref: {}
+  xrefLinks: []
 };
 
 class EntitySummary {
@@ -25,4 +17,4 @@ class EntitySummary {
   }
 }
 
-module.exports = { EntitySummary, DATASOURCES };
+module.exports = { EntitySummary };

src/server/external-services/gprofiler/gconvert/index.js

@@ -106,7 +106,7 @@ const gConvertResponseHandler = body =>  {
  * @param { object } userOptions - options
  * @return { object } list of unrecognized, object with duplicated and list of mapped IDs
  */
-const rawValidatorGconvert = ( query, userOptions ) => {
+const rawValidatorGconvert = ( query, userOptions = {} ) => {
 
   const defaultOptions = {
     'output': 'mini',

src/server/external-services/hgnc.js

@@ -1,7 +1,7 @@
 const { fetch } = require('../../util');
 const _ = require('lodash');
-const { HGNC_BASE_URL } = require('../../config');
-const { EntitySummary, DATASOURCES } = require('../../models/entity/summary');
+const { HGNC_BASE_URL, NS_GENECARDS, NS_HGNC_SYMBOL, NS_NCBI_GENE, NS_UNIPROT, IDENTIFIERS_URL } = require('../../config');
+const { EntitySummary } = require('../../models/entity/summary');
 const logger = require('../logger');
 
 //Could cache somewhere here.
@@ -20,9 +20,11 @@ const fetchBySymbol = symbol => {
 
 const fetchBySymbols = symbols => Promise.all( symbols.map(fetchBySymbol) );
 
+const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + '/' + localId;
+
 const getEntitySummary = async symbols => {
 
-  const summary = {};
+  const summary = [];
   if ( _.isEmpty( symbols ) ) return summary;
 
   const results = await fetchBySymbols( symbols );
@@ -31,26 +33,40 @@ const getEntitySummary = async symbols => {
   docList.forEach( doc => {
 
     const symbol = _.get( doc, 'symbol', '');
-    const xref = {
-      [DATASOURCES.GENECARDS] : symbol
-    };
+
     // Add database links
+    const xrefLinks = [{
+      "namespace": NS_GENECARDS,
+      "uri": createUri( NS_GENECARDS, symbol )
+    }, {
+      "namespace": NS_HGNC_SYMBOL,
+      "uri": createUri( NS_HGNC_SYMBOL, symbol )
+    }];
+
     if ( _.has( doc, 'entrez_id') ){
-      xref[DATASOURCES.NCBIGENE]  = _.get( doc, 'entrez_id');
+      xrefLinks.push({
+        "namespace": NS_NCBI_GENE,
+        "uri": createUri( NS_NCBI_GENE, _.get( doc, 'entrez_id') )
+      });
     }
+
     if ( _.has( doc, 'uniprot_ids') ){
-      xref[DATASOURCES.UNIPROT] = _.get( doc, 'uniprot_ids[0]', '');
+      xrefLinks.push({
+        "namespace": NS_UNIPROT,
+        "uri": createUri( NS_UNIPROT, _.get( doc, 'uniprot_ids') )
+      });
     }
+
     const eSummary = new EntitySummary({
-      dataSource: DATASOURCES.HGNC,
+      namespace: NS_HGNC_SYMBOL,
       displayName: _.get( doc, 'name', ''),
-      localID: symbol,
+      localId: symbol,
       aliases: _.get( doc, 'alias_name', []),
       aliasIds:_.get( doc, 'alias_symbol', []),
-      xref: xref
+      xrefLinks: xrefLinks
     });
 
-    return summary[ symbol ] = eSummary;
+    summary.push(eSummary);
   });
 
   return summary;

src/server/external-services/ncbi.js

@@ -1,9 +1,9 @@
 const { fetch } = require('../../util');
-const { NCBI_EUTILS_BASE_URL, PUB_CACHE_MAX_SIZE } = require('../../config');
+const { NCBI_EUTILS_BASE_URL, PUB_CACHE_MAX_SIZE, NS_GENECARDS, NS_HGNC_SYMBOL, NS_NCBI_GENE, IDENTIFIERS_URL } = require('../../config');
 const { URLSearchParams } = require('url');
 const QuickLRU = require('quick-lru');
 const _ = require('lodash');
-const { EntitySummary, DATASOURCES } = require('../../models/entity/summary');
+const { EntitySummary } = require('../../models/entity/summary');
 const logger = require('../logger');
 
 const pubCache = new QuickLRU({ maxSize: PUB_CACHE_MAX_SIZE });
@@ -79,9 +79,11 @@ const fetchByGeneIds = ( geneIds ) => {
     });
 };
 
+const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + '/' + localId;
+
 const getEntitySummary = async ( uids ) => {
 
-  const summary = {};
+  const summary = [];
   if ( _.isEmpty( uids ) ) return summary;
 
   const results = await fetchByGeneIds( uids );
@@ -90,25 +92,35 @@ const getEntitySummary = async ( uids ) => {
   result.uids.forEach( uid => {
     if( _.has( result, uid['error'] ) ) return;
     const doc = result[ uid ];
-    const xref = {};
+    const xrefLinks = [];
 
     // Fetch external database links first
-    if ( _.has( doc, 'name' ) ){
-      xref[DATASOURCES.HGNC] = _.get( doc, 'name' ,'');
-      xref[DATASOURCES.GENECARDS] = _.get( doc, 'name', '');
+    const localId = _.get( doc, 'name');
+    if( localId ){
+      [ NS_HGNC_SYMBOL, NS_GENECARDS ].forEach( namespace => {
+        xrefLinks.push({
+          "namespace": namespace,
+          "uri": createUri( namespace, localId )
+        });
+      });
     }
+    // push in NCBI xrefLink too
+    xrefLinks.push({
+      "namespace": NS_NCBI_GENE,
+      "uri": createUri( NS_NCBI_GENE, uid )
+    });
 
     const eSummary = new EntitySummary({
-      dataSource: DATASOURCES.NCBIGENE,
+      namespace: NS_NCBI_GENE,
       displayName: _.get( doc, 'description', ''),
-      localID: _.get( doc, 'uid', ''),
+      localId: uid,
       description: _.get( doc, 'summary', ''),
       aliases: _.get( doc, 'otherdesignations', '').split('|'),
       aliasIds: _.get( doc, 'otheraliases', '').split(',').map( a => a.trim() ),
-      xref: xref
+      xrefLinks: xrefLinks
     });
 
-    return summary[ uid ] = eSummary;
+    summary.push(eSummary);
   });
 
   return summary;