Update with most recent pull requests

src/client/common/config.js

@@ -21,7 +21,6 @@ const databases = [
   ['3DMET', 'http://identifiers.org/3dmet/', ''],
   ['Chemical Component Dictionary', 'http://identifiers.org/pdb-ccd/', ''],
   ['CAS', 'http://identifiers.org/cas/', ''],
-  ['Pathway Commons','/view?uri=http://pathwaycommons.org/pc2/',''],
   ['HPRD','	http://identifiers.org/hprd/',''],
   ['RefSeq','	http://identifiers.org/refseq/',''],
   ['NCBI Gene','http://identifiers.org/ncbigene/',''],

src/client/common/cy/tooltips/format-content.js

@@ -2,6 +2,7 @@ const h = require('hyperscript');
 const classNames = require('classnames');
 const _ = require('lodash');
 const config = require('../../config');
+const queryString = require('query-string');
 
 //Handle standard name related metadata fields
 const standardNameHandler = (pair) => makeTooltipItem(pair[1], 'Name: ');
@@ -41,17 +42,17 @@ const databaseHandler = (pair, expansionFunction) => {
 };
 
 //Handle interaction/Detailed views related fields
-const interactionHandlerTrim =(pair, expansionFunction) => {
+const interactionHandlerTrim =(pair, expansionFunction, title) => {
   let maxViews=8;
   const expansionLink = pair[1].length>maxViews? h('div.more-link', { onclick: () => expansionFunction(pair[0]) }, 'more »'):'';
   if (pair[1].length < 1) { return h('div.error'); }
-  return generateDetailedViewList(sortByDatabaseId(pair[1]), pair[1].length>maxViews, expansionLink,maxViews);
+  return generateDetailedViewList(sortByDatabaseId(pair[1]), pair[1].length>maxViews, expansionLink,maxViews,title);
 };
-const interactionHandler =(pair, expansionFunction) => {
+const interactionHandler =(pair, expansionFunction, title) => {
   let maxViews=8;
   const expansionLink = pair[1].length>maxViews? h('div.more-link', { onclick: () => expansionFunction(pair[0]) }, '« less'):'';
   if (pair[1].length < 1) { return h('div.error'); }
-  return generateDetailedViewList(sortByDatabaseId(pair[1]),false, expansionLink,maxViews);
+  return generateDetailedViewList(sortByDatabaseId(pair[1]),false, expansionLink,maxViews,title);
 };
 
 //Handle publication related fields
@@ -103,7 +104,7 @@ const metaDataKeyMap = new Map()
   * Sample Input : parseMetadata(['Standard Name', 'TP53'])
   * Sample Output : <div class='fake-paragraph'><div class='field-name'></div></div>
 */
-function parseMetadata(pair, trim = true, expansionFunction) {
+function parseMetadata(pair, trim = true, expansionFunction, title) {
   const doNotRender = ['Data Source', 'Data SourceTrim', 'Display Name'];
   let key = pair[0];
 
@@ -114,7 +115,7 @@ function parseMetadata(pair, trim = true, expansionFunction) {
 
   let handler = metaDataKeyMap.get(key);
   if (handler) {
-    return handler(pair, expansionFunction);
+    return handler(pair, expansionFunction, title);
   }
   else if (!(trim) && !doNotRender.includes(key)) {
     return defaultHandler(pair);
@@ -294,7 +295,7 @@ function generateIdList(dbIdObject, trim) {
  * Sample Input : generateDBLink('Reactome', 'R-HSA-59544', true)
  * Sample Output : <div class="fake-spacer"><a class="db-link-single-ref" href="http://identifiers.org/reactome/R-HSA-59544" target="_blank">Reactome</a></div>
  */
-function generateDBLink(dbName, dbId, isDbVisible, otherName) {
+function generateDBLink(dbName, dbId, isDbVisible) {
   //Get base url for dbid
   let db = config.databases;
   let className = '';
@@ -307,7 +308,7 @@ function generateDBLink(dbName, dbId, isDbVisible, otherName) {
   if (isDbVisible) {
     className = '-single-ref';
   }
-  let label = otherName ? otherName :(isDbVisible ? dbName :dbId);
+  let label = isDbVisible ? dbName :dbId;
 
   //Build reference url
   if (link.length === 1 && link[0][1]) {
@@ -430,17 +431,22 @@ function generateDatabaseList(sortedArray, trim, expansionLink) {
   //Generate list
   let renderValue = sortedArray.map(item => [generateIdList(item, trim)], this);
 
-  return formatRenderValue(sortedArray,renderValue,expansionLink,trim,true,'Links');
+  return formatRenderValue(sortedArray, renderValue, expansionLink, trim, true, 'Links');
 }
 
-function generateDetailedViewList(sortedArray, trim, expansionLink,maxViews) {
-  let name = sortedArray[0].database;
+function generateDetailedViewList(sortedArray, trim, expansionLink, maxViews, title) {
   let list = sortedArray[0].ids;
   if(trim){list=list.slice(0,maxViews);}
   //Generate list
-  let renderValue = list.map((data,index) => [generateDBLink(name, data, true,'Interaction '+(index+1))],this);
-
-  return formatRenderValue(sortedArray,renderValue,expansionLink,trim,false,'Detailed Views');
+  let renderValue = list.map((data,index) => [h('div.fake-spacer', 
+    h('a.db-link' ,{
+      href:'/view?',
+      search: queryString.stringify({uri:'http://pathwaycommons.org/pc2/'+data, title:title, removeInfoMenu:true}),
+      target: '_blank', 
+    }, 'Interaction '+(index+1))
+  )]);
+
+  return formatRenderValue(sortedArray, renderValue, expansionLink, trim, false, 'Detailed Views');
 }
 
 function formatRenderValue(sortedArray, renderValue, expansionLink, trim, list,name){

src/client/common/cy/tooltips/index.js

@@ -84,7 +84,7 @@ class MetadataTip {
     if (!(this.data)) { this.data = []; }
     return h('div.tooltip-image', [
       h('div.tooltip-heading', this.name),
-      h('div.tooltip-internal', h('div', (data).map(item => formatContent.parseMetadata(item, true, expandFunction)), this))
+      h('div.tooltip-internal', h('div', (data).map(item => formatContent.parseMetadata(item, true, expandFunction, this.name)), this))
     ]);
   }
 
@@ -111,7 +111,7 @@ class MetadataTip {
     if (!(this.data)) { this.data = []; }
     return h('div.tooltip-image', [
       h('div.tooltip-heading', this.name),
-      h('div.tooltip-internal', h('div', (data).map(item => formatContent.parseMetadata(item, !this.isExpanded(item[0]), getExpansionFunction(item)), this)))
+      h('div.tooltip-internal', h('div', (data).map(item => formatContent.parseMetadata(item, !this.isExpanded(item[0]), getExpansionFunction(item), this.name), this)))
     ]
     );
   }

src/client/features/interactions/filter-menu.js

@@ -15,7 +15,7 @@ class InteractionsFilterMenu extends React.Component {
       [
         h('div',{className:classNames(type,'interaction-filter-legend')}),
         h('h3.button-label',type),
-        h('i', {className: classNames('common-icon-button','material-icons',{ 'common-icon-button-active': !clicked})}, clicked ? 'close':'check')
+        h('i', {className: classNames('common-icon-button','material-icons','icon-cutoff',{ 'common-icon-button-active': !clicked})}, clicked ? 'close':'check')
       ]
     ));
     return h('div',[

src/client/features/search/index.js

@@ -67,7 +67,6 @@ class Search extends React.Component {
       genes: state.query.q.trim(),
       target: 'UNIPROT',
     };
-
     this.setState({
       landingLoading: true
     });

src/client/features/view/index.js

@@ -32,15 +32,20 @@ class View extends React.Component {
 
     ServerAPI.getGraphAndLayout(query.uri, 'latest').then(networkJSON => {
       const layoutConfig = getLayoutConfig(networkJSON.layout);
-      const componentConfig = _.merge({}, BaseNetworkView.config, { useSearchBar: true});
+      if(query.removeInfoMenu){
+        BaseNetworkView.config.toolbarButtons.splice(
+          _.findIndex(BaseNetworkView.config.toolbarButtons, entry=>entry.id==='showInfo'),1
+        );
+      }
 
+      const componentConfig = _.merge({},BaseNetworkView.config, { useSearchBar: true});
       this.setState({
         componentConfig: componentConfig,
         layoutConfig: layoutConfig,
         networkJSON: networkJSON.graph,
         networkMetadata: {
           uri: query.uri,
-          name: _.get(networkJSON, 'graph.pathwayMetadata.title.0', 'Unknown Network'),
+          name: query.title || _.get(networkJSON, 'graph.pathwayMetadata.title.0', 'Unknown Network'),
           datasource: _.get(networkJSON, 'graph.pathwayMetadata.dataSource.0', 'Unknown Data Source'),
           comments: networkJSON.graph.pathwayMetadata.comments,
           organism: networkJSON.graph.pathwayMetadata.organism

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

@@ -32,10 +32,6 @@ const ServerAPI = {
     return fetch(`/api/gene-query?${qs.stringify(query)}`, defaultFetchOpts).then(res => res.json());
   },
 
-  findUniprotId(query){
-  return fetch(`/pc-client/uniprotIdSearch?${qs.stringify(query)}`, defaultFetchOpts).then(res => res.json());
-  },
-
   getProteinInformation(uniprotId){
     return fetch(`https://www.ebi.ac.uk/proteins/api/proteins?offset=0&accession=${uniprotId}`,defaultFetchOpts).then(res => res.json());
   },

src/server/enrichment-map/emap/generateGraphInfo.js

@@ -20,7 +20,30 @@ const _ = require('lodash');
 
 // input ["GO:1902275", "GO:2001252", "GO:1905269", "GO:0051053"]
 // returns a cytoscape object
-const generateGraphInfo = (pathwayIdList) => {
+const generateGraphInfo = (pathwayIdList, cutoff = 0.375, JCWeight, OCWeight) => {
+  if (cutoff < 0 || cutoff > 1) { throw new Error('ERROR: cutoff out of range [0, 1]');}
+  if (isNaN(Number(cutoff))) { throw new Error('ERROR: cutoff is not a number'); }
+
+  if (JCWeight < 0 || JCWeight > 1) {
+    throw new Error('ERROR: JCWeight out of range [0, 1]');
+  }
+  if (OCWeight < 0 || OCWeight > 1) {
+    throw new Error('ERROR: OCWeight out of range [0, 1]');
+  }
+  if (JCWeight != undefined && isNaN(Number(JCWeight))) {throw new Error('ERROR: JCWeight should be a number');}
+  if (OCWeight != undefined && isNaN(Number(OCWeight))) {throw new Error('ERROR: OCWeight should be a number');}
+  if (OCWeight != undefined && JCWeight != undefined && Number(OCWeight) + Number(JCWeight) != 1) {
+    throw new Error('ERROR: OCWeight + JCWeight should be 1');
+  }
+  if (JCWeight === undefined && OCWeight === undefined) {
+    JCWeight = 0.5;
+    OCWeight = 0.5;
+  } else if (JCWeight === undefined) {
+    JCWeight = 1 - OCWeight;
+  } else if (OCWeight === undefined) {
+    OCWeight = 1 - JCWeight;
+  }
+
   // check unrecognized and duplicates, modify pathwayIdList
   const unrecognized = [];
   for (let i = 0; i < pathwayIdList.length; ++i) {
@@ -48,7 +71,7 @@ const generateGraphInfo = (pathwayIdList) => {
   _.forEach(nodeInfo, node => {
     elements.push({ data: { id: node.pathwayId } });
   });
-  const edgeInfo = generateEdgeInfo(pathwayIdList);
+  const edgeInfo = generateEdgeInfo(pathwayIdList, JCWeight, cutoff);
   _.forEach(edgeInfo, edge => {
     const sourceIndex = 0;
     const targetIndex = 1;
@@ -71,8 +94,3 @@ const generateGraphInfo = (pathwayIdList) => {
 
 
 module.exports = { generateGraphInfo };
-
-//simple testing
-//console.log(generateGraphInfo(["GO:1902275", "GO:2001252", "GO:1905269"]));
-// const result = generateGraphInfo(["GO:1902275", "GO:2001252", "GO:1905269"]);
-// console.log(JSON.stringify(result));

src/server/enrichment-map/emap/generateInfo.js

@@ -20,8 +20,8 @@ const fetchPathwayInfo = (pathwayList) => {
 // {edgeId: "GO:1902275_GO:0051053", intersection: [gene1], similarity: 0.1},
 // {edgeId: "GO:2001252_GO:0051053", intersection: [gene1], similarity: 0.1}]
 // cutoff = 0.375 unless specified
-const generateEdgeInfo = (pathwayIdList, cutoff = 0.375) => {
-  return filterEdges(pathwayListGraph(fetchPathwayInfo(pathwayIdList)), cutoff);
+const generateEdgeInfo = (pathwayIdList, JCWeight, cutoff = 0.375) => {
+  return filterEdges(pathwayListGraph(fetchPathwayInfo(pathwayIdList), JCWeight), cutoff);
 };
 
 

src/server/enrichment-map/emap/intersect.js

@@ -8,7 +8,7 @@ const _ = require('lodash');
 // JC/OC calculation
 // output: JSON object
 //        {edgeId: pathwayxyz_pathwayabc, intersection: [gene1, gene3], similarity: 0.6}
-const pathwayPairGraph = (pathway1, pathway2) => {
+const pathwayPairGraph = (pathway1, pathway2, JCWeight) => {
   let intersectionCount = 0;
   const intersection = [];
   _.forEach(pathway1.genes, gene => {
@@ -18,7 +18,7 @@ const pathwayPairGraph = (pathway1, pathway2) => {
     }
   });
   // JC/OC calculation
-  const similarity = 0.5*(intersectionCount/(pathway1.genes.length+pathway2.genes.length-intersectionCount))+0.5*(intersectionCount/Math.min(pathway1.genes.length, pathway2.genes.length));
+  const similarity = JCWeight*(intersectionCount/(pathway1.genes.length+pathway2.genes.length-intersectionCount))+(1-JCWeight)*(intersectionCount/Math.min(pathway1.genes.length, pathway2.genes.length));
   return {edgeId: pathway1.pathwayId+'_'+pathway2.pathwayId, intersection: intersection, similarity: similarity};
 };
 
@@ -35,11 +35,11 @@ const pathwayPairGraph = (pathway1, pathway2) => {
 // {edgeId: "pathway2_pathway3", intersection: [], similarity: 0.1},
 // {edgeId: "pathway2_pathway4", intersection: [], similarity: 0.1},
 // {edgeId: "pathway3_pathway4", intersection: [gene1], similarity: 0.1}]
-const pathwayListGraph = (pathwayList) => {
+const pathwayListGraph = (pathwayList, JCWeight) => {
   const ret = [];
   for (let i = 0; i < pathwayList.length; ++i) {
     for (let j = i + 1; j < pathwayList.length; ++j) {
-      ret.push(pathwayPairGraph(pathwayList[i], pathwayList[j]));
+      ret.push(pathwayPairGraph(pathwayList[i], pathwayList[j], JCWeight));
     }
   }
   return ret;

src/server/enrichment-map/enrichment/enrichment.js

@@ -40,7 +40,6 @@ const defaultSetting = {
   "threshold_algo": "fdr",
   "domain_size_type": "annotated",
   "custbg": [],
-  "custbg_cb": 0,
   "sf_GO:BP": 1,
   "sf_REAC": 1,
 };
@@ -55,24 +54,26 @@ const enrichment = (query, userSetting) => {
     const minSetSizeVal = Number(formData.min_set_size);
     const maxSetSizeVal = Number(formData.max_set_size);
     const thresholdAlgoVal = formData.threshold_algo;
-    const custbgCbVal = Number(formData.custbg_cb);
     if (orderedQueryVal != 0 && orderedQueryVal != 1) {
-      throw new Error('ERROR: orderedQuery should be 1 or 0');
+      reject(new Error('ERROR: orderedQuery should be 1 or 0'));
     }
     if (isNaN(userThrVal) || userThrVal > 1 || userThrVal < 0) {
-      throw new Error('ERROR: userThrVal should be a number [0, 1]')
+      reject(new Error('ERROR: userThrVal should be a number [0, 1]'));
     }
     if (isNaN(minSetSizeVal)) {
-      throw new Error('ERROR: minSetSize should be a number')
+      reject(new Error('ERROR: minSetSize should be a number'));
+    }
+    if (minSetSizeVal < 0) {
+      reject(new Error('ERROR: minSetSize should be >= 0'));
     }
     if (isNaN(maxSetSizeVal)) {
-      throw new Error('ERROR: maxSetSize should be a number');
+      reject(new Error('ERROR: maxSetSize should be a number'));
     }
-    if (thresholdAlgoVal != 'analytical' && thresholdAlgoVal != 'bonferroni' && thresholdAlgoVal != 'fdr') {
-      throw new Error('ERROR: thresholdAlgoVal should be one of analytical, bonferroni, fdr');
+    if (maxSetSizeVal < minSetSizeVal) {
+      reject(new Error('ERROR: maxSetSize should be >= minSetSize'));
     }
-    if (custbgCbVal != 0 && custbgCbVal != 1) {
-      throw new Error('ERROR: custbgCb should be 1 or 0')
+    if (thresholdAlgoVal != 'analytical' && thresholdAlgoVal != 'bonferroni' && thresholdAlgoVal != 'fdr') {
+      reject(new Error('ERROR: thresholdAlgoVal should be one of analytical, bonferroni, fdr'));
     }
 
     request.post({ url: gProfilerURL, formData: formData }, (err, httpResponse, gProfilerResponse) => {

src/server/enrichment-map/gene-validator/index.js

@@ -40,7 +40,8 @@ const validatorGconvert = (query, userOptions) => {
   const promise = new Promise((resolve, reject) => {
     const formData = _.assign({}, defaultOptions, userOptions, { query: query });
     formData.organism =  formData.organism.toLowerCase();
-    formData.target = convertGConvertNames(formData.target.toUpperCase());
+    const initialTarget = formData.target.toUpperCase();
+    formData.target = convertGConvertNames(initialTarget);
     const invalidInfo = {invalidTarget: '', invalidOrganism: ''};
     if (!validOrganism.includes(formData.organism)) {
       invalidInfo.invalidOrganism = formData.organism;
@@ -79,7 +80,7 @@ const validatorGconvert = (query, userOptions) => {
         }
       });
 
-      const ret = { options: {target: formData.target, organism: formData.organism}, unrecognized: unrecognized, duplicate: duplicate, geneInfo: geneInfo };
+      const ret = { options: {target: initialTarget, organism: formData.organism}, unrecognized: unrecognized, duplicate: duplicate, geneInfo: geneInfo };
       resolve(ret);
     });
   });

src/server/enrichment-map/gene-validator/validityInfo.js

@@ -253,6 +253,6 @@ const validOrganism = ['aaegypti',
   'vvinifera',
   'zmays'];
 
-const validTarget = ['ENSG', 'HGNC', 'HGNC_ACC', 'UNIPROTSWISSPROT', 'ENTREZGENE', 'ENTREZGENE_ACC'];
+const validTarget = ['ENSG', 'HGNC', 'HGNC_ACC', 'UNIPROTSWISSPROT', 'ENTREZGENE_ACC'];
 
 module.exports = {validOrganism, validTarget};

src/server/pathway-commons/index.js

@@ -77,7 +77,6 @@ const PathwayCommonsService = {
 };
 
 PathwayCommonsService.querySearch = _.memoize(search.querySearch, query => JSON.stringify(query));
-PathwayCommonsService.uniprotIdSearch = _.memoize(search.uniprotIdSearch, query => JSON.stringify(query));
 PathwayCommonsService.datasources = _.memoize(datasources);
 
 // expose core cpath2 client api

src/server/pathway-commons/search/index.js

@@ -67,23 +67,4 @@ const querySearch = async (query) => {
   return [];
 };
 
-const uniprotIdSearch = async (query) => {
-  const queries = await (processPhrase(sanitize(query.q.trim())));
-  const filteredQueries = queries.filter(entry=>entry.includes('xrefid'));
-  if(!_.isEmpty(filteredQueries)){
-    const searchResult = await search()
-      .query(query) //input query string
-      .q(filteredQueries)
-      .format('json')
-      .fetch();
-    const searchSuccess = searchResult != null
-    if (searchSuccess && searchResult.searchHit.length > 0) {
-      const filteredResults = searchResult.searchHit.filter(hit =>
-        hit.uri.startsWith('http://identifiers.org/uniprot/') 
-      );
-      return filteredResults.map(hit=>_.last(hit.uri.split('/'))); //Parses and returns the Uniprot id
-    }
-  } 
-  return [];
-};
-module.exports = {querySearch:querySearch,uniprotIdSearch:uniprotIdSearch};
+module.exports = {querySearch};

src/server/routes/pc.js

@@ -12,10 +12,6 @@ router.get('/querySearch', function (req, res) {
   pc.querySearch(req.query).then(r => res.json(r));
 });
 
-router.get('/uniprotIdSearch',function (req, res) {
-  pc.uniprotIdSearch(req.query).then(r => res.json(r));
-});
-
 router.get('/:path', function (req, res) {
   res.redirect('http://www.pathwaycommons.org/pc2/' + req.params.path + '?' + qs.stringify(req.query));
 });