Merge pull request #1453 from IgorRodchenkov/development

Preparing this app-ui for new PC v14 and Validator backend

.gitignore

@@ -14,4 +14,5 @@ src/scripts/jsonld/*
 src/*.gmt
 downloads/*
 public/img/pathways/*
-!/**/.gitkeep
+!/**/.gitkeep
+debug.log

package.json

@@ -1,6 +1,6 @@
 {
   "name": "app-ui",
-  "version": "3.8.0",
+  "version": "4.0.0",
   "description": "App UI",
   "repository": {
     "type": "git",

src/client/common/external-service-data.js

@@ -1,18 +1,18 @@
 const { IDENTIFIERS_URL } = require('../../config');
 
 let externalServiceData = [
-  {database:'Reactome', url:'http://identifiers.org/reactome/', search:''},
-  {database:'UniProt', url:'http://identifiers.org/uniprot/', search:''},
-  {database:'HGNC Symbol', url:'http://identifiers.org/hgnc.symbol/', search:''},
-  {database:'HGNC', url:'http://identifiers.org/hgnc/', search:''},
-  {database:'ChEBI', url:'http://identifiers.org/chebi/', search:''},
-  {database:'PubMed', url:'http://identifiers.org/pubmed/', search:''},
-  {database:'Ensembl', url:'http://identifiers.org/ensembl/', search:''},
-  {database:'NCBI Gene',url:'http://identifiers.org/ncbigene/',search:''},
-  {database:'Gene Cards',url:'http://identifiers.org/genecards/',search:''}
+  {database:'Reactome', url:'http://bioregistry.io/reactome:', search:''},
+  {database:'UniProt', url:'http://bioregistry.io/uniprot:', search:''},
+  {database:'HGNC Symbol', url:'http://bioregistry.io/hgnc.symbol:', search:''},
+  {database:'HGNC', url:'http://bioregistry.io/hgnc:', search:''},
+  {database:'ChEBI', url:'http://bioregistry.io/chebi:', search:''},
+  {database:'PubMed', url:'http://bioregistry.io/pubmed:', search:''},
+  {database:'Ensembl', url:'http://bioregistry.io/ensembl:', search:''},
+  {database:'NCBI Gene',url:'http://bioregistry.io/ncbigene:',search:''},
+  {database:'Gene Cards',url:'http://bioregistry.io/genecards:',search:''}
 ];
 
-let generateIdentifiersUrl = ( db, id ) => `${IDENTIFIERS_URL}/${db}/${id}`;
+let generateIdentifiersUrl = ( db, id ) => `${IDENTIFIERS_URL}/${db}:${id}`;
 
 module.exports = {
   externalServiceData,

src/client/features/interactions/interactions-edge-tooltip.js

@@ -73,7 +73,7 @@ class InteractionsEdgeTooltip extends React.Component {
     let publicationList = publications.map( publication => {
       let { id, title, firstAuthor, date, source } = publication;
       return h('div.cy-overflow-content', [
-        h('a.plain-link', { href: 'http://identifiers.org/pubmed/' + id, target: '_blank' }, title),
+        h('a.plain-link', { href: 'http://bioregistry.io/pubmed:' + id, target: '_blank' }, title),
         h('div', firstAuthor +  ' et al. | ' + source + ' - ' + new Date(date).getFullYear().toString())
       ]);
     });

src/client/features/paint/demo-pathway-results.json

@@ -282,7 +282,7 @@
               "ensembl": [
                 "ENST00000244741"
               ],
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "CDKN1A"
               ],
               "reactome": [
@@ -368,7 +368,7 @@
               "ensembl": [
                 "ENST00000244741"
               ],
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "CDKN1A"
               ],
               "reactome": [
@@ -418,13 +418,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein10458"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "PCBP4"
               ],
               "reactome": [
                 "R-HSA-6803382"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P57723"
               ]
             },
@@ -471,13 +471,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein10458"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "PCBP4"
               ],
               "reactome": [
                 "R-HSA-6803382"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P57723"
               ]
             },
@@ -648,13 +648,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein10457"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "ZNF385A"
               ],
               "reactome": [
                 "R-HSA-6803421"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "Q96PM9"
               ]
             },
@@ -728,13 +728,13 @@
               "Reactome DB_ID: 69683"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "TP53"
               ],
               "reactome": [
                 "R-HSA-69683"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P04637"
               ]
             },
@@ -801,7 +801,7 @@
               "ensembl": [
                 "ENSG00000124762"
               ],
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "CDKN1A"
               ],
               "reactome": [
@@ -860,13 +860,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein1393"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "CDKN1A"
               ],
               "reactome": [
                 "R-HSA-182585"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P38936"
               ]
             },
@@ -954,13 +954,13 @@
               "Reactome DB_ID: 69683"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "TP53"
               ],
               "reactome": [
                 "R-HSA-69683"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P04637"
               ]
             },
@@ -1024,13 +1024,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein10457"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "ZNF385A"
               ],
               "reactome": [
                 "R-HSA-6803421"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "Q96PM9"
               ]
             },
@@ -1104,13 +1104,13 @@
               "Reactome DB_ID: 69683"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "TP53"
               ],
               "reactome": [
                 "R-HSA-69683"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "P04637"
               ]
             },
@@ -1177,7 +1177,7 @@
               "ensembl": [
                 "ENSG00000124762"
               ],
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "CDKN1A"
               ],
               "reactome": [
@@ -1236,13 +1236,13 @@
               "REPLACED http://www.reactome.org/biopax/64/48887#Protein10457"
             ],
             "databaseIds": {
-              "hgnc symbol": [
+              "hgnc.symbol": [
                 "ZNF385A"
               ],
               "reactome": [
                 "R-HSA-6803421"
               ],
-              "uniprot knowledgebase": [
+              "uniprot": [
                 "Q96PM9"
               ]
             },

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

@@ -72,7 +72,7 @@ class PathwayNodeMetadataView extends React.Component {
     let publicationEles = publications.map(publication => {
       let { id, title, firstAuthor, date, source } = publication;
       return h('div.cy-overflow-content', [
-        h('a.plain-link', { href: 'http://identifiers.org/pubmed/' + id, target: '_blank'  }, title),
+        h('a.plain-link', { href: 'https://bioregistry.io/pubmed:' + id, target: '_blank'  }, title),
         h('div', firstAuthor +  ' et al. | ' + source + ' - ' + new Date(date).getFullYear().toString())
       ]);
     });

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

@@ -76,7 +76,7 @@ class PathwayNodeMetadataView extends React.Component {
     let publicationEles = publications.map(publication => {
       let { id, title, firstAuthor, date, source } = publication;
       return h('div.cy-overflow-content', [
-        h('a.plain-link', { href: 'http://identifiers.org/pubmed/' + id, target: '_blank'  }, title),
+        h('a.plain-link', { href: 'http://bioregistry.io/pubmed:' + id, target: '_blank'  }, title),
         h('div', firstAuthor +  ' et al. | ' + source + ' - ' + new Date(date).getFullYear().toString())
       ]);
     });

src/client/features/search/pathway-results-view.js

@@ -11,9 +11,7 @@ class PathwayResultsView extends React.Component {
   render(){
     let { searchHits: pathwayResults, controller, query , dataSources, hasFeature } = this.props;
     const curDatasource = query.datasource;
-    const sources = dataSources.filter( source => query.type === 'Pathway' ?
-      !source.notPathwayData && source.numPathways :
-      !source.notPathwayData && source.numInteractions );
+    const sources = dataSources.filter( source => query.type === 'Pathway' ? source.numPathways : source.numInteractions );
     const noPathwaysMsg = h( ErrorMessage, { title: 'Your search didn\'t match any pathways', footer: 'Try different keywords or gene names.'} );
 
     if( pathwayResults === null ){

src/client/router.js

@@ -79,27 +79,6 @@ module.exports = () => {
           return h(Features.Search, props);
         }
       }
-      // {
-      //   path: '/interactions',
-      //   render: props => {
-      //     return h(Features.Interactions, props);
-      //   }
-      // },
-      // {
-      //   path: '/enrichment',
-      //   render: props => {
-      //     return h(Features.Enrichment, props);
-      //   }
-      // },
-      // {
-      //   path: '/edit',
-      //   render: props => {
-      //     const editProps = _.assign({}, props, {
-      //       admin: true
-      //     });
-      //     return h(Features.Edit, editProps);
-      //   }
-      // }
     ].map( spec => h(Route, _.assign({ exact: true }, spec)) ))
   ]);
 };

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

@@ -114,8 +114,8 @@ const ServerAPI = {
 
   search(query){
     const queryClone=_.assign({},query);
-    if (/^((uniprot|hgnc):\w+|ncbi:[0-9]+)$/i.test(queryClone.q)) {
-      queryClone.q=queryClone.q.replace(/^(uniprot|ncbi|hgnc):/i,"");
+    if (/^((uniprot|hgnc|hgnc.symbol):\w+|ncbi:[0-9]+)$/i.test(queryClone.q)) {
+      queryClone.q=queryClone.q.replace(/^(uniprot|ncbi|hgnc|hgnc.symbol):/i,"");
     }
     return fetch(`/api/search`, {
       method: 'POST',

src/config.js

@@ -4,11 +4,10 @@ let defaults = {
   PORT: 3000,
   METADATA_CRON_SCHEDULE: '0 0 * * Monday', // update file from gprofiler etc. (Monday at midnight)
   PC_URL: 'https://www.pathwaycommons.org/',
-  XREF_SERVICE_URL: 'https://biopax.baderlab.org/',
   DOWNLOADS_FOLDER_NAME: 'downloads',
   GPROFILER_URL: "https://biit.cs.ut.ee/gprofiler/",
   GMT_ARCHIVE_URL: 'https://biit.cs.ut.ee/gprofiler/static/gprofiler_hsapiens.name.zip',
-  IDENTIFIERS_URL: 'https://identifiers.org',
+  IDENTIFIERS_URL: 'http://bioregistry.io',
   NCBI_EUTILS_BASE_URL: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils',
   NCBI_API_KEY: 'b99e10ebe0f90d815a7a99f18403aab08008', // for dev testing only (baderlabsysmonitor ncbi key)
   HGNC_BASE_URL: 'https://rest.genenames.org',

src/models/pathway/pathway-model.js

@@ -1,7 +1,6 @@
 const _ = require('lodash');
 
 // basic pathway model to serve the needs of the pathways view
-// TODO:
 //  - api to get entities,
 //  - compose each entity with entity metadata
 //  - get entity by id

src/scripts/cli.js

@@ -156,7 +156,7 @@ async function imagesFromGmtFile( fpath, store, get, parse, convert ) {
   }
 }
 
-// ambiguous: e.g. value[1] = 'name: t(4;14) translocations of FGFR3; datasource: reactome; organism: 9606; idtype: hgnc symbol'
+// ambiguous: e.g. value[1] = 'name: t(4;14) translocations of FGFR3; datasource: reactome; organism: 9606; idtype: hgnc.symbol'
 const parsePCGmtLine = line => {
   const extractFields = str => str.match(/^name:\s(?<name>.*);\sdatasource:\s(?<source>.*);\sorganism:\s(?<organism>.*);\sidtype:\s(?<idtype>.*)$/);
   const parseMeta = value => {

src/server/external-services/hgnc.js

@@ -20,7 +20,7 @@ const fetchBySymbol = symbol => {
 
 const fetchBySymbols = symbols => Promise.all( symbols.map(fetchBySymbol) );
 
-const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + '/' + localId;
+const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + ':' + localId;
 
 const getEntitySummary = async symbols => {
 

src/server/external-services/ncbi.js

@@ -148,7 +148,7 @@ const fetchByGeneIds = ( geneIds ) => {
   );
 };
 
-const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + '/' + localId;
+const createUri = ( namespace, localId ) => IDENTIFIERS_URL + '/' + namespace + ':' + localId;
 
 const rawMakeSummary = (ent) => {
   const xrefLinks = [];