gramene-search 1.4.6 → 1.5.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.4.6",
+  "version": "1.5.0",
   "description": "search wrapper for gramene.",
   "source": "src/index.js",
   "main": "dist/index.js",
@@ -28,7 +28,7 @@
     "flat-to-nested": "^1.1.1",
     "formik": "^3.0.0-next.8",
     "gramene-bins-client": "^2.3.3",
-    "gramene-dbxrefs": "^3.0.11",
+    "gramene-dbxrefs": "^3.0.12",
     "gramene-efp-browser": "^1.0.6",
     "gramene-genetree-vis": "^4.2.7",
     "gramene-mdview": "^2.0.6",
@@ -73,6 +73,7 @@
     "http-proxy-middleware": "latest",
     "parcel": "latest",
     "process": "^0.11.10",
+    "url": "^0.11.3",
     "util": "^0.12.5"
   },
   "repository": {

package/src/components/results/GeneList.js

@@ -134,60 +134,63 @@ function shouldShowClosestOrtholog(searchResult) {
   );
 }
 
+const allDetails = [
+  {
+    id: 'VEP',
+    label: 'Germplasm',
+    popup: 'Germplasm with protein truncating variants (PTVs)',
+    available: false
+  },
+  {
+    id: 'sequences',
+    label: 'Sequences',
+    popup: 'Gene/cDNA/protein fasta',
+    available: true
+  },
+  {
+    id: 'location',
+    label: 'Location',
+    popup: 'Genome Browser',
+    available: false
+  },
+  {
+    id: 'expression',
+    label: 'Expression',
+    popup: 'Gene Expression Atlas',
+    available: false
+  },
+  {
+    id: 'homology',
+    label: 'Homology',
+    popup: 'Gene Family Tree',
+    available: false
+  },
+  {
+    id: 'pathways',
+    label: 'Pathways',
+    popup: 'Plant Reactome Pathways',
+    available: false
+  },
+  {
+    id: 'pubs',
+    label: 'Papers',
+    popup: 'Curated Publications',
+    available: false
+  },
+  {
+    id: 'xrefs',
+    label: 'Xrefs',
+    popup: 'Database Cross-references',
+    available: false
+  }
+];
+
+
 class Gene extends React.Component {
   constructor(props) {
     super(props);
     this.state = {
-      details: [
-        // {
-        //   id: 'VEP',
-        //   label: 'Germplasm',
-        //   popup: 'Germplasm with protein truncating variants (PTVs)',
-        //   available: false
-        // },
-        {
-          id: 'sequences',
-          label: 'Sequences',
-          popup: 'Gene/cDNA/protein fasta',
-          available: true
-        },
-        {
-          id: 'location',
-          label: 'Location',
-          popup: 'Genome Browser',
-          available: false
-        },
-        {
-          id: 'expression',
-          label: 'Expression',
-          popup: 'Gene Expression Atlas',
-          available: false
-        },
-        {
-          id: 'homology',
-          label: 'Homology',
-          popup: 'Gene Family Tree',
-          available: false
-        },
-        {
-          id: 'pathways',
-          label: 'Pathways',
-          popup: 'Plant Reactome Pathways',
-          available: false
-        },
-        {
-          id: 'pubs',
-          label: 'Papers',
-          popup: 'Curated Publications',
-          available: false
-        },
-        {
-          id: 'xrefs',
-          label: 'Xrefs',
-          popup: 'Database Cross-references',
-          available: false
-        }
-      ],
+      details: allDetails.map(o => ({...o})).filter(d => props.config.details[d.id]),
       expandedDetail: props.expandedDetail
     };
     let hasData = {};
@@ -236,7 +239,7 @@ class Gene extends React.Component {
     return renderTairSummary(gene) || renderClosestOrtholog(gene);
   }
   render() {
-    const panSite = this.props.panSite;
+    const panSite = this.props.config.panSite;
     const searchResult = this.props.searchResult;
     const taxName = this.props.taxName;
     // let orthologs='';
@@ -303,9 +306,7 @@ const GeneList = props => {
       {props.grameneSearch.response.docs.map((g,idx) => (
         <Gene key={idx}
               searchResult={g}
-              ensemblURL={props.configuration.ensemblURL}
-              ensemblRest={props.configuration.ensemblRest}
-              panSite={props.configuration.panSite}
+              config={props.configuration}
               taxName={props.grameneTaxonomy[g.taxon_id].name}
               geneDocs={props.grameneGenes}
               requestGene={props.doRequestGrameneGene}

package/src/components/results/details/Location.js

@@ -156,7 +156,7 @@ class Location extends React.Component {
     }
     var gene = this.gene;
     let links = [
-      {name: 'Ensembl Browser', url: `${this.props.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`}
+      {name: 'Ensembl Browser', url: `${this.props.config.ensemblURL}/${gene.system_name}/Gene/Summary?g=${gene._id}`}
     ];
     if (gene.annotations.taxonomy.ancestors.includes(4557))
       links.push({name: 'Phytozome', url: `https://phytozome-next.jgi.doe.gov/report/gene/Sbicolor_v5_1/${jgiify(gene._id)}`})

package/src/components/results/details/location/dallianceBrowser.js

@@ -1,5 +1,6 @@
 import React from "react";
 import isEqual from "lodash/isEqual";
+
 // var ensemblREST = require('../../../../../package.json').gramene.ensemblREST;
 //const ensemblREST = 'http://data.gramene.org/ensembl63';
 // const ensemblREST = 'https://data.sorghumbase.org/ensembl2';
@@ -56,13 +57,13 @@ export default class DallianceBrowser extends React.Component {
         sources: [
           {
             name: 'DNA',
-            ensemblURI: this.props.ensemblRest,
+            ensemblURI: this.props.config.ensemblRest,
             species: g.system_name,
             tier_type: 'sequence'
           },
           {
             name: 'Genes',
-            uri: this.props.ensemblRest,
+            uri: this.props.config.ensemblRest,
             tier_type: 'ensembl',
             species: g.system_name,
             type: ['gene', 'transcript', 'exon', 'cds']
@@ -88,7 +89,7 @@ export default class DallianceBrowser extends React.Component {
         maxViewWidth: 1000000
       }
     );
-    
+
     browser.addViewListener(this.props.onViewChange);
   }
 
@@ -122,4 +123,4 @@ export default class DallianceBrowser extends React.Component {
 //   visibleRange: React.PropTypes.object.isRequired,
 //   expanded: React.PropTypes.bool,
 //   onViewChange: React.PropTypes.func.isRequired
-// };
+// };

package/src/demo.js

@@ -45,10 +45,20 @@ const panSites = [
     ensemblURL: 'https://ensembl.gramene.org',
     ensemblSite: 'https://ensembl.gramene.org',
     ensemblRest: 'https://data.gramene.org/ensembl68',
-    grameneData: 'https://data.gramene.org/v65',
+    grameneData: 'https://data.gramene.org/v68',
     ga: 'G-ZTEQBFCRXZ',
     targetTaxonId: 3702,
     alertText: 'Main site',
+    details: {
+      sequences: true,
+      VEP: false,
+      location: true,
+      expression: true,
+      homology: true,
+      pathways: true,
+      pubs: true,
+      xrefs: true
+    },
     panSite : {
       sorghum_bicolor : {
         url: "https://sorghumbase.org/genes?idList=",
@@ -84,6 +94,16 @@ const panSites = [
     ga: "G-Y7ZYG1R8QT",
     showViews: true,
     not_downtime: 'The search interface will be undergoing maintenance on Tuesday, July 20 from 3:00 - 4:00 PM EDT',
+    details: {
+      sequences: true,
+      VEP: false,
+      location: true,
+      expression: true,
+      homology: true,
+      pathways: true,
+      pubs: true,
+      xrefs: true
+    },
     renderAlert: () => (
         <Alert variant='primary'>
           Hufford et. al., 2021. &nbsp;
@@ -122,6 +142,16 @@ const panSites = [
     targetTaxonId: 4558003,
     alertText: 'Click the search icon in the menu bar or type / to search',
     showViews: true,
+    details: {
+      sequences: true,
+      VEP: true,
+      location: true,
+      expression: true,
+      homology: true,
+      pathways: true,
+      pubs: true,
+      xrefs: true
+    },
     panSite : {
       vitis_vinifera : {
         url: "https://vitis.gramene.org?idList=",
@@ -161,6 +191,16 @@ const panSites = [
     },
     targetTaxonId: 29760020,
     alertText: 'Grapevine site',
+    details: {
+      sequences: true,
+      VEP: false,
+      location: true,
+      expression: true,
+      homology: true,
+      pathways: true,
+      pubs: true,
+      xrefs: true
+    },
     panSite : {
       sorghum_bicolor : {
         url: "https://sorghumbase.org/genes?idList=",
@@ -187,8 +227,18 @@ const panSites = [
     ensemblRest: 'https://data.gramene.org/pansite-ensembl-87',
     grameneData: 'https://data.gramene.org/oryza_v5',
     targetTaxonId: 3702,
-    alertText: 'Rice site'
-  },
+    alertText: 'Rice site',
+    details: {
+      sequences: true,
+      VEP: false,
+      location: true,
+      expression: true,
+      homology: true,
+      pathways: true,
+      pubs: true,
+      xrefs: true
+    }
+  }
 ];
 const initialState = Object.assign({helpIsOn:false}, panSites[subsitelut[subsite]]);
 

package/src/index.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.gramene.org/v65/swagger';
+      gramene.defaultServer = 'https://data.gramene.org/v68/swagger';
     </script>
     <script async src="./static/gramene-dalliance/dalliance-all.js"></script>
     <script async src="https://plantreactome.gramene.org/DiagramJs/diagram/diagram.nocache.js"></script>

package/src/sorghum.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.sorghumbase.org/sorghum_v6/swagger';
+      gramene.defaultServer = 'https://data.sorghumbase.org/sorghum_v7/swagger';
     </script>
     <script async src="./static/gramene-dalliance/dalliance-all.js"></script>
     <script async src="https://plantreactome.gramene.org/DiagramJs/diagram/diagram.nocache.js"></script>
@@ -38,4 +38,4 @@
     }
 </script>
 </body>
-</html>
+</html>