gramene-search 1.6.27 → 1.6.29

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.6.27",
+  "version": "1.6.29",
   "description": "search wrapper for gramene",
   "source": "src/index.js",
   "main": "dist/index.js",
@@ -43,7 +43,6 @@
     "querystringify": "^2.2.0",
     "react": "^17.0.2",
     "react-bootstrap": "^2.7.2",
-    "react-bootstrap-typeahead": "^6.4.1",
     "react-debounce-input": "^3.2.5",
     "react-dom": "17.0.2",
     "react-ga4": "^2.1.0",

package/src/bundles/api.js

@@ -478,6 +478,43 @@ const grameneOrthologs = {
   selectGrameneOrthologs: state => state.grameneOrthologs
 };
 
+const grameneParalogs = {
+  name: 'grameneParalogs',
+  getReducer: () => {
+    const initialState = {};
+    return (state = initialState, {type, payload}) => {
+      let newState;
+      switch (type) {
+        case 'GRAMENE_PARALOGS_REQUESTED':
+          if (!state.hasOwnProperty(payload)) {
+            newState = Object.assign({}, state);
+            newState[payload] = [];
+            return newState;
+          }
+          break;
+        case 'GRAMENE_PARALOGS_RECEIVED':
+          return Object.assign({}, state, payload);
+      }
+      return state;
+    }
+  },
+  doRequestParalogs: (geneId,supertree,taxon_id) => ({dispatch, store}) => {
+    const paralogs = store.selectGrameneParalogs();
+    if (!paralogs.hasOwnProperty(geneId)) {
+      dispatch({type: 'GRAMENE_PARALOGS_REQUESTED', payload: geneId});
+      const API = store.selectGrameneAPI();
+      const q= supertree ? `supertree_attr_s:${supertree}` : `homology__within_species_paralog:${geneId}`;
+      fetch(`${API}/search?q=${q}&rows=100&fq=taxon_id:${taxon_id}`)
+        .then(res => res.json())
+        .then(res => {
+          let newParalogs = {};
+          newParalogs[geneId] = res.response.docs.map(d => d.id);
+          dispatch({type: 'GRAMENE_PARALOGS_RECEIVED', payload: newParalogs})
+        })
+    }
+  },
+  selectGrameneParalogs: state => state.grameneParalogs
+};
 
 // function selectFacetIDs(store, field) {
 //   const path = `grameneGenes.data.facet_counts.facet_fields.${field}`;
@@ -534,4 +571,4 @@ const grameneOrthologs = {
 // });
 
 
-export default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, curatedGenes, grameneGermplasm, grameneGeneAttribs, expressionSamples, expressionStudies];
+export default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, grameneParalogs, curatedGenes, grameneGermplasm, grameneGeneAttribs, expressionSamples, expressionStudies];

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

@@ -1,9 +1,6 @@
 import React, { useRef, useEffect, useState } from 'react'
 import {connect} from "redux-bundler-react";
 import {Tabs, Tab, Form, Row, Col} from 'react-bootstrap';
-import { Typeahead } from 'react-bootstrap-typeahead'; // ES2015
-// Import as a module in your JS
-import 'react-bootstrap-typeahead/css/Typeahead.css';
 import BAR, {haveBAR} from "gramene-efp-browser";
 
 function DynamicIframe(props) {
@@ -63,28 +60,29 @@ const Detail = props => {
   }, [props.expressionStudies]);
 
   let paralogs_url;
-  let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id || gene._id}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
+  let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${gene.atlas_id || gene._id}&localAPI=${isLocal}`;
   let paralogs = [];
-  if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {
-    paralogs = gene.homology.homologous_genes.within_species_paralog;
+  if (props.grameneParalogs && props.grameneParalogs[gene._id]) {
+    paralogs = props.grameneParalogs[gene._id];
+  } else {
+    props.doRequestParalogs(gene._id, gene.homology.supertree, gene.taxon_id);
   }
+  // if (gene.homology && gene.homology.homologous_genes && gene.homology.homologous_genes.within_species_paralog) {
+  //   paralogs = gene.homology.homologous_genes.within_species_paralog;
+  // }
   if (paralogs.length > 1 && atlasExperiment) {
     paralogs_url= `https://dev.gramene.org/static/atlasWidget.html?genes=${paralogs.join(' ')}&experiment=${atlasExperiment}&localAPI=${isLocal}`;
   }
-  const ref = useRef(null);
-  const ref2 = useRef(null);
   return <Tabs>
     {paralogs_url &&
       <Tab tabClassName="gxa" eventKey="paralogs" title={`Paralogs`} key="gxaparalogs">
-        <Typeahead clearButton size='sm'
-          id="experiment-selector"
-          ref={ref}
-          labelKey="experiment"
-          onChange={(exps) => {if (exps.length > 0) {setAtlasExperiment(exps[0]._id);setTimeout(() => ref.current?.clear(), 2000)}}}
-          placeholder="Choose an experiment..."
-          options={atlasExperimentList}
-          labelKey={(experiment) => `${experiment.type}: ${experiment.description || experiment._id}`}
-        />
+        <Form.Select aria-label='experiment selector'
+                     placeholder='Select experiment'
+                     onChange={(e) => setAtlasExperiment(e.target.value)}>
+          { atlasExperimentList.map((e,idx) =>
+            <option key={idx} value={e._id}>{e.type}: {e.description || e._id}</option>
+          )}
+        </Form.Select>
         <DynamicIframe url={paralogs_url}/>
       </Tab>
     }
@@ -96,15 +94,6 @@ const Detail = props => {
       {/*  checked={isLocal}*/}
       {/*  onChange={handleLocalAPIChange}*/}
       {/*/>*/}
-      <Typeahead clearButton size='sm'
-                 id="experiment-selector2"
-                 ref={ref}
-                 labelKey="experiment"
-                 onChange={(exps) => {if (exps.length > 0) {setAtlasExperiment(exps[0]._id);setTimeout(() => ref.current?.clear(), 2000)}}}
-                 placeholder="Choose an experiment..."
-                 options={atlasExperimentList}
-                 labelKey={(experiment) => `${experiment.type}: ${experiment.description || experiment._id}`}
-      />
       <DynamicIframe url={gene_url}/>
     </Tab>
     {haveBAR(gene) &&
@@ -114,8 +103,9 @@ const Detail = props => {
 };
 
 export default connect(
-  //'selectParalogExpression',
+  'selectGrameneParalogs',
   'selectExpressionStudies',
+  'doRequestParalogs',
   //'doRequestParalogExpression',
   Detail
 );

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

@@ -57,6 +57,14 @@ class Homology extends React.Component {
       name: `Paralogs of ${this.gene.name}`
     }))
   }
+  searchSupertree() {
+    this.props.doReplaceGrameneFilters(suggestionToFilters({
+      category: 'Gene Tree',
+      fq_field: 'supertree_attr_s',
+      fq_value: this.gene.homology.supertree,
+      name: this.gene.homology.supertree
+    }))
+  }
   orthologList() {
     return this.orthoParaList('ortholog');
   }
@@ -112,6 +120,14 @@ class Homology extends React.Component {
         handleClick: this.filterParalogs.bind(this)
       });
     }
+    if (this.gene.homology.supertree) {
+      x.push({
+        name: `Supertree`,
+        category: `Gene Tree`,
+        count: this.gene.homology.supertree,
+        handleClick: this.searchSupertree.bind(this)
+      })
+    }
     return x;
   }
   links() {