gramene-search 1.2.43 → 1.2.45

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.2.43",
+  "version": "1.2.45",
   "description": "search wrapper for gramene",
   "main": "dist/index.js",
   "scripts": {

package/src/bundles/filters.js

@@ -474,6 +474,15 @@ grameneFilters.reactGrameneFilters = createSelector(
       if (queryObject.hasOwnProperty('idList')) {
         return handleIdList(queryObject);
       }
+      if (queryObject.hasOwnProperty('fq_field') && queryObject.hasOwnProperty('fq_value')
+        && queryObject.hasOwnProperty('category') && queryObject.hasOwnProperty('name')) {
+        return {
+          type: 'BATCH_ACTIONS', actions: [
+            {type: 'GRAMENE_SEARCH_CLEARED'},
+            {type: 'GRAMENE_FILTER_ADDED', payload: queryObject}
+          ]
+        };
+      }
       const url = new URL(myUrl.href);
       if (url.pathname === '/genes') {
         return {type: 'GRAMENE_FILTERS_CLEARED'}

package/src/components/results/GeneList.js

@@ -8,6 +8,7 @@ import Location from './details/Location'
 import Pathways from "./details/Pathways"
 import Xrefs from "./details/Xrefs"
 import Publications from "./details/Publications"
+import {suggestionToFilters} from "../utils";
 import {GrFormPrevious, GrFormNextLink, GrFormNext, GrHpe} from 'react-icons/gr'
 import { Badge, OverlayTrigger, Tooltip } from 'react-bootstrap'
 
@@ -44,24 +45,34 @@ function trimSummary(summary) {
   }
 }
 
-const ClosestOrtholog = ({gene}) =>
+const ClosestOrthologCmp = (props) =>
 {
-  let name, desc, species;
+  let id, name, desc, species;
+  const gene = props.gene;
 
   if (gene.model_rep_id) {
     name = gene.model_rep_name || gene.model_rep_id;
     desc = gene.model_rep_description;
     species = gene.model_rep_species_name;
+    id = gene.model_rep_id;
   }
 
   else if (gene.closest_rep_id) {
     name = gene.closest_rep_name || gene.closest_rep_id;
     desc = gene.closest_rep_description;
     species = gene.closest_rep_species_name;
+    id = gene.closest_rep_id;
   }
 
   return (
-    <div className="closest-ortholog">
+    <div className="closest-ortholog" onClick={
+      props.doReplaceGrameneFilters(suggestionToFilters({
+        category: 'Gene',
+        fq_field: 'id',
+        fq_value: id,
+        name: name
+      }))
+    }>
       <h4>
         <span className="gene-id">{name}</span>
         <small className="species-name"> {species}</small>
@@ -71,6 +82,11 @@ const ClosestOrtholog = ({gene}) =>
   );
 };
 
+const ClosestOrtholog = connect(
+  'doReplaceGrameneFilters',
+  ClosestOrthologCmp
+);
+
 function renderClosestOrtholog(gene) {
 
   if (shouldShowClosestOrtholog(gene)) {

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

@@ -4,33 +4,11 @@ import {connect} from "redux-bundler-react";
 import TreeVis from "gramene-genetree-vis";
 import treesClient from "gramene-trees-client";
 import {Detail, Title, Description, Content, Explore, Links} from "./generic";
+import {suggestionToFilters} from "../../utils";
 import {Spinner, Alert} from "react-bootstrap";
 import '../../../../node_modules/gramene-genetree-vis/src/styles/msa.less';
 import '../../../../node_modules/gramene-genetree-vis/src/styles/tree.less';
 
-function suggestionToFilters(suggestion) {
-  return {
-    status: 'init',
-    rows: 20,
-    operation: 'AND',
-    negate: false,
-    leftIdx: 0,
-    rightIdx: 3,
-    children: [
-      {
-        fq_field: suggestion.fq_field,
-        fq_value: suggestion.fq_value,
-        name: suggestion.name,
-        category: suggestion.category,
-        leftIdx: 1,
-        rightIdx: 2,
-        negate: false,
-        marked: false
-      }
-    ]
-  }
-}
-
 class Homology extends React.Component {
   constructor(props) {
     super(props);

package/src/components/utils.js

@@ -0,0 +1,22 @@
+export const suggestionToFilters = (suggestion) => {
+  return {
+    status: 'init',
+    rows: 20,
+    operation: 'AND',
+    negate: false,
+    leftIdx: 0,
+    rightIdx: 3,
+    children: [
+      {
+        fq_field: suggestion.fq_field,
+        fq_value: suggestion.fq_value,
+        name: suggestion.name,
+        category: suggestion.category,
+        leftIdx: 1,
+        rightIdx: 2,
+        negate: false,
+        marked: false
+      }
+    ]
+  }
+}

package/src/demo.js

@@ -43,7 +43,7 @@ const panSites = [
     url: 'https://www.gramene.org',
     ensemblURL: 'https://ensembl.gramene.org',
     ensemblSite: 'https://ensembl.gramene.org',
-    ensemblRest: 'https://data.gramene.org/ensembl',
+    ensemblRest: 'https://data.gramene.org/ensembl66',
     grameneData: 'https://data.gramene.org/v66',
     targetTaxonId: 3702,
     alertText: 'Main site'
@@ -101,7 +101,7 @@ const panSites = [
     url: 'https://oryza.gramene.org',
     ensemblStie: 'https://ensembl-oryza.gramene.org',
     ensemblRest: 'https://data.gramene.org/pansite-ensembl-87',
-    grameneData: 'https://data.gramene.org/oryza_v4',
+    grameneData: 'https://data.gramene.org/oryza_v5',
     targetTaxonId: 3702,
     alertText: 'Rice site'
   },