gramene-search 1.6.27 → 1.6.29

package/.parcel-cache/snapshot-dc1da35000e13623.txt

@@ -1,2 +1,2 @@
-164935289
-1749746396350714000
+176344589
+1750133941590159000

package/dist/index.js

@@ -13,8 +13,6 @@ var $gXNCa$reactswitch = require("react-switch");
 var $gXNCa$reacticonsio5 = require("react-icons/io5");
 var $gXNCa$reacticonsbs = require("react-icons/bs");
 var $gXNCa$reacticonsgr = require("react-icons/gr");
-var $gXNCa$reactbootstraptypeahead = require("react-bootstrap-typeahead");
-require("react-bootstrap-typeahead/css/Typeahead.css");
 var $gXNCa$grameneefpbrowser = require("gramene-efp-browser");
 var $gXNCa$gramenegenetreevis = require("gramene-genetree-vis");
 var $gXNCa$lodashkeyBy = require("lodash/keyBy");
@@ -571,6 +569,47 @@ const $9d9aeaf9299e61a1$var$grameneOrthologs = {
         },
     selectGrameneOrthologs: (state)=>state.grameneOrthologs
 };
+const $9d9aeaf9299e61a1$var$grameneParalogs = {
+    name: 'grameneParalogs',
+    getReducer: ()=>{
+        const initialState = {};
+        return (state = initialState, { type: type, payload: payload })=>{
+            let newState;
+            switch(type){
+                case 'GRAMENE_PARALOGS_REQUESTED':
+                    if (!state.hasOwnProperty(payload)) {
+                        newState = Object.assign({}, state);
+                        newState[payload] = [];
+                        return newState;
+                    }
+                    break;
+                case 'GRAMENE_PARALOGS_RECEIVED':
+                    return Object.assign({}, state, payload);
+            }
+            return state;
+        };
+    },
+    doRequestParalogs: (geneId, supertree, taxon_id)=>({ dispatch: dispatch, store: store })=>{
+            const paralogs = store.selectGrameneParalogs();
+            if (!paralogs.hasOwnProperty(geneId)) {
+                dispatch({
+                    type: 'GRAMENE_PARALOGS_REQUESTED',
+                    payload: geneId
+                });
+                const API = store.selectGrameneAPI();
+                const q = supertree ? `supertree_attr_s:${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
+};
 var // function selectFacetIDs(store, field) {
 //   const path = `grameneGenes.data.facet_counts.facet_fields.${field}`;
 //   if (_.has(store,path)) {
@@ -631,6 +670,7 @@ $9d9aeaf9299e61a1$export$2e2bcd8739ae039 = [
     $9d9aeaf9299e61a1$var$grameneTaxonomy,
     $9d9aeaf9299e61a1$var$grameneTaxDist,
     $9d9aeaf9299e61a1$var$grameneOrthologs,
+    $9d9aeaf9299e61a1$var$grameneParalogs,
     $9d9aeaf9299e61a1$var$curatedGenes,
     $9d9aeaf9299e61a1$var$grameneGermplasm,
     $9d9aeaf9299e61a1$var$grameneGeneAttribs,
@@ -2211,8 +2251,6 @@ var $541b8b0d8c5501d2$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
-
-
 
 function $9e29a4f60318db7a$var$DynamicIframe(props) {
     // Create a ref for the iframe element
@@ -2262,12 +2300,14 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
         props.expressionStudies
     ]);
     let paralogs_url;
-    let gene_url = `https://dev.gramene.org/static/atlasWidget.html?genes=${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 = (0, $gXNCa$react.useRef)(null);
-    const ref2 = (0, $gXNCa$react.useRef)(null);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tabs), {
         children: [
             paralogs_url && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
@@ -2275,52 +2315,31 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
                 eventKey: "paralogs",
                 title: `Paralogs`,
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstraptypeahead.Typeahead), {
-                        clearButton: true,
-                        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}`
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Select, {
+                        "aria-label": "experiment selector",
+                        placeholder: "Select experiment",
+                        onChange: (e)=>setAtlasExperiment(e.target.value),
+                        children: atlasExperimentList.map((e, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("option", {
+                                value: e._id,
+                                children: [
+                                    e.type,
+                                    ": ",
+                                    e.description || e._id
+                                ]
+                            }, idx))
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
                         url: paralogs_url
                     })
                 ]
             }, "gxaparalogs"),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Tab), {
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "gxa",
                 eventKey: "gene",
                 title: "All Studies",
-                children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstraptypeahead.Typeahead), {
-                        clearButton: true,
-                        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}`
-                    }),
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
-                        url: gene_url
-                    })
-                ]
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($9e29a4f60318db7a$var$DynamicIframe, {
+                    url: gene_url
+                })
             }, "gxa"),
             (0, $gXNCa$grameneefpbrowser.haveBAR)(gene) && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tab), {
                 tabClassName: "eFP",
@@ -2333,8 +2352,7 @@ const $9e29a4f60318db7a$var$Detail = (props)=>{
         ]
     });
 };
-var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)(//'selectParalogExpression',
-'selectExpressionStudies', //'doRequestParalogExpression',
+var $9e29a4f60318db7a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneParalogs', 'selectExpressionStudies', 'doRequestParalogs', //'doRequestParalogExpression',
 $9e29a4f60318db7a$var$Detail);
 
 
@@ -2559,6 +2577,14 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             name: `Paralogs of ${this.gene.name}`
         }));
     }
+    searchSupertree() {
+        this.props.doReplaceGrameneFilters((0, $047461923b1badda$export$964d88edb00bbcaa)({
+            category: 'Gene Tree',
+            fq_field: 'supertree_attr_s',
+            fq_value: this.gene.homology.supertree,
+            name: this.gene.homology.supertree
+        }));
+    }
     orthologList() {
         return this.orthoParaList('ortholog');
     }
@@ -2603,6 +2629,12 @@ class $64fad37f770d2bfe$var$Homology extends (0, ($parcel$interopDefault($gXNCa$
             count: this.paralogs.length,
             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() {