gramene-search 1.2.96 → 1.4.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.2.96",
+  "version": "1.4.0",
   "description": "search wrapper for gramene",
   "source": "src/index.js",
   "main": "dist/index.js",
@@ -24,15 +24,15 @@
   "dependencies": {
     "ag-grid-community": "^31.1.1",
     "ag-grid-react": "^31.0.3",
-    "axios": "^0.21.1",
+    "axios": "^1.6.8",
     "flat-to-nested": "^1.1.1",
     "formik": "^3.0.0-next.8",
     "gramene-bins-client": "^2.3.3",
     "gramene-dbxrefs": "^3.0.11",
     "gramene-efp-browser": "^1.0.6",
-    "gramene-genetree-vis": "^4.1.18",
+    "gramene-genetree-vis": "^4.2.5",
     "gramene-mdview": "^2.0.6",
-    "gramene-search-vis": "^4.1.12",
+    "gramene-search-vis": "^4.2.4",
     "gramene-taxonomy-with-genomes": "^3.0.10",
     "gramene-trees-client": "^2.6.1",
     "lodash": "^4.17.15",
@@ -62,15 +62,18 @@
     "@babel/core": "latest",
     "@babel/preset-env": "latest",
     "@babel/preset-react": "latest",
-    "@parcel/config-default": "^2.0.0-rc.0",
-    "@parcel/core": "^2.8.0",
-    "@parcel/transformer-image": "^2.8.0",
-    "@parcel/transformer-js": "^2.8.0",
-    "@parcel/transformer-less": "^2.8.0",
+    "@parcel/config-default": "latest",
+    "@parcel/core": "latest",
+    "@parcel/transformer-image": "latest",
+    "@parcel/transformer-js": "latest",
+    "@parcel/transformer-less": "latest",
+    "assert": "^2.1.0",
     "buffer": "^5.7.1",
-    "http-proxy-middleware": "^2.0.6",
-    "parcel": "^2.8.0",
-    "process": "^0.11.10"
+    "console-browserify": "^1.2.0",
+    "http-proxy-middleware": "latest",
+    "parcel": "latest",
+    "process": "^0.11.10",
+    "util": "^0.12.5"
   },
   "repository": {
     "type": "git",

package/src/bundles/api.js

@@ -12,7 +12,7 @@ const facets = [
   "{!facet.limit='-1' facet.mincount='1' key='fixed_1000__bin'}fixed_1000__bin"
 ];
 const genomesOfInterest = '(taxon_id:2769) OR (taxon_id:3055) OR (taxon_id:3218) OR (taxon_id:3702) OR (taxon_id:3847) OR (taxon_id:4555) OR (taxon_id:4558) OR (taxon_id:4577) OR (taxon_id:13333) OR (taxon_id:15368) OR (taxon_id:29760) OR (taxon_id:39947) OR (taxon_id:55577) OR (taxon_id:88036) OR (taxon_id:214687)';
-
+const sites = ['main','oryza','maize','sorghum','grapevine'];
 const grameneSuggestions = createAsyncResourceBundle( {
   name: 'grameneSuggestions',
   actionBaseType: 'GRAMENE_SUGGESTIONS',
@@ -20,8 +20,13 @@ const grameneSuggestions = createAsyncResourceBundle( {
   getPromise: ({store}) => {
     const t = store.selectSuggestionsQuery().replaceAll(':',' ').trim();
     const g = store.selectGrameneGenomes();
-    return fetch(`${store.selectGrameneAPI()}/suggest?q={!boost b=relevance}name:${t}^5 ids:${t}^5 ids:${t}*^3 synonym:${t}^3 synonym:${t}*^2 text:${t}*^1`)
-      .then(res => res.json())
+    const q = `/suggest?q={!boost b=relevance}name:${t}^5 ids:${t}^5 ids:${t}*^3 synonym:${t}^3 synonym:${t}*^2 text:${t}*^1`;
+    // const promises = sites.map(site => fetch(`https://data.gramene.org/${site}${q}`));
+    // return Promise.all(promises)
+    return fetch(store.selectGrameneAPI() + q)
+      .then(res => {
+        return res.json()
+      })
       .then(suggestions => {
         if (Object.keys(g.active).length > 0) {
           suggestions.grouped.category.groups.forEach(group => {
@@ -221,6 +226,24 @@ curatedGenes.reactCuratedGenes = createSelector(
   }
 );
 
+const grameneGermplasm = createAsyncResourceBundle( {
+  name: 'grameneGermplasm',
+  actionBaseType: 'GRAMENE_GERMPLASM',
+  persist: true,
+  getPromise: ({store}) => {
+    return fetch(`${store.selectGrameneAPI()}/germplasm?rows=-1`)
+      .then(res => res.json())
+      .then(res => _.groupBy(res, 'ens_id'))
+  }
+});
+grameneGermplasm.reactGrameneGermplasm = createSelector(
+  'selectGrameneGermplasmShouldUpdate',
+  (shouldUpdate) => {
+    if (shouldUpdate) {
+      return { actionCreator: 'doFetchGrameneGermplasm' }
+    }
+  }
+);
 //
 // const grameneExpressionAssays = createAsyncResourceBundle( {
 //   name: 'grameneExpressionAssays',
@@ -510,4 +533,4 @@ const grameneOrthologs = {
 // });
 
 
-export default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, curatedGenes, grameneGeneAttribs, expressionSamples, expressionStudies];
+export default [grameneSuggestions, grameneSearch, grameneMaps, grameneTaxonomy, grameneTaxDist, grameneOrthologs, curatedGenes, grameneGermplasm, grameneGeneAttribs, expressionSamples, expressionStudies];

package/src/bundles/docs.js

@@ -10,11 +10,23 @@ const grameneDocs = {
       sequences: {},
       rnaSequences: {},
       pepSequences: {},
-      studies: {}
+      studies: {},
+      consequences: {}
     };
     return (state = initialState, {type, payload}) => {
       let newState;
       switch (type) {
+        case 'GRAMENE_CONSEQUENCES_REQUESTED':
+          if (!state.consequences.hasOwnProperty(payload)) {
+            newState = Object.assign({}, state);
+            newState.consequences[payload] = {};
+            return newState;
+          }
+          break;
+        case 'GRAMENE_CONSEQUENCES_RECEIVED':
+          newState = Object.assign({}, state);
+          newState.consequences = Object.assign({}, state.consequences, payload);
+          return newState;
         case 'GRAMENE_GENE_REQUESTED':
           if (!state.genes.hasOwnProperty(payload)) {
             newState = Object.assign({}, state);
@@ -37,14 +49,6 @@ const grameneDocs = {
           newState = Object.assign({}, state);
           newState.trees = Object.assign({}, state.trees, payload);
           return newState;
-        // case 'GRAMENE_PATHWAYS_REQUESTED':
-          // newState = Object.assign({}, state);
-          // payload.forEach(id => {
-          //   if (!state.pathways.hasOwnProperty(id)) {
-          //     newState.pathways[id] = {};
-          //   }
-          // });
-          // return newState;
         case 'GRAMENE_PATHWAYS_RECEIVED':
           newState = Object.assign({}, state);
           newState.pathways = Object.assign({}, state.pathways, payload);
@@ -116,6 +120,21 @@ const grameneDocs = {
       return state;
     }
   },
+  doRequestVEP: id => ({dispatch, store}) => {
+    const consequences = store.selectGrameneConsequences();
+    if (!consequences.hasOwnProperty(id)) {
+      dispatch({type: 'GRAMENE_CONSEQUENCES_REQUESTED', payload: id});
+      fetch(`${store.selectGrameneAPI()}/search?q=id:${id}&fl=id,VEP__*`)
+        .then(res => res.json())
+        .then(res => {
+          let genes = {};
+          res.response.docs.forEach(g => {
+            genes[g.id] = g;
+          });
+          dispatch({type: 'GRAMENE_CONSEQUENCES_RECEIVED', payload: genes})
+        })
+    }
+  },
   doRequestGrameneGene: id => ({dispatch, store}) => {
     const genes = store.selectGrameneGenes();
     if (!genes.hasOwnProperty(id)) {
@@ -297,6 +316,7 @@ const grameneDocs = {
     }
   },
   selectGrameneGenes: state => state.grameneDocs.genes,
+  selectGrameneConsequences: state => state.grameneDocs.consequences,
   selectGrameneTrees: state => state.grameneDocs.trees,
   selectGramenePathways: state => state.grameneDocs.pathways,
   selectParalogExpression: state => state.grameneDocs.expression,

package/src/components/results/GeneList.js

@@ -6,6 +6,7 @@ import Expression from './details/Expression'
 import Homology from './details/Homology'
 import Location from './details/Location'
 import Pathways from "./details/Pathways"
+import VEP from "./details/VEP"
 import Xrefs from "./details/Xrefs"
 import Publications from "./details/Publications"
 import Sequences from "./details/Sequences"
@@ -21,6 +22,7 @@ let inventory = {
   expression: Expression,
   homology: Homology,
   pathways: Pathways,
+  VEP: VEP,
   xrefs: Xrefs,
   pubs: Publications
 };
@@ -173,6 +175,12 @@ class Gene extends React.Component {
           popup: 'Curated Publications',
           available: false
         },
+        {
+          id: 'VEP',
+          label: 'Germplasm',
+          popup: 'Germplasm with protein truncating variants (PTVs)',
+          available: false
+        },
         {
           id: 'xrefs',
           label: 'Xrefs',

package/src/components/results/TaxDist.js

@@ -1,6 +1,6 @@
 import React from 'react'
 import { connect } from 'redux-bundler-react'
-import { Vis } from "gramene-search-vis"
+import Vis from "gramene-search-vis"
 import Selection from './selection.js'
 import '../../../node_modules/gramene-search-vis/styles/main.less';
 

package/src/components/results/details/VEP.css

@@ -0,0 +1,9 @@
+.button-like-link {
+    display: inline-block;
+    padding: 0;
+    background-color: #fff0;
+    color: #007bff;
+    text-decoration: underline;
+    border: none;
+    cursor: pointer;
+}

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

@@ -0,0 +1,102 @@
+import React, {useState, useEffect, useMemo} from 'react';
+import {connect} from "redux-bundler-react";
+import {Tabs, Tab, Form, Container, Row, Col, ToggleButton, ButtonGroup } from 'react-bootstrap';
+import * as console from "console";
+import { AgGridReact } from "ag-grid-react";
+import "ag-grid-community/styles/ag-grid.css";
+import "ag-grid-community/styles/ag-theme-quartz.css";
+import "./VEP.css";
+import {suggestionToFilters} from "../../utils";
+
+const metaRenderer = params => {
+  if (params.value.field === "germplasm") { // link to grin or SorgMutDB
+    if (params.value.germplasm_dbid) {
+      return <a target="_blank" href={`https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=${params.value.germplasm_dbid}`}>{params.value.pub_id}</a>;
+    }
+    return (
+      <form id={params.value.pub_id} action="https://www.depts.ttu.edu/igcast/sorbmutdb.php" method="post" target="_blank">
+        <input type="hidden" name="search" value={params.value.gene_id.replace('SORBI_3','Sobic.')} />
+        <input type="hidden" name="submit" value="Search" />
+        <button type="submit" className="button-like-link">SorbMutDB</button>
+      </form>
+    );
+  }
+  if (params.value.field === "search") { // search filter
+    const currentURL = new URL(window.location.href);
+    currentURL.search = '';
+    currentURL.searchParams.set('category', 'Germplasm');
+    currentURL.searchParams.set('fq_field',`VEP__merged__${study_info[params.value.pop_id].type}__attr_ss`);
+    currentURL.searchParams.set('fq_value',params.value.ens_id);
+    currentURL.searchParams.set('name', params.value.ens_id);
+
+    return <a href={currentURL.toString()}>{params.value.ens_id}</a>
+  }
+  return params.value.label
+}
+const sortByLabel = (valueA, valueB, nodeA, nodeB, isDescending) => {
+  if (valueA.label === valueB.label) return 0;
+  return (valueA.label > valueB.label) ? 1 : -1;
+}
+
+const study_info = {
+  '1' : {label: 'Purdue EMS', type: 'EMS'},
+  '2' : {label: 'USDA Lubbock EMS', type: 'EMS'},
+  '3' : {label: 'Lozano', type: 'NAT'},
+  '4' : {label: 'USDA Lubbock EMS', type: 'EMS'},
+  '5' : {label: 'Boatwright SAP', type: 'NAT'}
+};
+const Detail = props => {
+  const gene = props.geneDocs[props.searchResult.id];
+  if (props.grameneConsequences && props.grameneConsequences[gene._id] && props.grameneGermplasm) {
+    const germplasmLUT = props.grameneGermplasm;
+    const vep_obj = props.grameneConsequences[gene._id];
+    let accessionTable = [];
+    let tableFields = [
+      { field: 'Study/Population', cellRenderer: metaRenderer, comparator: sortByLabel},
+      { field: 'VEP consequence', cellRenderer: metaRenderer, comparator: sortByLabel},
+      { field: 'Allele Status', cellRenderer: metaRenderer, comparator: sortByLabel},
+      { field: 'Germplasm', cellRenderer: metaRenderer, comparator: sortByLabel},
+      { field: 'Other Genes', cellRenderer: metaRenderer, comparator: sortByLabel}
+    ];
+    Object.entries(vep_obj).forEach(([key,accessions]) => {
+      const parts = key.split("__");
+      if (parts[0] === "VEP") {
+        if (parts[1] !== "merged") {
+          accessions.forEach(ens_id => {
+            const germplasm = germplasmLUT[ens_id][0];
+            const accInfo = {
+              'Study/Population': {label: study_info[parts[3]].label},
+              'VEP consequence': {label: parts[1].replaceAll("_"," ")},
+              'Allele Status': {label: parts[2] === "het" ? "heterozygous" : "homozygous"},
+              'Germplasm': {field: 'germplasm', gene_id: props.searchResult.id, label: germplasm.pub_id, ...germplasm},
+              'Other Genes': {field: 'search', label: germplasm.ens_id, ...germplasm}
+            };
+            accessionTable.push(accInfo);
+          });
+        }
+      }
+    });
+    // const [rowData, setRowData] = useState(accessionTable);
+    // const [colDefs, setColDefs] = useState(tableFields);
+    const defaultColDef = useMemo(() => {
+      return {
+        filter: true
+      }
+    }, []);
+    return <div className="ag-theme-quartz" style={{height: `${44 * (accessionTable.length + 2)}px`}}>
+      <AgGridReact rowData={accessionTable} columnDefs={tableFields} defaultColDef={defaultColDef}/>
+    </div>
+  } else {
+      props.doRequestVEP(gene._id);
+      return <pre>loading</pre>;
+  }
+};
+
+export default connect(
+  'selectConfiguration',
+  'selectGrameneConsequences',
+  'selectGrameneGermplasm',
+  'doRequestVEP',
+  Detail
+);
+

package/src/demo.js

@@ -116,10 +116,10 @@ const panSites = [
     url: 'https://www.sorghumbase.org',
     ensemblURL: 'https://ensembl-dev.sorghumbase.org',
     ensemblSite: 'https://ensembl-dev.sorghumbase.org',
-    ensemblRest: 'https://data.gramene.org/pansite-ensembl',
-    grameneData: 'https://data.sorghumbase.org/sorghum_v6',
+    ensemblRest: 'https://data.gramene.org/pansite-ensembl-87',
+    grameneData: 'https://data.sorghumbase.org/sorghum_v7',
     ga: 'G-L5KXDCCZ16',
-    targetTaxonId: 4558,
+    targetTaxonId: 4558003,
     alertText: 'Click the search icon in the menu bar or type / to search',
     panSite : {
       vitis_vinifera : {

package/.parcel-cache/2126881b633272fa.txt

@@ -1,2 +0,0 @@
-458239591
-1709160133894321000

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