Merge branch 'feature/pathway_search' into feature/bar-chart-network

src/client/components/network-editor/controller.js

@@ -1,10 +1,10 @@
 import EventEmitter from 'eventemitter3';
 import Cytoscape from 'cytoscape'; // eslint-disable-line
 import _ from 'lodash';
-import MiniSearch from 'minisearch';
 
 import { DEFAULT_PADDING } from '../defaults';
 import { monkeyPatchMathRandom, restoreMathRandom } from '../../rng';
+import { SearchController } from './search-contoller';
 
 /**
  * The network editor controller contains all high-level model operations that the network
@@ -34,12 +34,13 @@ export class NetworkEditorController {
     /** @type {String} */
     this.networkIDStr = cy.data('id');
 
+    this.searchController = new SearchController(cy, this.bus);
+
     this.networkLoaded = false;
-    this.geneListIndexed = false;
 
     this.bus.on('networkLoaded', () => {
       this.networkLoaded = true;
-      this._indexGeneList();
+      this._fetchMinMaxRanks();
     });
   }
 
@@ -48,7 +49,19 @@ export class NetworkEditorController {
   }
 
   isGeneListIndexed() {
-    return this.geneListIndexed;
+    return this.searchController.isGeneListIndexed();
+  }
+
+  isPathwayListIndexed() {
+    return this.searchController.isPathwayListIndexed();
+  }
+
+  searchGenes(query) {
+    return this.searchController.searchGenes(query);
+  }
+
+  searchPathways(query) {
+    return this.searchController.searchPathways(query);
   }
 
   /**
@@ -107,45 +120,16 @@ export class NetworkEditorController {
     this.bus.emit('deletedSelectedElements', deletedEls);
   }
 
-  searchGenes(query) {
-    if (query && query.length > 0) {
-      return this.geneMiniSearch.search(query, { fields: ['gene'], prefix: true });
-    }
-
-    return [];
-  }
-
-  getGene(name) {
-    if (!this.isGeneListIndexed()) {
-      throw "The gene list hasn't been fecthed yet!";
-    }
-
-    const res = this.geneMiniSearch.search(name, { fields: ['gene'], prefix: true });
-
-    return res.length > 0 ? res[0] : {};
-  }
-
-  async _indexGeneList() {
-    const res = await this.fetchGeneList([]);
-    const genes = res ? res.genes : [];
-    this.minRank = res ? res.minRank : 0;
-    this.maxRank = res ? res.maxRank : 0;
-
-    if (genes && genes.length > 0) {
-      this.geneMiniSearch = new MiniSearch({
-        idField: 'gene',
-        fields: ['gene'], // fields to index for full-text search
-        storeFields: ['gene', 'rank'] // fields to return with search results
-      });
-      this.geneMiniSearch.addAll(genes);
-
-      this.lastGeneSet1 = res;
-      this.lastGeneSetNames1 = [];
-      this.geneListIndexed = true;
-      this.bus.emit('geneListIndexed');
-    }
+  async _fetchMinMaxRanks() {
+    const res = await fetch(`/api/${this.networkIDStr}/minmaxranks`);
+    const json = await res.json();
+    this.minRank = json ? json.minRank : 0;
+    this.maxRank = json ? json.maxRank : 0;
   }
 
+  /**
+   * Still needed by the gene sidebar.
+   */
   async fetchGeneList(geneSetNames) {
     geneSetNames = geneSetNames || [];
     const nameSet = new Set(geneSetNames);
@@ -165,11 +149,12 @@ export class NetworkEditorController {
         geneSets: geneSetNames
       })
     });
+
     if (res.ok) {
       const geneSet = await res.json();
       const rankedGenes = geneSet.genes.filter(g => g.rank);
       geneSet.genes = rankedGenes;
-      
+
       // We cache the last two queries because clicking on an 
       // edge queries for both source/target nodes.
       this.lastGeneSet2 = this.lastGeneSet1;
@@ -181,4 +166,5 @@ export class NetworkEditorController {
       return geneSet;
     }
   }
+
 }

src/client/components/network-editor/header.js

@@ -291,12 +291,13 @@ export function Header({ controller, classes, showControlPanel, isMobile, onShow
       <MobileMenu />
       <SearchDialog
         open={dialogName === SEARCH_DIALOG_ID}
+        controller={controller} 
         onClose={handleDialogClose}
       />
       <ShareMenu
         visible={menuName === SHARE_MENU_ID}
         target={anchorEl}
-        controller={controller} 
+        controller={controller}
         onClose={handleMenuClose}
         setSnackBarState={setSnackBarState}
       />

src/client/components/network-editor/index.js

@@ -63,6 +63,9 @@ async function loadNetwork(cy, controller, id) {
 
   console.log('Successful load from DB');
   console.log('End of editor sync initial phase');
+
+  // make the controller accessible from the chrome console for debugging purposes
+  window.controller = controller;
 }
 
 

src/client/components/network-editor/search-contoller.js

@@ -0,0 +1,101 @@
+import EventEmitter from 'eventemitter3';
+import Cytoscape from 'cytoscape'; // eslint-disable-line
+import _ from 'lodash';
+import MiniSearch from 'minisearch';
+
+export class SearchController {
+
+  constructor(cy, bus) {
+    this.networkIDStr = cy.data('id');
+    this.bus = bus || new EventEmitter();
+
+    this.genesReady = false;
+    this.pathwaysReady = false;
+
+    this.bus.on('networkLoaded', () => {
+      this.fetchAllGenesInNetwork();
+      this.fetchAllPathwaysInNetwork();
+    });
+  }
+
+  isGeneListIndexed() {
+    return this.genesReady;
+  }
+
+  isPathwayListIndexed() {
+    return this.pathwaysReady;
+  }
+
+  /**
+   * Fetches all the genes in the network.
+   */
+  async fetchAllGenesInNetwork() {
+    const res = await fetch(`/api/${this.networkIDStr}/genesforsearch`);
+
+    if (res.ok) {
+      this.geneMiniSearch = new MiniSearch({
+        idField: 'gene',
+        fields: ['gene'],
+        storeFields: ['gene', 'rank', 'pathwayNames']
+      });
+
+      const documents = await res.json();
+      this.geneMiniSearch.addAll(documents);
+
+      this.genesReady = true;
+      this.bus.emit('geneListIndexed');
+    }
+  }
+
+  /**
+   * Fetches all the genes in the network.
+   */
+  async fetchAllPathwaysInNetwork() {
+    const res = await fetch(`/api/${this.networkIDStr}/pathwaysforsearch`);
+
+    if (res.ok) {
+      // TODO add 'description' and 'leadingEdge'
+      this.pathwayMiniSearch = new MiniSearch({
+        idField: 'name',
+        fields: ['name'],
+        storeFields: ['name', 'padj', 'NES', 'pval', 'size', 'genes']
+      });
+
+      const documents = await res.json();
+
+      documents.map(doc => {
+        const i = doc.name.indexOf('%');
+        if(i > 0) {
+          doc.name = doc.name.substring(0, i);
+        }
+        doc.name = doc.name.toLowerCase();
+        return doc;
+      });
+
+      this.pathwayMiniSearch.addAll(documents);
+
+      this.pathwaysReady = true;
+      this.bus.emit('pathwayListIndexed');
+    }
+  }
+
+  searchGenes(query) {
+    if (!this.isGeneListIndexed()) {
+      throw "The gene list hasn't been fecthed yet!";
+    }
+    if (query && query.length > 0) {
+      return this.geneMiniSearch.search(query, { fields: ['gene'], prefix: true });
+    }
+    return [];
+  }
+
+  searchPathways(query) {
+    if (!this.isPathwayListIndexed()) {
+      throw "The pathway list hasn't been fecthed yet!";
+    }
+    if (query && query.length > 0) {
+      return this.pathwayMiniSearch.search(query, { fields: ['name'], prefix: true });
+    }
+    return [];
+  }
+}

src/client/components/network-editor/search-dialog.js

@@ -2,6 +2,7 @@ import React, { useRef, useState } from 'react';
 import PropTypes from 'prop-types';
 
 import theme from '../../theme';
+import { NetworkEditorController } from './controller';
 
 import { makeStyles } from '@material-ui/core/styles';
 
@@ -28,14 +29,16 @@ const useStyles = makeStyles((theme) => ({
 }));
 
 
-export const SearchDialog = ({ open, onClose }) => {
+export const SearchDialog = ({ open, controller, onClose }) => {
   const [searchValue, setSearchValue] = useState('');
   const [searchResult, setSearchResult] = useState(null);
   const [genes, setGenes] = useState(null);
 
   const searchValueRef = useRef(searchValue);
   searchValueRef.current = searchValue;
 
+  const cy = controller.cy;
+
   const classes = useStyles();
 
   const cancelSearch = () => {
@@ -46,13 +49,13 @@ export const SearchDialog = ({ open, onClose }) => {
     const query = val.trim();
 
     if (val.length > 0) {
-      // // Unselect Cy elements first
-      // const selectedEles = cy.elements().filter(':selected');
-      // selectedEles.unselect();
-      // // Now execute the search
-      // const res = controller.searchGenes(query);
-      // setSearchValue(val);
-      // setSearchResult(res);
+      // Unselect Cy elements first
+      const selectedEles = cy.elements().filter(':selected');
+      selectedEles.unselect();
+      // Now execute the search
+      const res = controller.searchGenes(query);
+      setSearchValue(val);
+      setSearchResult(res);
     } else {
       cancelSearch();
     }
@@ -82,6 +85,7 @@ export const SearchDialog = ({ open, onClose }) => {
 
 SearchDialog.propTypes = {
   open: PropTypes.bool,
+  controller: PropTypes.instanceOf(NetworkEditorController).isRequired,
   onClose: PropTypes.func.isRequired,
 };