Fuzzy search on genes (#473)

* proof of concept blueprint typeahead

* poc with fuzzysearch lib

* typeahead adds gene on enter

* add gene on menu click

* typeahead clears correctly

* cleanup

client/package-lock.json

@@ -2194,7 +2194,7 @@
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       "integrity": "sha1-/WU28rzhODb/o6VFjEkDpZe7O/U=",
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@@ -2627,7 +2627,7 @@
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       "dev": true,
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@@ -2664,7 +2664,7 @@
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-      "resolved": "http://registry.npmjs.org/browserify-rsa/-/browserify-rsa-4.0.1.tgz",
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@@ -2718,7 +2718,7 @@
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@@ -3394,7 +3394,7 @@
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-      "resolved": "http://registry.npmjs.org/create-hash/-/create-hash-1.2.0.tgz",
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@@ -3407,7 +3407,7 @@
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-      "resolved": "http://registry.npmjs.org/create-hmac/-/create-hmac-1.1.7.tgz",
+      "resolved": "https://registry.npmjs.org/create-hmac/-/create-hmac-1.1.7.tgz",
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@@ -4090,7 +4090,7 @@
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-      "resolved": "http://registry.npmjs.org/diffie-hellman/-/diffie-hellman-5.0.3.tgz",
+      "resolved": "https://registry.npmjs.org/diffie-hellman/-/diffie-hellman-5.0.3.tgz",
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       "dev": true,
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@@ -4705,7 +4705,7 @@
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-          "resolved": "http://registry.npmjs.org/load-json-file/-/load-json-file-2.0.0.tgz",
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@@ -4891,7 +4891,7 @@
     },
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-      "resolved": "http://registry.npmjs.org/events/-/events-1.1.1.tgz",
+      "resolved": "https://registry.npmjs.org/events/-/events-1.1.1.tgz",
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@@ -5206,7 +5206,7 @@
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     "finalhandler": {
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-      "resolved": "http://registry.npmjs.org/finalhandler/-/finalhandler-1.1.1.tgz",
+      "resolved": "https://registry.npmjs.org/finalhandler/-/finalhandler-1.1.1.tgz",
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@@ -5922,6 +5922,11 @@
       "integrity": "sha1-GwqzvVU7Kg1jmdKcDj6gslIHgyc=",
       "dev": true
     },
+    "fuzzysort": {
+      "version": "1.1.4",
+      "resolved": "https://registry.npmjs.org/fuzzysort/-/fuzzysort-1.1.4.tgz",
+      "integrity": "sha512-JzK/lHjVZ6joAg3OnCjylwYXYVjRiwTY6Yb25LvfpJHK8bjisfnZJ5bY8aVWwTwCXgxPNgLAtmHL+Hs5q1ddLQ=="
+    },
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@@ -5936,7 +5941,7 @@
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-      "resolved": "http://registry.npmjs.org/get-stream/-/get-stream-3.0.0.tgz",
+      "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-3.0.0.tgz",
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@@ -6323,7 +6328,7 @@
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-      "resolved": "http://registry.npmjs.org/html-webpack-plugin/-/html-webpack-plugin-3.2.0.tgz",
+      "resolved": "https://registry.npmjs.org/html-webpack-plugin/-/html-webpack-plugin-3.2.0.tgz",
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@@ -6399,7 +6404,7 @@
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     "http-errors": {
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-      "resolved": "http://registry.npmjs.org/http-errors/-/http-errors-1.6.3.tgz",
+      "resolved": "https://registry.npmjs.org/http-errors/-/http-errors-1.6.3.tgz",
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@@ -6622,7 +6627,7 @@
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-      "resolved": "http://registry.npmjs.org/is-builtin-module/-/is-builtin-module-1.0.0.tgz",
+      "resolved": "https://registry.npmjs.org/is-builtin-module/-/is-builtin-module-1.0.0.tgz",
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@@ -7629,7 +7634,7 @@
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-      "resolved": "http://registry.npmjs.org/json5/-/json5-0.5.1.tgz",
+      "resolved": "https://registry.npmjs.org/json5/-/json5-0.5.1.tgz",
       "integrity": "sha1-Hq3nrMASA0rYTiOWdn6tn6VJWCE=",
       "dev": true
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@@ -7719,7 +7724,7 @@
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-      "resolved": "http://registry.npmjs.org/load-json-file/-/load-json-file-1.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/load-json-file/-/load-json-file-1.1.0.tgz",
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@@ -8043,7 +8048,7 @@
       "dependencies": {
         "minimist": {
           "version": "1.2.0",
-          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
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@@ -8168,7 +8173,7 @@
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     "minimist": {
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-      "resolved": "http://registry.npmjs.org/minimist/-/minimist-0.0.8.tgz",
+      "resolved": "https://registry.npmjs.org/minimist/-/minimist-0.0.8.tgz",
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       "dev": true
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@@ -8213,7 +8218,7 @@
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-      "resolved": "http://registry.npmjs.org/mkdirp/-/mkdirp-0.5.1.tgz",
+      "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-0.5.1.tgz",
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@@ -9939,7 +9944,7 @@
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@@ -10647,7 +10652,7 @@
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-      "resolved": "http://registry.npmjs.org/readable-stream/-/readable-stream-2.3.6.tgz",
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@@ -11669,7 +11674,7 @@
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         "minimist": {
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-          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
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@@ -11856,7 +11861,7 @@
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     "sha.js": {
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-      "resolved": "http://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
+      "resolved": "https://registry.npmjs.org/sha.js/-/sha.js-2.4.11.tgz",
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       "dev": true,
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@@ -12310,7 +12315,7 @@
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     "strip-ansi": {
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-      "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
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@@ -12546,7 +12551,7 @@
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     "through": {
       "version": "2.3.8",
-      "resolved": "http://registry.npmjs.org/through/-/through-2.3.8.tgz",
+      "resolved": "https://registry.npmjs.org/through/-/through-2.3.8.tgz",
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       "dev": true
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@@ -13202,7 +13207,7 @@
       "dependencies": {
         "minimist": {
           "version": "1.2.0",
-          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
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@@ -13865,7 +13870,7 @@
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     "wrap-ansi": {
       "version": "2.1.0",
-      "resolved": "http://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz",
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@@ -13973,7 +13978,7 @@
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     "yargs": {
       "version": "11.1.0",
-      "resolved": "http://registry.npmjs.org/yargs/-/yargs-11.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-11.1.0.tgz",
       "integrity": "sha512-NwW69J42EsCSanF8kyn5upxvjp5ds+t3+udGBeTbFnERA+lF541DDpMawzo4z6W/QrzNM18D+BPMiOBibnFV5A==",
       "dev": true,
       "requires": {

client/package.json

@@ -34,6 +34,7 @@
     "d3": "^4.10.0",
     "d3-scale-chromatic": "^1.3.0",
     "font-color-contrast": "^1.0.3",
+    "fuzzysort": "^1.1.4",
     "gl-mat4": "^1.1.4",
     "gl-matrix": "^2.7.1",
     "key-pressed": "0.0.1",

client/src/components/geneExpression/index.js

@@ -4,14 +4,49 @@
 import React from "react";
 import _ from "lodash";
 import * as d3 from "d3";
+import fuzzysort from "fuzzysort";
+
 import { connect } from "react-redux";
-import { Button, Tooltip } from "@blueprintjs/core";
+import { MenuItem } from "@blueprintjs/core";
+import { Suggest } from "@blueprintjs/select";
 import HistogramBrush from "../brushableHistogram";
 import * as globals from "../../globals";
 import actions from "../../actions";
 import { postUserErrorToast } from "../framework/toasters";
 import ExpressionButtons from "./expressionButtons";
 
+const renderGene = (fuzzySortResult, { handleClick, modifiers, query }) => {
+  if (!modifiers.matchesPredicate) {
+    return null;
+  }
+  /* the fuzzysort wraps the object with other properties, like a score */
+  const gene = fuzzySortResult.obj;
+  const text = gene.name;
+
+  return (
+    <MenuItem
+      active={modifiers.active}
+      disabled={modifiers.disabled}
+      label={gene.n_counts}
+      key={gene.name}
+      onClick={g => {
+        /* this fires when user clicks a menu item */
+        handleClick(g);
+      }}
+      text={text}
+    />
+  );
+};
+
+const filterGenes = (query, genes) => {
+  /* fires on load, once, and then for each character typed into the input */
+  return fuzzysort.go(query, genes, {
+    key: "name",
+    limit: 5,
+    threshold: -10000 // don't return bad results
+  });
+};
+
 @connect(state => {
   const metadata = _.get(state.controls.world, "obsAnnotations", null);
   const ranges = _.get(state.controls.world, "summary.obs", null);
@@ -29,23 +64,9 @@ import ExpressionButtons from "./expressionButtons";
   };
 })
 class GeneExpression extends React.Component {
-  constructor(props) {
+  handleClick(g) {
-    super(props);
-    this.state = {
-      gene: ""
-    };
-  }
-
-  keyPress(e) {
-    if (e.keyCode === 13) {
-      this.handleClick();
-    }
-  }
-
-  handleClick() {
     const { world, dispatch, userDefinedGenes } = this.props;
-    const { gene } = this.state;
+    const gene = g.target;
-
     if (userDefinedGenes.indexOf(gene) !== -1) {
       postUserErrorToast("That gene already exists");
     } else if (userDefinedGenes.length > 15) {
@@ -60,13 +81,11 @@ class GeneExpression extends React.Component {
         type: "user defined gene",
         data: gene
       });
-      this.setState({ gene: "" });
     }
   }
 
   render() {
     const { world, userDefinedGenes, differential } = this.props;
-    const { gene } = this.state;
 
     return (
       <div>
@@ -87,27 +106,27 @@ class GeneExpression extends React.Component {
             style={{ padding: globals.leftSidebarSectionPadding }}
             className="bp3-control-group"
           >
-            <div className="bp3-input-group bp3-fill">
+            <Suggest
-              <input
+              closeOnSelect
-                onKeyDown={this.keyPress.bind(this)}
+              openOnKeyDown
-                onChange={e => {
+              resetOnSelect
-                  this.setState({ gene: e.target.value });
+              noResults={<MenuItem disabled text="No matching genes." />}
-                }}
+              onItemSelect={g => {
-                value={gene}
+                /* this happens on 'enter' */
-                type="text"
+                this.handleClick(g);
-                className="bp3-input"
+              }}
-                placeholder="Enter a gene name"
+              inputValueRenderer={g => {
-                style={{ paddingRight: 94 }}
+                return "";
-              />
+              }}
-            </div>
+              itemListPredicate={filterGenes}
-            <Tooltip
+              itemRenderer={renderGene.bind(this)}
-              content="Add a gene to see its expression levels"
+              items={
-              position="bottom"
+                world && world.varAnnotations
-            >
+                  ? world.varAnnotations
-              <Button intent="primary" onClick={this.handleClick.bind(this)}>
+                  : [{ name: "No genes", n_counts: "" }]
-                Add
+              }
-              </Button>
+              popoverProps={{ minimal: true }}
-            </Tooltip>
+            />
           </div>
           {world && userDefinedGenes.length > 0
             ? _.map(userDefinedGenes, (geneName, index) => {