Merge pull request #2264 from broadinstitute/ew-robust-pathway-autocomplete

Robustify search autocomplete to misformated pathways (SCP-6012)

Author: eweitz

app/javascript/components/explore/StudyGeneField.jsx

@@ -362,9 +362,9 @@ export default function StudyGeneField({
 }
 
 /** Last filtering applied before showing selectable autocomplete options */
-function finalFilterOptions(option, rawInput) {
+export function finalFilterOptions(option, rawInput) {
   const input = rawInput.toLowerCase()
-  const label = 'label' in option ? option.label.toLowerCase() : option.toLowerCase()
+  const label = 'label' in option ? option.label?.toLowerCase() : option.toLowerCase()
   const isPathway = option.data.isGene === false
   return isPathway || label.includes(input) // partial match
 }

app/javascript/lib/search-utils.js

@@ -39,8 +39,11 @@ function getPathwayIdsByName() {
 
   const pathwayCache = window.Ideogram.interactionCache
 
-  // Lower-quality pathways
-  const omittedPathways = ['WP1984', 'WP615', 'WP5096']
+  // Lower-quality or buggy pathways
+  const omittedPathways = [
+    'WP1984', 'WP615', 'WP5096',
+    'WP5520', 'WP5522', 'WP5523'
+  ]
 
   const pathwayIdsByName = {}
   const pathwayEntries = Object.entries(pathwayCache)

test/js/explore/study-gene-keyword.test.js

@@ -3,7 +3,9 @@ import React from 'react'
 import { render, waitFor, screen, fireEvent } from '@testing-library/react'
 import '@testing-library/jest-dom/extend-expect'
 
-import StudyGeneField, { getIsInvalidQuery, getIsEligibleForPathwayExplore } from 'components/explore/StudyGeneField'
+import StudyGeneField, {
+  getIsInvalidQuery, getIsEligibleForPathwayExplore, finalFilterOptions
+} from 'components/explore/StudyGeneField'
 import * as UserProvider from '~/providers/UserProvider'
 import { logStudyGeneSearch } from '~/lib/search-metrics'
 import * as MetricsApi from '~/lib/metrics-api'
@@ -152,5 +154,22 @@ describe('Search query display text', () => {
     )
 
   })
+
+  it('handles unexpected pathway data structures', () => {
+    // This tests pathway autocomplete handling for edge-case issues in
+    // upstreams WikiPathway data, which can occur upon upgrading Ideogram.js library
+    // to a new version that updates interactions cache data.  The resulting bug
+    // breaks the Explore page when the search box autocompletes an affected gene
+    // (e.g. TCF4) -- a low incidence, high severity bug.
+
+    const rawInput = 'TCF4'
+    const option = {
+      label: undefined,
+      value: 'WP5523',
+      data: { value: 'WP5523', isGene: false }
+    }
+    const isPathway = finalFilterOptions(option, rawInput)
+    expect(isPathway).toBe(true)
+  })
 })