Allow searching by gene name using linear synteny view

GMOD · Nov 29, 2023 · e2f2fbd · e2f2fbd
1 parent 0b51595
commit e2f2fbd
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Showing 4 changed files with 59 additions and 37 deletions.
diff --git a/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts b/plugins/linear-comparative-view/src/LaunchLinearSyntenyView.ts
@@ -1,8 +1,9 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel } from '@jbrowse/core/util'
-import { LinearSyntenyViewModel } from './LinearSyntenyView/model'
 import { when } from 'mobx'
 
+// locals
+import { LinearSyntenyViewModel } from './LinearSyntenyView/model'
 type LSV = LinearSyntenyViewModel
 
 export default function LaunchLinearSyntenyView(pluginManager: PluginManager) {
@@ -48,8 +49,12 @@ export default function LaunchLinearSyntenyView(pluginManager: PluginManager) {
         await Promise.all(
           views.map(async (data, idx) => {
             const view = model.views[idx]
-            const { loc, tracks = [] } = data
-            await view.navToLocString(loc)
+            const { assembly, loc, tracks = [] } = data
+            const asm = await assemblyManager.waitForAssembly(assembly)
+            if (!asm) {
+              throw new Error(`Assembly ${data.assembly} failed to load`)
+            }
+            await view.navToSearch({ input: loc, assembly: asm })
             tracks.forEach(track => tryTrack(view, track, idsNotFound))
           }),
         )

diff --git a/plugins/linear-genome-view/src/LinearGenomeView/model.ts b/plugins/linear-genome-view/src/LinearGenomeView/model.ts
@@ -54,6 +54,8 @@ import MenuOpenIcon from '@mui/icons-material/MenuOpen'
 import MiniControls from './components/MiniControls'
 import Header from './components/Header'
 import { generateLocations, parseLocStrings } from './util'
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { handleSelectedRegion } from '../searchUtils'
 // lazies
 const ReturnToImportFormDialog = lazy(
   () => import('@jbrowse/core/ui/ReturnToImportFormDialog'),
@@ -1315,6 +1317,26 @@ export function stateModelFactory(pluginManager: PluginManager) {
         )
       },
 
+      /**
+       * #action
+       * Performs a text index search, and navigates to it immediately if a
+       * single result is returned. Will pop up a search dialog if multiple
+       * results are returned
+       */
+      async navToSearch({
+        input,
+        assembly,
+      }: {
+        input: string
+        assembly: Assembly
+      }) {
+        await handleSelectedRegion({
+          input,
+          assembly,
+          model: self as LinearGenomeViewModel,
+        })
+      },
+
       /**
        * #action
        * Similar to `navToLocString`, but accepts parsed location objects

diff --git a/plugins/linear-genome-view/src/searchUtils.ts b/plugins/linear-genome-view/src/searchUtils.ts
@@ -41,38 +41,33 @@ export async function handleSelectedRegion({
   model: LinearGenomeViewModel
   assembly: Assembly
 }) {
-  try {
-    const allRefs = assembly?.allRefNamesWithLowerCase || []
-    const assemblyName = assembly.name
-    if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
-      await model.navToLocString(input, assembly.name)
-    } else {
-      const searchScope = model.searchScope(assemblyName)
-      const { textSearchManager } = getSession(model)
-      const results = await fetchResults({
-        queryString: input,
-        searchType: 'exact',
-        searchScope,
-        rankSearchResults: model.rankSearchResults,
-        textSearchManager,
-        assembly,
-      })
+  const allRefs = assembly?.allRefNamesWithLowerCase || []
+  const assemblyName = assembly.name
+  if (input.split(' ').every(entry => checkRef(entry, allRefs))) {
+    await model.navToLocString(input, assembly.name)
+  } else {
+    const searchScope = model.searchScope(assemblyName)
+    const { textSearchManager } = getSession(model)
+    const results = await fetchResults({
+      queryString: input,
+      searchType: 'exact',
+      searchScope,
+      rankSearchResults: model.rankSearchResults,
+      textSearchManager,
+      assembly,
+    })
 
-      if (results.length > 1) {
-        model.setSearchResults(results, input.toLowerCase(), assemblyName)
-      } else if (results.length === 1) {
-        await navToOption({
-          option: results[0],
-          model,
-          assemblyName,
-        })
-      } else {
-        await model.navToLocString(input, assemblyName)
-      }
+    if (results.length > 1) {
+      model.setSearchResults(results, input.toLowerCase(), assemblyName)
+    } else if (results.length === 1) {
+      await navToOption({
+        option: results[0],
+        model,
+        assemblyName,
+      })
+    } else {
+      await model.navToLocString(input, assemblyName)
     }
-  } catch (e) {
-    console.error(e)
-    getSession(model).notify(`${e}`, 'warning')
   }
 }
 

diff --git a/products/jbrowse-web/src/tests/JBrowse.test.tsx b/products/jbrowse-web/src/tests/JBrowse.test.tsx
@@ -17,7 +17,7 @@ jest.mock('../makeWorkerInstance', () => () => {})
 
 setup()
 
-const delay = { timeout: 15000 }
+const delay = { timeout: 30000 }
 
 beforeEach(() => {
   doBeforeEach()
@@ -70,7 +70,7 @@ test('assembly aliases', async () => {
     await findByTestId(hts('volvox_filtered_vcf_assembly_alias'), {}, delay),
   )
   await findByTestId('box-test-vcf-604453', {}, delay)
-}, 15000)
+}, 30000)
 
 test('nclist track test with long name', async () => {
   const { view, findByTestId, findByText } = await createView()
@@ -98,7 +98,7 @@ test('test sharing', async () => {
   expect(
     ((await findByLabelText('URL', {}, delay)) as HTMLInputElement).value,
   ).toBe('http://localhost/?session=share-abc&password=123')
-}, 15000)
+}, 30000)
 
 test('looks at about this track dialog', async () => {
   const { findByTestId, findAllByText, findByText } = await createView()
@@ -108,4 +108,4 @@ test('looks at about this track dialog', async () => {
   fireEvent.click(await findByTestId('track_menu_icon', {}, delay))
   fireEvent.click(await findByText('About track'))
   await findAllByText(/SQ/, {}, delay)
-}, 15000)
+}, 30000)