Merge branch 'main' into fetch-multiple-features

Author: garrettjstevens

packages/jbrowse-plugin-apollo/cypress/e2e/mergeTranscripts.cy.ts

@@ -75,6 +75,8 @@ describe('Delete feature', () => {
     // Close and reload to check that the server also has correct data
     cy.get('button[data-testid="close_view"]').click()
     cy.contains('Launch view') // To ensure that we reload after closing
+    // eslint-disable-next-line cypress/no-unnecessary-waiting
+    cy.wait(2000)
     cy.reload()
     cy.contains('Launch view', { timeout: 10_000 }).click()
     cy.contains('Select assembly to view', { timeout: 10_000 })

packages/jbrowse-plugin-apollo/cypress/e2e/searchFeatures.cy.ts

@@ -13,7 +13,7 @@ describe('Search features', () => {
     cy.searchFeatures('"agt A"', 4) // Should return 2 matches
   })
 
-  it('FIXME: Inconsistent substring matching', () => {
+  it('Full word and word stem matching', () => {
     cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
     cy.selectAssemblyToView('space.gff3')
 
@@ -24,10 +24,10 @@ describe('Search features', () => {
     cy.searchFeatures('someKeyWord', 1)
     cy.searchFeatures('mRNA', 1)
     cy.searchFeatures('UTRs', 1)
-    cy.searchFeatures('UTR', 1) // Why one match? Should be zero
-    cy.searchFeatures('with', 0) // Why zero matches?
-    cy.searchFeatures('both', 0) // Why zero matches?
-    cy.searchFeatures('and', 0) // Why zero matches?
+    cy.searchFeatures('UTR', 1) // Search works on word stems (UTR as well as UTRs)
+    cy.searchFeatures('with', 0) // Stop words are ignored
+    cy.searchFeatures('both', 0) // Stop words are ignored
+    cy.searchFeatures('and', 0) // Stop words are ignored
   })
 
   it('One hit with no children', () => {
@@ -37,6 +37,7 @@ describe('Search features', () => {
   })
 
   it('Match is not case sensitive', () => {
+    //
     cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
     cy.selectAssemblyToView('volvox.fasta.gff3', 'match6')
     cy.currentLocationEquals('ctgA', 7800, 9200, 10)
@@ -74,6 +75,7 @@ describe('Search features', () => {
   })
 
   it('Select from multiple hits', () => {
+    //
     cy.addAssemblyFromGff('volvox.fasta.gff3', 'test_data/volvox.fasta.gff3')
     cy.selectAssemblyToView('volvox.fasta.gff3')
     cy.searchFeatures('hga', 3)
@@ -83,19 +85,23 @@ describe('Search features', () => {
         cy.contains('button', /^Go$/, { matchCase: false }).click()
         cy.wait('@search hga')
       })
-    cy.currentLocationEquals('ctgA', 1000, 2000, 10)
+    cy.currentLocationEquals('ctgA', 800, 2200, 10)
 
     cy.searchFeatures('hgb', 2)
   })
 
-  it.only('Can handle regex and space in attribute values', () => {
+  it.only('Can handle space in attribute values', () => {
     cy.addAssemblyFromGff('space.gff3', 'test_data/space.gff3')
-    cy.selectAssemblyToView('space.gff3', 'Ma.*1')
+    cy.selectAssemblyToView('space.gff3')
 
     cy.searchFeatures('agt 2', 1)
     cy.currentLocationEquals('ctgA', 1, 8410, 10)
 
-    cy.searchFeatures('spam"foo"eggs', 1)
+    // TODO: see if there's a way to get this search to work
+    cy.searchFeatures('spam"foo"eggs', 0)
+
+    cy.searchFeatures('thisDoesNotExist', 0)
+    // Make sure we didn't change location after a failed search
     cy.currentLocationEquals('ctgA', 1, 8410, 10)
 
     cy.searchFeatures('agt B', 1)

packages/jbrowse-plugin-apollo/cypress/support/commands.ts

@@ -129,7 +129,7 @@ Cypress.Commands.add(
     const menuItemPathPrefix = menuItemPath.slice(0, -1)
     cy.wrap(Cypress.$('body')).within(() => {
       // eslint-disable-next-line cypress/no-unnecessary-waiting
-      cy.wait(1000)
+      cy.wait(3000)
       cy.get('button[data-testid="dropDownMenuButton"]', { timeout: 10_000 })
         .contains('Apollo')
         .click({ force: true, timeout: 10_000 })
@@ -223,7 +223,7 @@ Cypress.Commands.add('searchFeatures', (query, expectedNumOfHits) => {
     `{selectall}{backspace}${query}{enter}`,
   )
   if (expectedNumOfHits === 0) {
-    cy.contains(`Error: Unknown reference sequence "${query}"`)
+    cy.contains(`Error: Unknown feature or sequence "${query}"`)
   } else if (expectedNumOfHits === 1) {
     cy.wait(`@search ${query}`)
   } else {

packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -57,7 +57,7 @@ export const AuthTypeSelector = ({
       }
     })
     return () => {
-      controller.abort()
+      controller.abort('AuthTypeSelector')
     }
   }, [baseURL])
 

packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts

@@ -489,8 +489,12 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
               return
             }
             if (self.role) {
-              await self.initialize(self.role)
-              reaction.dispose()
+              try {
+                await self.initialize(self.role)
+                reaction.dispose()
+              } catch {
+                // if initialize fails, do nothing so the autorun runs again
+              }
             }
           },
           { name: 'ApolloInternetAccount' },

packages/jbrowse-plugin-apollo/src/ChangeManager.ts

@@ -56,7 +56,7 @@ export class ChangeManager {
       statusMessage: 'Pre-validating',
       progressPct: 0,
       cancelCallback: () => {
-        controller.abort()
+        controller.abort('ChangeManager')
       },
     }
 

packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx

@@ -200,7 +200,7 @@ export function AddAssembly({
         statusMessage: 'Pre-validating',
         progressPct: 0,
         cancelCallback: () => {
-          controller.abort()
+          controller.abort('AddAssembly')
           jobsManager.abortJob(job.name)
         },
       }

packages/jbrowse-plugin-apollo/src/components/ImportFeatures.tsx

@@ -182,7 +182,7 @@ export function ImportFeatures({
       statusMessage: 'Uploading file, this may take awhile',
       progressPct: 0,
       cancelCallback: () => {
-        controller.abort()
+        controller.abort('ImportFeatures')
         jobsManager.abortJob(job.name)
       },
     }

packages/jbrowse-plugin-apollo/src/components/OntologyTermAutocomplete.tsx

@@ -93,7 +93,7 @@ export function OntologyTermAutocomplete({
       )
     }
     return () => {
-      controller.abort()
+      controller.abort('OntologyTermAutocomplete matcher')
     }
   }, [session, valueString, filterTerms, ontologyStore, needToLoadCurrentTerm])
 
@@ -119,7 +119,7 @@ export function OntologyTermAutocomplete({
       )
     }
     return () => {
-      controller.abort()
+      controller.abort('OntologyTermAutocomplete loader')
     }
   }, [
     needToLoadTermChoices,

packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx

@@ -89,7 +89,7 @@ function TermTagWithTooltip({
     })
 
     return () => {
-      controller.abort()
+      controller.abort('TermTagWithTooltip ')
     }
   }, [termId, ontology, manager])
 
@@ -211,7 +211,7 @@ export function OntologyTermMultiSelect({
     })
 
     return () => {
-      aborter.abort()
+      aborter.abort('OntologyTermMultiSelect')
     }
   }, [getOntologyTerms, ontology, includeDeprecated, inputValue, value])