Load ontology configuration

Cypress tests updated so that they start with a configuration record already in the database. This should resolve issue #421
GMOD · Aug 14, 2024 · 3a70b30 · 3a70b30
1 parent 6fbe4ac
commit 3a70b30
Show file tree

Hide file tree

Showing 4 changed files with 69 additions and 33 deletions.
diff --git a/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts b/packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts
@@ -1,5 +1,6 @@
 describe('Different ways of editing features', () => {
   beforeEach(() => {
+    cy.addOntologies()
     cy.deleteAssemblies()
     cy.loginAsGuest()
   })
@@ -61,7 +62,7 @@ describe('Different ways of editing features', () => {
     })
   })
 
-  it.skip('Can add gene ontology attribute', () => {
+  it('Can add gene ontology attribute', () => {
     cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
     cy.selectAssemblyToView('onegene.fasta.gff3')
     cy.searchFeatures('gx1', 1)
@@ -142,7 +143,7 @@ describe('Different ways of editing features', () => {
     cy.contains('td', '=CDS1').should('not.exist')
   })
 
-  it.skip('Suggest only valid SO terms from dropdown', () => {
+  it('Suggest only valid SO terms from dropdown', () => {
     cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
     cy.selectAssemblyToView('onegene.fasta.gff3')
     cy.searchFeatures('gx1', 1)
@@ -160,7 +161,7 @@ describe('Different ways of editing features', () => {
     )
   })
 
-  it.skip('Can add child feature via table editor', () => {
+  it('Can add child feature via table editor', () => {
     cy.addAssemblyFromGff('onegene.fasta.gff3', 'test_data/onegene.fasta.gff3')
     cy.selectAssemblyToView('onegene.fasta.gff3')
     cy.searchFeatures('gx1', 1)

diff --git a/packages/jbrowse-plugin-apollo/cypress/support/commands.ts b/packages/jbrowse-plugin-apollo/cypress/support/commands.ts
@@ -16,6 +16,34 @@ Cypress.Commands.add('deleteAssemblies', () => {
   }
 })
 
+Cypress.Commands.add('addOntologies', () => {
+  cy.deleteMany({}, {collection: 'jbrowseconfigs'})
+  cy.insertOne({
+    'configuration': {
+      'ApolloPlugin': {
+        'ontologies': [
+          {
+            'name': 'Gene Ontology',
+            'version': 'full',
+            'source': {
+              'uri': 'https://release.geneontology.org/2023-06-11/ontology/go.json',
+              'locationType': 'UriLocation'
+            }
+          },
+          {
+            'name': 'Sequence Ontology',
+            'version': '3.1',
+            'source': {
+              'uri': 'http://localhost:9000/test_data/so-v3.1.json',
+              'locationType': 'UriLocation'
+            }
+          }
+        ]
+      }
+    }
+  }, {collection: 'jbrowseconfigs'})
+})
+
 Cypress.Commands.add('addAssemblyFromGff', (assemblyName, fin) => {
   cy.get('button[data-testid="dropDownMenuButton"]', { timeout: 10_000 })
     .contains('Apollo')

diff --git a/packages/jbrowse-plugin-apollo/cypress/support/index.d.ts b/packages/jbrowse-plugin-apollo/cypress/support/index.d.ts
@@ -2,6 +2,7 @@
 
 declare namespace Cypress {
   interface Chainable {
+    addOntologies(): Chainable<void> 
     loginAsGuest(): Chainable<void>
     deleteAssemblies(): Chainable<void>
     addAssemblyFromGff(assemblyName: string, fin: string): Chainable<void>

diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -18,6 +18,7 @@ import { Region, getSession, isElectron } from '@jbrowse/core/util'
 import { LocalPathLocation, UriLocation } from '@jbrowse/core/util/types/mst'
 import {
   Instance,
+  addDisposer,
   flow,
   getParentOfType,
   getRoot,
@@ -39,6 +40,7 @@ import {
   TextIndexFieldDefinition,
 } from '../OntologyManager'
 import { ApolloRootModel } from '../types'
+import { autorun } from 'mobx'
 
 export function clientDataStoreFactory(
   AnnotationFeatureExtended: typeof AnnotationFeature,
@@ -130,36 +132,40 @@ export function clientDataStoreFactory(
     }))
     .actions((self) => ({
       afterCreate() {
-        // Merge in the ontologies from our plugin configuration.
-        // Ontologies of a given name that are already in the session
-        // take precedence over the ontologies in the configuration.
-        const { ontologyManager, pluginConfiguration } = self
-        const configuredOntologies =
-          pluginConfiguration.ontologies as ConfigurationModel<
-            typeof OntologyRecordConfiguration
-          >[]
-
-        for (const ont of configuredOntologies || []) {
-          const [name, version, source, indexFields] = [
-            readConfObject(ont, 'name') as string,
-            readConfObject(ont, 'version') as string,
-            readConfObject(ont, 'source') as
-              | Instance<typeof LocalPathLocation>
-              | Instance<typeof UriLocation>,
-            readConfObject(
-              ont,
-              'textIndexFields',
-            ) as TextIndexFieldDefinition[],
-          ]
-          if (!ontologyManager.findOntology(name)) {
-            ontologyManager.addOntology(name, version, source, {
-              textIndexing: { indexFields },
-            })
-          }
-        }
-
-        // TODO: add in any configured ontology prefixes that we don't already
-        // have in the session (or hardcoded in the model)
+        addDisposer(
+          self,
+          autorun((reaction) => {
+            // Merge in the ontologies from our plugin configuration.
+            // Ontologies of a given name that are already in the session
+            // take precedence over the ontologies in the configuration.
+            const { ontologyManager, pluginConfiguration } = self
+            const configuredOntologies =
+              pluginConfiguration.ontologies as ConfigurationModel<
+                typeof OntologyRecordConfiguration
+              >[]
+            for (const ont of configuredOntologies || []) {
+              const [name, version, source, indexFields] = [
+                readConfObject(ont, 'name') as string,
+                readConfObject(ont, 'version') as string,
+                readConfObject(ont, 'source') as
+                  | Instance<typeof LocalPathLocation>
+                  | Instance<typeof UriLocation>,
+                readConfObject(
+                  ont,
+                  'textIndexFields',
+                ) as TextIndexFieldDefinition[],
+              ]
+              if (!ontologyManager.findOntology(name)) {
+                ontologyManager.addOntology(name, version, source, {
+                  textIndexing: { indexFields },
+                })
+              }
+            }
+            // TODO: add in any configured ontology prefixes that we don't already
+            // have in the session (or hardcoded in the model)
+            reaction.dispose()
+          }),
+        )
       },
     }))
     .views((self) => ({