Refactor Linear Apollo Display glyph drawing #725

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garrettjstevens wants to merge 16 commits into main from refactor_glyph_draw_lad

packages/apollo-collaboration-server/.development.env

-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,7 @@ MICROSOFT_CLIENT_ID=fabdd045-163c-4712-9d40-dbbb043b3090 @@
     MICROSOFT_CLIENT_SECRET=~Gr8Q~h6RTU7SMC-fjNxXy_~nabTD-ME_rFyLa.M
     DESCRIPTION=A server for Apollo development purposes
     PLUGIN_LOCATION=http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js
-    FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-v3.1.json
+    FEATURE_TYPE_ONTOLOGY_LOCATION=http://localhost:9000/test_data/so-2024-11-18.json
     LOG_LEVELS=error,warn,log,debug
     ALLOW_ROOT_USER=true
     ROOT_USER_PASSWORD=password
@@ Expand Down @@

packages/apollo-mst/src/AnnotationFeatureModel.ts

-Original file line number
+Diff line change
@@ Expand Up / @@ -291,40 +291,6 @@ export const AnnotationFeatureModel = types @@
             transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'),
           )
         },
-        get looksLikeGene(): boolean {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          const session = getSession(self) as any
-          const { apolloDataStore } = session
-          const { featureTypeOntology } = apolloDataStore.ontologyManager
-          if (!featureTypeOntology) {
-            return false
-          }
-          const children = self.children as Children
-          if (!children?.size) {
-            return false
-          }
-          const isGene =
-            featureTypeOntology.isTypeOf(self.type, 'gene') ||
-            featureTypeOntology.isTypeOf(self.type, 'pseudogene')
-          if (!isGene) {
-            return false
-          }
-          for (const [, child] of children) {
-            if (
-              featureTypeOntology.isTypeOf(child.type, 'transcript') ||
-              featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
-            ) {
-              const { children: grandChildren } = child
-              if (!grandChildren?.size) {
-                return false
-              }
-              return [...grandChildren.values()].some((grandchild) =>
-                featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
-              )
-            }
-          }
-          return false
-        },
       }))
       .actions((self) => ({
         setAttributes(attributes: Map<string, string[]>) {
@@ Expand Down @@

...ypress/cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-gene-model.png

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...ge-diff-screenshots/baseline/renderTrack.cy.ts-linear-apollo-display-canvas.png

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...reenshots/baseline/renderTrack.cy.ts-linear-apollo-six-frame-display-canvas.png

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.../cypress-image-diff-screenshots/baseline/renderTrack.cy.ts-seq-track-canvas.png

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...s-image-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-headless.png

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...mage-diff-screenshots/baseline/visualGeneModel.cy.ts-gene-model-interactive.png

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packages/jbrowse-plugin-apollo/cypress/data/so.json.gz

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

-Original file line number
+Diff line change
@@ -0,0 +1,75 @@
+    /* eslint-disable cypress/no-unnecessary-waiting */
+    describe('Simple tests for visuals', () => {
+      beforeEach(() => {
+        cy.loginAsGuest()
+      })
+      afterEach(() => {
+        cy.deleteAssemblies()
+      })
+      it('Shows correct gene model', () => {
+        cy.addAssemblyFromGff('so_types.gff3', 'test_data/so_types.gff3')
+        cy.selectAssemblyToView('so_types.gff3')
+        cy.get('body').then(($body) => {
+          if ($body.find('button[aria-label="Close drawer"]').length > 0) {
+            cy.get('button[aria-label="Close drawer"]').click()
+          }
+        })
+        cy.searchFeatures('TGGT1_200010', 1)
+        cy.wait(5000)
+        // This may fail locally due to differences in runtime such as installed
+        // fonts on. The snapshots used in this test are generated on GitHub Actions
+        cy.get('canvas[data-testid="overlayCanvas"]').compareSnapshot({
+          name: 'gene-model',
+          testThreshold: 0.03,
+        })
+      })
+      it('Shows different glyph types', () => {
+        cy.addAssemblyFromGff('glyph_types.gff3', 'test_data/glyph_types.gff3')
+        cy.selectAssemblyToView('glyph_types.gff3')
+        cy.contains('Open track selector').click()
+        cy.contains('Reference sequence (').click()
+        cy.contains('Annotations (').click()
+        cy.get('body').then(($body) => {
+          if ($body.find('button[aria-label="Close drawer"]').length > 0) {
+            cy.get('button[aria-label="Close drawer"]').click()
+          }
+        })
+        cy.wait(2000) // Wait for render
+        // This may fail locally due to differences in runtime such as installed
+        // fonts on. The snapshots used in this test are generated on GitHub Actions
+        cy.get('canvas[data-testid="seqTrackCanvas"]').compareSnapshot({
+          name: 'seq-track-canvas',
+          testThreshold: 0.03,
+        })
+        cy.get('[data-testid="track_menu_icon"]').last().click()
+        cy.contains('Display types').trigger('mouseover')
+        cy.contains('LinearApolloSixFrameDisplay').click()
+        cy.wait(2000) // Wait for render
+        // This may fail locally due to differences in runtime such as installed
+        // fonts on. The snapshots used in this test are generated on GitHub Actions
+        cy.get('canvas[data-testid="canvas"]').compareSnapshot({
+          name: 'linear-apollo-six-frame-display-canvas',
+          testThreshold: 0.03,
+        })
+        cy.get('[data-testid="track_menu_icon"]').last().click()
+        cy.contains('Display types').trigger('mouseover')
+        cy.contains('LinearApolloDisplay').click()
+        cy.get('button[data-testid="view_menu_icon"]', { timeout: 10_000 }).click({
+          force: true,
+          timeout: 10_000,
+        })
+        cy.contains('Show...', { timeout: 10_000 }).click()
+        cy.contains('Show all regions in assembly', { timeout: 10_000 }).click()
+        cy.wait(2000) // Wait for render
+        // This may fail locally due to differences in runtime such as installed
+        // fonts on. The snapshots used in this test are generated on GitHub Actions
+        cy.get('canvas[data-testid="canvas"]').compareSnapshot({
+          name: 'linear-apollo-display-canvas',
+          testThreshold: 0.03,
+        })
+      })
+    })

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

This file was deleted.

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

-Original file line number
+Diff line change
@@ Expand Up / @@ -76,7 +76,7 @@ Cypress.Commands.add('addOntologies', () => { @@
                   name: 'Sequence Ontology',
                   version: 'unversioned',
                   source: {
-                    uri: 'http://localhost:9000/test_data/so-v3.1.json',
+                    uri: 'http://localhost:9000/test_data/so-2024-11-18.json',
                     locationType: 'UriLocation',
                   },
                 },
@@ Expand All / @@ -86,6 +86,8 @@ Cypress.Commands.add('addOntologies', () => { @@
         },
         { collection: 'jbrowseconfigs' },
       )
+      // so.json.gz was generated from an IndexedDB dump using the script found at
+      // https://gist.github.com/loilo/ed43739361ec718129a15ae5d531095b
       cy.readFile('cypress/data/so.json.gz', null).then((soGZip: Buffer) => {
         cy.wrap<Promise<void>>(
           loadOntology(
@@ Expand Down @@

packages/jbrowse-plugin-apollo/jbrowse_config.json

-Original file line number
+Diff line change
@@ Expand Up / @@ -30,7 +30,7 @@ @@
               "name": "Sequence Ontology",
               "version": "3.1",
               "source": {
-                "uri": "test_data/so-v3.1.json",
+                "uri": "test_data/so-2024-11-18.json",
                 "locationType": "UriLocation"
               }
             }
@@ Expand Down @@

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