Load ontology synonyms into state tree

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -9,7 +9,7 @@ import { addDisposer, isAlive } from 'mobx-state-tree'
 
 import { ApolloSessionModel } from '../../session'
 import { baseModelFactory } from './base'
-import { getGlyph } from './getGlyph'
+import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs'
 
 export function layoutsModelFactory(
   pluginManager: PluginManager,
@@ -60,6 +60,48 @@ export function layoutsModelFactory(
           return
         })
       },
+      getGlyph(feature: AnnotationFeature) {
+        if (this.looksLikeGene(feature)) {
+          return geneGlyph
+        }
+        if (feature.children?.size) {
+          return genericChildGlyph
+        }
+        return boxGlyph
+      },
+      looksLikeGene(feature: AnnotationFeature): boolean {
+        const { featureTypeOntology } =
+          self.session.apolloDataStore.ontologyManager
+        if (!featureTypeOntology) {
+          return false
+        }
+        const { children } = feature
+        if (!children?.size) {
+          return false
+        }
+        const isGene = featureTypeOntology.isTypeOf(feature.type, 'gene')
+        if (!isGene) {
+          return false
+        }
+        for (const [, child] of children) {
+          if (featureTypeOntology.isTypeOf(child.type, 'mRNA')) {
+            const { children: grandChildren } = child
+            if (!grandChildren?.size) {
+              return false
+            }
+            const hasCDS = [...grandChildren.values()].some((grandchild) =>
+              featureTypeOntology.isTypeOf(grandchild.type, 'CDS'),
+            )
+            const hasExon = [...grandChildren.values()].some((grandchild) =>
+              featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
+            )
+            if (hasCDS && hasExon) {
+              return true
+            }
+          }
+        }
+        return false
+      },
     }))
     .actions((self) => ({
       addSeenFeature(feature: AnnotationFeature) {
@@ -94,10 +136,9 @@ export function layoutsModelFactory(
             ) {
               continue
             }
-            const rowCount = getGlyph(feature).getRowCount(
-              feature,
-              self.lgv.bpPerPx,
-            )
+            const rowCount = self
+              .getGlyph(feature)
+              .getRowCount(feature, self.lgv.bpPerPx)
             let startingRow = 0
             let placed = false
             while (!placed) {
@@ -174,10 +215,9 @@ export function layoutsModelFactory(
                 }
               }
               if (layoutFeature.hasDescendant(feature._id)) {
-                const row = getGlyph(layoutFeature).getRowForFeature(
-                  layoutFeature,
-                  feature,
-                )
+                const row = self
+                  .getGlyph(layoutFeature)
+                  .getRowForFeature(layoutFeature, feature)
                 if (row !== undefined) {
                   return {
                     layoutIndex: idx,

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -15,7 +15,6 @@ import type { CSSProperties } from 'react'
 import { Coord } from '../components'
 import { Glyph } from '../glyphs/Glyph'
 import { CanvasMouseEvent } from '../types'
-import { getGlyph } from './getGlyph'
 import { renderingModelFactory } from './rendering'
 import { Frame, getFrame } from '@jbrowse/core/util'
 
@@ -147,7 +146,7 @@ export function mouseEventsModelIntermediateFactory(
           return mousePosition
         }
         const [featureRow, topLevelFeature] = foundFeature
-        const glyph = getGlyph(topLevelFeature)
+        const glyph = self.getGlyph(topLevelFeature)
         const feature = glyph.getFeatureFromLayout(
           topLevelFeature,
           bp,
@@ -323,7 +322,7 @@ export function mouseEventsModelFactory(
         return []
       }
       const { topLevelFeature } = apolloHover
-      const glyph = getGlyph(topLevelFeature)
+      const glyph = self.getGlyph(topLevelFeature)
       return glyph.getContextMenuItems(self)
     },
   }))
@@ -483,7 +482,9 @@ export function mouseEventsModelFactory(
               if (apolloDragging) {
                 // NOTE: the glyph where the drag started is responsible for drawing the preview.
                 // it can call methods in other glyphs to help with this though.
-                const glyph = getGlyph(apolloDragging.feature.topLevelFeature)
+                const glyph = self.getGlyph(
+                  apolloDragging.feature.topLevelFeature,
+                )
                 glyph.drawDragPreview(self, ctx)
               }
             },

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -7,7 +7,6 @@ import { autorun } from 'mobx'
 import { Instance, addDisposer } from 'mobx-state-tree'
 
 import { ApolloSessionModel } from '../../session'
-import { getGlyph } from './getGlyph'
 import { layoutsModelFactory } from './layouts'
 
 export function renderingModelIntermediateFactory(
@@ -428,7 +427,7 @@ export function renderingModelFactory(
                   ) {
                     continue
                   }
-                  getGlyph(feature).draw(ctx, feature, row, self, idx)
+                  self.getGlyph(feature).draw(ctx, feature, row, self, idx)
                 }
               }
             }

packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts

@@ -5,7 +5,13 @@ import {
   UriLocation,
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
-import { Instance, addDisposer, getSnapshot, types } from 'mobx-state-tree'
+import {
+  Instance,
+  addDisposer,
+  flow,
+  getSnapshot,
+  types,
+} from 'mobx-state-tree'
 
 import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
@@ -19,6 +25,7 @@ export const OntologyRecordType = types
     version: 'unversioned',
     source: types.union(LocalPathLocation, UriLocation, BlobLocation),
     options: types.frozen<OntologyStoreOptions>(),
+    equivalentTypes: types.map(types.array(types.string)),
   })
   .volatile((_self) => ({
     dataStore: undefined as undefined | OntologyStore,
@@ -44,6 +51,43 @@ export const OntologyRecordType = types
         }),
       )
     },
+    setEquivalentTypes(type: string, equivalentTypes: string[]) {
+      self.equivalentTypes.set(type, equivalentTypes)
+    },
+  }))
+  .actions((self) => ({
+    loadEquivalentTypes: flow(function* loadEquivalentTypes(type: string) {
+      if (!self.dataStore) {
+        return
+      }
+      const terms = (yield self.dataStore.getTermsWithLabelOrSynonym(
+        type,
+      )) as unknown as OntologyTerm[]
+      const equivalents: string[] = terms
+        .map((term) => term.lbl)
+        .filter((term) => term != undefined)
+      console.log('loading', type, equivalents)
+      self.setEquivalentTypes(type, equivalents)
+    }),
+  }))
+  .views((self) => ({
+    isTypeOf(queryType: string, typeOf: string): boolean {
+      if (queryType === typeOf) {
+        return true
+      }
+      if (!self.dataStore) {
+        return false
+      }
+      const equivalents = self.equivalentTypes.get(typeOf)
+      if (!equivalents) {
+        void self.loadEquivalentTypes(typeOf)
+        return false
+      }
+      if (equivalents.includes(queryType)) {
+        return true
+      }
+      return false
+    },
   }))
 
 export const OntologyManagerType = types

packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx

@@ -21,7 +21,6 @@ import { FeatureAttributes } from './FeatureAttributes'
 import { featureContextMenuItems } from './featureContextMenuItems'
 import type { ContextMenuState } from './HybridGrid'
 import { NumberCell } from './NumberCell'
-import { getGlyph } from '../../LinearApolloDisplay/stateModel/getGlyph'
 
 const useStyles = makeStyles()((theme) => ({
   typeContent: {
@@ -134,7 +133,7 @@ export const Feature = observer(function Feature({
           displayState.setApolloHover({
             feature,
             topLevelFeature: getTopLevelFeature(feature),
-            glyph: getGlyph(getTopLevelFeature(feature)),
+            glyph: displayState.getGlyph(getTopLevelFeature(feature)),
           })
         }}
         className={