452 reactive sync ontology

packages/apollo-mst/src/AnnotationFeatureModel.ts

@@ -1,4 +1,4 @@
-import { intersection2 } from '@jbrowse/core/util'
+import { getSession, intersection2 } from '@jbrowse/core/util'
 import {
   IAnyModelType,
   IMSTMap,
@@ -109,7 +109,14 @@ export const AnnotationFeatureModel = types
       return false
     },
     get cdsLocations(): { min: number; max: number; phase: 0 | 1 | 2 }[][] {
-      if (self.type !== 'mRNA') {
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
+      const session = getSession(self) as any
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const { apolloDataStore } = session
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
+      const { featureTypeOntology } = apolloDataStore.ontologyManager
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+      if (!featureTypeOntology.isTypeOf(self.type, 'mRNA')) {
         throw new Error(
           'Only features of type "mRNA" or equivalent can calculate CDS locations',
         )
@@ -119,7 +126,8 @@ export const AnnotationFeatureModel = types
         throw new Error('no CDS or exons in mRNA')
       }
       const cdsChildren = [...children.values()].filter(
-        (child) => child.type === 'CDS',
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+        (child) => featureTypeOntology.isTypeOf(child.type, 'CDS'),
       )
       if (cdsChildren.length === 0) {
         throw new Error('no CDS in mRNA')
@@ -130,7 +138,8 @@ export const AnnotationFeatureModel = types
         const { max: cdsMax, min: cdsMin } = cds
         const locs: { min: number; max: number }[] = []
         for (const [, child] of children) {
-          if (child.type !== 'exon') {
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
+          if (!featureTypeOntology.isTypeOf(child.type, 'exon')) {
             continue
           }
           const [start, end] = intersection2(

packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptBasic.tsx

@@ -83,8 +83,11 @@
     const { notify } = session as unknown as AbstractSessionModel
     const currentAssembly = session.apolloDataStore.assemblies.get(assembly)
     const refData = currentAssembly?.getByRefName(refName)
-    const { changeManager } = session.apolloDataStore
-
+    const { changeManager, ontologyManager } = session.apolloDataStore
+    const { featureTypeOntology } = ontologyManager
+    if (!featureTypeOntology) {
+      throw new Error('featureTypeOntology is undefined')
+    }
     function handleStartChange(
       newStart: number,
       featureId: string,
@@ -100,10 +103,14 @@
       if (!subFeature?.children) {
         return
       }
+      if (!featureTypeOntology) {
+        throw new Error('featureTypeOntology is undefined')
+      }
       // Let's check CDS start and end values. And possibly update those too
       for (const child of subFeature.children) {
         if (
-          (child[1].type === 'CDS' || child[1].type === 'exon') &&
+          (featureTypeOntology.isTypeOf(child[1].type, 'CDS') ||
+            featureTypeOntology.isTypeOf(child[1].type, 'exon')) &&
           child[1].min === oldStart
         ) {
           const change = new LocationStartChange({
@@ -135,10 +142,14 @@
       if (!subFeature?.children) {
         return
       }
+      if (!featureTypeOntology) {
+        throw new Error('featureTypeOntology is undefined')
+      }
       // Let's check CDS start and end values. And possibly update those too
       for (const child of subFeature.children) {
         if (
-          (child[1].type === 'CDS' || child[1].type === 'exon') &&
+          (featureTypeOntology.isTypeOf(child[1].type, 'CDS') ||
+            featureTypeOntology.isTypeOf(child[1].type, 'exon')) &&
           child[1].max === oldEnd
         ) {
           const change = new LocationEndChange({
@@ -160,7 +171,7 @@
     const featureNew = feature
     let exonsArray: ExonInfo[] = []
     const traverse = (currentFeature: AnnotationFeature) => {
-      if (currentFeature.type === 'exon') {
+      if (featureTypeOntology.isTypeOf(currentFeature.type, 'exon')) {
         exonsArray.push({
           min: currentFeature.min + 1,
           max: currentFeature.max,
@@ -384,10 +395,10 @@
           {transcriptItems.map((item, index) => (
             <div key={index} style={{ display: 'flex', alignItems: 'center' }}>
               <span style={{ marginLeft: '20px', width: '50px' }}>
-                {item.type === 'three_prime_UTR'
+                {featureTypeOntology.isTypeOf(item.type, 'three_prime_UTR')
                   ? '3 UTR'
                   : // eslint-disable-next-line unicorn/no-nested-ternary
-                    item.type === 'five_prime_UTR'
+                    featureTypeOntology.isTypeOf(item.type, 'five_prime_UTR')
                     ? '5 UTR'
                     : 'CDS'}
               </span>
@@ -397,7 +408,7 @@
               <NumberTextField
                 margin="dense"
                 id={item.id}
-                disabled={item.type !== 'CDS'}
+                disabled={!featureTypeOntology.isTypeOf(item.type, 'CDS')}
                 style={{
                   width: '150px',
                   marginLeft: '8px',
@@ -419,7 +430,7 @@
               <NumberTextField
                 margin="dense"
                 id={item.id}
-                disabled={item.type !== 'CDS'}
+                disabled={!featureTypeOntology.isTypeOf(item.type, 'CDS')}
                 style={{
                   width: '150px',
                   backgroundColor:

packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/TranscriptSequence.tsx

@@ -12,6 +12,7 @@
 import React, { useState } from 'react'
 
 import { ApolloSessionModel } from '../session'
+import { OntologyRecord } from '../OntologyManager'
 
 export interface CDSInfo {
   id: string
@@ -28,6 +29,7 @@
 const getCDSInfo = (
   feature: AnnotationFeature,
   refData: ApolloRefSeqI,
+  featureTypeOntology: OntologyRecord,
 ): CDSInfo[] => {
   const CDSresult: CDSInfo[] = []
   const traverse = (
@@ -36,9 +38,9 @@
   ) => {
     if (
       isParentMRNA &&
-      (currentFeature.type === 'CDS' ||
-        currentFeature.type === 'three_prime_UTR' ||
-        currentFeature.type === 'five_prime_UTR')
+      (featureTypeOntology.isTypeOf(currentFeature.type, 'CDS') ||
+        featureTypeOntology.isTypeOf(currentFeature.type, 'three_prime_UTR') ||
+        featureTypeOntology.isTypeOf(currentFeature.type, 'five_prime_UTR'))
     ) {
       let startSeq = refData.getSequence(
         Number(currentFeature.min) - 2,
@@ -149,14 +151,22 @@
   if (!refSeq) {
     return null
   }
-  const transcriptItems = getCDSInfo(feature, refData)
+  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
+  if (!featureTypeOntology) {
+    throw new Error('featureTypeOntology is undefined')
+  }
+  const transcriptItems = getCDSInfo(feature, refData, featureTypeOntology)
   const { max, min } = feature
   let sequence = ''
   if (showSequence) {
-    getSequenceAsString(min, max)
+    getSequenceAsString(min, max, featureTypeOntology)
   }
 
-  function getSequenceAsString(start: number, end: number): string {
+  function getSequenceAsString(
+    start: number,
+    end: number,
+    featureTypeOntology: OntologyRecord,
+  ): string {
     sequence = refSeq?.getSequence(start, end) ?? ''
     if (sequence === '') {
       void session.apolloDataStore.loadRefSeq([
@@ -165,15 +175,18 @@
     } else {
       sequence = formatSequence(sequence, refName, start, end)
     }
-    getSequenceAsTextSegment(selectedOption) // For color coded sequence
+    getSequenceAsTextSegment(selectedOption, featureTypeOntology) // For color coded sequence
     return sequence
   }
 
   const handleSeqButtonClick = () => {
     setShowSequence(!showSequence)
   }
 
-  function getSequenceAsTextSegment(option: string) {
+  function getSequenceAsTextSegment(
+    option: string,
+    featureTypeOntology: OntologyRecord,
+  ) {
     let seqData = ''
     textSegments = []
     if (!refData) {
@@ -183,7 +196,7 @@
       case 'CDS': {
         textSegments.push({ text: `>${refName} : CDS\n`, color: 'black' })
         for (const item of transcriptItems) {
-          if (item.type === 'CDS') {
+          if (featureTypeOntology.isTypeOf(item.type, 'CDS')) {
             const refSeq: string = refData.getSequence(
               Number(item.min + 1),
               Number(item.max),
@@ -198,16 +211,16 @@
         textSegments.push({ text: `>${refName} : cDNA\n`, color: 'black' })
         for (const item of transcriptItems) {
           if (
-            item.type === 'CDS' ||
-            item.type === 'three_prime_UTR' ||
-            item.type === 'five_prime_UTR'
+            featureTypeOntology.isTypeOf(item.type, 'CDS') ||
+            featureTypeOntology.isTypeOf(item.type, 'three_prime_UTR') ||
+            featureTypeOntology.isTypeOf(item.type, 'five_prime_UTR')
           ) {
             const refSeq: string = refData.getSequence(
               Number(item.min + 1),
               Number(item.max),
             )
             seqData += item.strand === -1 && refSeq ? revcom(refSeq) : refSeq
-            if (item.type === 'CDS') {
+            if (featureTypeOntology.isTypeOf(item.type, 'CDS')) {
               textSegments.push({ text: seqData, color: cdsColor })
             } else {
               textSegments.push({ text: seqData, color: utrColor })
@@ -239,9 +252,9 @@
             textSegments.push({ text: seqData, color: 'black' })
           }
           if (
-            item.type === 'CDS' ||
-            item.type === 'three_prime_UTR' ||
-            item.type === 'five_prime_UTR'
+            featureTypeOntology.isTypeOf(item.type, 'CDS') ||
+            featureTypeOntology.isTypeOf(item.type, 'three_prime_UTR') ||
+            featureTypeOntology.isTypeOf(item.type, 'five_prime_UTR')
           ) {
             const refSeq: string = refData.getSequence(
               Number(item.min + 1),
@@ -274,10 +287,13 @@
     }
   }
 
-  function handleChangeSeqOption(e: SelectChangeEvent) {
+  function handleChangeSeqOption(
+    e: SelectChangeEvent,
+    featureTypeOntology: OntologyRecord,
+  ) {
     const option = e.target.value
     setSelectedOption(option)
-    getSequenceAsTextSegment(option)
+    getSequenceAsTextSegment(option, featureTypeOntology)
   }
 
   // Function to copy text to clipboard
@@ -329,7 +345,9 @@
         {showSequence && (
           <Select
             value={selectedOption}
-            onChange={handleChangeSeqOption}
+            onChange={(e: SelectChangeEvent) => {
+              handleChangeSeqOption(e, featureTypeOntology)
+            }}
             style={{ width: '150px', marginLeft: '15px', height: '25px' }}
           >
             <MenuItem value={'Select'}>Select</MenuItem>