Use "transcript" instead of "mRNA" for base ontology term (#516)

* Use "transcript" instead of "mRNA" for base term

* Remove console logs

Author: garrettjstevens

packages/apollo-mst/src/AnnotationFeatureModel.ts

@@ -134,21 +134,21 @@ export const AnnotationFeatureModel = types
       // 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')) {
+      if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
         throw new Error(
-          'Only features of type "mRNA" or equivalent can calculate CDS locations',
+          'Only features of type "transcript" or equivalent can calculate CDS locations',
         )
       }
       const children = self.children as Children
       if (!children) {
-        throw new Error('no CDS or exons in mRNA')
+        throw new Error('no CDS or exons in transcript')
       }
       const cdsChildren = [...children.values()].filter(
         // 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')
+        throw new Error('no CDS in transcript')
       }
       const transcriptParts: TranscriptParts[] = []
       for (const cds of cdsChildren) {

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

@@ -83,7 +83,12 @@ export const TranscriptBasicInformation = observer(
       return null
     }
 
-    const { strand, transcriptParts } = feature
+    let strand, transcriptParts
+    try {
+      ;({ strand, transcriptParts } = feature)
+    } catch {
+      return null
+    }
     const [firstLocation] = transcriptParts
 
     const locationData = firstLocation

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts

@@ -389,7 +389,14 @@ function getContextMenuItems(
       },
     },
   )
-  if (sourceFeature.type === 'mRNA' && isSessionModelWithWidgets(session)) {
+  const { featureTypeOntology } = session.apolloDataStore.ontologyManager
+  if (!featureTypeOntology) {
+    throw new Error('featureTypeOntology is undefined')
+  }
+  if (
+    featureTypeOntology.isTypeOf(sourceFeature.type, 'transcript') &&
+    isSessionModelWithWidgets(session)
+  ) {
     menuItems.push({
       label: 'Edit transcript details',
       onClick: () => {

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -110,19 +110,22 @@ function draw(
     topLevelFeatureHeight,
   )
 
-  // Draw lines on different rows for each mRNA
+  // Draw lines on different rows for each transcript
   let currentRow = 0
-  for (const [, mrna] of children) {
-    const isMrna = featureTypeOntology.isTypeOf(mrna.type, 'mRNA')
-    if (!isMrna) {
+  for (const [, transcript] of children) {
+    const isTranscript = featureTypeOntology.isTypeOf(
+      transcript.type,
+      'transcript',
+    )
+    if (!isTranscript) {
       currentRow += 1
       continue
     }
-    const { children: childrenOfmRNA, min } = mrna
-    if (!childrenOfmRNA) {
+    const { children: childrenOfTranscript, min } = transcript
+    if (!childrenOfTranscript) {
       continue
     }
-    for (const [, cds] of childrenOfmRNA) {
+    for (const [, cds] of childrenOfTranscript) {
       if (!featureTypeOntology.isTypeOf(cds.type, 'CDS')) {
         continue
       }
@@ -132,7 +135,7 @@ function draw(
           coord: min,
           regionNumber: displayedRegionIndex,
         })?.offsetPx ?? 0) - offsetPx
-      const widthPx = mrna.length / bpPerPx
+      const widthPx = transcript.length / bpPerPx
       const startPx = reversed ? minX - widthPx : minX
       const height =
         Math.round((currentRow + 1 / 2) * rowHeight) + row * rowHeight
@@ -149,20 +152,20 @@ function draw(
     theme?.palette.mode === 'dark' ? forwardFillDark : forwardFillLight
   const backwardFill =
     theme?.palette.mode === 'dark' ? backwardFillDark : backwardFillLight
-  // Draw exon and CDS for each mRNA
+  // Draw exon and CDS for each transcript
   currentRow = 0
   for (const [, child] of children) {
-    if (!featureTypeOntology.isTypeOf(child.type, 'mRNA')) {
+    if (!featureTypeOntology.isTypeOf(child.type, 'transcript')) {
       boxGlyph.draw(ctx, child, row, stateModel, displayedRegionIndex)
       currentRow += 1
       continue
     }
     for (const cdsRow of child.cdsLocations) {
-      const { _id, children: childrenOfmRNA } = child
-      if (!childrenOfmRNA) {
+      const { _id, children: childrenOfTranscript } = child
+      if (!childrenOfTranscript) {
         continue
       }
-      for (const [, exon] of childrenOfmRNA) {
+      for (const [, exon] of childrenOfTranscript) {
         if (!featureTypeOntology.isTypeOf(exon.type, 'exon')) {
           continue
         }
@@ -361,7 +364,7 @@ function getFeatureFromLayout(
     if (
       featureTypeOntology.isTypeOf(featureObj.type, 'CDS') &&
       featureObj.parent &&
-      featureTypeOntology.isTypeOf(featureObj.parent.type, 'mRNA')
+      featureTypeOntology.isTypeOf(featureObj.parent.type, 'transcript')
     ) {
       const { cdsLocations } = featureObj.parent
       for (const cdsLoc of cdsLocations) {
@@ -372,7 +375,7 @@ function getFeatureFromLayout(
         }
       }
 
-      // If mouse position is in the intron region, return the mRNA
+      // If mouse position is in the intron region, return the transcript
       return featureObj.parent
     }
     // If mouse position is in a feature that is not a CDS, return the feature
@@ -390,9 +393,9 @@ function getRowCount(
   if (!children) {
     return 1
   }
-  const isMrna = featureTypeOntology.isTypeOf(type, 'mRNA')
+  const isTranscript = featureTypeOntology.isTypeOf(type, 'transcript')
   let rowCount = 0
-  if (isMrna) {
+  if (isTranscript) {
     for (const [, child] of children) {
       const isCds = featureTypeOntology.isTypeOf(child.type, 'CDS')
       if (isCds) {
@@ -410,8 +413,8 @@ function getRowCount(
 /**
  * A list of all the subfeatures for each row for a given feature, as well as
  * the feature itself.
- * If the row contains an mRNA, the order is CDS -\> exon -\> mRNA -\> gene
- * If the row does not contain an mRNA, the order is subfeature -\> gene
+ * If the row contains a transcript, the order is CDS -\> exon -\> transcript -\> gene
+ * If the row does not contain an transcript, the order is subfeature -\> gene
  */
 function featuresForRow(
   feature: AnnotationFeature,
@@ -427,7 +430,7 @@ function featuresForRow(
   }
   const features: AnnotationFeature[][] = []
   for (const [, child] of children) {
-    if (!featureTypeOntology.isTypeOf(child.type, 'mRNA')) {
+    if (!featureTypeOntology.isTypeOf(child.type, 'transcript')) {
       features.push([child, feature])
       continue
     }
@@ -534,9 +537,9 @@ function getDraggableFeatureInfo(
     throw new Error('featureTypeOntology is undefined')
   }
   const isGene = featureTypeOntology.isTypeOf(feature.type, 'gene')
-  const isMrna = featureTypeOntology.isTypeOf(feature.type, 'mRNA')
+  const isTranscript = featureTypeOntology.isTypeOf(feature.type, 'transcript')
   const isCds = featureTypeOntology.isTypeOf(feature.type, 'CDS')
-  if (isGene || isMrna) {
+  if (isGene || isTranscript) {
     return
   }
   const { bp, refName, regionNumber, x } = mousePosition
@@ -560,12 +563,12 @@ function getDraggableFeatureInfo(
     return { feature, edge: 'max' }
   }
   if (isCds) {
-    const mRNA = feature.parent
-    if (!mRNA?.children) {
+    const transcript = feature.parent
+    if (!transcript?.children) {
       return
     }
     const exonChildren: AnnotationFeature[] = []
-    for (const child of mRNA.children.values()) {
+    for (const child of transcript.children.values()) {
       const childIsExon = featureTypeOntology.isTypeOf(child.type, 'exon')
       if (childIsExon) {
         exonChildren.push(child)

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

@@ -86,7 +86,7 @@ export function layoutsModelFactory(
           return false
         }
         for (const [, child] of children) {
-          if (featureTypeOntology.isTypeOf(child.type, 'mRNA')) {
+          if (featureTypeOntology.isTypeOf(child.type, 'transcript')) {
             const { children: grandChildren } = child
             if (!grandChildren?.size) {
               return false

packages/jbrowse-plugin-apollo/src/SixFrameFeatureDisplay/stateModel.ts

@@ -300,7 +300,9 @@ export function stateModelFactory(
             },
           )) {
             for (const [, childFeature] of feature.children ?? new Map()) {
-              if (featureTypeOntology.isTypeOf(childFeature.type, 'mRNA')) {
+              if (
+                featureTypeOntology.isTypeOf(childFeature.type, 'transcript')
+              ) {
                 for (const [, grandChildFeature] of childFeature.children ||
                   new Map()) {
                   let startingRow

packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -142,7 +142,7 @@ export function featureContextMenuItems(
       throw new Error('featureTypeOntology is undefined')
     }
     if (
-      featureTypeOntology.isTypeOf(feature.type, 'mRNA') &&
+      featureTypeOntology.isTypeOf(feature.type, 'transcript') &&
       isSessionModelWithWidgets(session)
     ) {
       menuItems.push({