Lint error fixes (#420)

* fixes

* fixes

* A few type changes

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>

packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts

@@ -50,14 +50,12 @@ export function gff3ToAnnotationFeature(
     if (type !== 'CDS') {
       throw new Error('GFF3 features has multiple locations but is not a CDS')
     }
-    const mins = gff3Feature
-      .map((f) => {
-        if (f.start === null) {
-          throw new Error(`feature does not have start: ${JSON.stringify(f)}`)
-        }
-        return f.start - 1
-      })
-      .filter<number>((m): m is number => m !== null)
+    const mins = gff3Feature.map((f) => {
+      if (f.start === null) {
+        throw new Error(`feature does not have start: ${JSON.stringify(f)}`)
+      }
+      return f.start - 1
+    })
     const maxes = gff3Feature
       .map((f) => f.end)
       .filter<number>((m): m is number => m !== null)

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

@@ -1,7 +1,7 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { AnnotationFeature, ApolloRefSeqI } from '@apollo-annotation/mst'
 import { AbstractSessionModel, getSession, revcom } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
-import { IAnyStateTreeNode, getRoot } from 'mobx-state-tree'
+import { getRoot } from 'mobx-state-tree'
 import React from 'react'
 
 import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
@@ -10,6 +10,7 @@ import { ApolloRootModel } from '../types'
 import { Attributes } from './Attributes'
 import { TranscriptBasicInformation } from './TranscriptBasic'
 import { TranscriptSequence } from './TranscriptSequence'
+import { ApolloTranscriptDetailsWidget as ApolloTranscriptDetailsWidgetState } from './model'
 
 export interface CDSInfo {
   id: string
@@ -29,8 +30,7 @@ export interface ExonInfo {
 
 export const getCDSInfo = (
   feature: AnnotationFeature,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  refData: any,
+  refData: ApolloRefSeqI,
 ): CDSInfo[] => {
   const CDSresult: CDSInfo[] = []
   const traverse = (
@@ -64,8 +64,8 @@ export const getCDSInfo = (
         max: (currentFeature.max + 1) as unknown as string,
         oldMin: (currentFeature.min + 1) as unknown as string,
         oldMax: (currentFeature.max + 1) as unknown as string,
-        startSeq: startSeq ?? '',
-        endSeq: endSeq ?? '',
+        startSeq: startSeq || '',
+        endSeq: endSeq || '',
       }
       CDSresult.push(oneCDS)
     }
@@ -104,7 +104,9 @@ export const getCDSInfo = (
 }
 
 export const ApolloTranscriptDetailsWidget = observer(
-  function ApolloTranscriptDetails(props: { model: IAnyStateTreeNode }) {
+  function ApolloTranscriptDetails(props: {
+    model: ApolloTranscriptDetailsWidgetState
+  }) {
     const { model } = props
     const { assembly, feature, refName } = model
     const session = getSession(model) as unknown as AbstractSessionModel
@@ -126,12 +128,12 @@ export const ApolloTranscriptDetailsWidget = observer(
     if (!refSeq) {
       return null
     }
-    const { end, start } = feature
+    const { max, min } = feature
 
-    const sequence = refSeq.getSequence(start, end)
+    const sequence = refSeq.getSequence(min, max)
     if (!sequence) {
       void apolloSession.apolloDataStore.loadRefSeq([
-        { assemblyName: assembly, refName, start, end },
+        { assemblyName: assembly, refName, start: min, end: max },
       ])
     }
 
@@ -140,21 +142,21 @@ export const ApolloTranscriptDetailsWidget = observer(
         <TranscriptBasicInformation
           feature={feature}
           session={apolloSession}
-          assembly={currentAssembly ? currentAssembly._id : ''}
+          assembly={currentAssembly._id || ''}
           refName={refName}
         />
         <hr />
         <Attributes
           feature={feature}
           session={apolloSession}
-          assembly={currentAssembly ? currentAssembly._id : ''}
+          assembly={currentAssembly._id || ''}
           editable={editable}
         />
         <hr />
         <TranscriptSequence
           feature={feature}
           session={apolloSession}
-          assembly={currentAssembly ? currentAssembly._id : ''}
+          assembly={currentAssembly._id || ''}
           refName={refName}
         />
       </>

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

@@ -19,13 +19,19 @@ import { NumberTextField } from './NumberTextField'
  * @param featureId -
  * @returns
  */
-function getFeatureFromId(feature: any, featureId: string): any | null {
+function getFeatureFromId(
+  feature: AnnotationFeature,
+  featureId: string,
+): AnnotationFeature | null {
   if (feature._id === featureId) {
     return feature
   }
   // Check if there is also childFeatures in parent feature and it's not empty
   // Let's get featureId from recursive method
-  for (const [, childFeature] of feature.children ?? new Map()) {
+  if (!feature.children) {
+    return null
+  }
+  for (const [, childFeature] of feature.children) {
     const subFeature = getFeatureFromId(childFeature, featureId)
     if (subFeature) {
       return subFeature
@@ -106,11 +112,12 @@ export const TranscriptBasicInformation = observer(
               newStart,
               assembly,
             })
-            return changeManager.submit(change)
+            changeManager.submit(change).catch(() => {
+              notify('Error updating feature start position')
+            })
           }
         }
       }
-      return
     }
 
     function handleEndChange(
@@ -123,7 +130,7 @@ export const TranscriptBasicInformation = observer(
         notify('Feature start cannot be greater than parent end', 'error')
         return
       }
-      if (subFeature.children) {
+      if (subFeature?.children) {
         // Let's check CDS start and end values. And possibly update those too
         for (const child of subFeature.children) {
           if (
@@ -138,11 +145,12 @@ export const TranscriptBasicInformation = observer(
               newEnd,
               assembly,
             })
-            return changeManager.submit(change)
+            changeManager.submit(change).catch(() => {
+              notify('Error updating feature end position')
+            })
           }
         }
       }
-      return
     }
 
     const featureNew = feature as unknown as AnnotationFeature
@@ -188,8 +196,8 @@ export const TranscriptBasicInformation = observer(
             max: dataPoint.max as unknown as string,
             oldMin: (dataPoint.min + 1) as unknown as string,
             oldMax: dataPoint.max as unknown as string,
-            startSeq: startSeq ?? '',
-            endSeq: endSeq ?? '',
+            startSeq: startSeq || '',
+            endSeq: endSeq || '',
           }
           // CDSresult.push(oneCDS)
           // Check if there is already an object with the same start and end
@@ -206,7 +214,7 @@ export const TranscriptBasicInformation = observer(
           }
 
           // Add possible UTRs
-          const foundExon = findExonInRange(
+          const foundExon: ExonInfo | null = findExonInRange(
             exonsArray,
             dataPoint.min + 1,
             dataPoint.max,
@@ -231,9 +239,11 @@ export const TranscriptBasicInformation = observer(
                 type: 'three_prime_UTR',
                 strand: Number(feature.strand),
                 min: (dataPoint.min + 1) as unknown as string,
-                max: foundExon.min + 1,
+                max: ((foundExon.min as unknown as number) +
+                  1) as unknown as string,
                 oldMin: (dataPoint.min + 1) as unknown as string,
-                oldMax: foundExon.min + 1,
+                oldMax: ((foundExon.min as unknown as number) +
+                  1) as unknown as string,
                 startSeq: '',
                 endSeq: '',
               }
@@ -302,9 +312,10 @@ export const TranscriptBasicInformation = observer(
             id: featureNew._id,
             type: 'five_prime_UTR',
             strand: Number(featureNew.strand),
-            min: (element.min + 1) as unknown as string,
+            min: ((element.min as unknown as number) + 1) as unknown as string,
             max: element.max,
-            oldMin: (element.min + 1) as unknown as string,
+            oldMin: ((element.min as unknown as number) +
+              1) as unknown as string,
             oldMax: element.max,
             startSeq: '',
             endSeq: '',
@@ -315,10 +326,12 @@ export const TranscriptBasicInformation = observer(
             id: featureNew._id,
             type: 'three_prime_UTR',
             strand: Number(featureNew.strand),
-            min: (element.min + 1) as unknown as string,
-            max: element.max + 1,
-            oldMin: (element.min + 1) as unknown as string,
-            oldMax: element.max + 1,
+            min: ((element.min as unknown as number) + 1) as unknown as string,
+            max: ((element.max as unknown as number) + 1) as unknown as string,
+            oldMin: ((element.min as unknown as number) +
+              1) as unknown as string,
+            oldMax: ((element.max as unknown as number) +
+              1) as unknown as string,
             startSeq: '',
             endSeq: '',
           }
@@ -395,9 +408,9 @@ export const TranscriptBasicInformation = observer(
                 }}
                 variant="outlined"
                 value={item.min}
-                onChangeCommitted={(newStart: number) =>
+                onChangeCommitted={(newStart: number) => {
                   handleStartChange(newStart, item.id, Number(item.oldMin))
-                }
+                }}
               />
               <span style={{ margin: '0 10px' }}>
                 {item.strand === -1 ? '-' : item.strand === 1 ? '+' : ''}
@@ -416,9 +429,9 @@ export const TranscriptBasicInformation = observer(
                 }}
                 variant="outlined"
                 value={item.max}
-                onChangeCommitted={(newEnd: number) =>
+                onChangeCommitted={(newEnd: number) => {
                   handleEndChange(newEnd, item.id, Number(item.oldMax))
-                }
+                }}
               />
               <span style={{ marginLeft: '8px', fontWeight: 'bold' }}>
                 {item.endSeq}

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

@@ -1,4 +1,4 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { AnnotationFeature, ApolloRefSeqI } from '@apollo-annotation/mst'
 import { splitStringIntoChunks } from '@apollo-annotation/shared'
 import { revcom } from '@jbrowse/core/util'
 import {
@@ -52,11 +52,11 @@ export const TranscriptSequence = observer(function TranscriptSequence({
   session: ApolloSessionModel
 }) {
   const currentAssembly = session.apolloDataStore.assemblies.get(assembly)
-  const refData = currentAssembly?.getByRefName(refName)
+  const refData = currentAssembly?.getByRefName(refName) as ApolloRefSeqI
   const [showSequence, setShowSequence] = useState(false)
   const [selectedOption, setSelectedOption] = useState('Select')
 
-  if (!(feature && currentAssembly)) {
+  if (!currentAssembly) {
     return null
   }
   const refSeq = currentAssembly.getByRefName(refName)
@@ -95,8 +95,8 @@ export const TranscriptSequence = observer(function TranscriptSequence({
         textSegments.push({ text: `>${refName} : CDS\n`, color: 'black' })
         for (const item of transcriptItems) {
           if (item.type === 'CDS') {
-            const refSeq: string | undefined = refData?.getSequence(
-              Number(item.min + 1),
+            const refSeq: string | undefined = refData.getSequence(
+              Number((item.min as unknown as number) + 1),
               Number(item.max),
             )
             seqData += item.strand === -1 && refSeq ? revcom(refSeq) : refSeq
@@ -113,8 +113,8 @@ export const TranscriptSequence = observer(function TranscriptSequence({
             item.type === 'three_prime_UTR' ||
             item.type === 'five_prime_UTR'
           ) {
-            const refSeq: string | undefined = refData?.getSequence(
-              Number(item.min + 1),
+            const refSeq: string | undefined = refData.getSequence(
+              Number((item.min as unknown as number) + 1),
               Number(item.max),
             )
             seqData += item.strand === -1 && refSeq ? revcom(refSeq) : refSeq
@@ -142,7 +142,7 @@ export const TranscriptSequence = observer(function TranscriptSequence({
             count != transcriptItems.length
           ) {
             // Intron etc. between CDS/UTRs. No need to check this on very last item
-            const refSeq: string | undefined = refData?.getSequence(
+            const refSeq: string | undefined = refData.getSequence(
               lastEnd + 1,
               Number(item.min) - 1,
             )
@@ -154,8 +154,8 @@ export const TranscriptSequence = observer(function TranscriptSequence({
             item.type === 'three_prime_UTR' ||
             item.type === 'five_prime_UTR'
           ) {
-            const refSeq: string | undefined = refData?.getSequence(
-              Number(item.min + 1),
+            const refSeq: string | undefined = refData.getSequence(
+              Number((item.min as unknown as number) + 1),
               Number(item.max),
             )
             seqData += item.strand === -1 && refSeq ? revcom(refSeq) : refSeq
@@ -185,7 +185,7 @@ export const TranscriptSequence = observer(function TranscriptSequence({
     }
   }
 
-  async function handleChangeSeqOption(e: SelectChangeEvent) {
+  function handleChangeSeqOption(e: SelectChangeEvent) {
     const option = e.target.value
     setSelectedOption(option)
     getSequenceAsTextSegment(option)
@@ -201,7 +201,7 @@ export const TranscriptSequence = observer(function TranscriptSequence({
         .then(() => {
           // console.log('Text copied to clipboard!')
         })
-        .catch((error_) => {
+        .catch((error_: unknown) => {
           console.error('Failed to copy text to clipboard', error_)
         })
     }

packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts

@@ -72,7 +72,7 @@ export interface ApolloFeatureDetailsWidget
 export interface ApolloFeatureDetailsWidgetSnapshot
   extends SnapshotIn<typeof ApolloFeatureDetailsWidgetModel> {}
 
-export const ApolloTranscriptDetails = types
+export const ApolloTranscriptDetailsModel = types
   .model('ApolloTranscriptDetails', {
     id: ElementId,
     type: types.literal('ApolloTranscriptDetails'),
@@ -123,3 +123,12 @@ export const ApolloTranscriptDetails = types
       )
     },
   }))
+
+// eslint disables because of
+// https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
+// eslint-disable-next-line @typescript-eslint/no-empty-interface
+export interface ApolloTranscriptDetailsWidget
+  extends Instance<typeof ApolloTranscriptDetailsModel> {}
+// eslint-disable-next-line @typescript-eslint/no-empty-interface
+export interface ApolloTranscriptDetailsWidgetSnapshot
+  extends SnapshotIn<typeof ApolloTranscriptDetailsModel> {}