jbrowse-plugin-msaview 2.0.3 → 2.0.5

package/src/LaunchMsaView/index.ts

@@ -1,51 +1,57 @@
 import PluginManager from '@jbrowse/core/PluginManager'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
+import { MenuItem } from '@jbrowse/core/ui'
+import { Feature, getContainingTrack, getSession } from '@jbrowse/core/util'
+import AddIcon from '@mui/icons-material/Add'
 import { IAnyModelType } from 'mobx-state-tree'
-import { getSession, getContainingTrack } from '@jbrowse/core/util'
 
 // icons
-import AddIcon from '@mui/icons-material/Add'
 
 // locals
 import LaunchMsaViewDialog from './components/LaunchMsaViewDialog'
 
+
 function isDisplay(elt: { name: string }): elt is DisplayType {
   return elt.name === 'LinearBasicDisplay'
 }
 
 function extendStateModel(stateModel: IAnyModelType) {
-  return stateModel.views(self => {
-    const superContextMenuItems = self.contextMenuItems
-    return {
-      contextMenuItems() {
-        const feature = self.contextMenuFeature
-        const track = getContainingTrack(self)
-        return [
-          ...superContextMenuItems(),
-          ...(feature
-            ? [
-                {
-                  label: 'Launch MSA view',
-                  icon: AddIcon,
-                  onClick: () => {
-                    const session = getSession(track)
-                    session.queueDialog(handleClose => [
-                      LaunchMsaViewDialog,
-                      {
-                        model: track,
-                        handleClose,
-                        feature,
-                      },
-                    ])
+  return stateModel.views(
+    (self: {
+      contextMenuItems: () => MenuItem[]
+      contextMenuFeature?: Feature
+    }) => {
+      const superContextMenuItems = self.contextMenuItems
+      return {
+        contextMenuItems() {
+          const feature = self.contextMenuFeature
+          const track = getContainingTrack(self)
+          return [
+            ...superContextMenuItems(),
+            ...(feature
+              ? [
+                  {
+                    label: 'Launch MSA view',
+                    icon: AddIcon,
+                    onClick: () => {
+                      getSession(track).queueDialog(handleClose => [
+                        LaunchMsaViewDialog,
+                        {
+                          model: track,
+                          handleClose,
+                          feature,
+                        },
+                      ])
+                    },
                   },
-                },
-              ]
-            : []),
-        ]
-      },
-    }
-  })
+                ]
+              : []),
+          ]
+        },
+      }
+    },
+  )
 }
 
 export default function LaunchMsaViewF(pluginManager: PluginManager) {

package/src/LaunchMsaView/util.ts

@@ -11,8 +11,8 @@ export function getTranscriptFeatures(feature: Feature) {
         f.get('subfeatures')?.some(f => f.get('type') === 'CDS'),
       )
 }
-export function getId(val?: Feature) {
-  return val === undefined ? '' : val.get('name') || val.get('id')
+export function getId(val?: Feature): string {
+  return val?.get('name') || val?.get('id') || ''
 }
 
 export function getTranscriptDisplayName(val?: Feature) {

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -1,9 +1,11 @@
 import React from 'react'
-import { JBrowsePluginMsaViewModel } from '../model'
+
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
 import { Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
+
+import { JBrowsePluginMsaViewModel } from '../model'
 
 // locals
 import RIDLink from './RIDLink'
@@ -48,9 +50,9 @@ const LoadingBLAST = observer(function LoadingBLAST2({
       <LoadingEllipses message="Running NCBI BLAST" variant="h5" />
       {error ? (
         <RIDError rid={rid} error={error} />
-      ) : rid ? (
+      ) : (rid ? (
         <RIDProgress rid={rid} progress={progress} />
-      ) : null}
+      ) : null)}
       <Typography>{processing || 'Initializing BLAST query'}</Typography>
     </div>
   )

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -1,4 +1,5 @@
 import React from 'react'
+
 import { observer } from 'mobx-react'
 import { MSAView } from 'react-msaview'
 

package/src/MsaViewPanel/components/RIDLink.tsx

@@ -1,5 +1,7 @@
 import React from 'react'
+
 import { Link, Typography } from '@mui/material'
+
 // locals
 import OpenInNewIcon from '../../OpenInNewIcon'
 import { BLAST_URL } from '../../utils/ncbiBlast'

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -1,10 +1,10 @@
-import { launchMSA } from '../utils/msa'
-import { queryBlast } from '../utils/ncbiBlast'
+import { JBrowsePluginMsaViewModel } from './model'
 import {
   makeId,
   strip,
 } from '../LaunchMsaView/components/NewNCBIBlastQuery/util'
-import { JBrowsePluginMsaViewModel } from './model'
+import { launchMSA } from '../utils/msa'
+import { queryBlast } from '../utils/ncbiBlast'
 
 export async function doLaunchBlast({
   self,
@@ -18,21 +18,39 @@ export async function doLaunchBlast({
     query,
     blastDatabase,
     blastProgram,
-    onProgress: arg => self.setProgress(arg),
-    onRid: rid => self.setRid(rid),
+    onProgress: arg => {
+      self.setProgress(arg)
+    },
+    onRid: rid => {
+      self.setRid(rid)
+    },
   })
 
   const sequence = [
     `>QUERY\n${query}`,
     ...hits
-      .map(h => [makeId(h.description[0]), strip(h.hsps[0].hseq)] as const)
+      .map(
+        h =>
+          [
+            makeId(
+              h.description[0] ?? {
+                accession: 'unknown',
+                id: 'unknown',
+                sciname: 'unknown',
+              },
+            ),
+            strip(h.hsps[0]?.hseq ?? ''),
+          ] as const,
+      )
       .map(([id, seq]) => `>${id}\n${seq}`),
   ].join('\n')
 
   const data = await launchMSA({
     algorithm: msaAlgorithm,
     sequence,
-    onProgress: arg => self.setProgress(arg),
+    onProgress: arg => {
+      self.setProgress(arg)
+    },
   })
   return data
 }

package/src/MsaViewPanel/genomeToMSA.ts

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
-import { checkHovered } from './util'
+
 import { JBrowsePluginMsaViewModel } from './model'
+import { checkHovered } from './util'
 
 export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
   const { hovered } = getSession(model)

package/src/MsaViewPanel/index.ts

@@ -1,4 +1,5 @@
 import { lazy } from 'react'
+
 import PluginManager from '@jbrowse/core/PluginManager'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 

package/src/MsaViewPanel/model.ts

@@ -1,15 +1,16 @@
-import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
-import { autorun } from 'mobx'
-import { MSAModelF } from 'react-msaview'
+import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 import { Feature, getSession } from '@jbrowse/core/util'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
+import { autorun } from 'mobx'
+import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
+import { MSAModelF } from 'react-msaview'
 
 // locals
 import { doLaunchBlast } from './doLaunchBlast'
 import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
-import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
+
 
 type LGV = LinearGenomeViewModel
 
@@ -199,7 +200,9 @@ export default function stateModelFactory() {
             label: 'Zoom to base level on click?',
             checked: self.zoomToBaseLevel,
             type: 'checkbox',
-            onClick: () => self.setZoomToBaseLevel(!self.zoomToBaseLevel),
+            onClick: () => {
+              self.setZoomToBaseLevel(!self.zoomToBaseLevel)
+            },
           },
         ]
       },
@@ -280,7 +283,7 @@ export default function stateModelFactory() {
             } else {
               const r =
                 assemblyManager
-                  .get(connectedView.assemblyNames[0])
+                  .get(connectedView.assemblyNames[0]!)
                   ?.getCanonicalRefName(r2.refName) ?? r2.refName
               connectedView.centerAt(r2.start, r)
             }

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -9,13 +9,13 @@ export function msaCoordToGenomeCoord({
   coord: number
 }) {
   const { transcriptToMsaMap } = model
-  if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+  if (transcriptToMsaMap === undefined) {
     return
   }
 
-  const c = mouseCol - 1
-  const k1 = model.globalCoordToRowSpecificSeqCoord('QUERY', c) || 0
-  const k2 = model.globalCoordToRowSpecificSeqCoord('QUERY', c + 1) || 0
+  const c = mouseCol
+  const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0
+  const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0
   const { refName, p2g } = transcriptToMsaMap
   const s = p2g[k1]
   const e = p2g[k2]

package/src/OpenInNewIcon.tsx

@@ -1,4 +1,5 @@
 import React from 'react'
+
 import { SvgIcon, SvgIconProps } from '@mui/material'
 
 export default function OpenInNewIcon(props: SvgIconProps) {

package/src/TextField2.tsx

@@ -1,4 +1,5 @@
 import React from 'react'
+
 import { TextField, TextFieldProps } from '@mui/material'
 
 function TextField2({ children, ...rest }: TextFieldProps) {

package/src/index.ts

@@ -7,9 +7,9 @@ import GridOn from '@mui/icons-material/GridOn'
 
 // locals
 import { version } from '../package.json'
-import MsaViewF from './MsaViewPanel'
-import LaunchMsaViewF from './LaunchMsaView'
 import AddHighlightModelF from './AddHighlightModel'
+import LaunchMsaViewF from './LaunchMsaView'
+import MsaViewF from './MsaViewPanel'
 
 export default class MsaViewPlugin extends Plugin {
   name = 'MsaViewPlugin'

package/src/utils/msa.ts

@@ -98,6 +98,7 @@ async function wait({
   algorithm: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     for (let i = 0; i < 10; i++) {
       await timeout(1000)
@@ -107,6 +108,8 @@ async function wait({
 
     if (result === 'FINISHED') {
       break
+    } else if (result.includes('FAILURE')) {
+      throw new Error(`Failed to run: jobId ${jobId}`)
     }
   }
 }

package/src/utils/ncbiBlast.ts

@@ -23,15 +23,26 @@ export async function queryBlast({
   })
   onRid(rid)
   await waitForRid({ rid, onProgress })
-  const ret = await jsonfetch(
+  const ret = (await jsonfetch(
     `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )
-  const hits = ret.BlastOutput2[0].report.results.search.hits as {
-    description: { accession: string; id: string; sciname: string }[]
-    hsps: { hseq: string }[]
-  }[]
-
-  return { rid, hits }
+  )) as {
+    BlastOutput2: {
+      report: {
+        results: {
+          search: {
+            hits: {
+              description: { accession: string; id: string; sciname: string }[]
+              hsps: { hseq: string }[]
+            }[]
+          }
+        }
+      }
+    }[]
+  }
+  return {
+    rid,
+    hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
+  }
 }
 
 async function initialQuery({
@@ -62,8 +73,8 @@ async function initialQuery({
   // the initial submission/query to the BLAST "REST API" does not return JSON
   // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
   // literally parsed from the text of the HTML that is returned
-  const rid = /^    RID = (.*$)/m.exec(res)?.[1]
-  const rtoe = /^    RTOE = (.*$)/m.exec(res)?.[1]
+  const rid = /^ {4}RID = (.*$)/m.exec(res)?.[1]
+  const rtoe = /^ {4}RTOE = (.*$)/m.exec(res)?.[1]
 
   if (!rid) {
     throw new Error('Failed to get RID from BLAST request')
@@ -78,6 +89,7 @@ async function waitForRid({
   rid: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     const iter = 20
     for (let i = 0; i < iter; i++) {