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GMOD · Sep 5, 2024 · 880efb8 · 880efb8
1 parent 8ca799b
commit 880efb8
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Showing 9 changed files with 195 additions and 390 deletions.
diff --git a/packages/core/assemblyManager/loadRefNameMap.ts b/packages/core/assemblyManager/loadRefNameMap.ts
diff --git a/packages/core/assemblyManager/util.ts b/packages/core/assemblyManager/util.ts
diff --git a/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx b/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx
@@ -100,7 +100,7 @@ const SaveTrackDataDialog = observer(function ({
  visibleRegions?: Region[]
  }
  const session = getSession(model)
- if (!features || !visibleRegions) {
+ if (!features || !visibleRegions?.length || !type) {
  return
  }
  const generator = options[type] || {
@@ -110,7 +110,7 @@ const SaveTrackDataDialog = observer(function ({
  await generator.callback({
  features,
  session,
- assemblyName: visibleRegions[0].assemblyName,
+ assemblyName: visibleRegions[0]!.assemblyName,
  }),
  )
  } catch (e) {
@@ -130,7 +130,12 @@ const SaveTrackDataDialog = observer(function ({
 
  <FormControl>
  <FormLabel>File type</FormLabel>
- <RadioGroup value={type} onChange={e => setType(e.target.value)}>
+ <RadioGroup
+ value={type}
+ onChange={e => {
+ setType(e.target.value)
+ }}
+ >
  {Object.entries(options).map(([key, val]) => (
  <FormControlLabel
  key={key}
@@ -165,7 +170,10 @@ const SaveTrackDataDialog = observer(function ({
  <DialogActions>
  <Button
  onClick={() => {
- const ext = options[type].extension
+ if (!type) {
+ return
+ }
+ const ext = options[type]?.extension || 'unknown'
  const blob = new Blob([str], { type: 'text/plain;charset=utf-8' })
  saveAs(blob, `jbrowse_track_data.${ext}`)
  }}
@@ -174,7 +182,13 @@ const SaveTrackDataDialog = observer(function ({
  Download
  </Button>
 
- <Button variant="contained" type="submit" onClick={() => handleClose()}>
+ <Button
+ variant="contained"
+ type="submit"
+ onClick={() => {
+ handleClose()
+ }}
+ >
  Close
  </Button>
  </DialogActions>

diff --git a/packages/core/pluggableElementTypes/models/saveTrackFileTypes/genbank.ts b/packages/core/pluggableElementTypes/models/saveTrackFileTypes/genbank.ts
@@ -45,20 +45,20 @@ function formatTags(f: Feature, parentId?: string, parentType?: string) {
  ...f
  .tags()
  .filter(tag => !coreFields.has(tag))
- .map(tag => [tag, fmt(f.get(tag))])
+ .map(tag => [tag, fmt(f.get(tag))] as const)
  .filter(tag => !!tag[1] && tag[0] !== parentType)
  .map(tag => `${blank}/${retitle[tag[0]] || tag[0]}="${tag[1]}"`),
  ].filter(f => !!f)
 }
 
-function rs(f: Feature, min: number) {
+function relativeStart(f: Feature, min: number) {
  return f.get('start') - min + 1
 }
-function re(f: Feature, min: number) {
+function relativeEnd(f: Feature, min: number) {
  return f.get('end') - min
 }
 function loc(f: Feature, min: number) {
- return `${rs(f, min)}..${re(f, min)}`
+ return `${relativeStart(f, min)}..${relativeEnd(f, min)}`
 }
 function formatFeat(
  f: Feature,
@@ -123,6 +123,9 @@ export async function stringifyGBK({
  session: AbstractSessionModel
  features: Feature[]
 }) {
+ if (!features.length) {
+ return ''
+ }
  const today = new Date()
  const month = today.toLocaleString('en-US', { month: 'short' }).toUpperCase()
  const day = today.toLocaleString('en-US', { day: 'numeric' })
@@ -132,15 +135,15 @@ export async function stringifyGBK({
  const start = min(features.map(f => f.get('start')))
  const end = max(features.map(f => f.get('end')))
  const length = end - start
- const refName = features[0].get('refName')
+ const refName = features[0]!.get('refName') || ''
 
  const l1 = [
- `${'LOCUS'.padEnd(12)}`,
+ 'LOCUS'.padEnd(12),
  `${refName}:${start + 1}..${end}`.padEnd(20),
- ` ${`${length} bp`}`.padEnd(15),
+ ` ${length} bp`.padEnd(15),
  ` ${'DNA'.padEnd(10)}`,
- `${'linear'.padEnd(10)}`,
- `${'UNK ' + date}`,
+ 'linear'.padEnd(10),
+ `UNK ${date}`,
  ].join('')
  const l2 = 'FEATURES Location/Qualifiers'
  const seq = await fetchSequence({

diff --git a/packages/core/pluggableElementTypes/models/saveTrackFileTypes/gff3.ts b/packages/core/pluggableElementTypes/models/saveTrackFileTypes/gff3.ts
@@ -54,7 +54,7 @@ function formatFeat(f: Feature, parentId?: string, parentRef?: string) {
  f
  .tags()
  .filter(tag => !coreFields.has(tag))
- .map(tag => [tag, fmt(f.get(tag))])
+ .map(tag => [tag, fmt(f.get(tag))] as const)
  .filter(tag => !!tag[1])
  .map(tag => `${retitle[tag[0]] || tag[0]}=${tag[1]}`)
  .join(';'),

diff --git a/packages/core/rpc/methods/CoreGetRegions.ts b/packages/core/rpc/methods/CoreGetRegions.ts
@@ -11,7 +11,7 @@ export default class CoreGetRegions extends RpcMethodType {
  args: {
  sessionId: string
  signal: RemoteAbortSignal
- adapterConfig: {}
+ adapterConfig: Record<string, unknown>
  },
  rpcDriver: string,
  ) {

diff --git a/packages/core/rpc/methods/CoreSaveFeatureData.ts b/packages/core/rpc/methods/CoreSaveFeatureData.ts
@@ -42,9 +42,9 @@ export default class CoreGetFeatures extends RpcMethodType {
  args: {
  sessionId: string
  regions: Region[]
- adapterConfig: {}
+ adapterConfig: Record<string, unknown>
  signal?: RemoteAbortSignal
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
  opts?: any
  },
  rpcDriver: string,