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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,