Include sessionAssemblies in session->"get assemblies()" and session-…

…>"get assemblyNames" (#3724)
GMOD · May 23, 2023 · d4b70fb · d4b70fb
1 parent c62df4a
commit d4b70fb
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Showing 4 changed files with 616 additions and 603 deletions.
diff --git a/packages/core/ui/AssemblySelector.tsx b/packages/core/ui/AssemblySelector.tsx
@@ -18,80 +18,78 @@ const useStyles = makeStyles()({
   },
 })
 
-const AssemblySelector = observer(
-  ({
-    session,
-    onChange,
-    selected,
-    InputProps,
-    TextFieldProps,
-    localStorageKey,
-    helperText = 'Select assembly to view',
-  }: {
-    session: AbstractSessionModel
-    helperText?: string
-    onChange: (arg: string) => void
-    selected?: string
-    localStorageKey?: string
-    InputProps?: IIP
-    TextFieldProps?: TFP
-  }) => {
-    const { classes } = useStyles()
-    const { assemblyNames, assemblyManager } = session
+const AssemblySelector = observer(function ({
+  session,
+  onChange,
+  selected,
+  InputProps,
+  TextFieldProps,
+  localStorageKey,
+  helperText = 'Select assembly to view',
+}: {
+  session: AbstractSessionModel
+  helperText?: string
+  onChange: (arg: string) => void
+  selected?: string
+  localStorageKey?: string
+  InputProps?: IIP
+  TextFieldProps?: TFP
+}) {
+  const { classes } = useStyles()
+  const { assemblyNames, assemblyManager } = session
 
-    // constructs a localstorage key based on host/path/config to help
-    // remember. non-config assists usage with e.g. embedded apps
-    const config = new URLSearchParams(window.location.search).get('config')
-    const [lastSelected, setLastSelected] =
-      typeof jest === 'undefined' && localStorageKey
-        ? useLocalStorage(
-            `lastAssembly-${[
-              window.location.host + window.location.pathname,
-              config,
-              localStorageKey,
-            ].join('-')}`,
-            selected,
-          )
-        : useState(selected)
+  // constructs a localstorage key based on host/path/config to help
+  // remember. non-config assists usage with e.g. embedded apps
+  const config = new URLSearchParams(window.location.search).get('config')
+  const [lastSelected, setLastSelected] =
+    typeof jest === 'undefined' && localStorageKey
+      ? useLocalStorage(
+          `lastAssembly-${[
+            window.location.host + window.location.pathname,
+            config,
+            localStorageKey,
+          ].join('-')}`,
+          selected,
+        )
+      : useState(selected)
 
-    const selection = assemblyNames.includes(lastSelected || '')
-      ? lastSelected
-      : selected
+  const selection = assemblyNames.includes(lastSelected || '')
+    ? lastSelected
+    : selected
 
-    useEffect(() => {
-      if (selection && selection !== selected) {
-        onChange(selection)
-      }
-    }, [selection, onChange, selected])
+  useEffect(() => {
+    if (selection && selection !== selected) {
+      onChange(selection)
+    }
+  }, [selection, onChange, selected])
 
-    const error = assemblyNames.length ? '' : 'No configured assemblies'
-    return (
-      <TextField
-        select
-        label="Assembly"
-        variant="outlined"
-        helperText={error || helperText}
-        value={selection || ''}
-        inputProps={{ 'data-testid': 'assembly-selector' }}
-        onChange={event => setLastSelected(event.target.value)}
-        error={!!error}
-        InputProps={InputProps}
-        disabled={!!error}
-        className={classes.importFormEntry}
-        {...TextFieldProps}
-      >
-        {assemblyNames.map(name => {
-          const assembly = assemblyManager.get(name)
-          const displayName = assembly ? getConf(assembly, 'displayName') : ''
-          return (
-            <MenuItem key={name} value={name}>
-              {displayName || name}
-            </MenuItem>
-          )
-        })}
-      </TextField>
-    )
-  },
-)
+  const error = assemblyNames.length ? '' : 'No configured assemblies'
+  return (
+    <TextField
+      select
+      label="Assembly"
+      variant="outlined"
+      helperText={error || helperText}
+      value={selection || ''}
+      inputProps={{ 'data-testid': 'assembly-selector' }}
+      onChange={event => setLastSelected(event.target.value)}
+      error={!!error}
+      InputProps={InputProps}
+      disabled={!!error}
+      className={classes.importFormEntry}
+      {...TextFieldProps}
+    >
+      {assemblyNames.map(name => {
+        const assembly = assemblyManager.get(name)
+        const displayName = assembly ? getConf(assembly, 'displayName') : ''
+        return (
+          <MenuItem key={name} value={name}>
+            {displayName || name}
+          </MenuItem>
+        )
+      })}
+    </TextField>
+  )
+})
 
 export default AssemblySelector
diff --git a/packages/web-core/src/BaseWebSession/index.ts b/packages/web-core/src/BaseWebSession/index.ts
@@ -19,6 +19,7 @@ import {
   getSnapshot,
   types,
   SnapshotIn,
+  Instance,
 } from 'mobx-state-tree'
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
 import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
@@ -92,6 +93,15 @@ export function BaseWebSession({
       get root() {
         return getParent<any>(self)
       },
+      /**
+       * #getter
+       * list of sessionAssemblies and jbrowse config assemblies, does not
+       * include temporaryAssemblies. basically the list to be displayed in a
+       * AssemblySelector dropdown
+       */
+      get assemblies(): Instance<BaseAssemblyConfigSchema[]> {
+        return [...self.jbrowse.assemblies, ...self.sessionAssemblies]
+      },
     }))
     .actions(self => ({
       /**

diff --git a/products/jbrowse-desktop/src/sessionModel/index.ts b/products/jbrowse-desktop/src/sessionModel/index.ts
@@ -68,10 +68,8 @@ export default function sessionModelFactory({
       /**
        * #getter
        */
-      get assemblyNames() {
-        return [...self.assemblies, ...self.sessionAssemblies].map(r =>
-          readConfObject(r, 'name'),
-        )
+      get assemblies(): Instance<BaseAssemblyConfigSchema[]> {
+        return [...self.jbrowse.assemblies, ...self.sessionAssemblies]
       },
       /**
        * #getter
@@ -95,6 +93,12 @@ export default function sessionModelFactory({
       },
     }))
     .views(self => ({
+      /**
+       * #getter
+       */
+      get assemblyNames(): string[] {
+        return self.assemblies.map(a => readConfObject(a, 'name'))
+      },
       /**
        * #getter
        */