@jbrowse/plugin-data-management 1.5.2 → 1.5.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.5.2",
+  "version": "1.5.6",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
+  "gitHead": "f3d36cfd90f7c5bdf86869d6698d8cb68a8e122f"
 }

package/src/AssemblyManager/AssemblyManager.tsx

@@ -1,6 +1,7 @@
 import React, { useState } from 'react'
 import { observer } from 'mobx-react'
 import { makeStyles } from '@material-ui/core/styles'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import {
   Button,
   Dialog,
@@ -52,7 +53,8 @@ const AssemblyManager = observer(
     const classes = useStyles()
     const [isFormOpen, setFormOpen] = useState(false)
     const [isAssemblyBeingEdited, setIsAssemblyBeingEdited] = useState(false)
-    const [assemblyBeingEdited, setAssemblyBeingEdited] = useState()
+    const [assemblyBeingEdited, setAssemblyBeingEdited] =
+      useState<AnyConfigurationModel>()
 
     const showAssemblyTable = !isFormOpen && !isAssemblyBeingEdited
 

package/src/AssemblyManager/AssemblyTable.tsx

@@ -42,11 +42,14 @@ const AssemblyTable = observer(
     setIsAssemblyBeingEdited,
     setAssemblyBeingEdited,
   }: {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    rootModel: any
+    rootModel: {
+      jbrowse: {
+        removeAssemblyConf: (arg: string) => void
+        assemblies: AnyConfigurationModel[]
+      }
+    }
     setIsAssemblyBeingEdited(arg: boolean): void
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    setAssemblyBeingEdited(arg: any): void
+    setAssemblyBeingEdited(arg: AnyConfigurationModel): void
   }) => {
     const classes = useStyles()
 
@@ -54,41 +57,39 @@ const AssemblyTable = observer(
       rootModel.jbrowse.removeAssemblyConf(name)
     }
 
-    const rows = rootModel.jbrowse.assemblies.map(
-      (assembly: AnyConfigurationModel) => {
-        const name = readConfObject(assembly, 'name')
-        const displayName = readConfObject(assembly, 'displayName')
-        const aliases = readConfObject(assembly, 'aliases')
-        return (
-          <TableRow key={name}>
-            <TableCell>{name}</TableCell>
-            <TableCell>{displayName}</TableCell>
-            <TableCell>{aliases ? aliases.toString() : ''}</TableCell>
-            <TableCell className={classes.buttonCell}>
-              <IconButton
-                data-testid={`${name}-edit`}
-                className={classes.button}
-                onClick={() => {
-                  setIsAssemblyBeingEdited(true)
-                  setAssemblyBeingEdited(assembly)
-                }}
-              >
-                <CreateIcon color="primary" />
-              </IconButton>
-              <IconButton
-                data-testid={`${name}-delete`}
-                className={classes.button}
-                onClick={() => {
-                  removeAssembly(name)
-                }}
-              >
-                <DeleteIcon color="error" />
-              </IconButton>
-            </TableCell>
-          </TableRow>
-        )
-      },
-    )
+    const rows = rootModel.jbrowse.assemblies.map(assembly => {
+      const name = readConfObject(assembly, 'name')
+      const displayName = readConfObject(assembly, 'displayName')
+      const aliases = readConfObject(assembly, 'aliases')
+      return (
+        <TableRow key={name}>
+          <TableCell>{name}</TableCell>
+          <TableCell>{displayName}</TableCell>
+          <TableCell>{aliases ? aliases.toString() : ''}</TableCell>
+          <TableCell className={classes.buttonCell}>
+            <IconButton
+              data-testid={`${name}-edit`}
+              className={classes.button}
+              onClick={() => {
+                setIsAssemblyBeingEdited(true)
+                setAssemblyBeingEdited(assembly)
+              }}
+            >
+              <CreateIcon color="primary" />
+            </IconButton>
+            <IconButton
+              data-testid={`${name}-delete`}
+              className={classes.button}
+              onClick={() => {
+                removeAssembly(name)
+              }}
+            >
+              <DeleteIcon color="error" />
+            </IconButton>
+          </TableCell>
+        </TableRow>
+      )
+    })
 
     return (
       <TableContainer component={Paper}>

package/src/PluginStoreWidget/components/InstalledPlugin.tsx

@@ -1,8 +1,6 @@
 import React, { useState } from 'react'
 import { observer } from 'mobx-react'
 import { getParent } from 'mobx-state-tree'
-
-import { makeStyles } from '@material-ui/core/styles'
 import {
   Button,
   Dialog,
@@ -13,6 +11,7 @@ import {
   ListItem,
   Tooltip,
   Typography,
+  makeStyles,
 } from '@material-ui/core'
 
 import CloseIcon from '@material-ui/icons/Close'
@@ -71,7 +70,9 @@ function PluginDialog({
       </DialogTitle>
       <DialogContent>
         <Typography>
-          Please confirm that you want to remove {plugin}:
+          Please confirm that you want to remove {plugin}. Note: if any
+          resources in this session still use this plugin, it may cause your
+          session to crash
         </Typography>
         <DialogActions>
           <Button
@@ -113,11 +114,11 @@ function InstalledPlugin({
   const [dialogPlugin, setDialogPlugin] = useState<string>()
 
   const session = getSession(model)
-
-  // @ts-ignore
-  const { sessionPlugins } = session
+  const { sessionPlugins } = session as unknown as {
+    sessionPlugins: BasePlugin[]
+  }
   const isSessionPlugin = sessionPlugins?.some(
-    (p: BasePlugin) => pluginManager.pluginMetadata[plugin.name].url === p.url,
+    p => pluginManager.pluginMetadata[plugin.name].url === p.url,
   )
 
   const rootModel = getParent(model, 3)
@@ -131,15 +132,11 @@ function InstalledPlugin({
           onClose={name => {
             if (name) {
               const pluginMetadata = pluginManager.pluginMetadata[plugin.name]
-              const pluginUrl =
-                pluginMetadata.url ||
-                pluginMetadata.esmUrl ||
-                pluginMetadata.umdUrl ||
-                pluginMetadata.cjsUrl
+
               if (adminMode) {
-                jbrowse.removePlugin(pluginUrl)
+                jbrowse.removePlugin(pluginMetadata)
               } else if (isSessionWithSessionPlugins(session)) {
-                session.removeSessionPlugin(pluginUrl)
+                session.removeSessionPlugin(pluginMetadata)
               }
             }
             setDialogPlugin(undefined)