@apollo-annotation/jbrowse-plugin-apollo 0.1.19 → 0.1.20

package/package.json

@@ -1,18 +1,18 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.1.19",
+  "version": "0.1.20",
   "description": "Apollo plugin for JBrowse 2",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
     "directory": "packages/jbrowse-plugin-apollo"
   },
-  "author": "JBrowse Team",
   "license": "Apache-2.0",
-  "keywords": [
-    "jbrowse",
-    "jbrowse2"
-  ],
+  "author": "JBrowse Team",
   "main": "dist/index.js",
   "module": "dist/index.esm.js",
   "typings": "dist/index.d.ts",
@@ -20,13 +20,6 @@
     "dist",
     "src"
   ],
-  "config": {
-    "jbrowse": {
-      "plugin": {
-        "name": "Apollo"
-      }
-    }
-  },
   "scripts": {
     "setup": "rimraf .jbrowse && jbrowse create .jbrowse",
     "clean": "rimraf dist",
@@ -47,13 +40,17 @@
     "prepack": "yarn build",
     "postversion": "git push --follow-tags"
   },
-  "jbrowse-plugin": {
-    "name": "Apollo"
+  "config": {
+    "jbrowse": {
+      "plugin": {
+        "name": "Apollo"
+      }
+    }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.1.19",
-    "@apollo-annotation/mst": "^0.1.19",
-    "@apollo-annotation/shared": "^0.1.19",
+    "@apollo-annotation/common": "^0.1.20",
+    "@apollo-annotation/mst": "^0.1.20",
+    "@apollo-annotation/shared": "^0.1.20",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",
@@ -74,18 +71,6 @@
     "socket.io-client": "^4.5.4",
     "tslib": "^2.3.1"
   },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.13.1",
-    "@mui/material": "^5.11.14",
-    "mobx": "^6.6.1",
-    "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.1.7",
-    "prop-types": "^15.8.1",
-    "react": "^18.2.0",
-    "react-dom": "^18.2.0",
-    "rxjs": "^7.4.0",
-    "tss-react": "^4.6.1"
-  },
   "devDependencies": {
     "@jbrowse/cli": "^2.6.2",
     "@jbrowse/core": "^2.13.1",
@@ -97,7 +82,7 @@
     "@types/file-saver": "^2",
     "@types/node": "^18.14.2",
     "@types/prop-types": "^15",
-    "@types/react": "^17.0.34",
+    "@types/react": "^18.3.4",
     "@types/react-dom": "^18",
     "cypress": "12.17.3",
     "cypress-mongodb": "^6.2.0",
@@ -123,7 +108,22 @@
     "tss-react": "^4.6.1",
     "typescript": "^5.5.3"
   },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.13.1",
+    "@mui/material": "^5.11.14",
+    "mobx": "^6.6.1",
+    "mobx-react": "^7.2.1",
+    "mobx-state-tree": "^5.1.7",
+    "prop-types": "^15.8.1",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
+    "rxjs": "^7.4.0",
+    "tss-react": "^4.6.1"
+  },
   "publishConfig": {
     "access": "public"
+  },
+  "jbrowse-plugin": {
+    "name": "Apollo"
   }
 }

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-/* eslint-disable import/no-named-as-default-member */
 // jsonpath triggers this rule for some reason. import { query } from 'jsonpath' does not work
 
 import { checkAbortSignal } from '@jbrowse/core/util'

package/src/components/AddAssembly.tsx

@@ -225,7 +225,7 @@ export function AddAssembly({
       const fileUploadChangeBase = {
         assembly: new ObjectID().toHexString(),
         assemblyName,
-        fileId,
+        fileIds: { fa: fileId },
       }
       change =
         fileType === FileType.GFF3 && importFeatures

package/src/components/ManageUsers.tsx

@@ -124,7 +124,26 @@ export function ManageUsers({
       headerName: 'Role',
       width: 140,
       type: 'singleSelect',
-      valueOptions: ['', 'readOnly', 'user', 'admin'],
+      valueOptions: ['readOnly', 'user', 'admin', 'none'],
+      getOptionLabel(value) {
+        switch (value) {
+          case 'readOnly': {
+            return 'Read-only'
+          }
+          case 'user': {
+            return 'User'
+          }
+          case 'admin': {
+            return 'Admin'
+          }
+          case 'none': {
+            return 'None'
+          }
+          default: {
+            return 'unknown'
+          }
+        }
+      },
       editable: true,
     },
     {

package/src/session/session.ts

@@ -323,7 +323,7 @@ export function extendSession(
                     if (Object.keys(filteredConfig).length === 0) {
                       filteredConfig = undefined
                     }
-                    let trackConfigSnapshot = getSnapshot(conf) as {
+                    const trackConfigSnapshot = getSnapshot(conf) as {
                       trackId: string
                       type: string
                     }
@@ -331,7 +331,7 @@ export function extendSession(
                       0,
                       trackId.length - sessionTrackIdentifier.length,
                     )
-                    trackConfigSnapshot = {
+                    const newTrackConfigSnapshot = {
                       ...trackConfigSnapshot,
                       trackId: newTrackId,
                     }
@@ -346,7 +346,7 @@ export function extendSession(
                           ...filteredConfig,
                           tracks: filteredConfig?.tracks && [
                             ...filteredConfig.tracks,
-                            trackConfigSnapshot,
+                            newTrackConfigSnapshot,
                           ],
                         },
                       })
@@ -357,6 +357,10 @@ export function extendSession(
                       const { notify } = self as unknown as AbstractSessionModel
                       notify('Track added', 'success')
                     }
+                    // @ts-expect-error This method is missing in the JB types
+                    self.deleteTrackConf(conf)
+                    // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                    jbrowse.addTrackConf(newTrackConfigSnapshot)
                   },
                   icon: SaveIcon,
                 },
@@ -396,6 +400,10 @@ export function extendSession(
                       const { notify } = self as unknown as AbstractSessionModel
                       notify('Track removed', 'success')
                     }
+                    // @ts-expect-error This method is missing in the JB types
+                    self.deleteTrackConf(conf)
+                    // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+                    jbrowse.deleteTrackConf(conf)
                   },
                   icon: SaveIcon,
                 },