Store autosave sessions in IndexedDB database (#4074)

GMOD · Dec 7, 2024 · 159a621 · 159a621
1 parent 55d3c6b
commit 159a621
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Showing 101 changed files with 3,990 additions and 3,453 deletions.
diff --git a/.ignore b/.ignore
@@ -23,3 +23,4 @@ test_data/config_demo.json
 plugins/spreadsheet-view/src/SpreadsheetView/test_data/1801160099-N32519_26611_S51_56704.hard-filtered.vcf
 website/docs/faq.md
 test_data/sars-cov2/ncbi_original.gff3
+plugins/data-management/src/UCSCTrackHub/ucscAssemblies.ts
diff --git a/config/jest/console.js b/config/jest/console.js
@@ -5,6 +5,7 @@ jest.spyOn(console, 'error').mockImplementation((...args) => {
   if (
     r.includes('volvox.2bit_404') ||
     r.includes('popupState') ||
+    r.includes('indexedDB') ||
     r.includes("Can't perform a React state update on an unmounted") ||
     r.includes('Unexpected return value from a callback ref') ||
     r.includes('A suspended resource finished loading inside a test') ||

diff --git a/packages/app-core/src/Assemblies/SessionAssembliesMixin.ts b/packages/app-core/src/Assemblies/SessionAssembliesMixin.ts
@@ -36,6 +36,28 @@ export function SessionAssembliesMixin(
           return self.sessionAssemblies[length - 1]
         },
 
+        /**
+         * #action
+         */
+        addAssembly(conf: AnyConfiguration) {
+          if (self.adminMode) {
+            self.jbrowse.addAssemblyConf(conf)
+          } else {
+            this.addSessionAssembly(conf)
+          }
+        },
+
+        /**
+         * #action
+         */
+        removeAssembly(name: string) {
+          if (self.adminMode) {
+            self.jbrowse.removeAssemblyConf(name)
+          } else {
+            this.removeSessionAssembly(name)
+          }
+        },
+
         /**
          * #action
          */

diff --git a/packages/app-core/src/JBrowseConfig/index.ts b/packages/app-core/src/JBrowseConfig/index.ts
@@ -150,5 +150,10 @@ export function JBrowseConfigF({
     defaultSession: types.optional(types.frozen(), {
       name: 'New Session',
     }),
+
+    /**
+     * #slot
+     */
+    preConfiguredSessions: types.array(types.frozen()),
   })
 }
diff --git a/packages/app-core/src/RootMenu/index.ts b/packages/app-core/src/RootMenu/index.ts
@@ -1,35 +1,39 @@
 import { types } from 'mobx-state-tree'
 
+import type { Menu, MenuAction } from '../menus'
 import type { MenuItem } from '@jbrowse/core/ui/Menu'
 
-export interface Menu {
-  label: string
-  menuItems: MenuItem[]
-}
-
 /**
  * #stateModel RootAppMenuMixin
  */
 export function RootAppMenuMixin() {
-  return types.model({}).actions(s => {
-    const self = s as { menus: Menu[] }
-    return {
+  return types
+    .model({})
+    .volatile(() => ({
+      mutableMenuActions: [] as MenuAction[],
+    }))
+    .actions(self => ({
       /**
        * #action
        */
       setMenus(newMenus: Menu[]) {
-        self.menus = newMenus
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
+          { type: 'setMenus', newMenus },
+        ]
       },
       /**
        * #action
        * Add a top-level menu
        *
        * @param menuName - Name of the menu to insert.
        *
-       * @returns The new length of the top-level menus array
        */
       appendMenu(menuName: string) {
-        return self.menus.push({ label: menuName, menuItems: [] })
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
+          { type: 'appendMenu', menuName },
+        ]
       },
       /**
        * #action
@@ -41,18 +45,16 @@ export function RootAppMenuMixin() {
        * end, e.g. `insertMenu('My Menu', -1)` will insert the menu as the
        * second-to-last one.
        *
-       * @returns The new length of the top-level menus array
        */
       insertMenu(menuName: string, position: number) {
-        self.menus.splice(
-          (position < 0 ? self.menus.length : 0) + position,
-          0,
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
           {
-            label: menuName,
-            menuItems: [],
+            type: 'insertMenu',
+            menuName,
+            position,
           },
-        )
-        return self.menus.length
+        ]
       },
       /**
        * #action
@@ -61,16 +63,16 @@ export function RootAppMenuMixin() {
        * @param menuName - Name of the top-level menu to append to.
        *
        * @param menuItem - Menu item to append.
-       *
-       * @returns The new length of the menu
        */
       appendToMenu(menuName: string, menuItem: MenuItem) {
-        const menu = self.menus.find(m => m.label === menuName)
-        if (!menu) {
-          self.menus.push({ label: menuName, menuItems: [menuItem] })
-          return 1
-        }
-        return menu.menuItems.push(menuItem)
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
+          {
+            type: 'appendToMenu',
+            menuName,
+            menuItem,
+          },
+        ]
       },
       /**
        * #action
@@ -83,19 +85,14 @@ export function RootAppMenuMixin() {
        * @param position - Position to insert menu item. If negative, counts
        * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
        * the second-to-last one.
-       *
-       * @returns The new length of the menu
        */
       insertInMenu(menuName: string, menuItem: MenuItem, position: number) {
-        const menu = self.menus.find(m => m.label === menuName)
-        if (!menu) {
-          self.menus.push({ label: menuName, menuItems: [menuItem] })
-          return 1
-        }
-        const insertPosition =
-          position < 0 ? menu.menuItems.length + position : position
-        menu.menuItems.splice(insertPosition, 0, menuItem)
-        return menu.menuItems.length
+        self.mutableMenuActions.push({
+          type: 'insertInMenu',
+          menuName,
+          menuItem,
+          position,
+        })
       },
       /**
        * #action
@@ -109,28 +106,14 @@ export function RootAppMenuMixin() {
        * @returns The new length of the sub-menu
        */
       appendToSubMenu(menuPath: string[], menuItem: MenuItem) {
-        let topMenu = self.menus.find(m => m.label === menuPath[0])
-        if (!topMenu) {
-          const idx = this.appendMenu(menuPath[0]!)
-          topMenu = self.menus[idx - 1]!
-        }
-        let { menuItems: subMenu } = topMenu
-        const pathSoFar = [menuPath[0]]
-        menuPath.slice(1).forEach(menuName => {
-          pathSoFar.push(menuName)
-          let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName)
-          if (!sm) {
-            const idx = subMenu.push({ label: menuName, subMenu: [] })
-            sm = subMenu[idx - 1]!
-          }
-          if (!('subMenu' in sm)) {
-            throw new Error(
-              `"${menuName}" in path "${pathSoFar}" is not a subMenu`,
-            )
-          }
-          subMenu = sm.subMenu
-        })
-        return subMenu.push(menuItem)
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
+          {
+            type: 'appendToSubMenu',
+            menuPath,
+            menuItem,
+          },
+        ]
       },
       /**
        * #action
@@ -144,38 +127,21 @@ export function RootAppMenuMixin() {
        * @param position - Position to insert menu item. If negative, counts
        * from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as
        * the second-to-last one.
-       *
-       * @returns The new length of the sub-menu
        */
       insertInSubMenu(
         menuPath: string[],
         menuItem: MenuItem,
         position: number,
       ) {
-        let topMenu = self.menus.find(m => m.label === menuPath[0])
-        if (!topMenu) {
-          const idx = this.appendMenu(menuPath[0]!)
-          topMenu = self.menus[idx - 1]!
-        }
-        let { menuItems: subMenu } = topMenu
-        const pathSoFar = [menuPath[0]]
-        menuPath.slice(1).forEach(menuName => {
-          pathSoFar.push(menuName)
-          let sm = subMenu.find(mi => 'label' in mi && mi.label === menuName)
-          if (!sm) {
-            const idx = subMenu.push({ label: menuName, subMenu: [] })
-            sm = subMenu[idx - 1]!
-          }
-          if (!('subMenu' in sm)) {
-            throw new Error(
-              `"${menuName}" in path "${pathSoFar}" is not a subMenu`,
-            )
-          }
-          subMenu = sm.subMenu
-        })
-        subMenu.splice(position, 0, menuItem)
-        return subMenu.length
+        self.mutableMenuActions = [
+          ...self.mutableMenuActions,
+          {
+            type: 'insertInSubMenu',
+            menuPath,
+            menuItem,
+            position,
+          },
+        ]
       },
-    }
-  })
+    }))
 }
diff --git a/packages/app-core/src/index.ts b/packages/app-core/src/index.ts
@@ -5,3 +5,4 @@ export * from './JBrowseConfig'
 export * from './JBrowseModel'
 export * from './Assemblies'
 export * from './RootMenu'
+export * from './menus'