@jbrowse/app-core 3.5.0 → 3.5.1

package/dist/JBrowseConfig/RootConfiguration.d.ts

@@ -0,0 +1,102 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function RootConfiguration({ pluginManager, }: {
+    pluginManager: PluginManager;
+}): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        defaultDriver: {
+            type: string;
+            description: string;
+            defaultValue: string;
+        };
+        drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    highResolutionScaling: {
+        type: string;
+        defaultValue: number;
+    };
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    shareURL: {
+        type: string;
+        defaultValue: string;
+    };
+    disableAnalytics: {
+        type: string;
+        defaultValue: boolean;
+    };
+    hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            trackNames: {
+                type: string;
+                defaultValue: boolean;
+            };
+            categories: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            categoryNames: {
+                type: string;
+                defaultValue: never[];
+            };
+            topLevelCategories: {
+                type: string;
+                defaultValue: boolean;
+            };
+            subCategories: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    theme: {
+        type: string;
+        defaultValue: {};
+    };
+    extraThemes: {
+        type: string;
+        defaultValue: {};
+    };
+    logoPath: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/JBrowseConfig/RootConfiguration.js

@@ -0,0 +1,46 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = RootConfiguration;
+const configuration_1 = require("@jbrowse/core/configuration");
+const RpcManager_1 = __importDefault(require("@jbrowse/core/rpc/RpcManager"));
+const product_core_1 = require("@jbrowse/product-core");
+function RootConfiguration({ pluginManager, }) {
+    return (0, configuration_1.ConfigurationSchema)('Root', {
+        rpc: RpcManager_1.default.configSchema,
+        highResolutionScaling: {
+            type: 'number',
+            defaultValue: 2,
+        },
+        formatDetails: (0, product_core_1.FormatDetailsConfigSchemaFactory)(),
+        formatAbout: (0, product_core_1.FormatAboutConfigSchemaFactory)(),
+        shareURL: {
+            type: 'string',
+            defaultValue: 'https://share.jbrowse.org/api/v1/',
+        },
+        disableAnalytics: {
+            type: 'boolean',
+            defaultValue: false,
+        },
+        hierarchical: (0, product_core_1.HierarchicalConfigSchemaFactory)(),
+        theme: {
+            type: 'frozen',
+            defaultValue: {},
+        },
+        extraThemes: {
+            type: 'frozen',
+            defaultValue: {},
+        },
+        logoPath: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '',
+                locationType: 'UriLocation',
+            },
+        },
+        ...pluginManager.pluginConfigurationNamespacedSchemas(),
+        ...pluginManager.pluginConfigurationUnnamespacedSchemas(),
+    });
+}

package/dist/JBrowseConfig/index.js

@@ -4,42 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.JBrowseConfigF = JBrowseConfigF;
-const configuration_1 = require("@jbrowse/core/configuration");
-const RpcManager_1 = __importDefault(require("@jbrowse/core/rpc/RpcManager"));
-const product_core_1 = require("@jbrowse/product-core");
 const mobx_state_tree_1 = require("mobx-state-tree");
+const RootConfiguration_1 = __importDefault(require("./RootConfiguration"));
 function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
     return mobx_state_tree_1.types.model('JBrowseConfig', {
-        configuration: (0, configuration_1.ConfigurationSchema)('Root', {
-            rpc: RpcManager_1.default.configSchema,
-            highResolutionScaling: {
-                type: 'number',
-                defaultValue: 2,
-            },
-            formatDetails: (0, product_core_1.FormatDetailsConfigSchemaFactory)(),
-            formatAbout: (0, product_core_1.FormatAboutConfigSchemaFactory)(),
-            shareURL: {
-                type: 'string',
-                defaultValue: 'https://share.jbrowse.org/api/v1/',
-            },
-            disableAnalytics: {
-                type: 'boolean',
-                defaultValue: false,
-            },
-            hierarchical: (0, product_core_1.HierarchicalConfigSchemaFactory)(),
-            theme: {
-                type: 'frozen',
-                defaultValue: {},
-            },
-            extraThemes: {
-                type: 'frozen',
-                defaultValue: {},
-            },
-            logoPath: {
-                type: 'fileLocation',
-                defaultValue: { uri: '', locationType: 'UriLocation' },
-            },
-            ...pluginManager.pluginConfigurationSchemas(),
+        configuration: (0, RootConfiguration_1.default)({
+            pluginManager,
         }),
         plugins: mobx_state_tree_1.types.array(mobx_state_tree_1.types.frozen()),
         assemblies: mobx_state_tree_1.types.array(assemblyConfigSchema),
@@ -51,5 +21,6 @@ function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
             name: 'New Session',
         }),
         preConfiguredSessions: mobx_state_tree_1.types.array(mobx_state_tree_1.types.frozen()),
+        ...pluginManager.pluginConfigurationRootSchemas(),
     });
 }

package/dist/ui/App/ViewMenu.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
 const CascadingMenu_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenu"));
+const hooks_1 = require("@jbrowse/core/ui/hooks");
 const util_1 = require("@jbrowse/core/util");
 const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
 const KeyboardArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardArrowUp"));
@@ -12,12 +13,10 @@ const KeyboardDoubleArrowDown_1 = __importDefault(require("@mui/icons-material/K
 const KeyboardDoubleArrowUp_1 = __importDefault(require("@mui/icons-material/KeyboardDoubleArrowUp"));
 const Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
 const material_1 = require("@mui/material");
-const hooks_1 = require("material-ui-popup-state/hooks");
 const mobx_react_1 = require("mobx-react");
 const ViewMenu = (0, mobx_react_1.observer)(function ({ model, IconButtonProps, IconProps, }) {
     const session = (0, util_1.getSession)(model);
     const popupState = (0, hooks_1.usePopupState)({
-        popupId: 'viewMenu',
         variant: 'popover',
     });
     return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.IconButton, { ...IconButtonProps, ...(0, hooks_1.bindTrigger)(popupState), "data-testid": "view_menu_icon", children: (0, jsx_runtime_1.jsx)(Menu_1.default, { ...IconProps, fontSize: "small" }) }), (0, jsx_runtime_1.jsx)(CascadingMenu_1.default, { ...(0, hooks_1.bindPopover)(popupState), onMenuItemClick: (_event, callback) => {

package/esm/JBrowseConfig/RootConfiguration.d.ts

@@ -0,0 +1,102 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function RootConfiguration({ pluginManager, }: {
+    pluginManager: PluginManager;
+}): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpc: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        defaultDriver: {
+            type: string;
+            description: string;
+            defaultValue: string;
+        };
+        drivers: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IMapType<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> | undefined, import("mobx-state-tree").ModelSnapshotType<Record<string, any>>, ({} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<Record<string, any>>> & import("mobx-state-tree/dist/internal").NonEmptyObject) | undefined>>, [undefined]>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    highResolutionScaling: {
+        type: string;
+        defaultValue: number;
+    };
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    shareURL: {
+        type: string;
+        defaultValue: string;
+    };
+    disableAnalytics: {
+        type: string;
+        defaultValue: boolean;
+    };
+    hierarchical: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            trackNames: {
+                type: string;
+                defaultValue: boolean;
+            };
+            categories: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+        defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+            categoryNames: {
+                type: string;
+                defaultValue: never[];
+            };
+            topLevelCategories: {
+                type: string;
+                defaultValue: boolean;
+            };
+            subCategories: {
+                type: string;
+                defaultValue: boolean;
+            };
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    theme: {
+        type: string;
+        defaultValue: {};
+    };
+    extraThemes: {
+        type: string;
+        defaultValue: {};
+    };
+    logoPath: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/JBrowseConfig/RootConfiguration.js

@@ -0,0 +1,40 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, } from '@jbrowse/product-core';
+export default function RootConfiguration({ pluginManager, }) {
+    return ConfigurationSchema('Root', {
+        rpc: RpcManager.configSchema,
+        highResolutionScaling: {
+            type: 'number',
+            defaultValue: 2,
+        },
+        formatDetails: FormatDetailsConfigSchemaFactory(),
+        formatAbout: FormatAboutConfigSchemaFactory(),
+        shareURL: {
+            type: 'string',
+            defaultValue: 'https://share.jbrowse.org/api/v1/',
+        },
+        disableAnalytics: {
+            type: 'boolean',
+            defaultValue: false,
+        },
+        hierarchical: HierarchicalConfigSchemaFactory(),
+        theme: {
+            type: 'frozen',
+            defaultValue: {},
+        },
+        extraThemes: {
+            type: 'frozen',
+            defaultValue: {},
+        },
+        logoPath: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '',
+                locationType: 'UriLocation',
+            },
+        },
+        ...pluginManager.pluginConfigurationNamespacedSchemas(),
+        ...pluginManager.pluginConfigurationUnnamespacedSchemas(),
+    });
+}

package/esm/JBrowseConfig/index.js

@@ -1,39 +1,9 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, } from '@jbrowse/product-core';
 import { types } from 'mobx-state-tree';
+import RootConfiguration from './RootConfiguration';
 export function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
     return types.model('JBrowseConfig', {
-        configuration: ConfigurationSchema('Root', {
-            rpc: RpcManager.configSchema,
-            highResolutionScaling: {
-                type: 'number',
-                defaultValue: 2,
-            },
-            formatDetails: FormatDetailsConfigSchemaFactory(),
-            formatAbout: FormatAboutConfigSchemaFactory(),
-            shareURL: {
-                type: 'string',
-                defaultValue: 'https://share.jbrowse.org/api/v1/',
-            },
-            disableAnalytics: {
-                type: 'boolean',
-                defaultValue: false,
-            },
-            hierarchical: HierarchicalConfigSchemaFactory(),
-            theme: {
-                type: 'frozen',
-                defaultValue: {},
-            },
-            extraThemes: {
-                type: 'frozen',
-                defaultValue: {},
-            },
-            logoPath: {
-                type: 'fileLocation',
-                defaultValue: { uri: '', locationType: 'UriLocation' },
-            },
-            ...pluginManager.pluginConfigurationSchemas(),
+        configuration: RootConfiguration({
+            pluginManager,
         }),
         plugins: types.array(types.frozen()),
         assemblies: types.array(assemblyConfigSchema),
@@ -45,5 +15,6 @@ export function JBrowseConfigF({ pluginManager, assemblyConfigSchema, }) {
             name: 'New Session',
         }),
         preConfiguredSessions: types.array(types.frozen()),
+        ...pluginManager.pluginConfigurationRootSchemas(),
     });
 }

package/esm/ui/App/ViewMenu.js

@@ -1,5 +1,6 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import CascadingMenu from '@jbrowse/core/ui/CascadingMenu';
+import { bindPopover, bindTrigger, usePopupState } from '@jbrowse/core/ui/hooks';
 import { getSession } from '@jbrowse/core/util';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
@@ -7,12 +8,10 @@ import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrow
 import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
 import MenuIcon from '@mui/icons-material/Menu';
 import { IconButton } from '@mui/material';
-import { bindPopover, bindTrigger, usePopupState, } from 'material-ui-popup-state/hooks';
 import { observer } from 'mobx-react';
 const ViewMenu = observer(function ({ model, IconButtonProps, IconProps, }) {
     const session = getSession(model);
     const popupState = usePopupState({
-        popupId: 'viewMenu',
         variant: 'popover',
     });
     return (_jsxs(_Fragment, { children: [_jsx(IconButton, { ...IconButtonProps, ...bindTrigger(popupState), "data-testid": "view_menu_icon", children: _jsx(MenuIcon, { ...IconProps, fontSize: "small" }) }), _jsx(CascadingMenu, { ...bindPopover(popupState), onMenuItemClick: (_event, callback) => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/app-core",
-  "version": "3.5.0",
+  "version": "3.5.1",
   "description": "JBrowse 2 code shared between the 'full featured' apps e.g. jbrowse-web and jbrowse-desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/product-core": "^3.5.0",
+    "@jbrowse/product-core": "^3.5.1",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "copy-to-clipboard": "^3.3.1",
@@ -59,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
+  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
 }