@jbrowse/product-core 2.18.0 → 3.0.0

package/dist/ui/AboutDialog.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function AboutDialog({ config, handleClose, }: {
     config: AnyConfigurationModel;
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/ui/AboutDialog.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.AboutDialog = AboutDialog;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -14,6 +14,5 @@ function AboutDialog({ config, handleClose, }) {
     const trackName = (0, tracks_1.getTrackName)(config, session);
     const { pluginManager } = (0, util_1.getEnv)(session);
     const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutDialogContents_1.default, { session, config });
-    return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
-        react_1.default.createElement(AboutComponent, { config: config })));
+    return ((0, jsx_runtime_1.jsx)(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl", children: (0, jsx_runtime_1.jsx)(AboutComponent, { config: config }) }));
 }

package/dist/ui/AboutDialogContents.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AboutDialogContents: ({ config, }: {
     config: AnyConfigurationModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AboutDialogContents;

package/dist/ui/AboutDialogContents.js

@@ -1,32 +1,10 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const configuration_1 = require("@jbrowse/core/configuration");
@@ -73,26 +51,17 @@ const AboutDialogContents = (0, mobx_react_1.observer)(function ({ config, }) {
         },
     }, { session, config });
     const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
-    return (react_1.default.createElement("div", { className: classes.content },
-        react_1.default.createElement(BaseCard_1.default, { title: "Configuration" },
-            !hideUris ? (react_1.default.createElement("span", { className: classes.button },
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        setShowRefNames(true);
-                    } }, "Show ref names"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        const snap = removeAttr(structuredClone(conf), 'baseUri');
-                        (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
-                        setCopied(true);
-                        setTimeout(() => {
-                            setCopied(false);
-                        }, 1000);
-                    } }, copied ? 'Copied to clipboard!' : 'Copy config'))) : null,
-            react_1.default.createElement(Attributes_1.default, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
-        ExtraPanel ? (react_1.default.createElement(BaseCard_1.default, { title: ExtraPanel.name },
-            react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
-        react_1.default.createElement(FileInfoPanel_1.default, { config: config }),
-        showRefNames ? (react_1.default.createElement(RefNameInfoDialog_1.default, { config: config, onClose: () => {
-                setShowRefNames(false);
-            } })) : null));
+    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.content, children: [(0, jsx_runtime_1.jsxs)(BaseCard_1.default, { title: "Configuration", children: [!hideUris ? ((0, jsx_runtime_1.jsxs)("span", { className: classes.button, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                    setShowRefNames(true);
+                                }, children: "Show ref names" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                    const snap = removeAttr(structuredClone(conf), 'baseUri');
+                                    (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
+                                    setCopied(true);
+                                    setTimeout(() => {
+                                        setCopied(false);
+                                    }, 1000);
+                                }, children: copied ? 'Copied to clipboard!' : 'Copy config' })] })) : null, (0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: confPostExt.config, omit: ['displays', 'baseUri', 'refNames', 'formatAbout', 'metadata'], hideUris: hideUris })] }), confPostExt.config.metadata ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Metadata", children: (0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: confPostExt.config.metadata, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris }) })) : null, ExtraPanel ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: ExtraPanel.name, children: (0, jsx_runtime_1.jsx)(ExtraPanel.Component, { config: config }) })) : null, (0, jsx_runtime_1.jsx)(FileInfoPanel_1.default, { config: config }), showRefNames ? ((0, jsx_runtime_1.jsx)(RefNameInfoDialog_1.default, { config: config, onClose: () => {
+                    setShowRefNames(false);
+                } })) : null] }));
 });
 exports.default = AboutDialogContents;

package/dist/ui/FileInfoPanel.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export default function FileInfoPanel({ config, }: {
     config: AnyConfigurationModel;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/ui/FileInfoPanel.js

@@ -1,33 +1,11 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = FileInfoPanel;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const configuration_1 = require("@jbrowse/core/configuration");
@@ -61,5 +39,5 @@ function FileInfoPanel({ config, }) {
                 .replaceAll('>', '&gt;')}</pre>`,
         }
         : info || {};
-    return (react_1.default.createElement(BaseCard_1.default, { title: "File info" }, error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : info === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading file data" })) : (react_1.default.createElement(Attributes_1.default, { attributes: details }))));
+    return ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "File info", children: error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : info === undefined ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Loading file data" })) : ((0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: details })) }));
 }

package/dist/ui/RefNameInfoDialog.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const RefNameInfoDialog: ({ config, onClose, }: {
     config: AnyConfigurationModel;
     onClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default RefNameInfoDialog;

package/dist/ui/RefNameInfoDialog.js

@@ -1,32 +1,10 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
@@ -92,21 +70,18 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
     })
         .filter(f => !!f)
         .join('\n');
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl" },
-        react_1.default.createElement(material_1.DialogContent, { className: classes.container }, error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : refNames === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading refNames" })) : (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    (0, copy_to_clipboard_1.default)(names
-                        .flatMap(([assemblyName, refNames]) => [
-                        `--- ${assemblyName} ---`,
-                        ...refNames,
-                    ])
-                        .filter(f => !!f)
-                        .join('\n'));
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 1000);
-                } }, copied ? 'Copied to clipboard!' : 'Copy ref names'),
-            react_1.default.createElement("pre", { className: classes.refNames }, result))))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl", children: (0, jsx_runtime_1.jsx)(material_1.DialogContent, { className: classes.container, children: error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : refNames === undefined ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Loading refNames" })) : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                            (0, copy_to_clipboard_1.default)(names
+                                .flatMap(([assemblyName, refNames]) => [
+                                `--- ${assemblyName} ---`,
+                                ...refNames,
+                            ])
+                                .filter(f => !!f)
+                                .join('\n'));
+                            setCopied(true);
+                            setTimeout(() => {
+                                setCopied(false);
+                            }, 1000);
+                        }, children: copied ? 'Copied to clipboard!' : 'Copy ref names' }), (0, jsx_runtime_1.jsx)("pre", { className: classes.refNames, children: result })] })) }) }));
 });
 exports.default = RefNameInfoDialog;

package/esm/Session/BaseSession.d.ts

@@ -1,5 +1,6 @@
 import type { BaseRootModelType } from '../RootModel/BaseRootModel';
 import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
@@ -18,40 +19,7 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     readonly adminMode: boolean;
     readonly textSearchManager: import("@jbrowse/core/util").TextSearchManager;
 } & {
-    readonly assemblies: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        aliases: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        refNameColors: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-        refNameAliases: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType;
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-        displayName: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "name">>>)[];
+    readonly assemblies: Instance<BaseAssemblyConfigSchema>[];
 } & {
     setSelection(thing: unknown): void;
     clearSelection(): void;

package/esm/Session/Connections.d.ts

@@ -1,5 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
 import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree';
 export declare function ConnectionManagementSessionMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -47,28 +48,7 @@ export declare function ConnectionManagementSessionMixin(pluginManager: PluginMa
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    readonly connections: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>)[];
+    readonly connections: BaseConnectionConfigModel[];
 } & {
     makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): ({
         name: string;