@jbrowse/plugin-data-management 2.17.0 → 2.18.0

package/dist/AddConnectionWidget/components/AddConnectionWidget.js

@@ -27,14 +27,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
-const mui_1 = require("tss-react/mui");
+const product_core_1 = require("@jbrowse/product-core");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-// locals
+const mui_1 = require("tss-react/mui");
 const ConfigureConnection_1 = __importDefault(require("./ConfigureConnection"));
 const ConnectionTypeSelect_1 = __importDefault(require("./ConnectionTypeSelect"));
-const product_core_1 = require("@jbrowse/product-core");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
         marginTop: theme.spacing(1),
@@ -58,7 +57,6 @@ const AddConnectionWidget = (0, mobx_react_1.observer)(function ({ model }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    // useMemo is needed for react@18+mobx-react@9, previous code called configScema.create directly in a setConfigModel useState hook setter but this caused infinite loop
     const configModel = (0, react_1.useMemo)(() => connectionType === null || connectionType === void 0 ? void 0 : connectionType.configSchema.create({ connectionId }, (0, util_1.getEnv)(model)), [connectionId, connectionType, model]);
     return (react_1.default.createElement("div", { className: classes.root },
         react_1.default.createElement(material_1.Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map(label => (react_1.default.createElement(material_1.Step, { key: label },

package/dist/AddConnectionWidget/components/ConfigureConnection.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { AbstractSessionModel } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
 declare const ConfigureConnection: ({ connectionType, model, session, }: {
     connectionType: ConnectionType;
     model: AnyConfigurationModel;

package/dist/AddConnectionWidget/components/ConfigureConnection.js

@@ -24,9 +24,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const plugin_config_1 = require("@jbrowse/plugin-config");
 const ui_1 = require("@jbrowse/core/ui");
+const plugin_config_1 = require("@jbrowse/plugin-config");
+const mobx_react_1 = require("mobx-react");
 const ConfigureConnection = (0, mobx_react_1.observer)(function ({ connectionType, model, session, }) {
     const ConfigEditorComponent = connectionType.configEditorComponent || plugin_config_1.ConfigurationEditor;
     return (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },

package/dist/AddConnectionWidget/components/ConnectionTypeSelect.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
     connectionTypeChoices: ConnectionType[];
     connectionType?: ConnectionType;

package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -27,10 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
+const OpenInNew_1 = __importDefault(require("@mui/icons-material/OpenInNew"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-// icons
-const OpenInNew_1 = __importDefault(require("@mui/icons-material/OpenInNew"));
 const ConnectionTypeSelect = (0, mobx_react_1.observer)(function ConnectionTypeSelect({ connectionTypeChoices, connectionType, setConnectionType, }) {
     const firstChoice = connectionTypeChoices[0];
     (0, react_1.useEffect)(() => {

package/dist/AddConnectionWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function AddConnectionWidgetF(pluginManager: PluginManager): void;

package/dist/AddConnectionWidget/index.js

@@ -27,9 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = AddConnectionWidgetF;
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('AddConnectionWidget', {});
 function AddConnectionWidgetF(pluginManager) {

package/dist/AddConnectionWidget/model.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_state_tree_1 = require("mobx-state-tree");
 exports.default = mobx_state_tree_1.types.model('AddConnectionModel', {
     id: mst_1.ElementId,
     type: mobx_state_tree_1.types.literal('AddConnectionWidget'),

package/dist/AddTrackWidget/components/AddTrackWidget.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const AddTrackSelector: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -27,9 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const DefaultAddTrackWorkflow_1 = __importDefault(require("./DefaultAddTrackWorkflow"));
 const PasteConfigWorkflow_1 = __importDefault(require("./PasteConfigWorkflow"));
 const AddTrackSelector = (0, mobx_react_1.observer)(function ({ model, }) {
@@ -41,7 +41,6 @@ const AddTrackSelector = (0, mobx_react_1.observer)(function ({ model, }) {
             .pluginManager.getAddTrackWorkflowElements()
             .map(w => [w.name, w.ReactComponent])),
     };
-    // make sure the selected value is in the list
     const val2 = ComponentMap[val] ? val : 'Default add track workflow';
     const Component = ComponentMap[val2];
     return (react_1.default.createElement(react_1.default.Fragment, null,

package/dist/AddTrackWidget/components/ConfirmTrack.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const ConfirmTrack: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/ConfirmTrack.js

@@ -27,15 +27,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const TextIndexingConfig_1 = __importDefault(require("./TextIndexingConfig"));
-const TrackTypeSelector_1 = __importDefault(require("./TrackTypeSelector"));
 const TrackAdapterSelector_1 = __importDefault(require("./TrackAdapterSelector"));
+const TrackTypeSelector_1 = __importDefault(require("./TrackTypeSelector"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
@@ -118,7 +118,6 @@ const ConfirmTrack = (0, mobx_react_1.observer)(function ConfirmTrack({ model, }
             }, TextFieldProps: {
                 fullWidth: true,
                 SelectProps: {
-                    // @ts-expect-error
                     SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
                 },
             } }),

package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const DefaultAddTrackWorkflow: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -27,13 +27,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-// locals
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
 const ConfirmTrack_1 = __importDefault(require("./ConfirmTrack"));
 const TrackSourceSelect_1 = __importDefault(require("./TrackSourceSelect"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({

package/dist/AddTrackWidget/components/PasteConfigWorkflow.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const PasteConfigAddTrackWorkflow: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -24,11 +24,11 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
-const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     textbox: {
         width: '100%',

package/dist/AddTrackWidget/components/TextIndexingConfig.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const TextIndexingConfig: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/TextIndexingConfig.js

@@ -27,12 +27,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
+const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-// icons
-const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     paper: {
         display: 'flex',
@@ -68,9 +67,7 @@ const TextIndexingConfig = (0, mobx_react_1.observer)(function ({ model, }) {
             react_1.default.createElement(material_1.CardContent, null,
                 react_1.default.createElement(material_1.InputLabel, null, section.label),
                 react_1.default.createElement(material_1.List, { disablePadding: true },
-                    section.values.map((val, idx) => (
-                    /* biome-ignore lint/suspicious/noArrayIndexKey: */
-                    react_1.default.createElement(material_1.ListItem, { key: `${val}-${idx}`, disableGutters: true },
+                    section.values.map((val, idx) => (react_1.default.createElement(material_1.ListItem, { key: `${val}-${idx}`, disableGutters: true },
                         react_1.default.createElement(material_1.TextField, { value: val, slotProps: {
                                 input: {
                                     endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },

package/dist/AddTrackWidget/components/TrackAdapterSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const TrackAdapterSelector: ({ model }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/TrackAdapterSelector.js

@@ -4,18 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
     },
 }));
-// collate adapters into a map with
-// key: category
-// value: array of adapters with that category
 function categorizeAdapters(adaptersList) {
     const map = {};
     adaptersList.forEach(adapter => {
@@ -36,14 +33,11 @@ const TrackAdapterSelector = (0, mobx_react_1.observer)(({ model }) => {
             model.setAdapterHint(event.target.value);
         }, slotProps: {
             select: {
-                // @ts-expect-error
                 SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
             },
         } }, Object.entries(categorizeAdapters(pluginManager
         .getAdapterElements()
         .filter(e => { var _a; return !((_a = e.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))).map(([key, val]) => {
-        // returning array avoids needing to use a react fragment which
-        // Select/TextField sub-elements disagree with
         return [
             react_1.default.createElement(material_1.ListSubheader, { key: key }, key),
             val.map(elt => (react_1.default.createElement(material_1.MenuItem, { key: elt.name, value: elt.name }, elt.displayName))),

package/dist/AddTrackWidget/components/TrackSourceSelect.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const TrackSourceSelect: ({ model, }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/TrackSourceSelect.js

@@ -6,9 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     paper: {
         padding: theme.spacing(2),

package/dist/AddTrackWidget/components/TrackTypeSelector.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const TrackTypeSelector: ({ model }: {
     model: AddTrackModel;
 }) => React.JSX.Element;

package/dist/AddTrackWidget/components/TrackTypeSelector.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
@@ -22,7 +22,6 @@ const TrackTypeSelector = (0, mobx_react_1.observer)(({ model }) => {
             model.setTrackType(event.target.value);
         }, slotProps: {
             select: {
-                // @ts-expect-error
                 SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
             },
         } }, trackTypes.map(({ name, displayName }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName)))));

package/dist/AddTrackWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function AddTrackWidgetF(pluginManager: PluginManager): void;

package/dist/AddTrackWidget/index.js

@@ -27,9 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = AddTrackWidgetF;
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('AddTrackWidget', {});
 function AddTrackWidgetF(pluginManager) {

package/dist/AddTrackWidget/model.d.ts

@@ -1,25 +1,13 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { FileLocation } from '@jbrowse/core/util/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { FileLocation } from '@jbrowse/core/util/types';
+import type { Instance } from 'mobx-state-tree';
 interface IndexingAttr {
     attributes: string[];
     exclude: string[];
 }
-/**
- * #stateModel AddTrackModel
- */
 export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     trackSource: string;
@@ -32,99 +20,30 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
 } & {
-    /**
-     * #action
-     */
     setAdapterHint(obj: string): void;
-    /**
-     * #action
-     */
     setTrackSource(str: string): void;
-    /**
-     * #action
-     */
     setTextIndexingConf(conf: IndexingAttr): void;
-    /**
-     * #action
-     */
     setTextIndexTrack(flag: boolean): void;
-    /**
-     * #action
-     */
     setTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setIndexTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setAssembly(str: string): void;
-    /**
-     * #action
-     */
     setTrackName(str: string): void;
-    /**
-     * #action
-     */
     setTrackType(str: string): void;
-    /**
-     * #action
-     */
     clearData(): void;
 } & {
-    /**
-     * #getter
-     */
     readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
-    /**
-     * #getter
-     */
     readonly trackName: string;
-    /**
-     * #getter
-     */
     readonly isFtp: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeTrackUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeIndexUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeUrl: boolean;
-    /**
-     * #getter
-     */
     readonly trackHttp: any;
-    /**
-     * #getter
-     */
     readonly indexHttp: any;
-    /**
-     * #getter
-     */
     readonly wrongProtocol: any;
-    /**
-     * #getter
-     */
     readonly unsupported: boolean;
-    /**
-     * #getter
-     */
     readonly assembly: any;
-    /**
-     * #getter
-     */
     readonly trackType: string;
 } & {
-    /**
-     * #getter
-     */
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AddTrackStateModel = ReturnType<typeof f>;