@jbrowse/plugin-data-management 2.2.0 → 2.2.1

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -8,12 +8,14 @@ const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const DefaultAddTrackWorkflow_1 = __importDefault(require("./DefaultAddTrackWorkflow"));
+const PasteConfigWorkflow_1 = __importDefault(require("./PasteConfigWorkflow"));
 function AddTrackSelector({ model }) {
     const [val, setVal] = (0, util_1.useLocalStorage)('trackSelector-choice', 'Default');
     const { pluginManager } = (0, util_1.getEnv)(model);
     const widgets = pluginManager.getElementTypesInGroup('add track workflow');
     const ComponentMap = {
         Default: DefaultAddTrackWorkflow_1.default,
+        'Add track JSON': PasteConfigWorkflow_1.default,
         ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
     };
     // make sure the selected value is in the list

package/dist/AddTrackWidget/components/AddTrackWidget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddTrackWidget.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/AddTrackWidget.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA6E;AAE7E,6CAA4D;AAI5D,wFAA+D;AAC/D,gFAAuD;AAEvD,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,sBAAe,EAAC,sBAAsB,EAAE,SAAS,CAAC,CAAA;IACxE,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,OAAO,GAAG,aAAa,CAAC,sBAAsB,CAClD,oBAAoB,CACK,CAAA;IAC3B,MAAM,YAAY,GAAG;QACnB,OAAO,EAAE,iCAAuB;QAChC,gBAAgB,EAAE,6BAAmB;QACrC,GAAG,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;KACX,CAAA;IAE1D,8CAA8C;IAC9C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;IAChD,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IACpC,OAAO,CACL;QACE,8BAAC,sBAAW;YACV,8BAAC,iBAAM,IAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAC/D,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClC,8BAAC,mBAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,IACvB,CAAC,CACO,CACZ,CAAC,CACK;YACT,8BAAC,yBAAc,qCAA4C,CAC/C;QAEd,yCAAM;QACN,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,gBAAgB,CAAC,CAAA"}

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

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -0,0 +1,66 @@
+"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;
+};
+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 mobx_react_1 = require("mobx-react");
+const useStyles = (0, mui_1.makeStyles)()({
+    textbox: {
+        width: '100%',
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+});
+function AddTrackWorkflow({ model }) {
+    const { classes } = useStyles();
+    const [val, setVal] = (0, react_1.useState)('');
+    const [error, setError] = (0, react_1.useState)();
+    return (react_1.default.createElement("div", null,
+        error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
+        react_1.default.createElement(material_1.TextField, { multiline: true, rows: 10, value: val, onChange: event => setVal(event.target.value), placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
+        react_1.default.createElement(material_1.Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    setError(undefined);
+                    const session = (0, util_1.getSession)(model);
+                    const conf = JSON.parse(val);
+                    const confs = Array.isArray(conf) ? conf : [conf];
+                    confs.forEach(c => session.addTrackConf(c));
+                    confs.forEach(c => c.trackId);
+                    model.clearData();
+                    session.hideWidget(model);
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+exports.default = (0, mobx_react_1.observer)(AddTrackWorkflow);
+//# sourceMappingURL=PasteConfigWorkflow.js.map

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js.map

@@ -0,0 +1 @@
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package/dist/AddTrackWidget/model.d.ts

@@ -46,6 +46,6 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
 } & {
     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 declare type AddTrackStateModel = ReturnType<typeof f>;
-export declare type AddTrackModel = Instance<AddTrackStateModel>;
+export type AddTrackStateModel = ReturnType<typeof f>;
+export type AddTrackModel = Instance<AddTrackStateModel>;
 export {};

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,7 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare type TreeNode = {
+export type TreeNode = {
     name: string;
     id: string;
     conf?: AnyConfigurationModel;
@@ -65,5 +65,5 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         tracks: AnyConfigurationModel[];
     }): TreeNode[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
-export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
+export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;

package/dist/PluginStoreWidget/model.d.ts

@@ -9,5 +9,5 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     clearFilterText(): void;
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type PluginStoreStateModel = ReturnType<typeof f>;
-export declare type PluginStoreModel = Instance<PluginStoreStateModel>;
+export type PluginStoreStateModel = ReturnType<typeof f>;
+export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -3,12 +3,14 @@ import { observer } from 'mobx-react';
 import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material';
 import { getEnv, useLocalStorage } from '@jbrowse/core/util';
 import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow';
+import PasteConfigWorkflow from './PasteConfigWorkflow';
 function AddTrackSelector({ model }) {
     const [val, setVal] = useLocalStorage('trackSelector-choice', 'Default');
     const { pluginManager } = getEnv(model);
     const widgets = pluginManager.getElementTypesInGroup('add track workflow');
     const ComponentMap = {
         Default: DefaultAddTrackWorkflow,
+        'Add track JSON': PasteConfigWorkflow,
         ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
     };
     // make sure the selected value is in the list

package/esm/AddTrackWidget/components/AddTrackWidget.js.map

@@ -1 +1 @@
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package/esm/AddTrackWidget/components/PasteConfigWorkflow.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -0,0 +1,41 @@
+import React, { useState } from 'react';
+import { Button, TextField } from '@mui/material';
+import { ErrorMessage } from '@jbrowse/core/ui';
+import { makeStyles } from 'tss-react/mui';
+import { getSession } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()({
+    textbox: {
+        width: '100%',
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+});
+function AddTrackWorkflow({ model }) {
+    const { classes } = useStyles();
+    const [val, setVal] = useState('');
+    const [error, setError] = useState();
+    return (React.createElement("div", null,
+        error ? React.createElement(ErrorMessage, { error: error }) : null,
+        React.createElement(TextField, { multiline: true, rows: 10, value: val, onChange: event => setVal(event.target.value), placeholder: 'Paste track config or array of track configs in JSON format', variant: "outlined", className: classes.textbox }),
+        React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    setError(undefined);
+                    const session = getSession(model);
+                    const conf = JSON.parse(val);
+                    const confs = Array.isArray(conf) ? conf : [conf];
+                    confs.forEach(c => session.addTrackConf(c));
+                    confs.forEach(c => c.trackId);
+                    model.clearData();
+                    session.hideWidget(model);
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+export default observer(AddTrackWorkflow);
+//# sourceMappingURL=PasteConfigWorkflow.js.map

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js.map

@@ -0,0 +1 @@
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package/esm/AddTrackWidget/model.d.ts

@@ -46,6 +46,6 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
 } & {
     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 declare type AddTrackStateModel = ReturnType<typeof f>;
-export declare type AddTrackModel = Instance<AddTrackStateModel>;
+export type AddTrackStateModel = ReturnType<typeof f>;
+export type AddTrackModel = Instance<AddTrackStateModel>;
 export {};

package/esm/AddTrackWidget/model.js

@@ -1,6 +1,6 @@
 import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { guessAdapter, guessTrackType, UNSUPPORTED, getFileName, } from '@jbrowse/core/util/tracks';
+import { guessAdapter, guessTrackType, getFileName, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,7 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare type TreeNode = {
+export type TreeNode = {
     name: string;
     id: string;
     conf?: AnyConfigurationModel;
@@ -65,5 +65,5 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         tracks: AnyConfigurationModel[];
     }): TreeNode[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
-export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
+export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;

package/esm/PluginStoreWidget/model.d.ts

@@ -9,5 +9,5 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     clearFilterText(): void;
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type PluginStoreStateModel = ReturnType<typeof f>;
-export declare type PluginStoreModel = Instance<PluginStoreStateModel>;
+export type PluginStoreStateModel = ReturnType<typeof f>;
+export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.2.0",
+  "version": "2.2.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
 }

package/src/AddTrackWidget/components/AddTrackWidget.tsx

@@ -7,6 +7,7 @@ import { getEnv, useLocalStorage } from '@jbrowse/core/util'
 // locals
 import { AddTrackModel } from '../model'
 import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow'
+import PasteConfigWorkflow from './PasteConfigWorkflow'
 
 function AddTrackSelector({ model }: { model: AddTrackModel }) {
   const [val, setVal] = useLocalStorage('trackSelector-choice', 'Default')
@@ -16,6 +17,7 @@ function AddTrackSelector({ model }: { model: AddTrackModel }) {
   ) as AddTrackWorkflowType[]
   const ComponentMap = {
     Default: DefaultAddTrackWorkflow,
+    'Add track JSON': PasteConfigWorkflow,
     ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
   } as { [key: string]: React.FC<{ model: AddTrackModel }> }
 

package/src/AddTrackWidget/components/PasteConfigWorkflow.tsx

@@ -0,0 +1,64 @@
+import React, { useState } from 'react'
+import { Button, TextField } from '@mui/material'
+import { ErrorMessage } from '@jbrowse/core/ui'
+import { makeStyles } from 'tss-react/mui'
+import { getSession } from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
+
+// locals
+import { AddTrackModel } from '../model'
+
+const useStyles = makeStyles()({
+  textbox: {
+    width: '100%',
+  },
+  submit: {
+    marginTop: 25,
+    marginBottom: 100,
+    display: 'block',
+  },
+})
+
+function AddTrackWorkflow({ model }: { model: AddTrackModel }) {
+  const { classes } = useStyles()
+  const [val, setVal] = useState('')
+  const [error, setError] = useState<unknown>()
+
+  return (
+    <div>
+      {error ? <ErrorMessage error={error} /> : null}
+      <TextField
+        multiline
+        rows={10}
+        value={val}
+        onChange={event => setVal(event.target.value)}
+        placeholder={
+          'Paste track config or array of track configs in JSON format'
+        }
+        variant="outlined"
+        className={classes.textbox}
+      />
+      <Button
+        variant="contained"
+        className={classes.submit}
+        onClick={() => {
+          try {
+            setError(undefined)
+            const session = getSession(model)
+            const conf = JSON.parse(val)
+            const confs = Array.isArray(conf) ? conf : [conf]
+            confs.forEach(c => session.addTrackConf(c))
+            confs.forEach(c => c.trackId)
+            model.clearData()
+            session.hideWidget(model)
+          } catch (e) {
+            setError(e)
+          }
+        }}
+      >
+        Submit
+      </Button>
+    </div>
+  )
+}
+export default observer(AddTrackWorkflow)

package/src/AddTrackWidget/model.ts

@@ -5,8 +5,8 @@ import { FileLocation } from '@jbrowse/core/util/types'
 import {
   guessAdapter,
   guessTrackType,
-  UNSUPPORTED,
   getFileName,
+  UNSUPPORTED,
 } from '@jbrowse/core/util/tracks'
 
 function isAbsoluteUrl(url = '') {

package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap

@@ -567,6 +567,28 @@ exports[`<PluginStoreWidget /> renders with the available plugins 1`] = `
                     WigglePlugin
                   </p>
                 </li>
+                <li
+                  class="MuiListItem-root MuiListItem-dense MuiListItem-gutters MuiListItem-padding css-ypie1g-MuiListItem-root"
+                >
+                  <svg
+                    aria-hidden="true"
+                    aria-label="This plugin was installed by an administrator, you cannot remove it."
+                    class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-1a34d00-MuiSvgIcon-root-lockedPluginTooltip"
+                    data-mui-internal-clone-element="true"
+                    data-testid="LockIcon"
+                    focusable="false"
+                    viewBox="0 0 24 24"
+                  >
+                    <path
+                      d="M18 8h-1V6c0-2.76-2.24-5-5-5S7 3.24 7 6v2H6c-1.1 0-2 .9-2 2v10c0 1.1.9 2 2 2h12c1.1 0 2-.9 2-2V10c0-1.1-.9-2-2-2zm-6 9c-1.1 0-2-.9-2-2s.9-2 2-2 2 .9 2 2-.9 2-2 2zm3.1-9H8.9V6c0-1.71 1.39-3.1 3.1-3.1 1.71 0 3.1 1.39 3.1 3.1v2z"
+                    />
+                  </svg>
+                  <p
+                    class="MuiTypography-root MuiTypography-body1 css-k0xfey-MuiTypography-root"
+                  >
+                    GCContentPlugin
+                  </p>
+                </li>
                 <li
                   class="MuiListItem-root MuiListItem-dense MuiListItem-gutters MuiListItem-padding css-ypie1g-MuiListItem-root"
                 >

package/src/__snapshots__/index.test.js.snap

@@ -1,9 +1,9 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`Data management adds config editor widget 1`] = `Object {}`;
+exports[`Data management adds config editor widget 1`] = `{}`;
 
-exports[`Data management adds connection add widget 1`] = `Object {}`;
+exports[`Data management adds connection add widget 1`] = `{}`;
 
-exports[`Data management adds hierarchical track selector 1`] = `Object {}`;
+exports[`Data management adds hierarchical track selector 1`] = `{}`;
 
-exports[`Data management adds track add widget 1`] = `Object {}`;
+exports[`Data management adds track add widget 1`] = `{}`;