@jbrowse/plugin-data-management 2.0.0 → 2.1.2

package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js

@@ -1,30 +1,13 @@
 "use strict";
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var material_1 = require("@mui/material");
-var mobx_react_1 = require("mobx-react");
-function CloseConnectionDialog(_a) {
-    var _b = _a.modalInfo, modalInfo = _b === void 0 ? {} : _b, setModalInfo = _a.setModalInfo;
-    var name = modalInfo.name, dereferenceTypeCount = modalInfo.dereferenceTypeCount, safelyBreakConnection = modalInfo.safelyBreakConnection;
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+function CloseConnectionDialog({ modalInfo = {}, setModalInfo, }) {
+    const { name, dereferenceTypeCount, safelyBreakConnection } = modalInfo;
     return (react_1.default.createElement(material_1.Dialog, { open: true },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Close connection \"",
@@ -33,19 +16,16 @@ function CloseConnectionDialog(_a) {
         react_1.default.createElement(material_1.DialogContent, null,
             dereferenceTypeCount ? (react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement(material_1.DialogContentText, null, "Closing this connection will close:"),
-                react_1.default.createElement(material_1.List, null, Object.entries(dereferenceTypeCount).map(function (_a) {
-                    var _b = __read(_a, 2), key = _b[0], value = _b[1];
-                    return (react_1.default.createElement(material_1.ListItem, { key: key }, "".concat(value, " ").concat(key)));
-                })))) : null,
+                react_1.default.createElement(material_1.List, null, Object.entries(dereferenceTypeCount).map(([key, value]) => (react_1.default.createElement(material_1.ListItem, { key: key }, `${value} ${key}`)))))) : null,
             react_1.default.createElement(material_1.DialogContentText, null, "Are you sure you want to close this connection?")),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: function () { return setModalInfo(); }, color: "primary" }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { onClick: () => setModalInfo(), color: "primary" }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", onClick: modalInfo
-                    ? function () {
+                    ? () => {
                         safelyBreakConnection === null || safelyBreakConnection === void 0 ? void 0 : safelyBreakConnection();
                         setModalInfo();
                     }
-                    : function () { }, color: "primary" }, "OK"))));
+                    : () => { }, color: "primary" }, "OK"))));
 }
 exports.default = (0, mobx_react_1.observer)(CloseConnectionDialog);
 //# sourceMappingURL=CloseConnectionDialog.js.map

package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CloseConnectionDialog.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CASsB;AACtB,2CAAqC;AAErC,SAAS,qBAAqB,CAAC,EAC7B,SAAS,GAAG,EAAE,EACd,YAAY,GAQb;IACC,MAAM,EAAE,IAAI,EAAE,oBAAoB,EAAE,qBAAqB,EAAE,GAAG,SAAS,CAAA;IACvE,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI;QACV,8BAAC,sBAAW;;YAAyB,IAAI;iBAAqB;QAC9D,8BAAC,wBAAa;YACX,oBAAoB,CAAC,CAAC,CAAC,CACtB;gBACE,8BAAC,4BAAiB,8CAEE;gBACpB,8BAAC,eAAI,QACF,MAAM,CAAC,OAAO,CAAC,oBAAoB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAC1D,8BAAC,mBAAQ,IAAC,GAAG,EAAE,GAAG,IAAG,GAAG,KAAK,IAAI,GAAG,EAAE,CAAY,CACnD,CAAC,CACG,CACN,CACJ,CAAC,CAAC,CAAC,IAAI;YACR,8BAAC,4BAAiB,0DAEE,CACN;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,YAAY,EAAE,EAAE,KAAK,EAAC,SAAS,aAE7C;YACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EACL,SAAS;oBACP,CAAC,CAAC,GAAG,EAAE;wBACH,qBAAqB,aAArB,qBAAqB,uBAArB,qBAAqB,EAAI,CAAA;wBACzB,YAAY,EAAE,CAAA;oBAChB,CAAC;oBACH,CAAC,CAAC,GAAG,EAAE,GAAE,CAAC,EAEd,KAAK,EAAC,SAAS,SAGR,CACK,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,qBAAqB,CAAC,CAAA"}

package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js

@@ -3,12 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var react_1 = __importDefault(require("react"));
-var material_1 = require("@mui/material");
-var mobx_react_1 = require("mobx-react");
-function DeleteConnectionDialog(_a) {
-    var deleteDialogDetails = _a.deleteDialogDetails, session = _a.session, handleClose = _a.handleClose;
-    var connectionConf = deleteDialogDetails.connectionConf, name = deleteDialogDetails.name;
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+function DeleteConnectionDialog({ deleteDialogDetails, session, handleClose, }) {
+    const { connectionConf, name } = deleteDialogDetails;
     return (react_1.default.createElement(material_1.Dialog, { open: true },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Delete connection \"",
@@ -17,8 +16,8 @@ function DeleteConnectionDialog(_a) {
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.DialogContentText, null, "Are you sure you want to delete this connection?")),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: function () { return handleClose(); }, color: "primary" }, "Cancel"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: function () {
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "primary" }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
                     var _a;
                     if (connectionConf) {
                         (_a = session.deleteConnection) === null || _a === void 0 ? void 0 : _a.call(session, connectionConf);

package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js.map

@@ -1 +1 @@
-{"version":3,"file":"DeleteConnectionDialog.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.tsx"],"names":[],"mappings":";;;;;AAAA,gDAAyB;AACzB,0CAOsB;AACtB,yCAAqC;AAIrC,SAAS,sBAAsB,CAAC,EAQ/B;QAPC,mBAAmB,yBAAA,EACnB,OAAO,aAAA,EACP,WAAW,iBAAA;IAMH,IAAA,cAAc,GAAW,mBAAmB,eAA9B,EAAE,IAAI,GAAK,mBAAmB,KAAxB,CAAwB;IACpD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI;QACV,8BAAC,sBAAW;;YAA0B,IAAI;iBAAqB;QAC/D,8BAAC,wBAAa;YACZ,8BAAC,4BAAiB,2DAEE,CACN;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,cAAM,OAAA,WAAW,EAAE,EAAb,CAAa,EAAE,KAAK,EAAC,SAAS,aAE5C;YACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE;;oBACP,IAAI,cAAc,EAAE;wBAClB,MAAA,OAAO,CAAC,gBAAgB,wDAAG,cAAc,CAAC,CAAA;qBAC3C;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,SAGM,CACK,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,sBAAsB,CAAC,CAAA"}
+{"version":3,"file":"DeleteConnectionDialog.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAOsB;AACtB,2CAAqC;AAIrC,SAAS,sBAAsB,CAAC,EAC9B,mBAAmB,EACnB,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,EAAE,cAAc,EAAE,IAAI,EAAE,GAAG,mBAAmB,CAAA;IACpD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI;QACV,8BAAC,sBAAW;;YAA0B,IAAI;iBAAqB;QAC/D,8BAAC,wBAAa;YACZ,8BAAC,4BAAiB,2DAEE,CACN;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,aAE5C;YACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;;oBACZ,IAAI,cAAc,EAAE;wBAClB,MAAA,OAAO,CAAC,gBAAgB,wDAAG,cAAc,CAAC,CAAA;qBAC3C;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,SAGM,CACK,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,sBAAsB,CAAC,CAAA"}

package/dist/HierarchicalTrackSelectorWidget/components/Header.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { HierarchicalTrackSelectorModel } from '../model';
+declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, assemblyIdx, }: {
+    model: HierarchicalTrackSelectorModel;
+    setHeaderHeight: (n: number) => void;
+    setAssemblyIdx: (n: number) => void;
+    assemblyIdx: number;
+}): JSX.Element;
+declare const _default: typeof HierarchicalTrackSelectorHeader;
+export default _default;

package/dist/HierarchicalTrackSelectorWidget/components/Header.js

@@ -0,0 +1,177 @@
+"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 mui_1 = require("tss-react/mui");
+const material_1 = require("@mui/material");
+// icons
+const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
+const Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
+const ShoppingCart_1 = __importDefault(require("@mui/icons-material/ShoppingCart"));
+const Icons_1 = require("@jbrowse/core/ui/Icons");
+// other
+const Menu_2 = __importDefault(require("@jbrowse/core/ui/Menu"));
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+// lazy components
+const CloseConnectionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./CloseConnectionDialog'))));
+const DeleteConnectionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./DeleteConnectionDialog'))));
+const ManageConnectionsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ManageConnectionsDialog'))));
+const ToggleConnectionsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ToggleConnectionsDialog'))));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    searchBox: {
+        margin: theme.spacing(2),
+    },
+    menuIcon: {
+        marginRight: theme.spacing(1),
+        marginBottom: 0,
+    },
+}));
+function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, assemblyIdx, }) {
+    const { classes } = useStyles();
+    const session = (0, util_1.getSession)(model);
+    const [connectionEl, setConnectionEl] = (0, react_1.useState)();
+    const [selectionEl, setSelectionEl] = (0, react_1.useState)();
+    const [menuEl, setMenuEl] = (0, react_1.useState)();
+    const [modalInfo, setModalInfo] = (0, react_1.useState)();
+    const [deleteDlgDetails, setDeleteDlgDetails] = (0, react_1.useState)();
+    const [connectionManagerOpen, setConnectionManagerOpen] = (0, react_1.useState)(false);
+    const [connectionToggleOpen, setConnectionToggleOpen] = (0, react_1.useState)(false);
+    const { assemblyNames } = model;
+    const assemblyName = assemblyNames[assemblyIdx];
+    function breakConnection(connectionConf, deletingConnection) {
+        const name = (0, configuration_1.readConfObject)(connectionConf, 'name');
+        // @ts-ignore
+        const result = session.prepareToBreakConnection(connectionConf);
+        if (result) {
+            const [safelyBreakConnection, dereferenceTypeCount] = result;
+            if (Object.keys(dereferenceTypeCount).length > 0) {
+                setModalInfo({
+                    connectionConf,
+                    safelyBreakConnection,
+                    dereferenceTypeCount,
+                    name,
+                });
+            }
+            else {
+                safelyBreakConnection();
+            }
+        }
+        if (deletingConnection) {
+            setDeleteDlgDetails({ name, connectionConf });
+        }
+    }
+    const connectionMenuItems = [
+        {
+            label: 'Turn on/off connections...',
+            onClick: () => setConnectionToggleOpen(true),
+        },
+    ];
+    if ((0, util_1.isSessionModelWithConnections)(session)) {
+        connectionMenuItems.unshift({
+            label: 'Add connection',
+            onClick: () => {
+                if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                }
+            },
+        });
+        connectionMenuItems.push({
+            label: 'Delete connections...',
+            onClick: () => setConnectionManagerOpen(true),
+        });
+    }
+    const assemblyMenuItems = assemblyNames.length > 1
+        ? [
+            {
+                label: 'Select assembly...',
+                subMenu: assemblyNames.map((name, idx) => ({
+                    label: name,
+                    onClick: () => setAssemblyIdx(idx),
+                })),
+            },
+        ]
+        : [];
+    const menuItems = [
+        {
+            label: 'Add track...',
+            onClick: () => {
+                if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                    session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                        view: model.view.id,
+                    }));
+                }
+            },
+        },
+        ...assemblyMenuItems,
+    ];
+    const items = (0, mobx_state_tree_1.getEnv)(model).pluginManager.evaluateExtensionPoint('TrackSelector-multiTrackMenuItems');
+    return (react_1.default.createElement("div", { ref: ref => setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0), "data-testid": "hierarchical_track_selector" },
+        react_1.default.createElement("div", { style: { display: 'flex' } },
+            (0, util_1.isSessionWithAddTracks)(session) && (react_1.default.createElement(material_1.IconButton, { className: classes.menuIcon, onClick: event => setMenuEl(event.currentTarget) },
+                react_1.default.createElement(Menu_1.default, null))),
+            session.makeConnection && (react_1.default.createElement(material_1.IconButton, { className: classes.menuIcon, onClick: event => setConnectionEl(event.currentTarget) },
+                react_1.default.createElement(Icons_1.Cable, null))),
+            model.selection.length ? (react_1.default.createElement(material_1.IconButton, { className: classes.menuIcon, onClick: event => setSelectionEl(event.currentTarget) },
+                react_1.default.createElement(material_1.Badge, { badgeContent: model.selection.length, color: "primary" },
+                    react_1.default.createElement(ShoppingCart_1.default, null)))) : null,
+            react_1.default.createElement(material_1.TextField, { className: classes.searchBox, label: "Filter tracks", value: model.filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+                    endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
+                        react_1.default.createElement(material_1.IconButton, { color: "secondary", onClick: model.clearFilterText },
+                            react_1.default.createElement(Clear_1.default, null)))),
+                } })),
+        react_1.default.createElement(Menu_2.default, { anchorEl: connectionEl, open: Boolean(connectionEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setConnectionEl(undefined);
+            }, onClose: () => setConnectionEl(undefined), menuItems: connectionMenuItems }),
+        react_1.default.createElement(Menu_2.default, { anchorEl: menuEl, open: Boolean(menuEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setMenuEl(undefined);
+            }, onClose: () => setMenuEl(undefined), menuItems: menuItems }),
+        react_1.default.createElement(Menu_2.default, { anchorEl: selectionEl, open: Boolean(selectionEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setSelectionEl(undefined);
+            }, onClose: () => setSelectionEl(undefined), menuItems: [
+                { label: 'Clear', onClick: () => model.clearSelection() },
+                ...items.map(item => ({
+                    ...item,
+                    ...('onClick' in item
+                        ? { onClick: () => item.onClick(model) }
+                        : {}),
+                })),
+            ] }),
+        react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+            modalInfo ? (react_1.default.createElement(CloseConnectionDialog, { modalInfo: modalInfo, setModalInfo: setModalInfo })) : null,
+            deleteDlgDetails ? (react_1.default.createElement(DeleteConnectionDialog, { handleClose: () => setDeleteDlgDetails(undefined), deleteDialogDetails: deleteDlgDetails, session: session })) : null,
+            connectionManagerOpen ? (react_1.default.createElement(ManageConnectionsDialog, { handleClose: () => setConnectionManagerOpen(false), breakConnection: breakConnection, session: session })) : null,
+            connectionToggleOpen ? (react_1.default.createElement(ToggleConnectionsDialog, { handleClose: () => setConnectionToggleOpen(false), session: session, breakConnection: breakConnection, assemblyName: assemblyName })) : null)));
+}
+exports.default = (0, mobx_react_1.observer)(HierarchicalTrackSelectorHeader);
+//# sourceMappingURL=Header.js.map

package/dist/HierarchicalTrackSelectorWidget/components/Header.js.map

@@ -0,0 +1 @@
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