@jbrowse/plugin-data-management 1.7.11 → 2.1.0

package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js

@@ -1,46 +1,30 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _react = _interopRequireDefault(require("react"));
-
-var _core = require("@material-ui/core");
-
-var _mobxReact = require("mobx-react");
-
-function DeleteConnectionDialog(_ref) {
-  var deleteDialogDetails = _ref.deleteDialogDetails,
-      session = _ref.session,
-      handleClose = _ref.handleClose;
-  var connectionConf = deleteDialogDetails.connectionConf,
-      name = deleteDialogDetails.name;
-  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
-    open: true
-  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Delete connection \"", name, "\""), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, /*#__PURE__*/_react.default.createElement(_core.DialogContentText, null, "Are you sure you want to delete this connection?")), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
-    onClick: function onClick() {
-      return handleClose();
-    },
-    color: "primary"
-  }, "Cancel"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-    variant: "contained",
-    color: "primary",
-    onClick: function onClick() {
-      if (connectionConf) {
-        var _session$deleteConnec;
-
-        (_session$deleteConnec = session.deleteConnection) === null || _session$deleteConnec === void 0 ? void 0 : _session$deleteConnec.call(session, connectionConf);
-      }
-
-      handleClose();
-    }
-  }, "OK")));
+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;
+    return (react_1.default.createElement(material_1.Dialog, { open: true },
+        react_1.default.createElement(material_1.DialogTitle, null,
+            "Delete connection \"",
+            name,
+            "\""),
+        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 () {
+                    var _a;
+                    if (connectionConf) {
+                        (_a = session.deleteConnection) === null || _a === void 0 ? void 0 : _a.call(session, connectionConf);
+                    }
+                    handleClose();
+                } }, "OK"))));
 }
-
-var _default = (0, _mobxReact.observer)(DeleteConnectionDialog);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(DeleteConnectionDialog);
+//# sourceMappingURL=DeleteConnectionDialog.js.map

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

@@ -0,0 +1 @@
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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 +1,209 @@
+"use strict";
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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 __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 __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var mui_1 = require("tss-react/mui");
+var material_1 = require("@mui/material");
+// icons
+var Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
+var Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
+var ShoppingCart_1 = __importDefault(require("@mui/icons-material/ShoppingCart"));
+var Icons_1 = require("@jbrowse/core/ui/Icons");
+// other
+var Menu_2 = __importDefault(require("@jbrowse/core/ui/Menu"));
+var util_1 = require("@jbrowse/core/util");
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_react_1 = require("mobx-react");
+var mobx_state_tree_1 = require("mobx-state-tree");
+// lazy components
+var CloseConnectionDialog = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./CloseConnectionDialog')); }); });
+var DeleteConnectionDialog = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./DeleteConnectionDialog')); }); });
+var ManageConnectionsDialog = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./ManageConnectionsDialog')); }); });
+var ToggleConnectionsDialog = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./ToggleConnectionsDialog')); }); });
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+    searchBox: {
+        margin: theme.spacing(2),
+    },
+    menuIcon: {
+        marginRight: theme.spacing(1),
+        marginBottom: 0,
+    },
+}); });
+function HierarchicalTrackSelectorHeader(_a) {
+    var model = _a.model, setHeaderHeight = _a.setHeaderHeight, setAssemblyIdx = _a.setAssemblyIdx, assemblyIdx = _a.assemblyIdx;
+    var classes = useStyles().classes;
+    var session = (0, util_1.getSession)(model);
+    var _b = __read((0, react_1.useState)(), 2), connectionEl = _b[0], setConnectionEl = _b[1];
+    var _c = __read((0, react_1.useState)(), 2), selectionEl = _c[0], setSelectionEl = _c[1];
+    var _d = __read((0, react_1.useState)(), 2), menuEl = _d[0], setMenuEl = _d[1];
+    var _e = __read((0, react_1.useState)(), 2), modalInfo = _e[0], setModalInfo = _e[1];
+    var _f = __read((0, react_1.useState)(), 2), deleteDlgDetails = _f[0], setDeleteDlgDetails = _f[1];
+    var _g = __read((0, react_1.useState)(false), 2), connectionManagerOpen = _g[0], setConnectionManagerOpen = _g[1];
+    var _h = __read((0, react_1.useState)(false), 2), connectionToggleOpen = _h[0], setConnectionToggleOpen = _h[1];
+    var assemblyNames = model.assemblyNames;
+    var assemblyName = assemblyNames[assemblyIdx];
+    function breakConnection(connectionConf, deletingConnection) {
+        var name = (0, configuration_1.readConfObject)(connectionConf, 'name');
+        // @ts-ignore
+        var result = session.prepareToBreakConnection(connectionConf);
+        if (result) {
+            var _a = __read(result, 2), safelyBreakConnection = _a[0], dereferenceTypeCount = _a[1];
+            if (Object.keys(dereferenceTypeCount).length > 0) {
+                setModalInfo({
+                    connectionConf: connectionConf,
+                    safelyBreakConnection: safelyBreakConnection,
+                    dereferenceTypeCount: dereferenceTypeCount,
+                    name: name,
+                });
+            }
+            else {
+                safelyBreakConnection();
+            }
+        }
+        if (deletingConnection) {
+            setDeleteDlgDetails({ name: name, connectionConf: connectionConf });
+        }
+    }
+    var connectionMenuItems = [
+        {
+            label: 'Turn on/off connections...',
+            onClick: function () { return setConnectionToggleOpen(true); },
+        },
+    ];
+    if ((0, util_1.isSessionModelWithConnections)(session)) {
+        connectionMenuItems.unshift({
+            label: 'Add connection',
+            onClick: function () {
+                if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                }
+            },
+        });
+        connectionMenuItems.push({
+            label: 'Delete connections...',
+            onClick: function () { return setConnectionManagerOpen(true); },
+        });
+    }
+    var assemblyMenuItems = assemblyNames.length > 1
+        ? [
+            {
+                label: 'Select assembly...',
+                subMenu: assemblyNames.map(function (name, idx) { return ({
+                    label: name,
+                    onClick: function () { return setAssemblyIdx(idx); },
+                }); }),
+            },
+        ]
+        : [];
+    var menuItems = __spreadArray([
+        {
+            label: 'Add track...',
+            onClick: function () {
+                if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                    session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                        view: model.view.id,
+                    }));
+                }
+            },
+        }
+    ], __read(assemblyMenuItems), false);
+    var items = (0, mobx_state_tree_1.getEnv)(model).pluginManager.evaluateExtensionPoint('TrackSelector-multiTrackMenuItems');
+    return (react_1.default.createElement("div", { ref: function (ref) { return 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: function (event) { return setMenuEl(event.currentTarget); } },
+                react_1.default.createElement(Menu_1.default, null))),
+            session.makeConnection && (react_1.default.createElement(material_1.IconButton, { className: classes.menuIcon, onClick: function (event) { return 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: function (event) { return 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: function (event) { return 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: function (_, callback) {
+                callback();
+                setConnectionEl(undefined);
+            }, onClose: function () { return setConnectionEl(undefined); }, menuItems: connectionMenuItems }),
+        react_1.default.createElement(Menu_2.default, { anchorEl: menuEl, open: Boolean(menuEl), onMenuItemClick: function (_, callback) {
+                callback();
+                setMenuEl(undefined);
+            }, onClose: function () { return setMenuEl(undefined); }, menuItems: menuItems }),
+        react_1.default.createElement(Menu_2.default, { anchorEl: selectionEl, open: Boolean(selectionEl), onMenuItemClick: function (_, callback) {
+                callback();
+                setSelectionEl(undefined);
+            }, onClose: function () { return setSelectionEl(undefined); }, menuItems: __spreadArray([
+                { label: 'Clear', onClick: function () { return model.clearSelection(); } }
+            ], __read(items.map(function (item) { return (__assign(__assign({}, item), ('onClick' in item
+                ? { onClick: function () { return item.onClick(model); } }
+                : {}))); })), false) }),
+        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: function () { return setDeleteDlgDetails(undefined); }, deleteDialogDetails: deleteDlgDetails, session: session })) : null,
+            connectionManagerOpen ? (react_1.default.createElement(ManageConnectionsDialog, { handleClose: function () { return setConnectionManagerOpen(false); }, breakConnection: breakConnection, session: session })) : null,
+            connectionToggleOpen ? (react_1.default.createElement(ToggleConnectionsDialog, { handleClose: function () { return 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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package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts

@@ -1,3 +1,4 @@
+/// <reference types="react" />
 import { HierarchicalTrackSelectorModel } from '../model';
 declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overrideDimensions, }: {
     model: HierarchicalTrackSelectorModel;