@jbrowse/plugin-data-management 2.1.0 → 2.1.3

package/dist/HierarchicalTrackSelectorWidget/components/Node.js

@@ -22,129 +22,97 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 material_1 = require("@mui/material");
-var mui_1 = require("tss-react/mui");
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
 // icons
-var ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
-var ArrowRight_1 = __importDefault(require("@mui/icons-material/ArrowRight"));
-var MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
-var Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
-var util_1 = require("@jbrowse/core/util");
-var configuration_1 = require("@jbrowse/core/configuration");
-var util_2 = require("./util");
-var useStyles = (0, mui_1.makeStyles)()(function (theme) {
-    var _a, _b;
-    return ({
-        compactCheckbox: {
-            padding: 0,
-        },
-        checkboxLabel: {
-            marginRight: 0,
-            '&:hover': {
-                backgroundColor: '#eee',
-            },
-        },
-        contrastColor: {
-            color: theme.palette.secondary.contrastText,
+const ArrowDropDown_1 = __importDefault(require("@mui/icons-material/ArrowDropDown"));
+const ArrowRight_1 = __importDefault(require("@mui/icons-material/ArrowRight"));
+const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
+const Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_2 = require("./util");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    compactCheckbox: {
+        padding: 0,
+    },
+    checkboxLabel: {
+        marginRight: 0,
+        '&:hover': {
+            backgroundColor: '#eee',
         },
-        // this accordionBase element's small padding is used to give a margin to
-        // accordionColor it a "margin" because the virtualized elements can't really
-        // use margin in a conventional way (it doesn't affect layout)
-        accordionBase: {
-            display: 'flex',
-        },
-        accordionCard: {
-            padding: 3,
-            cursor: 'pointer',
-            display: 'flex',
-        },
-        nestingLevelMarker: {
-            position: 'absolute',
-            borderLeft: '1.5px solid #555',
-        },
-        // accordionColor set's display:flex so that the child accordionText use
-        // vertically centered text
-        accordionColor: {
-            // @ts-ignore
-            background: (_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.main,
-            // @ts-ignore
-            color: (_b = theme.palette.tertiary) === null || _b === void 0 ? void 0 : _b.contrastText,
-            width: '100%',
-            display: 'flex',
-            paddingLeft: 5,
-        },
-        // margin:auto 0 to center text vertically
-        accordionText: {
-            margin: 'auto 0',
-        },
-    });
-});
-function treeToMap(tree, map) {
-    if (map === void 0) { map = new Map(); }
+    },
+    contrastColor: {
+        color: theme.palette.secondary.contrastText,
+    },
+    // this accordionBase element's small padding is used to give a margin to
+    // accordionColor it a "margin" because the virtualized elements can't really
+    // use margin in a conventional way (it doesn't affect layout)
+    accordionBase: {
+        display: 'flex',
+    },
+    accordionCard: {
+        padding: 3,
+        cursor: 'pointer',
+        display: 'flex',
+    },
+    nestingLevelMarker: {
+        position: 'absolute',
+        borderLeft: '1.5px solid #555',
+    },
+    // accordionColor set's display:flex so that the child accordionText use
+    // vertically centered text
+    accordionColor: {
+        background: theme.palette.tertiary.main,
+        color: theme.palette.tertiary.contrastText,
+        width: '100%',
+        display: 'flex',
+        paddingLeft: 5,
+    },
+    // margin:auto 0 to center text vertically
+    accordionText: {
+        margin: 'auto 0',
+    },
+}));
+function treeToMap(tree, map = new Map()) {
     if (tree.id && tree.children.length) {
         map.set(tree.id, tree);
     }
-    for (var i = 0; i < tree.children.length; i++) {
-        var node = tree.children[i];
+    for (let i = 0; i < tree.children.length; i++) {
+        const node = tree.children[i];
         treeToMap(node, map);
     }
     return map;
 }
-function isUnsupported(name) {
-    if (name === void 0) { name = ''; }
+function isUnsupported(name = '') {
     return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
 }
 // An individual node in the track selector. Note: manually sets cursor:
 // pointer improves usability for what can be clicked
 function Node(props) {
     var _a, _b;
-    var data = props.data, isOpen = props.isOpen, style = props.style, setOpen = props.setOpen;
-    var checked = data.checked, conf = data.conf, drawerPosition = data.drawerPosition, id = data.id, isLeaf = data.isLeaf, model = data.model, name = data.name, nestingLevel = data.nestingLevel, onChange = data.onChange, selected = data.selected, toggleCollapse = data.toggleCollapse, tree = data.tree;
-    var classes = useStyles().classes;
-    var width = 10;
-    var _c = __read((0, react_1.useState)(null), 2), menuEl = _c[0], setMenuEl = _c[1];
-    var _d = __read((0, react_1.useState)(), 2), info = _d[0], setInfo = _d[1];
-    var marginLeft = nestingLevel * width + (isLeaf ? width : 0);
-    var description = (conf && (0, configuration_1.readConfObject)(conf, ['description'])) || '';
+    const { data, isOpen, style, setOpen } = props;
+    const { checked, conf, drawerPosition, id, isLeaf, model, name, nestingLevel, onChange, selected, toggleCollapse, tree, } = data;
+    const { classes } = useStyles();
+    const width = 10;
+    const [menuEl, setMenuEl] = (0, react_1.useState)(null);
+    const [info, setInfo] = (0, react_1.useState)();
+    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
+    const description = (conf && (0, configuration_1.readConfObject)(conf, ['description'])) || '';
     return (react_1.default.createElement("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined },
-        new Array(nestingLevel).fill(0).map(function (_, idx) { return (react_1.default.createElement("div", { key: "mark-".concat(idx), style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker })); }),
-        react_1.default.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, onClick: function () {
+        new Array(nestingLevel).fill(0).map((_, idx) => (react_1.default.createElement("div", { key: `mark-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
+        react_1.default.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, onClick: () => {
                 if (!menuEl) {
                     toggleCollapse(id);
                     setOpen(!isOpen);
                 }
             }, style: {
-                marginLeft: marginLeft,
+                marginLeft,
                 whiteSpace: 'nowrap',
                 width: '100%',
             } },
@@ -153,55 +121,53 @@ function Node(props) {
                     react_1.default.createElement(material_1.Typography, null,
                         isOpen ? react_1.default.createElement(ArrowDropDown_1.default, null) : react_1.default.createElement(ArrowRight_1.default, null),
                         name,
-                        react_1.default.createElement(material_1.IconButton, { onClick: function (event) {
+                        react_1.default.createElement(material_1.IconButton, { onClick: event => {
                                 setMenuEl(event.currentTarget);
                                 event.stopPropagation();
                             }, className: classes.contrastColor },
                             react_1.default.createElement(MoreHoriz_1.default, null))))) : (react_1.default.createElement(react_1.default.Fragment, null,
                     react_1.default.createElement(material_1.Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
-                        react_1.default.createElement(material_1.FormControlLabel, { className: classes.checkboxLabel, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: function () { return onChange(id); }, disabled: isUnsupported(name), inputProps: {
+                        react_1.default.createElement(material_1.FormControlLabel, { className: classes.checkboxLabel, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: isUnsupported(name), inputProps: {
                                     // @ts-ignore
-                                    'data-testid': "htsTrackEntry-".concat(id),
+                                    'data-testid': `htsTrackEntry-${id}`,
                                 } }), label: react_1.default.createElement("div", { style: {
                                     background: selected ? '#cccc' : undefined,
                                     padding: 1,
                                 } }, name) })),
-                    react_1.default.createElement(material_1.IconButton, { onClick: function (e) { return setInfo({ target: e.currentTarget, id: id, conf: conf }); }, style: { padding: 0 }, color: "secondary", "data-testid": "htsTrackEntryMenu-".concat(id) },
+                    react_1.default.createElement(material_1.IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, color: "secondary", "data-testid": `htsTrackEntryMenu-${id}` },
                         react_1.default.createElement(MoreHoriz_1.default, null)))),
                 menuEl ? (react_1.default.createElement(Menu_1.default, { anchorEl: menuEl, menuItems: [
                         {
                             label: 'Add to selection',
-                            onClick: function () {
-                                return model.addToSelection((0, util_2.getAllChildren)(treeToMap(tree).get(id)));
-                            },
+                            onClick: () => model.addToSelection((0, util_2.getAllChildren)(treeToMap(tree).get(id))),
                         },
                         {
                             label: 'Remove from selection',
-                            onClick: function () {
-                                return model.removeFromSelection((0, util_2.getAllChildren)(treeToMap(tree).get(id)));
-                            },
+                            onClick: () => model.removeFromSelection((0, util_2.getAllChildren)(treeToMap(tree).get(id))),
                         },
-                    ], onMenuItemClick: function (_event, callback) {
+                    ], onMenuItemClick: (_event, callback) => {
                         callback();
                         setMenuEl(null);
-                    }, open: Boolean(menuEl), onClose: function () { return setMenuEl(null); } })) : null,
-                info ? (react_1.default.createElement(Menu_1.default, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: __spreadArray(__spreadArray(__spreadArray([], __read((((_b = (_a = (0, util_1.getSession)(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) ||
-                        [])), false), [
+                    }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null,
+                info ? (react_1.default.createElement(Menu_1.default, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
+                        ...(((_b = (_a = (0, util_1.getSession)(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) ||
+                            []),
                         {
                             label: 'Add to selection',
-                            onClick: function () { return model.addToSelection([info.conf]); },
-                        }
-                    ], false), __read((selected
-                        ? [
-                            {
-                                label: 'Remove from selection',
-                                onClick: function () { return model.removeFromSelection([info.conf]); },
-                            },
-                        ]
-                        : [])), false), onMenuItemClick: function (_event, callback) {
+                            onClick: () => model.addToSelection([info.conf]),
+                        },
+                        ...(selected
+                            ? [
+                                {
+                                    label: 'Remove from selection',
+                                    onClick: () => model.removeFromSelection([info.conf]),
+                                },
+                            ]
+                            : []),
+                    ], onMenuItemClick: (_event, callback) => {
                         callback();
                         setInfo(undefined);
-                    }, open: Boolean(info), onClose: function () { return setInfo(undefined); } })) : null))));
+                    }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null))));
 }
 exports.default = Node;
 //# sourceMappingURL=Node.js.map

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

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package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js

@@ -3,13 +3,13 @@ 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 mui_1 = require("tss-react/mui");
-var Close_1 = __importDefault(require("@mui/icons-material/Close"));
-var mobx_react_1 = require("mobx-react");
-var configuration_1 = require("@jbrowse/core/configuration");
-var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const mobx_react_1 = require("mobx-react");
+const configuration_1 = require("@jbrowse/core/configuration");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     closeButton: {
         position: 'absolute',
         right: theme.spacing(1),
@@ -20,13 +20,12 @@ var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
         width: 500,
         margin: theme.spacing(4),
     },
-}); });
-function ToggleConnectionDialog(_a) {
-    var session = _a.session, handleClose = _a.handleClose, assemblyName = _a.assemblyName, breakConnection = _a.breakConnection;
-    var classes = useStyles().classes;
-    var connections = session.connections, _b = session.connectionInstances, instances = _b === void 0 ? [] : _b;
-    var assemblySpecificConnections = connections.filter(function (c) {
-        var configAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+}));
+function ToggleConnectionDialog({ session, handleClose, assemblyName, breakConnection, }) {
+    const { classes } = useStyles();
+    const { connections, connectionInstances: instances = [] } = session;
+    const assemblySpecificConnections = connections.filter(c => {
+        const configAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
         if (configAssemblyNames.length === 0) {
             return true;
         }
@@ -35,15 +34,15 @@ function ToggleConnectionDialog(_a) {
     return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose, maxWidth: "lg" },
         react_1.default.createElement(material_1.DialogTitle, null,
             "Turn on/off connections",
-            react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: function () { return handleClose(); } },
+            react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
                 react_1.default.createElement(Close_1.default, null))),
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null, "Use the checkbox to turn on/off connections"),
             react_1.default.createElement("div", { className: classes.connectionContainer },
-                assemblySpecificConnections.map(function (conf) {
-                    var name = (0, configuration_1.readConfObject)(conf, 'name');
-                    var found = instances.find(function (conn) { return name === conn.name; });
-                    return (react_1.default.createElement(material_1.FormControlLabel, { key: conf.connectionId, control: react_1.default.createElement(material_1.Checkbox, { checked: !!found, onChange: function () {
+                assemblySpecificConnections.map(conf => {
+                    const name = (0, configuration_1.readConfObject)(conf, 'name');
+                    const found = instances.find(conn => name === conn.name);
+                    return (react_1.default.createElement(material_1.FormControlLabel, { key: conf.connectionId, control: react_1.default.createElement(material_1.Checkbox, { checked: !!found, onChange: () => {
                                 var _a;
                                 if (found) {
                                     breakConnection(conf);
@@ -57,7 +56,7 @@ function ToggleConnectionDialog(_a) {
                     "No connections found for ",
                     assemblyName)) : null)),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: function () { return handleClose(); }, variant: "contained", color: "primary" }, "Close"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
 }
 exports.default = (0, mobx_react_1.observer)(ToggleConnectionDialog);
 //# sourceMappingURL=ToggleConnectionsDialog.js.map

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

@@ -1 +1 @@
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package/dist/HierarchicalTrackSelectorWidget/components/util.js

@@ -3,9 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getAllChildren = void 0;
 function getAllChildren(subtree) {
     // @ts-ignore
-    return ((subtree === null || subtree === void 0 ? void 0 : subtree.children.map(function (t) {
-        return t.children.length ? getAllChildren(t) : t.conf;
-    })) || []).flat(Infinity);
+    return ((subtree === null || subtree === void 0 ? void 0 : subtree.children.map(t => t.children.length ? getAllChildren(t) : t.conf)) || []).flat(Infinity);
 }
 exports.getAllChildren = getAllChildren;
 //# sourceMappingURL=util.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":";;;AAGA,SAAgB,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,UAAA,CAAC;QACrB,OAAA,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B;IAAzE,CAAyE,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC;AAPD,wCAOC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":";;;AAGA,SAAgB,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC;AAPD,wCAOC"}

package/dist/HierarchicalTrackSelectorWidget/configSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-var configSchema = (0, configuration_1.ConfigurationSchema)('HierarchicalTrackSelectorWidget', {});
+const configuration_1 = require("@jbrowse/core/configuration");
+const configSchema = (0, configuration_1.ConfigurationSchema)('HierarchicalTrackSelectorWidget', {});
 exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/HierarchicalTrackSelectorWidget/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,IAAM,YAAY,GAAG,IAAA,mCAAmB,EAAC,iCAAiC,EAAE,EAAE,CAAC,CAAA;AAC/E,kBAAe,YAAY,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EAAC,iCAAiC,EAAE,EAAE,CAAC,CAAA;AAC/E,kBAAe,YAAY,CAAA"}

package/dist/HierarchicalTrackSelectorWidget/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = exports.stateModelFactory = void 0;
-var model_1 = __importDefault(require("./model"));
+const model_1 = __importDefault(require("./model"));
 exports.stateModelFactory = model_1.default;
-var configSchema_1 = __importDefault(require("./configSchema"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 exports.configSchema = configSchema_1.default;
 //# sourceMappingURL=index.js.map

package/dist/HierarchicalTrackSelectorWidget/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/index.ts"],"names":[],"mappings":";;;;;;AAAA,kDAA2E;AAGlE,4BAHF,eAAiB,CAGE;AAF1B,gEAAyC;AAEb,uBAFrB,sBAAY,CAEqB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/index.ts"],"names":[],"mappings":";;;;;;AAAA,oDAA2E;AAGlE,4BAHF,eAAiB,CAGE;AAF1B,kEAAyC;AAEb,uBAFrB,sBAAY,CAEqB"}