@jbrowse/plugin-data-management 2.10.2 → 2.11.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/AddConnectionWidget/components/ConnectionTypeSelect.d.ts +1 -1
- package/dist/AssemblyManager/AssemblyEditor.d.ts +1 -5
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.d.ts +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js +2 -2
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.d.ts +4 -4
- package/dist/HierarchicalTrackSelectorWidget/components/dialogs/ManageConnectionsDialog.js +6 -3
- package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js +11 -11
- package/dist/HierarchicalTrackSelectorWidget/components/tree/DropdownTrackSelector.d.ts +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabelMenu.d.ts +2 -2
- package/dist/HierarchicalTrackSelectorWidget/model.d.ts +2 -6
- package/dist/HierarchicalTrackSelectorWidget/model.js +3 -3
- package/dist/ucsc-trackhub/doConnect.js +1 -1
- package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts +1 -1
- package/esm/AssemblyManager/AssemblyEditor.d.ts +1 -5
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalFab.d.ts +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js +2 -2
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.d.ts +4 -4
- package/esm/HierarchicalTrackSelectorWidget/components/dialogs/ManageConnectionsDialog.js +6 -3
- package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js +11 -11
- package/esm/HierarchicalTrackSelectorWidget/components/tree/DropdownTrackSelector.d.ts +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabelMenu.d.ts +2 -2
- package/esm/HierarchicalTrackSelectorWidget/model.d.ts +2 -6
- package/esm/HierarchicalTrackSelectorWidget/model.js +3 -3
- package/esm/ucsc-trackhub/doConnect.js +1 -1
- package/package.json +3 -3
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@@ -2,7 +2,7 @@ import React from 'react';
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import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
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declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
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connectionTypeChoices: ConnectionType[];
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connectionType?: ConnectionType
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connectionType?: ConnectionType;
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setConnectionType: (c?: ConnectionType) => void;
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}) => React.JSX.Element;
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export default ConnectionTypeSelect;
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@@ -1,10 +1,6 @@
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import React from 'react';
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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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declare const AssemblyEditor: ({ assembly, }: {
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assembly?:
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[x: string]: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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setSubschema(slotName: string, data: unknown): any;
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} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
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assembly?: AnyConfigurationModel;
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}) => React.JSX.Element;
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export default AssemblyEditor;
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@@ -49,7 +49,7 @@ const HierarchicalFab = (0, mobx_react_1.observer)(function ({ model, }) {
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}
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const hasConnections = (0, util_1.isSessionModelWithConnections)(session);
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const hasAddTrack = (0, util_1.isSessionWithAddTracks)(session);
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return
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return hasAddTrack || hasConnections ? (react_1.default.createElement(react_1.default.Fragment, null,
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react_1.default.createElement(material_1.Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
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react_1.default.createElement(Add_1.default, null)),
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react_1.default.createElement(material_1.Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) },
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@@ -66,6 +66,6 @@ const HierarchicalFab = (0, mobx_react_1.observer)(function ({ model, }) {
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view: model.view.id,
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}));
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}
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} }, "Add track")) : null))) : null
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} }, "Add track")) : null))) : null;
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});
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exports.default = HierarchicalFab;
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@@ -38,7 +38,7 @@ const AutoSizedHierarchicalTree = ({ tree, model, offset, }) => {
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return typeof jest === 'undefined' ? (react_1.default.createElement(react_virtualized_auto_sizer_1.default, { disableWidth: true }, args => (react_1.default.createElement(HierarchicalTree_1.default, { height: (args.height || offset) - offset, model: model, tree: tree })))) : (react_1.default.createElement(HierarchicalTree_1.default, { height: 9000, model: model, tree: tree }));
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};
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const Wrapper = ({ overrideDimensions, children, }) => {
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return overrideDimensions ? (react_1.default.createElement("div", { style: { ...overrideDimensions } }, children)) : (
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return overrideDimensions ? (react_1.default.createElement("div", { style: { ...overrideDimensions } }, children)) : (children);
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};
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const HierarchicalTrackSelectorContainer = (0, mobx_react_1.observer)(function ({ model, toolbarHeight, overrideDimensions, }) {
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return (react_1.default.createElement(Wrapper, { overrideDimensions: overrideDimensions },
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@@ -1,10 +1,10 @@
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import React from 'react';
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declare const CloseConnectionDialog: ({ modalInfo, onClose, }: {
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modalInfo?: {
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name?: string
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dereferenceTypeCount?: Record<string, number
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safelyBreakConnection?: (
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}
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name?: string;
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dereferenceTypeCount?: Record<string, number>;
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safelyBreakConnection?: () => void;
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};
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onClose: () => void;
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}) => React.JSX.Element;
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export default CloseConnectionDialog;
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@@ -17,6 +17,11 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
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width: 500,
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},
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}));
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function DisabledButton() {
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return (react_1.default.createElement(material_1.Tooltip, { title: "Unable to delete connection in config file as non-admin user" },
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react_1.default.createElement(material_1.IconButton, null,
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react_1.default.createElement(Close_1.default, { color: "disabled" }))));
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}
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const ManageConnectionsDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, breakConnection, }) {
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const { classes } = useStyles();
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const { adminMode, connections, sessionConnections } = session;
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@@ -28,9 +33,7 @@ const ManageConnectionsDialog = (0, mobx_react_1.observer)(function ({ session,
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const name = (0, configuration_1.readConfObject)(conf, 'name');
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return (react_1.default.createElement(material_1.Typography, { key: `conn-${name}` },
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adminMode || (sessionConnections === null || sessionConnections === void 0 ? void 0 : sessionConnections.includes(conf)) ? (react_1.default.createElement(material_1.IconButton, { onClick: () => breakConnection(conf, true) },
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react_1.default.createElement(Close_1.default, { color: "error" }))) : (react_1.default.createElement(
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react_1.default.createElement(material_1.IconButton, null,
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react_1.default.createElement(Close_1.default, { color: "disabled" })))),
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react_1.default.createElement(Close_1.default, { color: "error" }))) : (react_1.default.createElement(DisabledButton, null)),
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name));
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}),
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!connections.length ? (react_1.default.createElement(material_1.Typography, null, "No connections found")) : null)),
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@@ -43,7 +43,7 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
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{
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field: 'name',
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hideable: false,
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renderCell:
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renderCell: params => {
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const { value, row } = params;
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const { id, conf } = row;
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return (react_1.default.createElement("div", { className: classes.cell },
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},
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...filteredNonMetadataKeys.map(e => {
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var _a;
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return
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return {
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field: e,
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width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
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renderCell:
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renderCell: params => {
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const val = params.value;
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return val ? react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val }) : '';
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return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
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},
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}
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};
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}),
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...filteredMetadataKeys.map(e => {
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var _a;
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return
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return {
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field: `metadata.${e}`,
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headerName: ['name', ...filteredNonMetadataKeys].includes(e)
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? `${e} (from metadata)`
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: e,
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width: (_a = widthsDebounced['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
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valueGetter: (
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renderCell:
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const val = params.
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return val ? react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val }) : '';
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valueGetter: (_, row) => `${row.metadata[e]}`,
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renderCell: params => {
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const val = params.value;
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return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
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}
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};
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}),
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];
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return (react_1.default.createElement(react_1.default.Fragment, null,
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model: HierarchicalTrackSelectorModel;
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tracks: AnyConfigurationModel[];
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extraMenuItems: MenuItem[];
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onClick?: (
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onClick?: () => void;
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}) => React.JSX.Element | null;
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declare const TrackLabelMenu: ({ id, trackId, stopPropagation, model, setOpen, conf, }: {
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stopPropagation?: boolean;
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setOpen?: (
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setOpen?: (arg: boolean) => void;
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export default TrackLabelMenu;
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panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
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}, {
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* #property
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const facetedModel_1 = require("./facetedModel");
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// for settings that are config dependent
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function postNoConfigF() {
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return typeof window !== 'undefined'
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? [window.location.host, window.location.pathname].join('-')
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: 'empty';
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}
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// for settings that are not config dependent
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? [
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postNoConfigF(),
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...this.configAndSessionTrackConfigurations,
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...connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks),
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...((connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks)) || []),
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/**
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session.notifyError(`${(0, configuration_1.getConf)(self, 'name')}: "${e}"`, e);
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}
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import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
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declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
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import React from 'react';
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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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declare const AssemblyEditor: ({ assembly, }: {
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[x: string]: any;
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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setSubschema(slotName: string, data: unknown): any;
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} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
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return hasAddTrack || hasConnections ? (React.createElement(React.Fragment, null,
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React.createElement(Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
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React.createElement(AddIcon, null)),
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} }, "Add track")) : null))) : null
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} }, "Add track")) : null))) : null;
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return overrideDimensions ? (React.createElement("div", { style: { ...overrideDimensions } }, children)) : (children);
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};
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const HierarchicalTrackSelectorContainer = observer(function ({ model, toolbarHeight, overrideDimensions, }) {
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return (React.createElement(Wrapper, { overrideDimensions: overrideDimensions },
|
|
@@ -1,10 +1,10 @@
|
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1
1
|
import React from 'react';
|
|
2
2
|
declare const CloseConnectionDialog: ({ modalInfo, onClose, }: {
|
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3
3
|
modalInfo?: {
|
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4
|
-
name?: string
|
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5
|
-
dereferenceTypeCount?: Record<string, number
|
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6
|
-
safelyBreakConnection?: (
|
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7
|
-
}
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4
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+
name?: string;
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5
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+
dereferenceTypeCount?: Record<string, number>;
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6
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+
safelyBreakConnection?: () => void;
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7
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+
};
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onClose: () => void;
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9
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}) => React.JSX.Element;
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export default CloseConnectionDialog;
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@@ -12,6 +12,11 @@ const useStyles = makeStyles()(theme => ({
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width: 500,
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},
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}));
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+
function DisabledButton() {
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+
return (React.createElement(Tooltip, { title: "Unable to delete connection in config file as non-admin user" },
|
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+
React.createElement(IconButton, null,
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18
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+
React.createElement(CloseIcon, { color: "disabled" }))));
|
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+
}
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const ManageConnectionsDialog = observer(function ({ session, handleClose, breakConnection, }) {
|
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16
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const { classes } = useStyles();
|
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17
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const { adminMode, connections, sessionConnections } = session;
|
|
@@ -23,9 +28,7 @@ const ManageConnectionsDialog = observer(function ({ session, handleClose, break
|
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23
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|
const name = readConfObject(conf, 'name');
|
|
24
29
|
return (React.createElement(Typography, { key: `conn-${name}` },
|
|
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adminMode || (sessionConnections === null || sessionConnections === void 0 ? void 0 : sessionConnections.includes(conf)) ? (React.createElement(IconButton, { onClick: () => breakConnection(conf, true) },
|
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26
|
-
React.createElement(CloseIcon, { color: "error" }))) : (React.createElement(
|
|
27
|
-
React.createElement(IconButton, null,
|
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28
|
-
React.createElement(CloseIcon, { color: "disabled" })))),
|
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31
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+
React.createElement(CloseIcon, { color: "error" }))) : (React.createElement(DisabledButton, null)),
|
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29
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|
name));
|
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30
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|
}),
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34
|
!connections.length ? (React.createElement(Typography, null, "No connections found")) : null)),
|
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@@ -38,7 +38,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
|
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38
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|
{
|
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39
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|
field: 'name',
|
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40
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|
hideable: false,
|
|
41
|
-
renderCell:
|
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41
|
+
renderCell: params => {
|
|
42
42
|
const { value, row } = params;
|
|
43
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|
const { id, conf } = row;
|
|
44
44
|
return (React.createElement("div", { className: classes.cell },
|
|
@@ -49,29 +49,29 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
|
|
|
49
49
|
},
|
|
50
50
|
...filteredNonMetadataKeys.map(e => {
|
|
51
51
|
var _a;
|
|
52
|
-
return
|
|
52
|
+
return {
|
|
53
53
|
field: e,
|
|
54
54
|
width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
|
|
55
|
-
renderCell:
|
|
55
|
+
renderCell: params => {
|
|
56
56
|
const val = params.value;
|
|
57
|
-
return val ? React.createElement(SanitizedHTML, { className: classes.cell, html: val }) : '';
|
|
57
|
+
return val ? (React.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
|
|
58
58
|
},
|
|
59
|
-
}
|
|
59
|
+
};
|
|
60
60
|
}),
|
|
61
61
|
...filteredMetadataKeys.map(e => {
|
|
62
62
|
var _a;
|
|
63
|
-
return
|
|
63
|
+
return {
|
|
64
64
|
field: `metadata.${e}`,
|
|
65
65
|
headerName: ['name', ...filteredNonMetadataKeys].includes(e)
|
|
66
66
|
? `${e} (from metadata)`
|
|
67
67
|
: e,
|
|
68
68
|
width: (_a = widthsDebounced['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
|
|
69
|
-
valueGetter: (
|
|
70
|
-
renderCell:
|
|
71
|
-
const val = params.
|
|
72
|
-
return val ? React.createElement(SanitizedHTML, { className: classes.cell, html: val }) : '';
|
|
69
|
+
valueGetter: (_, row) => `${row.metadata[e]}`,
|
|
70
|
+
renderCell: params => {
|
|
71
|
+
const val = params.value;
|
|
72
|
+
return val ? (React.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
|
|
73
73
|
},
|
|
74
|
-
}
|
|
74
|
+
};
|
|
75
75
|
}),
|
|
76
76
|
];
|
|
77
77
|
return (React.createElement(React.Fragment, null,
|
|
@@ -6,7 +6,7 @@ declare const DropdownTrackSelector: ({ model, tracks, extraMenuItems, children,
|
|
|
6
6
|
model: HierarchicalTrackSelectorModel;
|
|
7
7
|
tracks: AnyConfigurationModel[];
|
|
8
8
|
extraMenuItems: MenuItem[];
|
|
9
|
-
onClick?: (
|
|
9
|
+
onClick?: () => void;
|
|
10
10
|
children: React.ReactElement;
|
|
11
11
|
}) => React.JSX.Element | null;
|
|
12
12
|
export default DropdownTrackSelector;
|
|
@@ -4,9 +4,9 @@ import { HierarchicalTrackSelectorModel } from '../../model';
|
|
|
4
4
|
declare const TrackLabelMenu: ({ id, trackId, stopPropagation, model, setOpen, conf, }: {
|
|
5
5
|
id: string;
|
|
6
6
|
trackId: string;
|
|
7
|
-
stopPropagation?: boolean
|
|
7
|
+
stopPropagation?: boolean;
|
|
8
8
|
conf: AnyConfigurationModel;
|
|
9
|
-
setOpen?: (
|
|
9
|
+
setOpen?: (arg: boolean) => void;
|
|
10
10
|
model: HierarchicalTrackSelectorModel;
|
|
11
11
|
}) => React.JSX.Element;
|
|
12
12
|
export default TrackLabelMenu;
|
|
@@ -45,13 +45,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
|
|
|
45
45
|
panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
46
46
|
}, {
|
|
47
47
|
visible: Record<string, boolean>;
|
|
48
|
-
widths: Record<string, number | undefined>;
|
|
49
|
-
* #property
|
|
50
|
-
*/
|
|
48
|
+
widths: Record<string, number | undefined>;
|
|
51
49
|
useShoppingCart: boolean;
|
|
52
|
-
filters: import("mobx").ObservableMap<string, string[]>;
|
|
53
|
-
* #property
|
|
54
|
-
*/
|
|
50
|
+
filters: import("mobx").ObservableMap<string, string[]>;
|
|
55
51
|
} & {
|
|
56
52
|
setFilter(key: string, value: string[]): void;
|
|
57
53
|
setPanelWidth(width: number): void;
|
|
@@ -10,13 +10,13 @@ import { findSubCategories, findTopLevelCategories } from './util';
|
|
|
10
10
|
import { facetedStateTreeF } from './facetedModel';
|
|
11
11
|
// for settings that are config dependent
|
|
12
12
|
function postNoConfigF() {
|
|
13
|
-
return typeof window !== undefined
|
|
13
|
+
return typeof window !== 'undefined'
|
|
14
14
|
? [window.location.host, window.location.pathname].join('-')
|
|
15
15
|
: 'empty';
|
|
16
16
|
}
|
|
17
17
|
// for settings that are not config dependent
|
|
18
18
|
function postF() {
|
|
19
|
-
return typeof window !== undefined
|
|
19
|
+
return typeof window !== 'undefined'
|
|
20
20
|
? [
|
|
21
21
|
postNoConfigF(),
|
|
22
22
|
new URLSearchParams(window.location.search).get('config'),
|
|
@@ -329,7 +329,7 @@ export default function stateTreeFactory(pluginManager) {
|
|
|
329
329
|
const { connectionInstances = [] } = getSession(self);
|
|
330
330
|
return [
|
|
331
331
|
...this.configAndSessionTrackConfigurations,
|
|
332
|
-
...connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks),
|
|
332
|
+
...((connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks)) || []),
|
|
333
333
|
];
|
|
334
334
|
},
|
|
335
335
|
/**
|
|
@@ -121,7 +121,7 @@ export async function doConnect(self) {
|
|
|
121
121
|
}
|
|
122
122
|
catch (e) {
|
|
123
123
|
console.error(e);
|
|
124
|
-
session.
|
|
124
|
+
session.notifyError(`${getConf(self, 'name')}: "${e}"`, e);
|
|
125
125
|
(_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
|
|
126
126
|
}
|
|
127
127
|
}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-data-management",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.11.0",
|
|
4
4
|
"description": "JBrowse 2 linear genome view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -38,7 +38,7 @@
|
|
|
38
38
|
"dependencies": {
|
|
39
39
|
"@gmod/ucsc-hub": "^0.3.0",
|
|
40
40
|
"@mui/icons-material": "^5.0.1",
|
|
41
|
-
"@mui/x-data-grid": "^
|
|
41
|
+
"@mui/x-data-grid": "^7.0.0",
|
|
42
42
|
"react-virtualized-auto-sizer": "^1.0.2",
|
|
43
43
|
"react-vtree": "^3.0.0-beta.1",
|
|
44
44
|
"react-window": "^1.8.6"
|
|
@@ -60,5 +60,5 @@
|
|
|
60
60
|
"distModule": "esm/index.js",
|
|
61
61
|
"srcModule": "src/index.ts",
|
|
62
62
|
"module": "esm/index.js",
|
|
63
|
-
"gitHead": "
|
|
63
|
+
"gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
|
|
64
64
|
}
|