@jbrowse/plugin-data-management 4.1.3 → 4.1.5

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Files changed (15) hide show
  1. package/esm/AddTrackWidget/components/doSubmit.js +3 -1
  2. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts +1 -1
  3. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js +3 -1
  4. package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.js +4 -6
  5. package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js +25 -3
  6. package/esm/HierarchicalTrackSelectorWidget/components/tree/trackListStyles.d.ts +2 -2
  7. package/esm/HierarchicalTrackSelectorWidget/configSchema.d.ts +1 -1
  8. package/esm/HierarchicalTrackSelectorWidget/facetedModel.js +3 -2
  9. package/esm/HierarchicalTrackSelectorWidget/util.d.ts +1 -0
  10. package/esm/HierarchicalTrackSelectorWidget/util.js +7 -0
  11. package/esm/JB2TrackHubConnection/configSchema.d.ts +3 -3
  12. package/esm/JB2TrackHubConnection/model.d.ts +5 -5
  13. package/esm/UCSCTrackHubConnection/configSchema.d.ts +3 -3
  14. package/esm/UCSCTrackHubConnection/model.d.ts +5 -5
  15. package/package.json +7 -7
package/esm/AddTrackWidget/components/doSubmit.js CHANGED
@@ -31,7 +31,9 @@ export function doSubmit({ model }) {
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  else if (trackConfig && trackAdapter) {
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  const { trackId } = trackConfig;
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  session.addTrackConf(trackConfig);
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- view?.showTrack?.(trackId);
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+ if (view?.assemblyNames?.includes(model.assembly)) {
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+ view.showTrack(trackId);
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+ }
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  if (isElectron &&
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  textIndexTrack &&
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  isSupportedIndexingAdapter(trackAdapter.type)) {
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts CHANGED
@@ -2,7 +2,7 @@ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  declare const ShoppingCart: ({ model, }: {
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  model: {
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  clearSelection: () => void;
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- selection: AnyConfigurationModel[];
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+ selection: (AnyConfigurationModel | undefined)[];
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  };
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  }) => import("react/jsx-runtime").JSX.Element | null;
8
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  export default ShoppingCart;
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js CHANGED
@@ -19,7 +19,9 @@ const ShoppingCart = observer(function ShoppingCart({ model, }) {
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  model.clearSelection();
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  },
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  },
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- ...(selection.every(elt => canEdit(elt.trackId))
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+ ...(selection
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+ .filter((elt) => !!elt)
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+ .every(elt => canEdit(elt.trackId))
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  ? [
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  {
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  label: 'Delete tracks',
package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDataGrid.js CHANGED
@@ -1,13 +1,11 @@
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  import { jsx as _jsx } from "react/jsx-runtime";
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  import { useMemo, useState, useTransition } from 'react';
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- import { getEnv } from '@jbrowse/core/util';
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- import { getRoot, resolveIdentifier } from '@jbrowse/mobx-state-tree';
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+ import { notEmpty } from '@jbrowse/core/util';
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  import { DataGrid } from '@mui/x-data-grid';
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  import { transaction } from 'mobx';
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  import { observer } from 'mobx-react';
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  import { computeInitialWidths } from "./computeInitialWidths.js";
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  const FacetedDataGrid = observer(function FacetedDataGrid({ model, columns, shownTrackIds, selection, }) {
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- const { pluginManager } = getEnv(model);
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  const { view, faceted } = model;
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  const { rows, useShoppingCart, showOptions, filteredRows, filteredNonMetadataKeys, filteredMetadataKeys, visible, } = faceted;
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  const [, startTransition] = useTransition();
@@ -44,9 +42,9 @@ const FacetedDataGrid = observer(function FacetedDataGrid({ model, columns, show
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  });
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  }
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  else {
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- const root = getRoot(model);
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- const schema = pluginManager.pluggableConfigSchemaType('track');
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- model.setSelection([...userSelectedIds.ids].map(id => resolveIdentifier(schema, root, id)));
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+ model.setSelection([...userSelectedIds.ids]
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+ .map(id => model.allTrackConfigurationTrackIdSet.get(id))
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+ .filter(notEmpty));
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  }
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  });
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  }, rowSelectionModel: rowSelectionModel, columns: columnsWithWidths }));
package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js CHANGED
@@ -19,11 +19,33 @@ const useStyles = makeStyles()({
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  width: 5,
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  },
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  });
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+ function HighlightText({ text, query, className, }) {
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+ if (!query || !text) {
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+ return _jsx("span", { className: className, children: text });
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+ }
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+ const lowerText = text.toLowerCase();
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+ const lowerQuery = query.toLowerCase();
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+ const parts = [];
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+ let lastIndex = 0;
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+ let idx = lowerText.indexOf(lowerQuery, lastIndex);
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+ while (idx !== -1) {
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+ if (idx > lastIndex) {
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+ parts.push(text.slice(lastIndex, idx));
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+ }
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+ parts.push(_jsx("mark", { style: { background: '#FFEB3B' }, children: text.slice(idx, idx + query.length) }, idx));
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+ lastIndex = idx + query.length;
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+ idx = lowerText.indexOf(lowerQuery, lastIndex);
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+ }
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+ if (lastIndex < text.length) {
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+ parts.push(text.slice(lastIndex));
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+ }
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+ return _jsx("span", { className: className, children: parts });
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+ }
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  const frac = 0.75;
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  const FacetedSelector = observer(function FacetedSelector({ model, }) {
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  const { classes } = useStyles();
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  const { selection, shownTrackIds, faceted } = model;
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- const { rows, panelWidth, showFilters, filteredNonMetadataKeys, filteredMetadataKeys, } = faceted;
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+ const { rows, panelWidth, showFilters, filterText, filteredNonMetadataKeys, filteredMetadataKeys, } = faceted;
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  const columns = [
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  {
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  field: 'name',
@@ -39,7 +61,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
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  field: e,
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  renderCell: params => {
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  const val = params.value;
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- return val ? (_jsx(SanitizedHTML, { className: classes.cell, html: val })) : ('');
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+ return val ? (_jsx(HighlightText, { className: classes.cell, text: val, query: filterText })) : ('');
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  },
44
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  };
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  }),
@@ -52,7 +74,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
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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 ? (_jsx(SanitizedHTML, { className: classes.cell, html: val })) : ('');
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+ return val ? (_jsx(HighlightText, { className: classes.cell, text: val, query: filterText })) : ('');
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  },
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  };
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  }),
package/esm/HierarchicalTrackSelectorWidget/components/tree/trackListStyles.d.ts CHANGED
@@ -6,8 +6,8 @@ export declare const useSmallBadgeStyles: (_params?: unknown, muiStyleOverridesP
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  } | undefined) => {
7
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  classes: Record<"margin" | "smallBadge", string>;
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  theme: import("@mui/material").Theme;
9
- css: import("node_modules/@jbrowse/core/src/util/tss-react/types").Css;
10
- cx: import("node_modules/@jbrowse/core/src/util/tss-react/types").Cx;
9
+ css: import("@jbrowse/core/util/tss-react/types").Css;
10
+ cx: import("@jbrowse/core/util/tss-react/types").Cx;
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  };
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  export declare const badgeAnchorOrigin: {
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  readonly vertical: "bottom";
package/esm/HierarchicalTrackSelectorWidget/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
1
+ declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
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  export default configSchema;
package/esm/HierarchicalTrackSelectorWidget/facetedModel.js CHANGED
@@ -5,7 +5,7 @@ import { addDisposer, getParent, types } from '@jbrowse/mobx-state-tree';
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  import { autorun, observable } from 'mobx';
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  import { getRowStr } from "./components/faceted/util.js";
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  import { findNonSparseKeys, getRootKeys } from "./facetedUtil.js";
8
- import { matches } from "./util.js";
8
+ import { matches, matchesMetadata } from "./util.js";
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  const nonMetadataKeys = ['category', 'adapter', 'description'];
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  export function facetedStateTreeF() {
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  return types
@@ -58,7 +58,8 @@ export function facetedStateTreeF() {
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  const session = getSession(self);
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  const { allTrackConfigurations, filterText } = self;
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  return allTrackConfigurations
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- .filter(conf => matches(filterText, conf, session))
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+ .filter(conf => matches(filterText, conf, session) ||
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+ matchesMetadata(filterText, conf))
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  .map(track => ({
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  id: track.trackId,
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  conf: track,
package/esm/HierarchicalTrackSelectorWidget/util.d.ts CHANGED
@@ -3,6 +3,7 @@ import type { AbstractSessionModel } from '@jbrowse/core/util';
3
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  export declare function hasAnyOverlap<T>(a1?: T[], a2?: T[]): boolean;
4
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  export declare function hasAllOverlap<T>(a1?: T[], a2?: T[]): boolean;
5
5
  export declare function matches(query: string, conf: AnyConfigurationModel, session: AbstractSessionModel): boolean;
6
+ export declare function matchesMetadata(query: string, conf: AnyConfigurationModel): boolean;
6
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  interface Node {
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  children: Node[];
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  id: string;
package/esm/HierarchicalTrackSelectorWidget/util.js CHANGED
@@ -19,6 +19,13 @@ export function matches(query, conf, session) {
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  return (getTrackName(conf, session).toLowerCase().includes(queryLower) ||
20
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  categories.some(c => c.toLowerCase().includes(queryLower)));
21
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  }
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+ export function matchesMetadata(query, conf) {
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+ const queryLower = query.toLowerCase();
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+ const description = (readConfObject(conf, 'description') || '');
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+ const metadata = (conf.metadata || {});
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+ return (description.toLowerCase().includes(queryLower) ||
27
+ Object.values(metadata).some(v => typeof v === 'string' && v.toLowerCase().includes(queryLower)));
28
+ }
22
29
  export function findSubCategories(obj, paths, depth = 0) {
23
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  let hasSubs = false;
24
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  for (const elt of obj) {
package/esm/JB2TrackHubConnection/configSchema.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- declare const JB2TrackHubConnection: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
1
+ declare const JB2TrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
2
  configJsonLocation: {
3
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  type: string;
4
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  defaultValue: {
@@ -12,7 +12,7 @@ declare const JB2TrackHubConnection: import("node_modules/@jbrowse/core/src/conf
12
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  defaultValue: never[];
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  description: string;
14
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
15
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  name: {
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  type: string;
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  defaultValue: string;
@@ -23,5 +23,5 @@ declare const JB2TrackHubConnection: import("node_modules/@jbrowse/core/src/conf
23
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  defaultValue: never[];
24
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  description: string;
25
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
26
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
27
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  export default JB2TrackHubConnection;
package/esm/JB2TrackHubConnection/model.d.ts CHANGED
@@ -2,7 +2,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  export default function JB2TrackHubConnection(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
3
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  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
4
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  tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
5
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
5
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
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  name: {
7
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  type: string;
8
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  defaultValue: string;
@@ -13,9 +13,9 @@ export default function JB2TrackHubConnection(pluginManager: PluginManager): imp
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  defaultValue: never[];
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  description: string;
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  };
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- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>;
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+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
17
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  } & {
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- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
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+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
19
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  configJsonLocation: {
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  type: string;
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  defaultValue: {
@@ -29,7 +29,7 @@ export default function JB2TrackHubConnection(pluginManager: PluginManager): imp
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  defaultValue: never[];
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  description: string;
31
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  };
32
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
32
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  name: {
34
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  type: string;
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  defaultValue: string;
@@ -40,7 +40,7 @@ export default function JB2TrackHubConnection(pluginManager: PluginManager): imp
40
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  defaultValue: never[];
41
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  description: string;
42
42
  };
43
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
43
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
44
44
  type: import("@jbrowse/mobx-state-tree").ISimpleType<"JB2TrackHubConnection">;
45
45
  }, {
46
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  connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
package/esm/UCSCTrackHubConnection/configSchema.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- declare const UCSCTrackHubConnection: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
1
+ declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
2
  hubTxtLocation: {
3
3
  type: string;
4
4
  defaultValue: {
@@ -12,7 +12,7 @@ declare const UCSCTrackHubConnection: import("node_modules/@jbrowse/core/src/con
12
12
  defaultValue: never[];
13
13
  description: string;
14
14
  };
15
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
15
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
16
16
  name: {
17
17
  type: string;
18
18
  defaultValue: string;
@@ -23,5 +23,5 @@ declare const UCSCTrackHubConnection: import("node_modules/@jbrowse/core/src/con
23
23
  defaultValue: never[];
24
24
  description: string;
25
25
  };
26
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
26
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
27
27
  export default UCSCTrackHubConnection;
package/esm/UCSCTrackHubConnection/model.d.ts CHANGED
@@ -2,7 +2,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
3
3
  name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
4
4
  tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
5
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
5
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
6
6
  name: {
7
7
  type: string;
8
8
  defaultValue: string;
@@ -13,9 +13,9 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
13
13
  defaultValue: never[];
14
14
  description: string;
15
15
  };
16
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>;
16
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
17
17
  } & {
18
- configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
18
+ configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
19
19
  hubTxtLocation: {
20
20
  type: string;
21
21
  defaultValue: {
@@ -29,7 +29,7 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
29
29
  defaultValue: never[];
30
30
  description: string;
31
31
  };
32
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
32
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
33
33
  name: {
34
34
  type: string;
35
35
  defaultValue: string;
@@ -40,7 +40,7 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
40
40
  defaultValue: never[];
41
41
  description: string;
42
42
  };
43
- }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
43
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
44
44
  type: import("@jbrowse/mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
45
45
  }, {
46
46
  connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-data-management",
3
- "version": "4.1.3",
3
+ "version": "4.1.5",
4
4
  "type": "module",
5
5
  "description": "JBrowse 2 linear genome view",
6
6
  "keywords": [
@@ -23,15 +23,15 @@
23
23
  "dependencies": {
24
24
  "@gmod/ucsc-hub": "^2.0.3",
25
25
  "@jbrowse/mobx-state-tree": "^5.5.0",
26
- "@mui/icons-material": "^7.3.7",
27
- "@mui/material": "^7.3.7",
28
- "@mui/x-data-grid": "^8.26.0",
26
+ "@mui/icons-material": "^7.3.8",
27
+ "@mui/material": "^7.3.8",
28
+ "@mui/x-data-grid": "^8.27.1",
29
29
  "deepmerge": "^4.3.1",
30
30
  "mobx": "^6.15.0",
31
31
  "mobx-react": "^9.2.1",
32
- "@jbrowse/core": "^4.1.3",
33
- "@jbrowse/plugin-config": "^4.1.3",
34
- "@jbrowse/product-core": "^4.1.3"
32
+ "@jbrowse/plugin-config": "^4.1.5",
33
+ "@jbrowse/core": "^4.1.5",
34
+ "@jbrowse/product-core": "^4.1.5"
35
35
  },
36
36
  "peerDependencies": {
37
37
  "react": ">=18.0.0"