@jbrowse/plugin-data-management 2.4.0 → 2.4.2
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/AddTrackWidget/components/ConfirmTrack.js +1 -1
- package/dist/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js +1 -1
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -1
- package/dist/AddTrackWidget/components/TrackTypeSelector.js +1 -1
- package/dist/AddTrackWidget/components/TrackTypeSelector.js.map +1 -1
- package/dist/AddTrackWidget/model.js +5 -5
- package/dist/AddTrackWidget/model.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.js +9 -9
- package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js +0 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js +2 -2
- package/dist/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/util.js +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/util.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/index.d.ts +2 -4
- package/dist/HierarchicalTrackSelectorWidget/index.js +4 -2
- package/dist/HierarchicalTrackSelectorWidget/index.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/model.d.ts +1 -1
- package/dist/HierarchicalTrackSelectorWidget/model.js +15 -6
- package/dist/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/dist/PluginStoreWidget/components/InstalledPluginsList.js +4 -4
- package/dist/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -1
- package/dist/PluginStoreWidget/components/PluginCard.js +2 -1
- package/dist/PluginStoreWidget/components/PluginCard.js.map +1 -1
- package/dist/index.d.ts +2 -3
- package/dist/index.js.map +1 -1
- package/dist/ucsc-trackhub/ucscTrackHub.d.ts +1 -2
- package/dist/ucsc-trackhub/ucscTrackHub.js +11 -11
- package/dist/ucsc-trackhub/ucscTrackHub.js.map +1 -1
- package/esm/AddTrackWidget/components/ConfirmTrack.js +1 -1
- package/esm/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js +1 -1
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -1
- package/esm/AddTrackWidget/components/TrackTypeSelector.js +1 -1
- package/esm/AddTrackWidget/components/TrackTypeSelector.js.map +1 -1
- package/esm/AddTrackWidget/model.js +5 -5
- package/esm/AddTrackWidget/model.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.js +9 -9
- package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js +0 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js +2 -2
- package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/util.js +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/util.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/index.d.ts +2 -4
- package/esm/HierarchicalTrackSelectorWidget/index.js +2 -1
- package/esm/HierarchicalTrackSelectorWidget/index.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/model.d.ts +1 -1
- package/esm/HierarchicalTrackSelectorWidget/model.js +15 -6
- package/esm/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/esm/PluginStoreWidget/components/InstalledPluginsList.js +4 -4
- package/esm/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -1
- package/esm/PluginStoreWidget/components/PluginCard.js +2 -1
- package/esm/PluginStoreWidget/components/PluginCard.js.map +1 -1
- package/esm/index.d.ts +2 -3
- package/esm/index.js.map +1 -1
- package/esm/ucsc-trackhub/ucscTrackHub.d.ts +1 -2
- package/esm/ucsc-trackhub/ucscTrackHub.js +9 -10
- package/esm/ucsc-trackhub/ucscTrackHub.js.map +1 -1
- package/package.json +2 -2
- package/src/AddConnectionWidget/components/AddConnectionWidget.test.tsx +4 -4
- package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.tsx.snap +1 -1
- package/src/AddTrackWidget/components/ConfirmTrack.tsx +1 -1
- package/src/AddTrackWidget/components/TrackAdapterSelector.tsx +1 -1
- package/src/AddTrackWidget/components/TrackTypeSelector.tsx +1 -1
- package/src/AddTrackWidget/index.test.tsx +2 -2
- package/src/AddTrackWidget/model.ts +5 -5
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.tsx +4 -4
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx +1 -1
- package/src/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.tsx +9 -9
- package/src/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.tsx +4 -5
- package/src/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.tsx +0 -2
- package/src/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.tsx +4 -4
- package/src/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.tsx +1 -1
- package/src/HierarchicalTrackSelectorWidget/components/util.ts +1 -1
- package/src/HierarchicalTrackSelectorWidget/index.ts +7 -4
- package/src/HierarchicalTrackSelectorWidget/model.ts +14 -6
- package/src/PluginStoreWidget/components/InstalledPluginsList.tsx +7 -5
- package/src/PluginStoreWidget/components/PluginCard.tsx +2 -3
- package/src/PluginStoreWidget/components/PluginStoreWidget.test.tsx +3 -3
- package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.tsx.snap +1 -1
- package/src/index.ts +5 -5
- package/src/ucsc-trackhub/ucscTrackHub.ts +9 -10
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@@ -4,7 +4,15 @@ import { dedupe, getSession, getEnv, } from '@jbrowse/core/util';
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import { getTrackName } from '@jbrowse/core/util/tracks';
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import { ElementId } from '@jbrowse/core/util/types/mst';
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function hasAnyOverlap(a1 = [], a2 = []) {
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-
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+
// shortcut case is that arrays are single entries, and are equal
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// long case is that we use a set
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if (a1[0] === a2[0]) {
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return true;
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}
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else {
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const s1 = new Set(a1);
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return a2.some(a => s1.has(a));
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}
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}
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export function matches(query, conf, session) {
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const categories = readConfObject(conf, 'category');
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@@ -70,7 +78,7 @@ export function generateHierarchy(model, trackConfigurations, collapsed, extra)
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id: conf.trackId,
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name: getTrackName(conf, session),
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conf,
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checked:
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checked: tracks.some(f => f.configuration === conf),
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children: [],
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});
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});
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@@ -124,7 +132,7 @@ export default function stateTreeFactory(pluginManager) {
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return undefined;
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}
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for (const display of trackConf.displays) {
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if (viewType.displayTypes.
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if (viewType.displayTypes.some(d => d.name === display.type)) {
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return trackConf;
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}
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}
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@@ -143,9 +151,10 @@ export default function stateTreeFactory(pluginManager) {
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const refseq = self.getRefSeqTrackConf(assemblyName);
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// filter out tracks that don't match the current assembly (check all
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// assembly aliases) and display types
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return
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return [
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...(refseq ? [refseq] : []),
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...filterTracks(tracks, self, assemblyName),
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-
]
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];
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},
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get assemblyNames() {
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var _a;
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@@ -170,7 +179,7 @@ export default function stateTreeFactory(pluginManager) {
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const assembly = assemblyManager.get(assemblyName);
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const conns = (assembly &&
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(connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.map(c => ({
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// @ts-
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// @ts-expect-error
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id: getSnapshot(c).configuration,
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name: getConf(c, 'name'),
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children: this.connectionHierarchy(assemblyName, c),
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@@ -1 +1 @@
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1
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-
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1
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+
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@@ -4,11 +4,11 @@ import { List, Typography } from '@mui/material';
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4
4
|
import InstalledPlugin from './InstalledPlugin';
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5
5
|
function InstalledPluginsList({ pluginManager, model, }) {
|
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6
6
|
const { plugins } = pluginManager;
|
|
7
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-
const corePlugins = plugins
|
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7
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+
const corePlugins = new Set(plugins
|
|
8
8
|
.filter(p => { var _a; return (_a = pluginManager.pluginMetadata[p.name]) === null || _a === void 0 ? void 0 : _a.isCore; })
|
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9
|
-
.map(p => p.name);
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|
10
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-
const externalPlugins = plugins.filter(plugin => !corePlugins.
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11
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-
return (React.createElement(List, null, externalPlugins.length ? (externalPlugins
|
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9
|
+
.map(p => p.name));
|
|
10
|
+
const externalPlugins = plugins.filter(plugin => !corePlugins.has(plugin.name));
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11
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+
return (React.createElement(List, null, externalPlugins.length > 0 ? (externalPlugins
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12
12
|
.filter(plugin => plugin.name.toLowerCase().includes(model.filterText.toLowerCase()))
|
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13
13
|
.map(plugin => (React.createElement(InstalledPlugin, { key: plugin.name, plugin: plugin, model: model, pluginManager: pluginManager })))) : (React.createElement(Typography, null, "No plugins currently installed"))));
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14
14
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}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"InstalledPluginsList.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/InstalledPluginsList.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAGhD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,SAAS,oBAAoB,CAAC,EAC5B,aAAa,EACb,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,aAAa,CAAA;IAEjC,MAAM,WAAW,GAAG,OAAO;
|
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1
|
+
{"version":3,"file":"InstalledPluginsList.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/InstalledPluginsList.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAGhD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,SAAS,oBAAoB,CAAC,EAC5B,aAAa,EACb,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,aAAa,CAAA;IAEjC,MAAM,WAAW,GAAG,IAAI,GAAG,CACzB,OAAO;SACJ,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,aAAa,CAAC,cAAc,CAAC,CAAC,CAAC,IAAI,CAAC,0CAAE,MAAM,CAAA,EAAA,CAAC;SACzD,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CACpB,CAAA;IAED,MAAM,eAAe,GAAG,OAAO,CAAC,MAAM,CACpC,MAAM,CAAC,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CACxC,CAAA;IAED,OAAO,CACL,oBAAC,IAAI,QACF,eAAe,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAC5B,eAAe;SACZ,MAAM,CAAC,MAAM,CAAC,EAAE,CACf,MAAM,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CACnE;SACA,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACb,oBAAC,eAAe,IACd,GAAG,EAAE,MAAM,CAAC,IAAI,EAChB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,KAAK,EACZ,aAAa,EAAE,aAAa,GAC5B,CACH,CAAC,CACL,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,yCAA4C,CACxD,CACI,CACR,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
|
|
@@ -30,7 +30,8 @@ export default observer(function PluginCard({ plugin, model, adminMode, }) {
|
|
|
30
30
|
const { classes } = useStyles();
|
|
31
31
|
const session = getSession(model);
|
|
32
32
|
const { pluginManager } = getEnv(model);
|
|
33
|
-
const
|
|
33
|
+
const { runtimePluginDefinitions } = pluginManager;
|
|
34
|
+
const isInstalled = runtimePluginDefinitions.some(d => d.url === plugin.url);
|
|
34
35
|
const [tempDisabled, setTempDisabled] = useState(false);
|
|
35
36
|
const disableButton = isInstalled || tempDisabled;
|
|
36
37
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"PluginCard.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/PluginCard.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAEL,2BAA2B,GAC5B,MAAM,0BAA0B,CAAA;AACjC,OAAO,EACL,IAAI,EACJ,WAAW,EACX,WAAW,EACX,MAAM,EACN,IAAI,EACJ,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,UAAU,MAAM,4BAA4B,CAAA;AACnD,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAC7C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAKjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,MAAM,EAAE,KAAK;KACd;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,OAAO;QACnB,WAAW,EAAE,OAAO;KACrB;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,GAAG;KAChB;IACD,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,MAAM,EAAE,WAAW;KACpB;CACF,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC1C,MAAM,EACN,KAAK,EACL,SAAS,GAKV;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,
|
|
1
|
+
{"version":3,"file":"PluginCard.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/PluginCard.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAEL,2BAA2B,GAC5B,MAAM,0BAA0B,CAAA;AACjC,OAAO,EACL,IAAI,EACJ,WAAW,EACX,WAAW,EACX,MAAM,EACN,IAAI,EACJ,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,UAAU,MAAM,4BAA4B,CAAA;AACnD,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAC7C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAKjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,MAAM,EAAE,KAAK;KACd;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,OAAO;QACnB,WAAW,EAAE,OAAO;KACrB;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,GAAG;KAChB;IACD,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,MAAM,EAAE,WAAW;KACpB;CACF,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC1C,MAAM,EACN,KAAK,EACL,SAAS,GAKV;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,wBAAwB,EAAE,GAAG,aAAa,CAAA;IAClD,MAAM,WAAW,GAAG,wBAAwB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,MAAM,CAAC,GAAG,CAAC,CAAA;IAC5E,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvD,MAAM,aAAa,GAAG,WAAW,IAAI,YAAY,CAAA;IAEjD,8DAA8D;IAC9D,MAAM,SAAS,GAAG,SAAS,CAAM,KAAK,EAAE,CAAC,CAAC,CAAA;IAC1C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,CAAA;IAE7B,OAAO,CACL,oBAAC,IAAI,IAAC,OAAO,EAAC,UAAU,EAAC,GAAG,EAAE,MAAM,CAAC,IAAI,EAAE,SAAS,EAAE,OAAO,CAAC,IAAI;QAChE,oBAAC,WAAW;YACV,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;gBAC/B,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI;oBACtB,oBAAC,IAAI,IACH,IAAI,EAAE,GAAG,MAAM,CAAC,QAAQ,SAAS,EACjC,MAAM,EAAC,QAAQ,EACf,GAAG,EAAC,UAAU,IAEb,MAAM,CAAC,IAAI,CACP,CACI,CACT;YACN,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;gBAC/B,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,GAAI;gBAC/C,oBAAC,UAAU,QAAE,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAc,CAChD;YACN,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI,mBAA2B;YAC9D,oBAAC,UAAU,QAAE,MAAM,CAAC,WAAW,CAAc,CACjC;QACd,oBAAC,WAAW;YACV,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,aAAa,EACvB,SAAS,EAAE,WAAW,CAAC,CAAC,CAAC,oBAAC,SAAS,OAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,OAAG,EACpD,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,SAAS,EAAE;wBACb,OAAO,CAAC,SAAS,CAAC,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;qBAC1D;yBAAM,IAAI,2BAA2B,CAAC,OAAO,CAAC,EAAE;wBAC/C,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAA;qBACjC;oBACD,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvB,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAC/B,CACG,CACT,CACR,CAAA;AACH,CAAC,CAAC,CAAA"}
|
package/esm/index.d.ts
CHANGED
|
@@ -1,8 +1,6 @@
|
|
|
1
1
|
/// <reference types="react" />
|
|
2
2
|
import Plugin from '@jbrowse/core/Plugin';
|
|
3
3
|
import PluginManager from '@jbrowse/core/PluginManager';
|
|
4
|
-
import { AddTrackModel } from './AddTrackWidget/model';
|
|
5
|
-
import { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
|
|
6
4
|
declare const SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
|
|
7
5
|
rootModel?: unknown;
|
|
8
6
|
onClose: () => void;
|
|
@@ -27,4 +25,5 @@ export default class extends Plugin {
|
|
|
27
25
|
configure(_pluginManager: PluginManager): void;
|
|
28
26
|
}
|
|
29
27
|
export { AssemblyManager, SetDefaultSession };
|
|
30
|
-
export
|
|
28
|
+
export { type AddTrackModel } from './AddTrackWidget/model';
|
|
29
|
+
export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,uBAAuB,MAAM,iBAAiB,CAAA;AACrD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAE9C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,uBAAuB,MAAM,iBAAiB,CAAA;AACrD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAE9C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,gCAAgC,MAAM,mCAAmC,CAAA;AAEhF,MAAM,iBAAiB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAA;AAEnE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,CAAA;AAE/D,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,sBAAsB,CAAA;QAE7B,YAAO,GAAG;YACR,eAAe;YACf,iBAAiB;SAClB,CAAA;IAWH,CAAC;IATC,OAAO,CAAC,aAA4B;QAClC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,eAAe,CAAC,aAAa,CAAC,CAAA;QAC9B,gCAAgC,CAAC,aAAa,CAAC,CAAA;QAC/C,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C;AAED,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,CAAA"}
|
|
@@ -1,7 +1,5 @@
|
|
|
1
1
|
import { TrackDbFile } from '@gmod/ucsc-hub';
|
|
2
2
|
import { FileLocation } from '@jbrowse/core/util';
|
|
3
|
-
import ucscAssemblies from './ucscAssemblies';
|
|
4
|
-
export { ucscAssemblies };
|
|
5
3
|
export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
|
|
6
4
|
export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
|
|
7
5
|
export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
|
|
@@ -22,3 +20,4 @@ export declare function makeLoc2(first: string, alt?: string): {
|
|
|
22
20
|
locationType: string;
|
|
23
21
|
};
|
|
24
22
|
export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
|
|
23
|
+
export { default as ucscAssemblies } from './ucscAssemblies';
|
|
@@ -1,8 +1,6 @@
|
|
|
1
1
|
import { isUriLocation, objectHash } from '@jbrowse/core/util';
|
|
2
2
|
import { openLocation } from '@jbrowse/core/util/io';
|
|
3
3
|
import { generateUnsupportedTrackConf, generateUnknownTrackConf, } from '@jbrowse/core/util/tracks';
|
|
4
|
-
import ucscAssemblies from './ucscAssemblies';
|
|
5
|
-
export { ucscAssemblies };
|
|
6
4
|
export async function fetchHubFile(hubLocation) {
|
|
7
5
|
try {
|
|
8
6
|
const hubFileText = await openLocation(hubLocation).readFile('utf8');
|
|
@@ -44,18 +42,18 @@ export function makeLoc2(first, alt) {
|
|
|
44
42
|
};
|
|
45
43
|
}
|
|
46
44
|
export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
|
|
45
|
+
var _a;
|
|
47
46
|
const tracks = [];
|
|
48
|
-
trackDb.
|
|
49
|
-
|
|
50
|
-
const
|
|
51
|
-
const parentTrackKeys = [
|
|
47
|
+
for (const [trackName, track] of trackDb.entries()) {
|
|
48
|
+
const trackKeys = [...track.keys()];
|
|
49
|
+
const parentTrackKeys = new Set([
|
|
52
50
|
'superTrack',
|
|
53
51
|
'compositeTrack',
|
|
54
52
|
'container',
|
|
55
53
|
'view',
|
|
56
|
-
];
|
|
57
|
-
if (trackKeys.some(key => parentTrackKeys.
|
|
58
|
-
|
|
54
|
+
]);
|
|
55
|
+
if (trackKeys.some(key => parentTrackKeys.has(key))) {
|
|
56
|
+
continue;
|
|
59
57
|
}
|
|
60
58
|
const parentTracks = [];
|
|
61
59
|
let currentTrackName = trackName;
|
|
@@ -77,7 +75,7 @@ export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapte
|
|
|
77
75
|
trackId: `ucsc-trackhub-${objectHash(res)}`,
|
|
78
76
|
assemblyNames: [assemblyName],
|
|
79
77
|
});
|
|
80
|
-
}
|
|
78
|
+
}
|
|
81
79
|
return tracks;
|
|
82
80
|
}
|
|
83
81
|
function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter) {
|
|
@@ -289,4 +287,5 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
|
|
|
289
287
|
return generateUnknownTrackConf(name, baseTrackType, categories);
|
|
290
288
|
}
|
|
291
289
|
}
|
|
290
|
+
export { default as ucscAssemblies } from './ucscAssemblies';
|
|
292
291
|
//# sourceMappingURL=ucscTrackHub.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ucscTrackHub.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscTrackHub.ts"],"names":[],"mappings":"AAEA,OAAO,EAAgB,aAAa,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EACL,4BAA4B,EAC5B,wBAAwB,GACzB,MAAM,2BAA2B,CAAA;
|
|
1
|
+
{"version":3,"file":"ucscTrackHub.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscTrackHub.ts"],"names":[],"mappings":"AAEA,OAAO,EAAgB,aAAa,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EACL,4BAA4B,EAC5B,wBAAwB,GACzB,MAAM,2BAA2B,CAAA;AAElC,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,WAAyB;IAC1D,IAAI;QACF,MAAM,WAAW,GAAG,MAAM,YAAY,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;QAClD,OAAO,IAAI,OAAO,CAAC,WAAW,CAAC,CAAA;KAChC;IAAC,OAAO,KAAK,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,yCAAyC,KAAK,GAAG,CAAC,CAAA;KACnE;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,eAAe,GAAG,MAAM,YAAY,CAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACvE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,eAAe,CAAC,CAAA;AACzC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,IAAI,GAAG,MAAM,YAAY,CAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5D,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,IAAI,CAAC,CAAA;AAC9B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,KAAa,EAAE,IAAqB;IAC1D,OAAO;QACL,GAAG,EAAE,IAAI,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI;QAClC,YAAY,EAAE,aAAa;KAC5B,CAAA;AACH,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,KAAa,EAAE,GAAW,EAAE,IAAqB;IAC1E,OAAO,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;AAC1D,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,KAAa,EAAE,GAAY;IAClD,OAAO,KAAK;QACV,CAAC,CAAC;YACE,GAAG,EAAE,KAAK;YACV,YAAY,EAAE,WAAW;SAC1B;QACH,CAAC,CAAC;YACE,GAAG,EAAE,GAAG;YACR,YAAY,EAAE,aAAa;SAC5B,CAAA;AACP,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,OAAoB,EACpB,UAAwB,EACxB,YAAoB,EACpB,eAAoB;;IAEpB,MAAM,MAAM,GAAQ,EAAE,CAAA;IAEtB,KAAK,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE;QAClD,MAAM,SAAS,GAAG,CAAC,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC,CAAA;QACnC,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC;YAC9B,YAAY;YACZ,gBAAgB;YAChB,WAAW;YACX,MAAM;SACP,CAAC,CAAA;QACF,IAAI,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE;YACnD,SAAQ;SACT;QACD,MAAM,YAAY,GAAG,EAAE,CAAA;QACvB,IAAI,gBAAgB,GAAG,SAAS,CAAA;QAChC,GAAG;YACD,gBAAgB,GAAG,CAAA,MAAA,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,0CAAE,GAAG,CAAC,QAAQ,CAAC,KAAI,EAAE,CAAA;YACrE,IAAI,gBAAgB,EAAE;gBACpB,CAAC;gBAAA,CAAC,gBAAgB,CAAC,GAAG,gBAAgB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACjD,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAA;aACjD;SACF,QAAQ,gBAAgB,EAAC;QAC1B,YAAY,CAAC,OAAO,EAAE,CAAA;QACtB,MAAM,UAAU,GAAG,YAAY;aAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,GAAG,CAAC,YAAY,CAAC,CAAC;aAC9B,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,eAAe,CACzB,KAAK,EACL,UAAU,EACV,UAAU,EACV,OAAO,EACP,eAAe,CAChB,CAAA;QACD,MAAM,CAAC,IAAI,CAAC;YACV,GAAG,GAAG;YACN,OAAO,EAAE,iBAAiB,UAAU,CAAC,GAAG,CAAC,EAAE;YAC3C,aAAa,EAAE,CAAC,YAAY,CAAC;SAC9B,CAAC,CAAA;KACH;IAED,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,eAAe,CACtB,KAAe,EACf,UAAoB,EACpB,UAAwB,EACxB,OAAoB,EACpB,eAAoB;;IAEpB,IAAI,SAAS,GAAG,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAChD,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,EAAE,CAAA;IAClD,MAAM,KAAK,GAAG,aAAa,CAAC,UAAU,CAAC,CAAA;IACvC,IAAI,CAAC,SAAS,EAAE;QACd,SAAS,GAAG,MAAA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,0CAAE,GAAG,CAAC,MAAM,CAAC,CAAA;KAChE;IACD,IAAI,aAAa,GAAG,CAAA,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,KAAI,EAAE,CAAA;IAClD,IAAI,aAAa,KAAK,KAAK,IAAI,UAAU,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;QACxE,aAAa,GAAG,MAAM,CAAA;KACvB;IACD,MAAM,eAAe,GAAG,KAAK;QAC3B,CAAC,CAAC,OAAO,CAAC,UAAU,EAAE,UAAU,CAAC;QACjC,CAAC,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAA;IAExB,QAAQ,aAAa,EAAE;QACrB,KAAK,KAAK;YACR,OAAO;gBACL,IAAI,EAAE,iBAAiB;gBACvB,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC;gBAC7B,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,eAAe;oBAC5B,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK;4BACb,CAAC,CAAC,UAAU,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,EAAE,UAAU,CAAC;4BACzD,CAAC,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,CAAC;qBAC9C;iBACF;aACF,CAAA;QAEH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,UAAU;YACb,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,mBAAmB;gBACzB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QAEH,KAAK,MAAM;YACT,OAAO;gBACL,IAAI,EAAE,iBAAiB;gBACvB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,aAAa;oBACnB,YAAY,EAAE,eAAe;oBAC7B,YAAY,EAAE,KAAK;wBACjB,CAAC,CAAC,UAAU,CAAC,UAAU,EAAE,UAAU,GAAG,OAAO,EAAE,UAAU,CAAC;wBAC1D,CAAC,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,OAAO,CAAC;oBAC9C,eAAe;iBAChB;aACF,CAAA;QAEH,KAAK,eAAe;YAClB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,gBAAgB;YACnB,OAAO,4BAA4B,CAAC,IAAI,EAAE,aAAa,EAAE,UAAU,CAAC,CAAA;QACtE,KAAK,UAAU;YACb,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,iBAAiB;oBACvB,aAAa,EAAE,eAAe;oBAC9B,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK;4BACb,CAAC,CAAC,UAAU,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,EAAE,UAAU,CAAC;4BACzD,CAAC,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,CAAC;qBAC9C;iBACF;aACF,CAAA;QAEH,KAAK,KAAK;YACR,OAAO;gBACL,IAAI,EAAE,UAAU;gBAChB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,eAAe;iBAC7B;aACF,CAAA;QAEH,oBAAoB;QACpB,kBAAkB;QAClB,kBAAkB;QAClB,yBAAyB;QACzB,kBAAkB;QAClB,qBAAqB;QACrB,uBAAuB;QACvB,kBAAkB;QAClB,6BAA6B;QAC7B,uBAAuB;QACvB,6BAA6B;QAC7B,wBAAwB;QACxB,0BAA0B;QAC1B;YACE,OAAO,wBAAwB,CAAC,IAAI,EAAE,aAAa,EAAE,UAAU,CAAC,CAAA;KACnE;AACH,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,kBAAkB,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-data-management",
|
|
3
|
-
"version": "2.4.
|
|
3
|
+
"version": "2.4.2",
|
|
4
4
|
"description": "JBrowse 2 linear genome view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -61,5 +61,5 @@
|
|
|
61
61
|
"distModule": "esm/index.js",
|
|
62
62
|
"srcModule": "src/index.ts",
|
|
63
63
|
"module": "esm/index.js",
|
|
64
|
-
"gitHead": "
|
|
64
|
+
"gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
|
|
65
65
|
}
|
|
@@ -47,8 +47,8 @@ describe('<AddConnectionWidget />', () => {
|
|
|
47
47
|
|
|
48
48
|
it('can handle a custom UCSC trackHub URL', async () => {
|
|
49
49
|
const mockFetch = async (url: RequestInfo | URL) => {
|
|
50
|
-
// @ts-
|
|
51
|
-
const urlText = url.href
|
|
50
|
+
// @ts-expect-error
|
|
51
|
+
const urlText = url.href || url
|
|
52
52
|
let responseText = ''
|
|
53
53
|
if (urlText.endsWith('hub.txt')) {
|
|
54
54
|
responseText = `hub TestHub
|
|
@@ -98,8 +98,8 @@ type bigWig
|
|
|
98
98
|
|
|
99
99
|
it('can handle a custom JBrowse 1 data directory URL', async () => {
|
|
100
100
|
const mockFetch = async (url: RequestInfo | URL) => {
|
|
101
|
-
// @ts-
|
|
102
|
-
const urlText = url.href
|
|
101
|
+
// @ts-expect-error
|
|
102
|
+
const urlText = url.href || url
|
|
103
103
|
let responseText = ''
|
|
104
104
|
if (urlText.endsWith('trackList.json')) {
|
|
105
105
|
responseText = '{}'
|
|
@@ -68,7 +68,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
|
|
|
68
68
|
class="MuiFormControl-root MuiFormControl-fullWidth MuiTextField-root css-wb57ya-MuiFormControl-root-MuiTextField-root"
|
|
69
69
|
>
|
|
70
70
|
<label
|
|
71
|
-
class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-colorPrimary MuiFormLabel-filled MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined css-
|
|
71
|
+
class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-colorPrimary MuiFormLabel-filled MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined css-1jy569b-MuiFormLabel-root-MuiInputLabel-root"
|
|
72
72
|
data-shrink="true"
|
|
73
73
|
for="mui-1"
|
|
74
74
|
id="mui-1-label"
|
|
@@ -44,7 +44,7 @@ const TrackAdapterSelector = observer(({ model }: { model: AddTrackModel }) => {
|
|
|
44
44
|
fullWidth
|
|
45
45
|
onChange={event => model.setAdapterHint(event.target.value)}
|
|
46
46
|
SelectProps={{
|
|
47
|
-
// @ts-
|
|
47
|
+
// @ts-expect-error
|
|
48
48
|
SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
|
|
49
49
|
}}
|
|
50
50
|
>
|
|
@@ -30,7 +30,7 @@ const TrackTypeSelector = observer(({ model }: { model: AddTrackModel }) => {
|
|
|
30
30
|
fullWidth
|
|
31
31
|
onChange={event => model.setTrackType(event.target.value)}
|
|
32
32
|
SelectProps={{
|
|
33
|
-
// @ts-
|
|
33
|
+
// @ts-expect-error
|
|
34
34
|
SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
|
|
35
35
|
}}
|
|
36
36
|
>
|
|
@@ -53,9 +53,9 @@ const realLocation = window.location
|
|
|
53
53
|
|
|
54
54
|
// https://stackoverflow.com/a/60110508/2129219
|
|
55
55
|
function setWindowLoc(loc: string) {
|
|
56
|
-
// @ts-
|
|
56
|
+
// @ts-expect-error
|
|
57
57
|
delete window.location
|
|
58
|
-
// @ts-
|
|
58
|
+
// @ts-expect-error
|
|
59
59
|
window.location = new URL(loc)
|
|
60
60
|
}
|
|
61
61
|
|
|
@@ -104,18 +104,18 @@ export default function f(pluginManager: PluginManager) {
|
|
|
104
104
|
get isFtp() {
|
|
105
105
|
const { trackData: track, indexTrackData: index } = self
|
|
106
106
|
return !!(
|
|
107
|
-
// @ts-
|
|
107
|
+
// @ts-expect-error
|
|
108
108
|
(index?.uri?.startsWith('ftp://') || track?.uri?.startsWith('ftp://'))
|
|
109
109
|
)
|
|
110
110
|
},
|
|
111
111
|
|
|
112
112
|
get isRelativeTrackUrl() {
|
|
113
|
-
// @ts-
|
|
113
|
+
// @ts-expect-error
|
|
114
114
|
const uri = self.trackData?.uri
|
|
115
115
|
return uri ? !isAbsoluteUrl(uri) : false
|
|
116
116
|
},
|
|
117
117
|
get isRelativeIndexUrl() {
|
|
118
|
-
// @ts-
|
|
118
|
+
// @ts-expect-error
|
|
119
119
|
const uri = self.indexTrackData?.uri
|
|
120
120
|
return uri ? !isAbsoluteUrl(uri) : false
|
|
121
121
|
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@@ -124,11 +124,11 @@ export default function f(pluginManager: PluginManager) {
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},
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get trackHttp() {
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// @ts-
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+
// @ts-expect-error
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return self.trackData?.uri?.startsWith('http://')
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},
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get indexHttp() {
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// @ts-
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// @ts-expect-error
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@@ -9,7 +9,7 @@ import HierarchicalTrackSelector from './HierarchicalTrackSelector'
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jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
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// @ts-
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+
// @ts-expect-error
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window.requestIdleCallback = cb => cb()
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window.cancelIdleCallback = () => {}
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@@ -20,7 +20,7 @@ test('renders nothing with no assembly', () => {
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const { container } = render(
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<ThemeProvider theme={createJBrowseTheme()}>
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-
{/* @ts-
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+
{/* @ts-expect-error*/}
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<HierarchicalTrackSelector model={model} />
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</ThemeProvider>,
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)
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@@ -76,7 +76,7 @@ test('renders with a couple of uncategorized tracks', async () => {
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const { container, findByTestId } = render(
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<ThemeProvider theme={createJBrowseTheme()}>
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-
{/* @ts-
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+
{/* @ts-expect-error*/}
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<HierarchicalTrackSelector model={model} />
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</ThemeProvider>,
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)
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@@ -139,7 +139,7 @@ test('renders with a couple of categorized tracks', async () => {
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const { container, findByTestId } = render(
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<ThemeProvider theme={createJBrowseTheme()}>
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-
{/* @ts-
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+
{/* @ts-expect-error*/}
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<HierarchicalTrackSelector model={model} />
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</ThemeProvider>,
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)
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@@ -65,7 +65,7 @@ function FacetFilter({
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className={classes.select}
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value={filters[column.field]}
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onChange={event => {
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-
// @ts-
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+
// @ts-expect-error
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const { options } = event.target
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const val: string[] = []
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const len = options.length
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@@ -105,28 +105,28 @@ export default function FacetFilters({
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}) {
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const facets = columns.slice(1)
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const uniqs = facets.map(() => new Map<string, number>())
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|
-
|
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|
-
facets.
|
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|
+
for (const row of rows) {
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|
+
for (const [index, column] of facets.entries()) {
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|
const elt = uniqs[index]
|
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|
const key = `${row[column.field] || ''}`
|
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112
|
const val = elt.get(key)
|
|
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|
// we don't allow filtering on empty yet
|
|
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|
if (key) {
|
|
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|
-
if (val
|
|
116
|
-
elt.set(key, val + 1)
|
|
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|
-
} else {
|
|
115
|
+
if (val === undefined) {
|
|
118
116
|
elt.set(key, 1)
|
|
117
|
+
} else {
|
|
118
|
+
elt.set(key, val + 1)
|
|
119
119
|
}
|
|
120
120
|
}
|
|
121
|
-
}
|
|
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|
-
}
|
|
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|
+
}
|
|
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|
+
}
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|
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123
|
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|
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|
return (
|
|
125
125
|
<div>
|
|
126
126
|
{facets.map((column, index) => (
|
|
127
127
|
<FacetFilter
|
|
128
128
|
key={column.field}
|
|
129
|
-
vals={
|
|
129
|
+
vals={[...uniqs[index]]}
|
|
130
130
|
column={column}
|
|
131
131
|
width={width}
|
|
132
132
|
dispatch={dispatch}
|
|
@@ -99,11 +99,10 @@ export default observer(function FacetedSelector({
|
|
|
99
99
|
|
|
100
100
|
const filteredMetadataKeys = useMemo(
|
|
101
101
|
() =>
|
|
102
|
-
[...new Set(rows.
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
: rows.map(r => r.metadata[f]).filter(f => !!f).length > 5,
|
|
102
|
+
[...new Set(rows.flatMap(row => getRootKeys(row.metadata)))].filter(f =>
|
|
103
|
+
!hideSparse
|
|
104
|
+
? true
|
|
105
|
+
: rows.map(r => r.metadata[f]).filter(f => !!f).length > 5,
|
|
107
106
|
),
|
|
108
107
|
[hideSparse, rows],
|
|
109
108
|
)
|
|
@@ -73,8 +73,6 @@ export default observer(function HamburgerMenu({
|
|
|
73
73
|
deletingConnection?: boolean,
|
|
74
74
|
) {
|
|
75
75
|
const name = readConfObject(connectionConf, 'name')
|
|
76
|
-
|
|
77
|
-
// @ts-ignore
|
|
78
76
|
const result = session.prepareToBreakConnection(connectionConf)
|
|
79
77
|
if (result) {
|
|
80
78
|
const [safelyBreakConnection, dereferenceTypeCount] = result
|
|
@@ -70,7 +70,7 @@ export default observer(function HierarchicalTree({
|
|
|
70
70
|
}
|
|
71
71
|
|
|
72
72
|
while (true) {
|
|
73
|
-
// @ts-
|
|
73
|
+
// @ts-expect-error
|
|
74
74
|
const parentMeta = yield
|
|
75
75
|
|
|
76
76
|
for (let i = 0; i < parentMeta.node.children.length; i++) {
|
|
@@ -83,7 +83,7 @@ export default observer(function HierarchicalTree({
|
|
|
83
83
|
)
|
|
84
84
|
|
|
85
85
|
useEffect(() => {
|
|
86
|
-
// @ts-
|
|
86
|
+
// @ts-expect-error
|
|
87
87
|
treeRef.current.recomputeTree({
|
|
88
88
|
refreshNodes: true,
|
|
89
89
|
useDefaultHeight: true,
|
|
@@ -91,9 +91,9 @@ export default observer(function HierarchicalTree({
|
|
|
91
91
|
}, [tree, filterText])
|
|
92
92
|
return (
|
|
93
93
|
<>
|
|
94
|
-
{/* @ts-
|
|
94
|
+
{/* @ts-expect-error */}
|
|
95
95
|
<VariableSizeTree ref={treeRef} treeWalker={treeWalker} height={height}>
|
|
96
|
-
{/* @ts-
|
|
96
|
+
{/* @ts-expect-error */}
|
|
97
97
|
{Node}
|
|
98
98
|
</VariableSizeTree>
|
|
99
99
|
</>
|
|
@@ -17,7 +17,7 @@ export interface NodeData {
|
|
|
17
17
|
}
|
|
18
18
|
|
|
19
19
|
export function getAllChildren(subtree?: TreeNode): AnyConfigurationModel[] {
|
|
20
|
-
// @ts-
|
|
20
|
+
// @ts-expect-error
|
|
21
21
|
return (
|
|
22
22
|
subtree?.children.map(t =>
|
|
23
23
|
t.children.length ? getAllChildren(t) : (t.conf as AnyConfigurationModel),
|
|
@@ -1,12 +1,9 @@
|
|
|
1
|
-
import stateModelFactory
|
|
1
|
+
import stateModelFactory from './model'
|
|
2
2
|
import configSchema from './configSchema'
|
|
3
3
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
4
4
|
import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
|
|
5
5
|
import { lazy } from 'react'
|
|
6
6
|
|
|
7
|
-
export { stateModelFactory, configSchema }
|
|
8
|
-
export type { HierarchicalTrackSelectorModel }
|
|
9
|
-
|
|
10
7
|
export default (pluginManager: PluginManager) => {
|
|
11
8
|
pluginManager.addWidgetType(() => {
|
|
12
9
|
return new WidgetType({
|
|
@@ -20,3 +17,9 @@ export default (pluginManager: PluginManager) => {
|
|
|
20
17
|
})
|
|
21
18
|
})
|
|
22
19
|
}
|
|
20
|
+
|
|
21
|
+
export {
|
|
22
|
+
type HierarchicalTrackSelectorModel,
|
|
23
|
+
default as stateModelFactory,
|
|
24
|
+
} from './model'
|
|
25
|
+
export { default as configSchema } from './configSchema'
|