@jbrowse/plugin-data-management 2.2.2 → 2.3.1
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/AddTrackWidget.js +28 -5
- package/dist/AddTrackWidget/components/AddTrackWidget.js.map +1 -1
- package/dist/AddTrackWidget/components/ConfirmTrack.d.ts +2 -3
- package/dist/AddTrackWidget/components/ConfirmTrack.js +30 -177
- package/dist/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map +1 -1
- package/dist/AddTrackWidget/components/TextIndexingConfig.d.ts +6 -0
- package/dist/AddTrackWidget/components/TextIndexingConfig.js +109 -0
- package/dist/AddTrackWidget/components/TextIndexingConfig.js.map +1 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.d.ts +6 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js +50 -0
- package/dist/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.d.ts +6 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.js +27 -0
- package/dist/AddTrackWidget/components/TrackTypeSelector.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +3 -4
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +3 -1
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -1
- package/dist/HierarchicalTrackSelectorWidget/model.d.ts +2 -1
- package/dist/HierarchicalTrackSelectorWidget/model.js +5 -5
- package/dist/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/dist/ucsc-trackhub/index.d.ts +2 -2
- package/dist/ucsc-trackhub/index.js.map +1 -1
- package/dist/ucsc-trackhub/model.d.ts +3 -2
- package/dist/ucsc-trackhub/model.js +41 -40
- package/dist/ucsc-trackhub/model.js.map +1 -1
- package/dist/ucsc-trackhub/ucscAssemblies.js.map +1 -1
- package/esm/AddTrackWidget/components/AddTrackWidget.js +6 -6
- package/esm/AddTrackWidget/components/AddTrackWidget.js.map +1 -1
- package/esm/AddTrackWidget/components/ConfirmTrack.d.ts +2 -3
- package/esm/AddTrackWidget/components/ConfirmTrack.js +28 -175
- package/esm/AddTrackWidget/components/ConfirmTrack.js.map +1 -1
- package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map +1 -1
- package/esm/AddTrackWidget/components/TextIndexingConfig.d.ts +6 -0
- package/esm/AddTrackWidget/components/TextIndexingConfig.js +81 -0
- package/esm/AddTrackWidget/components/TextIndexingConfig.js.map +1 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.d.ts +6 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js +45 -0
- package/esm/AddTrackWidget/components/TrackAdapterSelector.js.map +1 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.d.ts +6 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.js +22 -0
- package/esm/AddTrackWidget/components/TrackTypeSelector.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +3 -4
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +3 -1
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -1
- package/esm/HierarchicalTrackSelectorWidget/model.d.ts +2 -1
- package/esm/HierarchicalTrackSelectorWidget/model.js +5 -5
- package/esm/HierarchicalTrackSelectorWidget/model.js.map +1 -1
- package/esm/ucsc-trackhub/index.d.ts +2 -2
- package/esm/ucsc-trackhub/index.js.map +1 -1
- package/esm/ucsc-trackhub/model.d.ts +3 -2
- package/esm/ucsc-trackhub/model.js +41 -40
- package/esm/ucsc-trackhub/model.js.map +1 -1
- package/esm/ucsc-trackhub/ucscAssemblies.js.map +1 -1
- package/package.json +3 -4
- package/src/AddTrackWidget/components/AddTrackWidget.test.tsx +3 -4
- package/src/AddTrackWidget/components/AddTrackWidget.tsx +6 -9
- package/src/AddTrackWidget/components/ConfirmTrack.tsx +36 -296
- package/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx +0 -1
- package/src/AddTrackWidget/components/TextIndexingConfig.tsx +134 -0
- package/src/AddTrackWidget/components/TrackAdapterSelector.tsx +73 -0
- package/src/AddTrackWidget/components/TrackTypeSelector.tsx +46 -0
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx +4 -4
- package/src/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.tsx +5 -1
- package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap +1 -1
- package/src/HierarchicalTrackSelectorWidget/model.ts +7 -7
- package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap +0 -22
- package/src/ucsc-trackhub/{index.js → index.ts} +0 -0
- package/src/ucsc-trackhub/model.ts +119 -0
- package/src/ucsc-trackhub/{ucscAssemblies.js → ucscAssemblies.ts} +0 -0
- package/src/ucsc-trackhub/model.js +0 -125
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@@ -29,7 +29,7 @@ function filterTracks(tracks, self, assemblyName) {
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return hasAnyOverlap(compatDisplays, trackDisplays);
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});
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}
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-
export function generateHierarchy(model, trackConfigurations, collapsed) {
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export function generateHierarchy(model, trackConfigurations, collapsed, extra) {
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const hierarchy = { children: [] };
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const { filterText, view } = model;
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const session = getSession(model);
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@@ -49,7 +49,7 @@ export function generateHierarchy(model, trackConfigurations, collapsed) {
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for (let i = 0; i < categories.length; i++) {
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const category = categories[i];
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const ret = currLevel.children.find(c => c.name === category);
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const id = categories.slice(0, i + 1).join(',');
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const id = extra + '-' + categories.slice(0, i + 1).join(',');
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if (!ret) {
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const n = {
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children: [],
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@@ -166,7 +166,7 @@ export default function stateTreeFactory(pluginManager) {
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const { assemblyManager } = getSession(self);
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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.
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(connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.map(c => ({
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// @ts-ignore
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id: getSnapshot(c).configuration,
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name: getConf(c, 'name'),
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@@ -174,7 +174,7 @@ export default function stateTreeFactory(pluginManager) {
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state: {
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expanded: true,
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},
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})))) ||
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})).filter(f => f.children.length))) ||
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[];
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return {
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name: 'Root',
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@@ -188,7 +188,7 @@ export default function stateTreeFactory(pluginManager) {
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connectionHierarchy(assemblyName, connection) {
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return generateHierarchy(
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
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self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed, connection.name);
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},
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}));
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}
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@@ -1 +1 @@
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-
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+
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@@ -1,2 +1,2 @@
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1
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-
export { default as modelFactory } from
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2
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-
export { default as configSchema } from
|
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1
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+
export { default as modelFactory } from './model';
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2
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+
export { default as configSchema } from './configSchema';
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.
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1
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+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,SAAS,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
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@@ -1,4 +1,5 @@
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1
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-
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1
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+
import PluginManager from '@jbrowse/core/PluginManager';
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2
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+
export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
|
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2
3
|
name: import("mobx-state-tree").ISimpleType<string>;
|
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3
4
|
tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
|
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4
5
|
} & {
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@@ -23,5 +24,5 @@ export default function UCSCTrackHubConnection(pluginManager: any): import("mobx
|
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23
24
|
} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
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24
25
|
clear(): void;
|
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25
26
|
} & {
|
|
26
|
-
connect(): void
|
|
27
|
+
connect(): Promise<void>;
|
|
27
28
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
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@@ -2,81 +2,82 @@ import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/
|
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2
2
|
import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
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3
3
|
import { getSession } from '@jbrowse/core/util';
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4
4
|
import { types } from 'mobx-state-tree';
|
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5
|
+
// locals
|
|
5
6
|
import configSchema from './configSchema';
|
|
6
7
|
import { fetchGenomesFile, fetchHubFile, fetchTrackDbFile, generateTracks, } from './ucscTrackHub';
|
|
7
8
|
export default function UCSCTrackHubConnection(pluginManager) {
|
|
8
|
-
return types
|
|
9
|
-
.model({
|
|
9
|
+
return types
|
|
10
|
+
.compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
|
|
10
11
|
configuration: ConfigurationReference(configSchema),
|
|
11
12
|
type: types.literal('UCSCTrackHubConnection'),
|
|
12
|
-
})
|
|
13
|
+
}))
|
|
13
14
|
.actions(self => ({
|
|
14
|
-
connect() {
|
|
15
|
-
const connectionName = getConf(self, 'name');
|
|
16
|
-
const hubFileLocation = getConf(self, 'hubTxtLocation');
|
|
15
|
+
async connect() {
|
|
17
16
|
const session = getSession(self);
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
const
|
|
17
|
+
try {
|
|
18
|
+
const connectionName = getConf(self, 'name');
|
|
19
|
+
const hubFileLocation = getConf(self, 'hubTxtLocation');
|
|
20
|
+
const hubFile = await fetchHubFile(hubFileLocation);
|
|
21
|
+
const genomeFile = hubFile.get('genomesFile');
|
|
22
|
+
if (!genomeFile) {
|
|
23
|
+
throw new Error('genomesFile not found on hub');
|
|
24
|
+
}
|
|
25
|
+
const hubUri = new URL(hubFileLocation.uri, hubFileLocation.baseUri);
|
|
26
|
+
const genomesFileLocation = hubUri
|
|
21
27
|
? {
|
|
22
|
-
uri: new URL(
|
|
28
|
+
uri: new URL(genomeFile, hubUri).href,
|
|
23
29
|
locationType: 'UriLocation',
|
|
24
30
|
}
|
|
25
31
|
: {
|
|
26
|
-
localPath:
|
|
32
|
+
localPath: genomeFile,
|
|
27
33
|
locationType: 'LocalPathLocation',
|
|
28
34
|
};
|
|
29
|
-
|
|
30
|
-
hubFile,
|
|
31
|
-
fetchGenomesFile(genomesFileLocation),
|
|
32
|
-
]);
|
|
33
|
-
})
|
|
34
|
-
.then(([hubFile, genomesFile]) => {
|
|
35
|
+
const genomesFile = await fetchGenomesFile(genomesFileLocation);
|
|
35
36
|
const trackDbData = [];
|
|
36
37
|
for (const [genomeName, genome] of genomesFile) {
|
|
37
38
|
const assemblyNames = getConf(self, 'assemblyNames');
|
|
38
39
|
if (assemblyNames.length > 0 &&
|
|
39
40
|
!assemblyNames.includes(genomeName)) {
|
|
40
|
-
|
|
41
|
+
continue;
|
|
41
42
|
}
|
|
42
|
-
const
|
|
43
|
-
if (!
|
|
43
|
+
const conf = session.assemblies.find(a => readConfObject(a, 'name') === genomeName);
|
|
44
|
+
if (!conf) {
|
|
44
45
|
throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
|
|
45
46
|
}
|
|
46
|
-
const
|
|
47
|
+
const trackDb = genome.get('trackDb');
|
|
48
|
+
if (!trackDb) {
|
|
49
|
+
throw new Error('genomesFile not found on hub');
|
|
50
|
+
}
|
|
51
|
+
const trackDbFileLocation = hubUri
|
|
47
52
|
? {
|
|
48
|
-
uri: new URL(
|
|
53
|
+
uri: new URL(trackDb, new URL(genomeFile, hubUri)).href,
|
|
49
54
|
locationType: 'UriLocation',
|
|
50
55
|
}
|
|
51
56
|
: {
|
|
52
|
-
localPath:
|
|
57
|
+
localPath: trackDb,
|
|
53
58
|
locationType: 'LocalPathLocation',
|
|
54
59
|
};
|
|
55
|
-
trackDbData.push(
|
|
60
|
+
trackDbData.push([
|
|
56
61
|
trackDbFileLocation,
|
|
57
|
-
fetchTrackDbFile(trackDbFileLocation),
|
|
62
|
+
await fetchTrackDbFile(trackDbFileLocation),
|
|
58
63
|
genomeName,
|
|
59
|
-
|
|
60
|
-
])
|
|
64
|
+
conf,
|
|
65
|
+
]);
|
|
61
66
|
}
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
.then(trackDbData => {
|
|
65
|
-
for (const [trackDbFileLocation, trackDbFile, genomeName, assemblyConf,] of trackDbData) {
|
|
66
|
-
const sequenceAdapter = readConfObject(assemblyConf, [
|
|
67
|
+
for (const [trackDbFileLocation, trackDbFile, genomeName, conf,] of trackDbData) {
|
|
68
|
+
const sequenceAdapter = readConfObject(conf, [
|
|
67
69
|
'sequence',
|
|
68
70
|
'adapter',
|
|
69
71
|
]);
|
|
70
|
-
|
|
71
|
-
self.addTrackConfs(tracks);
|
|
72
|
+
self.addTrackConfs(generateTracks(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter));
|
|
72
73
|
}
|
|
73
|
-
}
|
|
74
|
-
|
|
75
|
-
console.error(
|
|
76
|
-
session.notify(`There was a problem connecting to the UCSC Track Hub "${self.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${
|
|
74
|
+
}
|
|
75
|
+
catch (e) {
|
|
76
|
+
console.error(e);
|
|
77
|
+
session.notify(`There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`, 'error');
|
|
77
78
|
session.breakConnection(self.configuration);
|
|
78
|
-
}
|
|
79
|
+
}
|
|
79
80
|
},
|
|
80
|
-
}))
|
|
81
|
+
}));
|
|
81
82
|
}
|
|
82
83
|
//# sourceMappingURL=model.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EACL,sBAAsB,EACtB,cAAc,EACd,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EACL,gBAAgB,EAChB,YAAY,EACZ,gBAAgB,EAChB,cAAc,GACf,MAAM,gBAAgB,CAAA;AAEvB,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,aAA4B;IACzE,OAAO,KAAK;SACT,OAAO,CACN,wBAAwB,EACxB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;YACX,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI;gBACF,MAAM,cAAc,GAAG,OAAO,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;gBAC5C,MAAM,eAAe,GAAG,OAAO,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,aAAa;qBAC5B;oBACH,CAAC,CAAC;wBACE,SAAS,EAAE,UAAU;wBACrB,YAAY,EAAE,mBAAmB;qBAClC,CAAA;gBACL,MAAM,WAAW,GAAG,MAAM,gBAAgB,CAAC,mBAAmB,CAAC,CAAA;gBAC/D,MAAM,WAAW,GAAG,EAAE,CAAA;gBACtB,KAAK,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,IAAI,WAAW,EAAE;oBAC9C,MAAM,aAAa,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;oBACpD,IACE,aAAa,CAAC,MAAM,GAAG,CAAC;wBACxB,CAAC,aAAa,CAAC,QAAQ,CAAC,UAAU,CAAC,EACnC;wBACA,SAAQ;qBACT;oBACD,MAAM,IAAI,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAClC,CAAC,CAAC,EAAE,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC,KAAK,UAAU,CAC9C,CAAA;oBACD,IAAI,CAAC,IAAI,EAAE;wBACT,MAAM,IAAI,KAAK,CACb,6BAA6B,UAAU,2CAA2C,cAAc,GAAG,CACpG,CAAA;qBACF;oBACD,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;oBACrC,IAAI,CAAC,OAAO,EAAE;wBACZ,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;qBAChD;oBACD,MAAM,mBAAmB,GAAG,MAAM;wBAChC,CAAC,CAAC;4BACE,GAAG,EAAE,IAAI,GAAG,CAAC,OAAO,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI;4BACvD,YAAY,EAAE,aAAa;yBAC5B;wBACH,CAAC,CAAC;4BACE,SAAS,EAAE,OAAO;4BAClB,YAAY,EAAE,mBAAmB;yBAClC,CAAA;oBACL,WAAW,CAAC,IAAI,CAAC;wBACf,mBAAmB;wBACnB,MAAM,gBAAgB,CAAC,mBAAmB,CAAC;wBAC3C,UAAU;wBACV,IAAI;qBACI,CAAC,CAAA;iBACZ;gBACD,KAAK,MAAM,CACT,mBAAmB,EACnB,WAAW,EACX,UAAU,EACV,IAAI,EACL,IAAI,WAAW,EAAE;oBAChB,MAAM,eAAe,GAAG,cAAc,CAAC,IAAI,EAAE;wBAC3C,UAAU;wBACV,SAAS;qBACV,CAAC,CAAA;oBACF,IAAI,CAAC,aAAa,CAChB,cAAc,CACZ,WAAW,EACX,mBAAmB,EACnB,UAAU,EACV,eAAe,CAChB,CACF,CAAA;iBACF;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CACZ,yDAAyD,IAAI,CAAC,aAAa,CAAC,IAAI,6FAA6F,CAAC,GAAG,EACjL,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5C;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ucscAssemblies.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscAssemblies.
|
|
1
|
+
{"version":3,"file":"ucscAssemblies.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscAssemblies.ts"],"names":[],"mappings":"AAAA,yEAAyE;AACzE,yFAAyF;AACzF,oDAAoD;AAEpD,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;QAoMP,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-data-management",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.3.1",
|
|
4
4
|
"description": "JBrowse 2 linear genome view",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -51,9 +51,8 @@
|
|
|
51
51
|
"mobx": "^6.0.0",
|
|
52
52
|
"mobx-react": "^7.0.0",
|
|
53
53
|
"mobx-state-tree": "^5.0.0",
|
|
54
|
-
"prop-types": "^15.0.0",
|
|
55
54
|
"react": ">=16.8.0",
|
|
56
|
-
"tss-react": "^
|
|
55
|
+
"tss-react": "^4.0.0"
|
|
57
56
|
},
|
|
58
57
|
"publishConfig": {
|
|
59
58
|
"access": "public"
|
|
@@ -61,5 +60,5 @@
|
|
|
61
60
|
"distModule": "esm/index.js",
|
|
62
61
|
"srcModule": "src/index.ts",
|
|
63
62
|
"module": "esm/index.js",
|
|
64
|
-
"gitHead": "
|
|
63
|
+
"gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
|
|
65
64
|
}
|
|
@@ -103,16 +103,15 @@ describe('<AddTrackWidget />', () => {
|
|
|
103
103
|
})
|
|
104
104
|
fireEvent.click(getAllByTestId('addTrackNextButton')[0])
|
|
105
105
|
fireEvent.mouseDown(getByTestId('adapterTypeSelect'))
|
|
106
|
-
const bamAdapter = await findByText('
|
|
106
|
+
const bamAdapter = await findByText('BAM adapter')
|
|
107
107
|
fireEvent.click(bamAdapter)
|
|
108
108
|
fireEvent.change(getByTestId('trackNameInput'), {
|
|
109
109
|
target: { value: 'Test track name' },
|
|
110
110
|
})
|
|
111
111
|
fireEvent.mouseDown(getByTestId('trackTypeSelect'))
|
|
112
|
-
fireEvent.click(await findByText('
|
|
112
|
+
fireEvent.click(await findByText('Feature track'))
|
|
113
113
|
fireEvent.mouseDown(getByTestId('assemblyNameSelect'))
|
|
114
|
-
|
|
115
|
-
fireEvent.click(volMyt1[1])
|
|
114
|
+
fireEvent.click((await findAllByText('volMyt1'))[1])
|
|
116
115
|
fireEvent.click(getAllByTestId('addTrackNextButton')[0])
|
|
117
116
|
expect(session.sessionTracks.length).toBe(2)
|
|
118
117
|
})
|
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
import React from 'react'
|
|
1
|
+
import React, { useState } from 'react'
|
|
2
2
|
import { observer } from 'mobx-react'
|
|
3
3
|
import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material'
|
|
4
|
-
import {
|
|
5
|
-
import { getEnv, useLocalStorage } from '@jbrowse/core/util'
|
|
4
|
+
import { getEnv } from '@jbrowse/core/util'
|
|
6
5
|
|
|
7
6
|
// locals
|
|
8
7
|
import { AddTrackModel } from '../model'
|
|
@@ -10,19 +9,17 @@ import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow'
|
|
|
10
9
|
import PasteConfigWorkflow from './PasteConfigWorkflow'
|
|
11
10
|
|
|
12
11
|
function AddTrackSelector({ model }: { model: AddTrackModel }) {
|
|
13
|
-
const [val, setVal] =
|
|
12
|
+
const [val, setVal] = useState('Default add track workflow')
|
|
14
13
|
const { pluginManager } = getEnv(model)
|
|
15
|
-
const widgets = pluginManager.
|
|
16
|
-
'add track workflow',
|
|
17
|
-
) as AddTrackWorkflowType[]
|
|
14
|
+
const widgets = pluginManager.getAddTrackWorkflowElements()
|
|
18
15
|
const ComponentMap = {
|
|
19
|
-
Default: DefaultAddTrackWorkflow,
|
|
16
|
+
'Default add track workflow': DefaultAddTrackWorkflow,
|
|
20
17
|
'Add track JSON': PasteConfigWorkflow,
|
|
21
18
|
...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
|
|
22
19
|
} as { [key: string]: React.FC<{ model: AddTrackModel }> }
|
|
23
20
|
|
|
24
21
|
// make sure the selected value is in the list
|
|
25
|
-
const val2 = ComponentMap[val] ? val : 'Default'
|
|
22
|
+
const val2 = ComponentMap[val] ? val : 'Default add track workflow'
|
|
26
23
|
const Component = ComponentMap[val2]
|
|
27
24
|
return (
|
|
28
25
|
<>
|