@jbrowse/plugin-data-management 3.0.5 → 3.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. package/dist/AddTrackWidget/components/PasteConfigWorkflow.js +4 -4
  2. package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts +5 -2
  3. package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js +4 -1
  4. package/dist/UCSCTrackHub/configSchema.js +11 -0
  5. package/dist/UCSCTrackHub/doConnect.js +10 -0
  6. package/esm/AddTrackWidget/components/PasteConfigWorkflow.js +4 -4
  7. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts +5 -2
  8. package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js +4 -1
  9. package/esm/UCSCTrackHub/configSchema.js +11 -0
  10. package/esm/UCSCTrackHub/doConnect.js +10 -0
  11. package/package.json +5 -5
package/dist/AddTrackWidget/components/PasteConfigWorkflow.js CHANGED
@@ -33,12 +33,12 @@ const PasteConfigAddTrackWorkflow = (0, mobx_react_1.observer)(function ({ model
33
33
  if ((0, util_1.isSessionWithAddTracks)(session) &&
34
34
  (0, util_1.isSessionModelWithWidgets)(session)) {
35
35
  (0, mobx_1.transaction)(() => {
36
- confs.forEach(c => {
36
+ for (const c of confs) {
37
37
  session.addTrackConf(c);
38
- });
39
- confs.forEach(c => {
38
+ }
39
+ for (const c of confs) {
40
40
  model.view.showTrack(c.trackId);
41
- });
41
+ }
42
42
  model.clearData();
43
43
  });
44
44
  session.hideWidget(model);
package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts CHANGED
@@ -1,5 +1,8 @@
1
- import type { HierarchicalTrackSelectorModel } from '../model';
1
+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
2
  declare const ShoppingCart: ({ model, }: {
3
- model: HierarchicalTrackSelectorModel;
3
+ model: {
4
+ clearSelection: () => void;
5
+ selection: AnyConfigurationModel[];
6
+ };
4
7
  }) => import("react/jsx-runtime").JSX.Element | null;
5
8
  export default ShoppingCart;
package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js CHANGED
@@ -29,7 +29,10 @@ const ShoppingCart = (0, mobx_react_1.observer)(function ({ model, }) {
29
29
  {
30
30
  label: 'Delete tracks',
31
31
  onClick: () => {
32
- selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
32
+ var _a;
33
+ for (const s of selection) {
34
+ (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
35
+ }
33
36
  },
34
37
  },
35
38
  ]
package/dist/UCSCTrackHub/configSchema.js CHANGED
@@ -19,5 +19,16 @@ const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTra
19
19
  },
20
20
  }, {
21
21
  baseConfiguration: models_1.baseConnectionConfig,
22
+ preProcessSnapshot: snap => {
23
+ return snap.uri
24
+ ? {
25
+ ...snap,
26
+ hubTxtLocation: {
27
+ uri: snap.uri,
28
+ baseUri: snap.baseUri,
29
+ },
30
+ }
31
+ : snap;
32
+ },
22
33
  });
23
34
  exports.default = UCSCTrackHubConnection;
package/dist/UCSCTrackHub/doConnect.js CHANGED
@@ -49,6 +49,16 @@ async function doConnect(self) {
49
49
  },
50
50
  },
51
51
  },
52
+ ...(genome.data.chromAliasBb
53
+ ? {
54
+ refNameAliases: {
55
+ adapter: {
56
+ type: 'BigBedAdapter',
57
+ uri: (0, util_2.resolve)(genome.data.chromAliasBb, hubUri),
58
+ },
59
+ },
60
+ }
61
+ : {}),
52
62
  });
53
63
  }
54
64
  const asm2 = assemblyManager.get(genomeName);
package/esm/AddTrackWidget/components/PasteConfigWorkflow.js CHANGED
@@ -31,12 +31,12 @@ const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
31
31
  if (isSessionWithAddTracks(session) &&
32
32
  isSessionModelWithWidgets(session)) {
33
33
  transaction(() => {
34
- confs.forEach(c => {
34
+ for (const c of confs) {
35
35
  session.addTrackConf(c);
36
- });
37
- confs.forEach(c => {
36
+ }
37
+ for (const c of confs) {
38
38
  model.view.showTrack(c.trackId);
39
- });
39
+ }
40
40
  model.clearData();
41
41
  });
42
42
  session.hideWidget(model);
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.d.ts CHANGED
@@ -1,5 +1,8 @@
1
- import type { HierarchicalTrackSelectorModel } from '../model';
1
+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
2
2
  declare const ShoppingCart: ({ model, }: {
3
- model: HierarchicalTrackSelectorModel;
3
+ model: {
4
+ clearSelection: () => void;
5
+ selection: AnyConfigurationModel[];
6
+ };
4
7
  }) => import("react/jsx-runtime").JSX.Element | null;
5
8
  export default ShoppingCart;
package/esm/HierarchicalTrackSelectorWidget/components/ShoppingCart.js CHANGED
@@ -24,7 +24,10 @@ const ShoppingCart = observer(function ({ model, }) {
24
24
  {
25
25
  label: 'Delete tracks',
26
26
  onClick: () => {
27
- selection.forEach(s => { var _a; return (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s); });
27
+ var _a;
28
+ for (const s of selection) {
29
+ (_a = session.deleteTrackConf) === null || _a === void 0 ? void 0 : _a.call(session, s);
30
+ }
28
31
  },
29
32
  },
30
33
  ]
package/esm/UCSCTrackHub/configSchema.js CHANGED
@@ -17,5 +17,16 @@ const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
17
17
  },
18
18
  }, {
19
19
  baseConfiguration: baseConnectionConfig,
20
+ preProcessSnapshot: snap => {
21
+ return snap.uri
22
+ ? {
23
+ ...snap,
24
+ hubTxtLocation: {
25
+ uri: snap.uri,
26
+ baseUri: snap.baseUri,
27
+ },
28
+ }
29
+ : snap;
30
+ },
20
31
  });
21
32
  export default UCSCTrackHubConnection;
package/esm/UCSCTrackHub/doConnect.js CHANGED
@@ -46,6 +46,16 @@ export async function doConnect(self) {
46
46
  },
47
47
  },
48
48
  },
49
+ ...(genome.data.chromAliasBb
50
+ ? {
51
+ refNameAliases: {
52
+ adapter: {
53
+ type: 'BigBedAdapter',
54
+ uri: resolve(genome.data.chromAliasBb, hubUri),
55
+ },
56
+ },
57
+ }
58
+ : {}),
49
59
  });
50
60
  }
51
61
  const asm2 = assemblyManager.get(genomeName);
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-data-management",
3
- "version": "3.0.5",
3
+ "version": "3.2.0",
4
4
  "description": "JBrowse 2 linear genome view",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -37,9 +37,9 @@
37
37
  },
38
38
  "dependencies": {
39
39
  "@gmod/ucsc-hub": "^1.0.0",
40
- "@jbrowse/core": "^3.0.5",
41
- "@jbrowse/plugin-config": "^3.0.5",
42
- "@jbrowse/product-core": "^3.0.5",
40
+ "@jbrowse/core": "^3.2.0",
41
+ "@jbrowse/plugin-config": "^3.2.0",
42
+ "@jbrowse/product-core": "^3.2.0",
43
43
  "@mui/icons-material": "^6.0.0",
44
44
  "@mui/material": "^6.0.0",
45
45
  "@mui/x-data-grid": "^7.0.0",
@@ -61,5 +61,5 @@
61
61
  "distModule": "esm/index.js",
62
62
  "srcModule": "src/index.ts",
63
63
  "module": "esm/index.js",
64
- "gitHead": "a03749efe19e51609922272b845a331897346789"
64
+ "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
65
65
  }