@jbrowse/plugin-legacy-jbrowse 5.0.0-beta.8 → 5.0.0-beta.9

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 (7) hide show
  1. package/esm/JBrowse1Connection/configSchema.d.ts +41 -25
  2. package/esm/JBrowse1Connection/model.d.ts +60 -37
  3. package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts +20 -22
  4. package/esm/NCListAdapter/NCListAdapter.d.ts +1 -1
  5. package/esm/NCListAdapter/NCListAdapter.js +4 -4
  6. package/esm/NCListAdapter/configSchema.d.ts +12 -18
  7. package/package.json +4 -4
package/esm/JBrowse1Connection/configSchema.d.ts CHANGED
@@ -17,35 +17,51 @@
17
17
  * ```
18
18
  */
19
19
  declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
20
- /**
21
- * #slot
22
- */
23
- readonly dataDirLocation: {
24
- readonly type: "fileLocation";
25
- readonly defaultValue: {
26
- readonly uri: "https://mysite.com/jbrowse/data/";
27
- readonly locationType: "UriLocation";
28
- };
29
- readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
30
- };
31
- /**
32
- * #slot
33
- */
34
- readonly assemblyNames: {
35
- readonly description: "name of the assembly the connection belongs to, should be a single entry";
36
- readonly type: "stringArray";
37
- readonly defaultValue: readonly [];
20
+ assemblyNames: {
21
+ type: "stringArray";
22
+ } & {
23
+ defaultValue: unknown;
24
+ };
25
+ connectionId: {
26
+ type: "string";
27
+ } & {
28
+ defaultValue: string;
29
+ };
30
+ dataDirLocation: {
31
+ type: "fileLocation";
32
+ } & {
33
+ defaultValue: unknown;
34
+ };
35
+ name: {
36
+ type: "string";
37
+ } & {
38
+ defaultValue: string;
39
+ };
40
+ type: {
41
+ type: "string";
42
+ } & {
43
+ defaultValue: string;
38
44
  };
39
45
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
40
46
  readonly name: {
41
- readonly type: "string";
42
- readonly defaultValue: "nameOfConnection";
43
- readonly description: "a unique name for this connection";
47
+ type: "string";
48
+ } & {
49
+ defaultValue: string;
44
50
  };
45
51
  readonly assemblyNames: {
46
- readonly type: "stringArray";
47
- readonly defaultValue: readonly [];
48
- readonly description: "optional list of names of assemblies in this connection";
52
+ type: "stringArray";
53
+ } & {
54
+ defaultValue: unknown;
55
+ };
56
+ type: {
57
+ type: "string";
58
+ } & {
59
+ defaultValue: string;
60
+ };
61
+ connectionId: {
62
+ type: "string";
63
+ } & {
64
+ defaultValue: string;
49
65
  };
50
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
66
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
51
67
  export default JBrowse1Connection;
package/esm/JBrowse1Connection/model.d.ts CHANGED
@@ -8,44 +8,76 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
8
8
  tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
9
9
  configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
10
10
  readonly name: {
11
- readonly type: "string";
12
- readonly defaultValue: "nameOfConnection";
13
- readonly description: "a unique name for this connection";
11
+ type: "string";
12
+ } & {
13
+ defaultValue: string;
14
14
  };
15
15
  readonly assemblyNames: {
16
- readonly type: "stringArray";
17
- readonly defaultValue: readonly [];
18
- readonly description: "optional list of names of assemblies in this connection";
16
+ type: "stringArray";
17
+ } & {
18
+ defaultValue: unknown;
19
19
  };
20
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>;
20
+ type: {
21
+ type: "string";
22
+ } & {
23
+ defaultValue: string;
24
+ };
25
+ connectionId: {
26
+ type: "string";
27
+ } & {
28
+ defaultValue: string;
29
+ };
30
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>;
21
31
  silent: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
22
32
  }, "configuration" | "type"> & {
23
33
  configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
24
- readonly dataDirLocation: {
25
- readonly type: "fileLocation";
26
- readonly defaultValue: {
27
- readonly uri: "https://mysite.com/jbrowse/data/";
28
- readonly locationType: "UriLocation";
29
- };
30
- readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
34
+ assemblyNames: {
35
+ type: "stringArray";
36
+ } & {
37
+ defaultValue: unknown;
31
38
  };
32
- readonly assemblyNames: {
33
- readonly description: "name of the assembly the connection belongs to, should be a single entry";
34
- readonly type: "stringArray";
35
- readonly defaultValue: readonly [];
39
+ connectionId: {
40
+ type: "string";
41
+ } & {
42
+ defaultValue: string;
43
+ };
44
+ dataDirLocation: {
45
+ type: "fileLocation";
46
+ } & {
47
+ defaultValue: unknown;
48
+ };
49
+ name: {
50
+ type: "string";
51
+ } & {
52
+ defaultValue: string;
53
+ };
54
+ type: {
55
+ type: "string";
56
+ } & {
57
+ defaultValue: string;
36
58
  };
37
59
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
38
60
  readonly name: {
39
- readonly type: "string";
40
- readonly defaultValue: "nameOfConnection";
41
- readonly description: "a unique name for this connection";
61
+ type: "string";
62
+ } & {
63
+ defaultValue: string;
42
64
  };
43
65
  readonly assemblyNames: {
44
- readonly type: "stringArray";
45
- readonly defaultValue: readonly [];
46
- readonly description: "optional list of names of assemblies in this connection";
66
+ type: "stringArray";
67
+ } & {
68
+ defaultValue: unknown;
69
+ };
70
+ type: {
71
+ type: "string";
72
+ } & {
73
+ defaultValue: string;
74
+ };
75
+ connectionId: {
76
+ type: "string";
77
+ } & {
78
+ defaultValue: string;
47
79
  };
48
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>>;
80
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>;
49
81
  type: import("@jbrowse/mobx-state-tree").ILiteralType<"JBrowse1Connection">;
50
82
  }, {
51
83
  loading: boolean;
@@ -57,18 +89,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
57
89
  setLoading(loading: boolean): void;
58
90
  } & {
59
91
  afterAttach(): void;
60
- addTrackConf(trackConf: Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
61
- setSubschema(slotName: string, data: Record<string, unknown>): any;
62
- setSlot(slotName: string, value: unknown): void;
63
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
64
- addTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
65
- setSubschema(slotName: string, data: Record<string, unknown>): any;
66
- setSlot(slotName: string, value: unknown): void;
67
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
68
- setTrackConfs(trackConfs: (Record<string, unknown> | (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
69
- setSubschema(slotName: string, data: Record<string, unknown>): any;
70
- setSlot(slotName: string, value: unknown): void;
71
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
92
+ addTrackConf(trackConf: Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel): any;
93
+ addTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
94
+ setTrackConfs(trackConfs: (Record<string, unknown> | import("@jbrowse/core/configuration").AnyConfigurationModel)[]): void;
72
95
  } & {
73
96
  connect(): Promise<void>;
74
97
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED
@@ -18,32 +18,30 @@
18
18
  * ```
19
19
  */
20
20
  declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
21
- /**
22
- * #slot
23
- */
21
+ type: {
22
+ type: "string";
23
+ } & {
24
+ defaultValue: string;
25
+ };
24
26
  readonly namesIndexLocation: {
25
- readonly type: "fileLocation";
26
- readonly defaultValue: {
27
- readonly uri: "/volvox/names";
28
- readonly locationType: "UriLocation";
29
- };
30
- readonly description: "the location of the JBrowse1 names index data directory";
27
+ type: "fileLocation";
28
+ } & {
29
+ defaultValue: unknown;
31
30
  };
32
- /**
33
- * #slot
34
- */
35
31
  readonly tracks: {
36
- readonly type: "stringArray";
37
- readonly defaultValue: readonly [];
38
- readonly description: "List of tracks covered by text search adapter";
32
+ type: "stringArray";
33
+ } & {
34
+ defaultValue: unknown;
39
35
  };
40
- /**
41
- * #slot
42
- */
43
36
  readonly assemblyNames: {
44
- readonly type: "stringArray";
45
- readonly defaultValue: readonly [];
46
- readonly description: "List of assemblies covered by text search adapter";
37
+ type: "stringArray";
38
+ } & {
39
+ defaultValue: unknown;
40
+ };
41
+ textSearchAdapterId: {
42
+ type: "string";
43
+ } & {
44
+ defaultValue: string;
47
45
  };
48
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
46
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
49
47
  export default _default;
package/esm/NCListAdapter/NCListAdapter.d.ts CHANGED
@@ -14,7 +14,7 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
14
14
  /**
15
15
  * Fetch features for a certain region.
16
16
  * @param region -
17
- * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
17
+ * @param opts - [signal] optional signalling object for aborting the fetch
18
18
  * @returns Observable of Feature objects in the region
19
19
  */
20
20
  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/esm/NCListAdapter/NCListAdapter.js CHANGED
@@ -1,7 +1,7 @@
1
1
  import NCListStore from '@gmod/nclist';
2
2
  import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
3
+ import { checkAbortSignal } from '@jbrowse/core/util/aborting';
3
4
  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
4
- import { checkStopToken } from '@jbrowse/core/util/stopToken';
5
5
  import { RemoteFile } from 'generic-filehandle2';
6
6
  import NCListFeature from './NCListFeature.js';
7
7
  export default class NCListAdapter extends BaseFeatureDataAdapter {
@@ -23,14 +23,14 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
23
23
  /**
24
24
  * Fetch features for a certain region.
25
25
  * @param region -
26
- * @param opts - [stopToken] optional stopTokenling object for aborting the fetch
26
+ * @param opts - [signal] optional signalling object for aborting the fetch
27
27
  * @returns Observable of Feature objects in the region
28
28
  */
29
29
  getFeatures(region, opts = {}) {
30
30
  return ObservableCreate(async (observer) => {
31
- const { stopToken } = opts;
31
+ const { signal } = opts;
32
32
  for await (const feature of this.nclist.getFeatures(region)) {
33
- checkStopToken(stopToken);
33
+ checkAbortSignal(signal);
34
34
  observer.next(this.wrapFeature(feature));
35
35
  }
36
36
  observer.complete();
package/esm/NCListAdapter/configSchema.d.ts CHANGED
@@ -16,26 +16,20 @@
16
16
  * ```
17
17
  */
18
18
  declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
19
- /**
20
- * #slot
21
- * URL of a JBrowse 1 NCList `trackData.json`, with `{refseq}` standing in
22
- * for the reference sequence name — the per-reference directory layout
23
- * `flatfile-to-json.pl` and `biodb-to-json.pl` write.
24
- */
19
+ type: {
20
+ type: "string";
21
+ } & {
22
+ defaultValue: string;
23
+ };
25
24
  readonly rootUrlTemplate: {
26
- readonly type: "fileLocation";
27
- readonly defaultValue: {
28
- readonly uri: "/path/to/my/{refseq}/trackData.json";
29
- readonly locationType: "UriLocation";
30
- };
25
+ type: "fileLocation";
26
+ } & {
27
+ defaultValue: unknown;
31
28
  };
32
- /**
33
- * #slot
34
- */
35
29
  readonly refNames: {
36
- readonly type: "stringArray";
37
- readonly defaultValue: readonly [];
38
- readonly description: "List of refNames used by the NCList used for aliasing";
30
+ type: "stringArray";
31
+ } & {
32
+ defaultValue: unknown;
39
33
  };
40
- }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
34
+ }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
41
35
  export default NCListAdapter;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-legacy-jbrowse",
3
- "version": "5.0.0-beta.8",
3
+ "version": "5.0.0-beta.9",
4
4
  "type": "module",
5
5
  "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
6
6
  "keywords": [
@@ -22,12 +22,12 @@
22
22
  ],
23
23
  "dependencies": {
24
24
  "@gmod/nclist": "^3.0.14",
25
- "@jbrowse/mobx-state-tree": "^6.5.1",
25
+ "@jbrowse/mobx-state-tree": "^6.5.2",
26
26
  "generic-filehandle2": "^2.4.0",
27
27
  "mobx": "^7.0.3",
28
28
  "rxjs": "^7.8.2",
29
- "@jbrowse/add-track-core": "^5.0.0-beta.8",
30
- "@jbrowse/core": "^5.0.0-beta.8"
29
+ "@jbrowse/add-track-core": "^5.0.0-beta.9",
30
+ "@jbrowse/core": "^5.0.0-beta.9"
31
31
  },
32
32
  "publishConfig": {
33
33
  "access": "public"