@jbrowse/plugin-trix 2.16.1 → 2.18.0

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Files changed (13) hide show
  1. package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts +5 -9
  2. package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js +2 -9
  3. package/dist/TrixTextSearchAdapter/configSchema.d.ts +0 -15
  4. package/dist/TrixTextSearchAdapter/configSchema.js +1 -22
  5. package/dist/index.d.ts +1 -1
  6. package/dist/index.js +1 -1
  7. package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts +5 -9
  8. package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js +3 -10
  9. package/esm/TrixTextSearchAdapter/configSchema.d.ts +0 -15
  10. package/esm/TrixTextSearchAdapter/configSchema.js +1 -22
  11. package/esm/index.d.ts +1 -1
  12. package/esm/index.js +1 -1
  13. package/package.json +2 -2
package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts CHANGED
@@ -1,19 +1,15 @@
1
1
  import Trix from '@gmod/trix';
2
- import { BaseTextSearchAdapter, BaseAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
3
2
  import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
4
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
5
- import PluginManager from '@jbrowse/core/PluginManager';
6
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
3
+ import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
4
+ import type PluginManager from '@jbrowse/core/PluginManager';
5
+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
6
+ import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
7
+ import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
8
  export default class TrixTextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
8
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  indexingAttributes?: string[];
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  trixJs: Trix;
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  tracksNames?: string[];
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  constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
12
- /**
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- * Returns list of results
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- * @param args - search options/arguments include: search query
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- * limit of results to return, searchType...prefix | full | exact", etc.
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- */
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13
  searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
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  freeResources(): void;
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  }
package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js CHANGED
@@ -4,16 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
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  Object.defineProperty(exports, "__esModule", { value: true });
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  const trix_1 = __importDefault(require("@gmod/trix"));
7
- const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
8
- const io_1 = require("@jbrowse/core/util/io");
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  const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
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8
  const configuration_1 = require("@jbrowse/core/configuration");
9
+ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
10
+ const io_1 = require("@jbrowse/core/util/io");
11
11
  function decodeURIComponentNoThrow(uri) {
12
12
  try {
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  return decodeURIComponent(uri);
14
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  }
15
15
  catch (e) {
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- // avoid throwing exception on a failure to decode URI component
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  return uri;
18
17
  }
19
18
  }
@@ -38,17 +37,11 @@ class TrixTextSearchAdapter extends BaseAdapter_1.BaseAdapter {
38
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  }
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  this.trixJs = new trix_1.default((0, io_1.openLocation)(ixxFilePath, pluginManager), (0, io_1.openLocation)(ixFilePath, pluginManager), 1500);
40
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  }
41
- /**
42
- * Returns list of results
43
- * @param args - search options/arguments include: search query
44
- * limit of results to return, searchType...prefix | full | exact", etc.
45
- */
46
40
  async searchIndex(args) {
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41
  const query = args.queryString.toLowerCase();
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  const strs = query.split(' ');
49
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  const results = await this.trixJs.search(query);
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44
  const formatted = results
51
- // if multi-word search try to filter out relevant items
52
45
  .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
53
46
  .map(([term, data]) => {
54
47
  const result = JSON.parse(data.replaceAll('|', ','));
package/dist/TrixTextSearchAdapter/configSchema.d.ts CHANGED
@@ -1,7 +1,4 @@
1
1
  declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
- /**
3
- * #slot
4
- */
5
2
  ixFilePath: {
6
3
  type: string;
7
4
  defaultValue: {
@@ -10,9 +7,6 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
10
7
  };
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8
  description: string;
12
9
  };
13
- /**
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- * #slot
15
- */
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10
  ixxFilePath: {
17
11
  type: string;
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12
  defaultValue: {
@@ -21,9 +15,6 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
21
15
  };
22
16
  description: string;
23
17
  };
24
- /**
25
- * #slot
26
- */
27
18
  metaFilePath: {
28
19
  type: string;
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20
  defaultValue: {
@@ -32,17 +23,11 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
32
23
  };
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24
  description: string;
34
25
  };
35
- /**
36
- * #slot
37
- */
38
26
  tracks: {
39
27
  type: string;
40
28
  defaultValue: never[];
41
29
  description: string;
42
30
  };
43
- /**
44
- * #slot
45
- */
46
31
  assemblyNames: {
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  type: string;
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  defaultValue: never[];
package/dist/TrixTextSearchAdapter/configSchema.js CHANGED
@@ -1,46 +1,28 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  const configuration_1 = require("@jbrowse/core/configuration");
4
- /**
5
- * #config TrixTextSearchAdapter
6
- */
7
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
4
+ function x() { }
8
5
  const TrixTextSearchAdapter = (0, configuration_1.ConfigurationSchema)('TrixTextSearchAdapter', {
9
- /**
10
- * #slot
11
- */
12
6
  ixFilePath: {
13
7
  type: 'fileLocation',
14
8
  defaultValue: { uri: 'out.ix', locationType: 'UriLocation' },
15
9
  description: 'the location of the trix ix file',
16
10
  },
17
- /**
18
- * #slot
19
- */
20
11
  ixxFilePath: {
21
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  type: 'fileLocation',
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13
  defaultValue: { uri: 'out.ixx', locationType: 'UriLocation' },
23
14
  description: 'the location of the trix ixx file',
24
15
  },
25
- /**
26
- * #slot
27
- */
28
16
  metaFilePath: {
29
17
  type: 'fileLocation',
30
18
  defaultValue: { uri: 'meta.json', locationType: 'UriLocation' },
31
19
  description: 'the location of the metadata json file for the trix index',
32
20
  },
33
- /**
34
- * #slot
35
- */
36
21
  tracks: {
37
22
  type: 'stringArray',
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23
  defaultValue: [],
39
24
  description: 'List of tracks covered by text search adapter',
40
25
  },
41
- /**
42
- * #slot
43
- */
44
26
  assemblyNames: {
45
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  type: 'stringArray',
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  defaultValue: [],
@@ -48,9 +30,6 @@ const TrixTextSearchAdapter = (0, configuration_1.ConfigurationSchema)('TrixText
48
30
  },
49
31
  }, {
50
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  explicitlyTyped: true,
51
- /**
52
- * #identifier
53
- */
54
33
  explicitIdentifier: 'textSearchAdapterId',
55
34
  });
56
35
  exports.default = TrixTextSearchAdapter;
package/dist/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import Plugin from '@jbrowse/core/Plugin';
2
- import PluginManager from '@jbrowse/core/PluginManager';
2
+ import type PluginManager from '@jbrowse/core/PluginManager';
3
3
  export default class TrixPlugin extends Plugin {
4
4
  name: string;
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  install(pluginManager: PluginManager): void;
package/dist/index.js CHANGED
@@ -26,8 +26,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  return (mod && mod.__esModule) ? mod : { "default": mod };
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  };
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  Object.defineProperty(exports, "__esModule", { value: true });
29
- const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
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  const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
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+ const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
31
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  const configSchema_1 = __importDefault(require("./TrixTextSearchAdapter/configSchema"));
32
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  class TrixPlugin extends Plugin_1.default {
33
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  constructor() {
package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts CHANGED
@@ -1,19 +1,15 @@
1
1
  import Trix from '@gmod/trix';
2
- import { BaseTextSearchAdapter, BaseAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
3
2
  import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
4
- import { AnyConfigurationModel } from '@jbrowse/core/configuration';
5
- import PluginManager from '@jbrowse/core/PluginManager';
6
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
3
+ import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
4
+ import type PluginManager from '@jbrowse/core/PluginManager';
5
+ import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
6
+ import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
7
+ import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
8
  export default class TrixTextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
8
9
  indexingAttributes?: string[];
9
10
  trixJs: Trix;
10
11
  tracksNames?: string[];
11
12
  constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
12
- /**
13
- * Returns list of results
14
- * @param args - search options/arguments include: search query
15
- * limit of results to return, searchType...prefix | full | exact", etc.
16
- */
17
13
  searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
18
14
  freeResources(): void;
19
15
  }
package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js CHANGED
@@ -1,14 +1,13 @@
1
1
  import Trix from '@gmod/trix';
2
- import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
3
- import { openLocation } from '@jbrowse/core/util/io';
4
2
  import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
5
- import { readConfObject, } from '@jbrowse/core/configuration';
3
+ import { readConfObject } from '@jbrowse/core/configuration';
4
+ import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
5
+ import { openLocation } from '@jbrowse/core/util/io';
6
6
  function decodeURIComponentNoThrow(uri) {
7
7
  try {
8
8
  return decodeURIComponent(uri);
9
9
  }
10
10
  catch (e) {
11
- // avoid throwing exception on a failure to decode URI component
12
11
  return uri;
13
12
  }
14
13
  }
@@ -33,17 +32,11 @@ export default class TrixTextSearchAdapter extends BaseAdapter {
33
32
  }
34
33
  this.trixJs = new Trix(openLocation(ixxFilePath, pluginManager), openLocation(ixFilePath, pluginManager), 1500);
35
34
  }
36
- /**
37
- * Returns list of results
38
- * @param args - search options/arguments include: search query
39
- * limit of results to return, searchType...prefix | full | exact", etc.
40
- */
41
35
  async searchIndex(args) {
42
36
  const query = args.queryString.toLowerCase();
43
37
  const strs = query.split(' ');
44
38
  const results = await this.trixJs.search(query);
45
39
  const formatted = results
46
- // if multi-word search try to filter out relevant items
47
40
  .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
48
41
  .map(([term, data]) => {
49
42
  const result = JSON.parse(data.replaceAll('|', ','));
package/esm/TrixTextSearchAdapter/configSchema.d.ts CHANGED
@@ -1,7 +1,4 @@
1
1
  declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
2
- /**
3
- * #slot
4
- */
5
2
  ixFilePath: {
6
3
  type: string;
7
4
  defaultValue: {
@@ -10,9 +7,6 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
10
7
  };
11
8
  description: string;
12
9
  };
13
- /**
14
- * #slot
15
- */
16
10
  ixxFilePath: {
17
11
  type: string;
18
12
  defaultValue: {
@@ -21,9 +15,6 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
21
15
  };
22
16
  description: string;
23
17
  };
24
- /**
25
- * #slot
26
- */
27
18
  metaFilePath: {
28
19
  type: string;
29
20
  defaultValue: {
@@ -32,17 +23,11 @@ declare const TrixTextSearchAdapter: import("@jbrowse/core/configuration/configu
32
23
  };
33
24
  description: string;
34
25
  };
35
- /**
36
- * #slot
37
- */
38
26
  tracks: {
39
27
  type: string;
40
28
  defaultValue: never[];
41
29
  description: string;
42
30
  };
43
- /**
44
- * #slot
45
- */
46
31
  assemblyNames: {
47
32
  type: string;
48
33
  defaultValue: never[];
package/esm/TrixTextSearchAdapter/configSchema.js CHANGED
@@ -1,44 +1,26 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- /**
3
- * #config TrixTextSearchAdapter
4
- */
5
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
2
+ function x() { }
6
3
  const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
7
- /**
8
- * #slot
9
- */
10
4
  ixFilePath: {
11
5
  type: 'fileLocation',
12
6
  defaultValue: { uri: 'out.ix', locationType: 'UriLocation' },
13
7
  description: 'the location of the trix ix file',
14
8
  },
15
- /**
16
- * #slot
17
- */
18
9
  ixxFilePath: {
19
10
  type: 'fileLocation',
20
11
  defaultValue: { uri: 'out.ixx', locationType: 'UriLocation' },
21
12
  description: 'the location of the trix ixx file',
22
13
  },
23
- /**
24
- * #slot
25
- */
26
14
  metaFilePath: {
27
15
  type: 'fileLocation',
28
16
  defaultValue: { uri: 'meta.json', locationType: 'UriLocation' },
29
17
  description: 'the location of the metadata json file for the trix index',
30
18
  },
31
- /**
32
- * #slot
33
- */
34
19
  tracks: {
35
20
  type: 'stringArray',
36
21
  defaultValue: [],
37
22
  description: 'List of tracks covered by text search adapter',
38
23
  },
39
- /**
40
- * #slot
41
- */
42
24
  assemblyNames: {
43
25
  type: 'stringArray',
44
26
  defaultValue: [],
@@ -46,9 +28,6 @@ const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
46
28
  },
47
29
  }, {
48
30
  explicitlyTyped: true,
49
- /**
50
- * #identifier
51
- */
52
31
  explicitIdentifier: 'textSearchAdapterId',
53
32
  });
54
33
  export default TrixTextSearchAdapter;
package/esm/index.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import Plugin from '@jbrowse/core/Plugin';
2
- import PluginManager from '@jbrowse/core/PluginManager';
2
+ import type PluginManager from '@jbrowse/core/PluginManager';
3
3
  export default class TrixPlugin extends Plugin {
4
4
  name: string;
5
5
  install(pluginManager: PluginManager): void;
package/esm/index.js CHANGED
@@ -1,5 +1,5 @@
1
- import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
2
1
  import Plugin from '@jbrowse/core/Plugin';
2
+ import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
3
3
  import configSchema from './TrixTextSearchAdapter/configSchema';
4
4
  export default class TrixPlugin extends Plugin {
5
5
  constructor() {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-trix",
3
- "version": "2.16.1",
3
+ "version": "2.18.0",
4
4
  "description": "JBrowse 2 trix text search adapter",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -52,5 +52,5 @@
52
52
  "distModule": "esm/index.js",
53
53
  "srcModule": "src/index.ts",
54
54
  "module": "esm/index.js",
55
- "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
55
+ "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
56
56
  }