npm - @jbrowse/plugin-legacy-jbrowse - Versions diffs - 2.4.1 → 2.5.0 - Mend

@jbrowse/plugin-legacy-jbrowse 2.4.1 → 2.5.0

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 (16) hide show

package/dist/JBrowse1Connection/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,33 @@
-declare const JBrowse1Connection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    dataDirLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
 export default JBrowse1Connection;

package/dist/JBrowse1Connection/model.d.ts CHANGED Viewed

@@ -3,7 +3,32 @@ export default function (pluginManager: PluginManager): import("mobx-state-tree"
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        dataDirLocation: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+            description: string;
+        };
+        assemblyNames: {
+            description: string;
+            type: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
     afterAttach(): void;

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseTextSearchAdapter, BaseTextSearchArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import HttpMap from './HttpMap';
@@ -26,7 +26,7 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter implements Ba
      * @param query - string query
      */
     loadIndexFile(query: string): Promise<IndexFile>;
-    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
+    searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
     formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
     freeResources(): void;
 }

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"JBrowse1TextSearchAdapter.js","sourceRoot":"","sources":["../../src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAIgD;AAChD,uFAA6D;AAC7D,+DAGoC;AACpC,wDAA+B;AAkB/B,wCAAwC;AACxC,MAAqB,yBACnB,SAAQ,yBAAW;IAOnB,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC/D,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,UAAU,CAAA;QACnC,IAAI,CAAC,OAAO,GAAG,IAAI,iBAAO,CAAC;YACzB,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG;SAChD,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,aAAa,CAAC,KAAa;QAC/B,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAwB;QACxC,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,IAAI,CAAC,MAAM,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,CAAC,CAAA;QACvE,MAAM,GAAG,GAAG,WAAW,CAAC,WAAW,EAAE,CAAA;QACrC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;QAC7C,OAAO,OAAO,CAAC,GAAG,CAAC;YACjB,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,MAAM,EAAE,UAAU,CAAC;YACtD,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;IACD,aAAa,CAAC,OAAsB,EAAE,MAAgB,EAAE,UAAmB;QACzE,OAAO;YACL,GAAG,CAAC,UAAU,KAAK,OAAO;gBACxB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAChB,MAAM,CAAC,EAAE,CACP,IAAI,qBAAU,CAAC;oBACb,KAAK,EAAE,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM;oBACxD,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;iBAClC,CAAC,CACL,CAAC;YACN,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC5B,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACtB,MAAM,UAAU,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBAC5B,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACvB,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;gBACrB,MAAM,SAAS,GAAG,GAAG,OAAO,IAAI,IAAI,IAAI,KAAK,IAAI,GAAG,EAAE,CAAA;gBACtD,OAAO,IAAI,qBAAU,CAAC;oBACpB,SAAS,EAAE,SAAS;oBACpB,KAAK,EAAE,IAAI;oBACX,gBAAgB,EAAE,MAAM;oBACxB,aAAa,EAAE,MAAM;oBACrB,OAAO,EAAE,MAAM,CAAC,UAAU,CAAC;iBAC5B,CAAC,CAAA;YACJ,CAAC,CAAC;SACH,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,KAAK,kBAAkB,CAAC,CAAA;IAC9D,CAAC;IAED,aAAa,KAAI,CAAC;CACnB;AAtED,4CAsEC"}

package/dist/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,30 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    namesIndexLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    tracks: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
 export default _default;

package/dist/NCListAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,21 @@
-declare const NCListAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    rootUrlTemplate: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    refNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default NCListAdapter;

package/esm/JBrowse1Connection/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,33 @@
-declare const JBrowse1Connection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    dataDirLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        type: string;
+        defaultValue: string;
+        description: string;
+    };
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
 export default JBrowse1Connection;

package/esm/JBrowse1Connection/model.d.ts CHANGED Viewed

@@ -3,7 +3,32 @@ export default function (pluginManager: PluginManager): import("mobx-state-tree"
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        dataDirLocation: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+            description: string;
+        };
+        assemblyNames: {
+            description: string;
+            type: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
     type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
 }, {
     afterAttach(): void;

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseTextSearchAdapter, BaseTextSearchArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import HttpMap from './HttpMap';
@@ -26,7 +26,7 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter implements Ba
      * @param query - string query
      */
     loadIndexFile(query: string): Promise<IndexFile>;
-    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
+    searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
     formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
     freeResources(): void;
 }

package/esm/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/JBrowse1TextSearchAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,30 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    namesIndexLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    tracks: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    assemblyNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "textSearchAdapterId">>;
 export default _default;

package/esm/NCListAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,2 +1,21 @@
-declare const NCListAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    rootUrlTemplate: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    refNames: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default NCListAdapter;

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.4.1",
+  "version": "2.5.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }

package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts CHANGED Viewed

@@ -4,61 +4,46 @@ import first from '../../test_data/names/0.json'
 import last from '../../test_data/names/f.json'
 import HttpMap from './HttpMap'
-describe('test JBrowse1 hash implementation', () => {
-  test('read from meta', async () => {
-    function mockFetch(url: string): Promise<Response> {
-      let response = {}
-      if (url.includes('names/meta.json')) {
-        response = meta
-      }
-      return Promise.resolve(new Response(JSON.stringify(response)))
-    }
-    const rootTemplate = path
-      .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-      .replace(/\\/g, '\\\\')
+test('read from meta', async () => {
+  const rootTemplate = path
+    .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
+    .replace(/\\/g, '\\\\')
-    const spy = jest.spyOn(global, 'fetch')
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    spy.mockImplementation(mockFetch as any)
-    const hashMap = new HttpMap({
-      url: rootTemplate,
-    })
+  jest.spyOn(global, 'fetch').mockImplementation(url => {
+    const response = `${url}`.includes('names/meta.json') ? meta : {}
+    return Promise.resolve(new Response(JSON.stringify(response)))
+  })
+  const hashMap = new HttpMap({ url: rootTemplate })
+  await hashMap.getBucket('apple')
-    await hashMap.getBucket('apple')
+  // test compress and hash hex characters are set after initial search
+  expect(await hashMap.getHashHexCharacters()).toBe(1)
+  expect(await hashMap.getCompress()).toBe(0)
+})
+test('get bucket contents', async () => {
+  const rootTemplate = path
+    .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
+    .replace(/\\/g, '\\\\')
-    // test compress and hash hex characters are set after initial search
-    expect(await hashMap.getHashHexCharacters()).toBe(1)
-    expect(await hashMap.getCompress()).toBe(0)
-  })
-  test('get bucket contents', async () => {
-    function mockFetch(url: string): Promise<Response> {
-      let response = {}
-      if (url.includes('names/meta.json')) {
-        response = meta
-      }
-      if (url.includes('names/0.json')) {
-        response = first
-      }
-      if (url.includes('names/f.json')) {
-        response = last
-      }
-      return Promise.resolve(new Response(JSON.stringify(response)))
+  const spy = jest.spyOn(global, 'fetch')
+  spy.mockImplementation(url => {
+    let response = {}
+    if (`${url}`.includes('names/meta.json')) {
+      response = meta
     }
-    const rootTemplate = path
-      .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-      .replace(/\\/g, '\\\\')
-    const spy = jest.spyOn(global, 'fetch')
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    spy.mockImplementation(mockFetch as any)
-    const hashMap = new HttpMap({
-      url: rootTemplate,
-    })
+    if (`${url}`.includes('names/0.json')) {
+      response = first
+    }
+    if (`${url}`.includes('names/f.json')) {
+      response = last
+    }
+    return Promise.resolve(new Response(JSON.stringify(response)))
+  })
+  const hashMap = new HttpMap({ url: rootTemplate })
-    await hashMap.getBucket('apple')
-    expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/0.json`)
+  await hashMap.getBucket('apple')
+  expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/0.json`)
-    await hashMap.getBucket('apple3')
-    expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/f.json`)
-  })
+  await hashMap.getBucket('apple3')
+  expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/f.json`)
 })

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts CHANGED Viewed

@@ -6,15 +6,15 @@ import last from '../../test_data/names/f.json'
 import Adapter from './JBrowse1TextSearchAdapter'
 import configSchema from './configSchema'
-function mockFetch(url: string) {
+function mockFetch(url: RequestInfo | URL) {
   let response = {}
-  if (url.includes('names/meta.json')) {
+  if (`${url}`.includes('names/meta.json')) {
     response = meta
   }
-  if (url.includes('names/0.json')) {
+  if (`${url}`.includes('names/0.json')) {
     response = first
   }
-  if (url.includes('names/f.json')) {
+  if (`${url}`.includes('names/f.json')) {
     response = last
   }
   return Promise.resolve(new Response(JSON.stringify(response)))
@@ -26,8 +26,7 @@ const rootTemplate = path
 test('search upper case', async () => {
   const spy = jest.spyOn(global, 'fetch')
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  spy.mockImplementation(mockFetch as any)
+  spy.mockImplementation(mockFetch)
   const adapter = new Adapter(
     configSchema.create({
@@ -65,8 +64,7 @@ test('search upper case', async () => {
 test('search lower case', async () => {
   const spy = jest.spyOn(global, 'fetch')
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  spy.mockImplementation(mockFetch as any)
+  spy.mockImplementation(mockFetch)
   const adapter = new Adapter(
     configSchema.create({

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import {
   BaseTextSearchAdapter,
-  BaseArgs,
+  BaseTextSearchArgs,
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
@@ -57,7 +57,7 @@ export default class JBrowse1TextSearchAdapter
     return this.httpMap.getBucket(query)
   }
-  async searchIndex(args: BaseArgs) {
+  async searchIndex(args: BaseTextSearchArgs) {
     const { searchType, queryString } = args
     const tracks = this.tracksNames || (await this.httpMap.getTrackNames())
     const str = queryString.toLowerCase()