@apollo-annotation/cli 1.1.1 → 1.1.2

package/dist/commands/export/gff3.js

@@ -1,8 +1,7 @@
 import { Readable } from 'node:stream';
 import { Args, Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static description = 'Export the annotations for an assembly to stdout as gff3';
     static examples = [
@@ -25,43 +24,22 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { args } = await this.parse(Get);
-        const access = await this.getAccess();
         const assembly = await idReader([args.assembly]);
-        const [assemblyId] = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
+        const [assemblyId] = await this.convertAssemblyNameToId(assembly);
         if (!assemblyId) {
             this.error(`Invalid assembly name or id: ${args.assembly}`);
         }
-        const url = new URL(localhostToAddress(`${access.address}/export/getID`));
         const searchParams = new URLSearchParams({
             assembly: assemblyId,
         });
-        url.search = searchParams.toString();
-        const uri = url.toString();
-        const auth = {
-            headers: {
-                authorization: `Bearer ${access.accessToken}`,
-            },
-        };
-        const response = await fetch(uri, auth);
-        if (!response.ok) {
-            const newErrorMessage = await createFetchErrorMessage(response, 'Error when exporting ID');
-            throw new Error(newErrorMessage);
-        }
-        const { exportID } = (await response.json());
-        const exportURL = new URL(localhostToAddress(`${access.address}/export`));
+        const { exportID } = (await this.get(`export/getID?${searchParams.toString()}`));
         const params = {
             exportID,
             assemblyId,
             includeFASTA: this.flags['include-fasta'] ? 'true' : 'false',
         };
         const exportSearchParams = new URLSearchParams(params);
-        exportURL.search = exportSearchParams.toString();
-        const exportUri = exportURL.toString();
-        const responseExport = await fetch(exportUri, auth);
-        if (!responseExport.ok) {
-            const newErrorMessage = await createFetchErrorMessage(responseExport, 'Error when exporting gff');
-            throw new Error(newErrorMessage);
-        }
+        const responseExport = await this.fetch(`export?${exportSearchParams.toString()}`);
         const { body } = responseExport;
         if (body) {
             const readable = Readable.from(body);

package/dist/commands/export/gff3.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gff3.js","sourceRoot":"","sources":["../../../src/commands/export/gff3.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AAEtC,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEzC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,WAAW,GAChB,0DAA0D,CAAA;IAE5D,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,oCAAoC;YACjD,OAAO,EAAE,2DAA2D;SACrE;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,QAAQ,EAAE,IAAI,CAAC,MAAM,CAAC;YACpB,WAAW,EAAE,iDAAiD;YAC9D,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC;YAC7B,WAAW,EAAE,kCAAkC;YAC/C,OAAO,EAAE,KAAK;SACf,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAA;QAChD,MAAM,CAAC,UAAU,CAAC,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,QAAQ,CAAC,CAAA;QACjE,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,IAAI,CAAC,KAAK,CAAC,gCAAgC,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAA;QAC7D,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,eAAe,CAAC;YACvC,QAAQ,EAAE,UAAU;SACrB,CAAC,CAAA;QACF,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAClC,gBAAgB,YAAY,CAAC,QAAQ,EAAE,EAAE,CAC1C,CAAyB,CAAA;QAE1B,MAAM,MAAM,GAA2B;YACrC,QAAQ;YACR,UAAU;YACV,YAAY,EAAE,IAAI,CAAC,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO;SAC7D,CAAA;QACD,MAAM,kBAAkB,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAA;QAEtD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,KAAK,CACrC,UAAU,kBAAkB,CAAC,QAAQ,EAAE,EAAE,CAC1C,CAAA;QACD,MAAM,EAAE,IAAI,EAAE,GAAG,cAAc,CAAA;QAC/B,IAAI,IAAI,EAAE,CAAC;YACT,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACpC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;QAC/B,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;QACrC,CAAC;IACH,CAAC"}

package/dist/commands/feature/add-child.d.ts

@@ -7,10 +7,10 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        start: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        end: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        start: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
+        end: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
+        type: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
     private addChild;

package/dist/commands/feature/add-child.d.ts.map

@@ -1 +1 @@
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package/dist/commands/feature/add-child.js

@@ -1,8 +1,7 @@
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Add a child feature (e.g. add an exon to an mRNA)';
     static description = 'See the other commands under `apollo feature` \
@@ -48,27 +47,16 @@ to retrive the parent ID of interest and to populate the child feature with attr
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess();
-        const res = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        const feature = JSON.parse(await res.text());
-        const childRes = await this.addChild(access.address, access.accessToken, feature, flags.start - 1, flags.end, flags.type);
-        if (!childRes.ok) {
-            const errorMessage = await createFetchErrorMessage(childRes, 'Add child failed');
-            throw new Error(errorMessage);
-        }
+        const feature = await this.getFeatureById(featureId);
+        await this.addChild(feature, flags.start - 1, flags.end, flags.type);
     }
-    async addChild(address, accessToken, parentFeature, min, max, type) {
+    async addChild(parentFeature, min, max, type) {
         const pMin = parentFeature.min;
         const pMax = parentFeature.max;
         if (min < pMin || max > pMax) {
             this.error(`Error: Child feature coordinates (${min + 1}-${max}) cannot extend beyond parent coordinates (${pMin + 1}-${pMax})`);
         }
-        const res = await queryApollo(address, accessToken, 'refSeqs');
-        const refSeqs = (await res.json());
+        const refSeqs = (await this.get('refSeqs'));
         const { refSeq, _id } = parentFeature;
         let assembly = '';
         for (const x of refSeqs) {
@@ -90,21 +78,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
             },
             parentFeatureId: _id,
         };
-        const url = new URL(localhostToAddress(`${address}/changes`));
-        const auth = {
-            method: 'POST',
-            body: JSON.stringify(change),
-            headers: {
-                authorization: `Bearer ${accessToken}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const response = await fetch(url, auth);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        return response;
+        await this.post('changes', JSON.stringify(change));
     }
 }
 //# sourceMappingURL=add-child.js.map

package/dist/commands/feature/add-child.js.map

@@ -1 +1 @@
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package/dist/commands/feature/add.d.ts

@@ -1,6 +1,5 @@
 import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import type { SerializedAddFeatureChange } from '@apollo-annotation/shared';
-import { type Response } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
 interface BaseFeatureJSON {
     min: number;
@@ -21,26 +20,21 @@ export default class Add extends BaseCommand<typeof Add> {
         command: string;
     }[];
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        refSeq: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        min: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        max: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        'feature-json-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        refSeq: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        min: import("@oclif/core/interfaces").OptionFlag<number | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        max: import("@oclif/core/interfaces").OptionFlag<number | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        type: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        'feature-json-file': import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     static args: {
-        'feature-json': import("@oclif/core/lib/interfaces/parser.js").Arg<string | undefined, Record<string, unknown>>;
+        'feature-json': import("@oclif/core/interfaces").Arg<string | undefined, Record<string, unknown>>;
     };
     run(): Promise<void>;
     addFeatureFromJSON(featureJSONString: string): Promise<void>;
     makeFeatureSnapshot(details: FeatureJSON, ids: string[]): AnnotationFeatureSnapshot;
     addFeatureFromFlags(refSeqNameOrId: string, min: number, max: number, type: string, assemblyNameOrId?: string): Promise<void>;
     getAssemblyAndRefSeqIds(refSeqNameOrId: string, assemblyNameOrId?: string): Promise<[string, string]>;
-    getAssembly(assemblyNameOrId: string): Promise<{
-        _id: string;
-        name: string;
-        aliases?: string[];
-    }>;
     getRefSeq(refSeqNameOrId: string, assemblyId?: string): Promise<{
         _id: string;
         name: string;
@@ -48,11 +42,6 @@ export default class Add extends BaseCommand<typeof Add> {
         aliases?: string[];
     }>;
     submitChange(change: SerializedAddFeatureChange): Promise<void>;
-    fetch(endpoint: string, options?: {
-        method?: string;
-        body?: string;
-        headers?: Record<string, string>;
-    }): Promise<Response>;
 }
 export {};
 //# sourceMappingURL=add.d.ts.map

package/dist/commands/feature/add.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"add.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/add.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AACvE,OAAO,KAAK,EAEV,0BAA0B,EAC3B,MAAM,2BAA2B,CAAA;AAIlC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,UAAU,eAAe;IACvB,GAAG,EAAE,MAAM,CAAA;IACX,GAAG,EAAE,MAAM,CAAA;IACX,IAAI,EAAE,MAAM,CAAA;IACZ,QAAQ,CAAC,EAAE,eAAe,EAAE,CAAA;IAC5B,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;CACvB;AAED,UAAU,WAAY,SAAQ,eAAe;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAA;IACjB,MAAM,EAAE,MAAM,CAAA;CACf;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAuC;IACrD,MAAM,CAAC,WAAW,SAGnB;IAEC,MAAM,CAAC,QAAQ;;;QAqBd;IAED,MAAM,CAAC,KAAK;;;;;;;MAmCX;IAED,MAAM,CAAC,IAAI;;MAKV;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;IA2C3B,kBAAkB,CAAC,iBAAiB,EAAE,MAAM;IA2ElD,mBAAmB,CACjB,OAAO,EAAE,WAAW,EACpB,GAAG,EAAE,MAAM,EAAE,GACZ,yBAAyB;IAqBtB,mBAAmB,CACvB,cAAc,EAAE,MAAM,EACtB,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,gBAAgB,CAAC,EAAE,MAAM;IAsBrB,uBAAuB,CAC3B,cAAc,EAAE,MAAM,EACtB,gBAAgB,CAAC,EAAE,MAAM,GACxB,OAAO,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IA4BtB,SAAS,CACb,cAAc,EAAE,MAAM,EACtB,UAAU,CAAC,EAAE,MAAM,GAClB,OAAO,CAAC;QACT,GAAG,EAAE,MAAM,CAAA;QACX,IAAI,EAAE,MAAM,CAAA;QACZ,QAAQ,EAAE,MAAM,CAAA;QAChB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAA;KACnB,CAAC;IA+BI,YAAY,CAAC,MAAM,EAAE,0BAA0B;CAItD"}

package/dist/commands/feature/add.js

@@ -1,9 +1,7 @@
 import { readFile } from 'node:fs/promises';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress } from '../../utils.js';
 export default class Add extends BaseCommand {
     static summary = 'Add one or more features to Apollo';
     static description = `A single simple feature can be added using the --min, --max, etc. flags.
@@ -212,49 +210,16 @@ To add multiple features, features with more details, or features with children,
         const refSeqDocument = await this.getRefSeq(refSeqNameOrId, assemblyDocument._id);
         return [assemblyDocument._id, refSeqDocument._id];
     }
-    async getAssembly(assemblyNameOrId) {
-        if (ObjectId.isValid(assemblyNameOrId)) {
-            const response = await this.fetch(`assemblies/${assemblyNameOrId}`);
-            if (!response.ok) {
-                const errorMessage = await createFetchErrorMessage(response, `Could not find assembly: "${assemblyNameOrId}"`);
-                this.error(errorMessage);
-            }
-            return response.json();
-        }
-        const response = await this.fetch('assemblies');
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, `Could not find assembly: "${assemblyNameOrId}"`);
-            this.error(errorMessage);
-        }
-        const assemblies = (await response.json());
-        for (const assembly of assemblies) {
-            if (assembly.name === assemblyNameOrId ||
-                assembly.aliases?.includes(assemblyNameOrId)) {
-                return assembly;
-            }
-        }
-        throw new Error(`Could not find assembly: "${assemblyNameOrId}"`);
-    }
     async getRefSeq(refSeqNameOrId, assemblyId) {
         if (ObjectId.isValid(refSeqNameOrId)) {
-            const response = await this.fetch(`refSeqs/${refSeqNameOrId}`);
-            if (!response.ok) {
-                const errorMessage = await createFetchErrorMessage(response, `Could not find refSeq: "${refSeqNameOrId}"`);
-                this.error(errorMessage);
-            }
-            return response.json();
+            return (await this.get(`refSeqs/${refSeqNameOrId}`));
         }
         let endpoint = 'refSeqs';
         if (assemblyId) {
             const searchParams = new URLSearchParams({ assembly: assemblyId });
             endpoint = `${endpoint}?${searchParams.toString()}`;
         }
-        const response = await this.fetch(endpoint);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, `Could not find refSeq: "${refSeqNameOrId}"`);
-            this.error(errorMessage);
-        }
-        const refSeqs = (await response.json());
+        const refSeqs = (await this.get(endpoint));
         for (const refSeq of refSeqs) {
             if (refSeq.name === refSeqNameOrId ||
                 refSeq.aliases?.includes(refSeqNameOrId)) {
@@ -264,26 +229,8 @@ To add multiple features, features with more details, or features with children,
         throw new Error(`Could not find refSeq: "${refSeqNameOrId}"`);
     }
     async submitChange(change) {
-        const options = { method: 'POST', body: JSON.stringify(change) };
-        const response = await this.fetch('changes', options);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'Could not add feature');
-            this.error(errorMessage);
-        }
-        this.log(await response.text());
-    }
-    async fetch(endpoint, options) {
-        const { address, accessToken } = await this.getAccess();
-        const url = new URL(localhostToAddress(`${address}/${endpoint}`));
-        const optionsWithAuth = {
-            ...options,
-            headers: {
-                authorization: `Bearer ${accessToken}`,
-                'Content-Type': 'application/json',
-                ...options?.headers,
-            },
-        };
-        return fetch(url, optionsWithAuth);
+        const result = await this.post('changes', JSON.stringify(change));
+        this.log(JSON.stringify(result));
     }
 }
 function parseFeatureJSON(featureJSONString) {

package/dist/commands/feature/add.js.map

@@ -1 +1 @@
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package/dist/commands/feature/check.d.ts

@@ -7,9 +7,10 @@ export default class Check extends BaseCommand<typeof Check> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
+    keepAssemblies(assembly: string | undefined): Promise<string[]>;
 }
 //# sourceMappingURL=check.d.ts.map

package/dist/commands/feature/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/check.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAEmE;IAErF,MAAM,CAAC,QAAQ;;;QASd;IAED,MAAM,CAAC,KAAK;;;MAUX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAiDlC"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/check.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAEmE;IAErF,MAAM,CAAC,QAAQ;;;QASd;IAED,MAAM,CAAC,KAAK;;;MAUX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;IAwC3B,cAAc,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;CAatE"}

package/dist/commands/feature/check.js

@@ -1,7 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Check extends BaseCommand {
     static summary = 'Get check results';
     static description = 'Use this command to view which features fail checks along with the reason for failing.\
@@ -29,21 +28,19 @@ Use `apollo assembly check` for managing which checks should be applied to an as
     };
     async run() {
         const { flags } = await this.parse(Check);
-        const access = await this.getAccess();
         let keepFeatures = new Set();
         if (flags['feature-id'] !== undefined) {
             keepFeatures = new Set(await idReader(flags['feature-id']));
         }
-        const keepAsmId = await keepAssemblies(access.address, access.accessToken, flags.assembly);
-        const res = await queryApollo(access.address, access.accessToken, 'refseqs');
-        const refseq = (await res.json());
+        const keepAsmId = await this.keepAssemblies(flags.assembly);
+        const refseq = (await this.get('refseqs'));
         const refseqId = new Set();
         for (const x of refseq) {
             if (keepAsmId.includes(x['assembly'])) {
                 refseqId.add(x['_id']);
             }
         }
-        const checks = await getChecks(access.address, access.accessToken);
+        const checks = (await this.get('checks'));
         const results = [];
         for (const chk of checks) {
             let keep = false;
@@ -65,35 +62,19 @@ Use `apollo assembly check` for managing which checks should be applied to an as
         results.sort((a, b) => (a.start < b.start ? -1 : 1));
         this.log(JSON.stringify(results, null, 2));
     }
-}
-async function keepAssemblies(address, accessToken, assembly) {
-    let keepAssembly = [];
-    if (assembly === undefined) {
-        const res = await queryApollo(address, accessToken, 'assemblies');
-        const asm = (await res.json());
-        for (const x of asm) {
-            keepAssembly.push(x._id);
+    async keepAssemblies(assembly) {
+        let keepAssembly = [];
+        if (assembly === undefined) {
+            const asm = (await this.get('assemblies'));
+            for (const x of asm) {
+                keepAssembly.push(x._id);
+            }
         }
+        else {
+            const ids = await idReader([assembly]);
+            keepAssembly = await this.convertAssemblyNameToId(ids);
+        }
+        return keepAssembly;
     }
-    else {
-        const ids = await idReader([assembly]);
-        keepAssembly = await convertAssemblyNameToId(address, accessToken, ids);
-    }
-    return keepAssembly;
-}
-async function getChecks(address, token) {
-    const url = new URL(localhostToAddress(`${address}/checks`));
-    const auth = {
-        headers: {
-            authorization: `Bearer ${token}`,
-            'Content-Type': 'application/json',
-        },
-    };
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
-        throw new Error(errorMessage);
-    }
-    return (await response.json());
 }
 //# sourceMappingURL=check.js.map

package/dist/commands/feature/check.js.map

@@ -1 +1 @@
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+{"version":3,"file":"check.js","sourceRoot":"","sources":["../../../src/commands/feature/check.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAyB;IAC1D,MAAM,CAAC,OAAO,GAAG,mBAAmB,CAAA;IACpC,MAAM,CAAC,WAAW,GAChB;uFACmF,CAAA;IAErF,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,wCAAwC;YACrD,OAAO,EAAE,qCAAqC;SAC/C;QACD;YACE,WAAW,EAAE,sCAAsC;YACnD,OAAO,EAAE,6CAA6C;SACvD;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,YAAY,EAAE,KAAK,CAAC,MAAM,CAAC;YACzB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,0CAA0C;YACvD,QAAQ,EAAE,IAAI;SACf,CAAC;QACF,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,8BAA8B;SAC5C,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;QAEzC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,IAAI,KAAK,CAAC,YAAY,CAAC,KAAK,SAAS,EAAE,CAAC;YACtC,YAAY,GAAG,IAAI,GAAG,CAAC,MAAM,QAAQ,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC7D,CAAC;QAED,MAAM,SAAS,GAAa,MAAM,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;QAErE,MAAM,MAAM,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAa,CAAA;QACtD,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAU,CAAA;QAClC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,IAAI,SAAS,CAAC,QAAQ,CAAC,CAAC,CAAC,UAA4B,CAAC,CAAC,EAAE,CAAC;gBACxD,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,KAAuB,CAAC,CAAC,CAAA;YAC1C,CAAC;QACH,CAAC;QAED,MAAM,MAAM,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAA0B,CAAA;QAClE,MAAM,OAAO,GAA0B,EAAE,CAAA;QACzC,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;YACzB,IAAI,IAAI,GAAG,KAAK,CAAA;YAChB,IAAI,KAAK,CAAC,YAAY,CAAC,KAAK,SAAS,EAAE,CAAC;gBACtC,IAAI,GAAG,IAAI,CAAA;YACb,CAAC;iBAAM,IAAI,GAAG,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;gBACjC,KAAK,MAAM,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,CAAC;oBACxB,IAAI,CAAC,KAAK,SAAS,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,EAAE,CAAC;wBACtD,IAAI,GAAG,IAAI,CAAA;wBACX,MAAK;oBACP,CAAC;gBACH,CAAC;YACH,CAAC;YACD,IAAI,IAAI,IAAI,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;gBACrC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACnB,CAAC;QACH,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACpD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,cAAc,CAAC,QAA4B;QAC/C,IAAI,YAAY,GAAa,EAAE,CAAA;QAC/B,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;YAC3B,MAAM,GAAG,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAA6B,CAAA;YACtE,KAAK,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;gBACpB,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;YACtC,YAAY,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,GAAG,CAAC,CAAA;QACxD,CAAC;QACD,OAAO,YAAY,CAAA;IACrB,CAAC"}

package/dist/commands/feature/copy.d.ts

@@ -7,10 +7,10 @@ export default class Copy extends BaseCommand<typeof Copy> {
         command: string;
     }[];
     static flags: {
-        'feature-id': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        refseq: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        start: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-id': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        refseq: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        start: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
     private copyFeature;

package/dist/commands/feature/copy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/copy.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AASlD,MAAM,CAAC,OAAO,OAAO,IAAK,SAAQ,WAAW,CAAC,OAAO,IAAI,CAAC;IACxD,MAAM,CAAC,OAAO,SAAuC;IACrD,MAAM,CAAC,WAAW,SAGmC;IAErD,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;;;MAsBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YA0DnB,WAAW;CA8C1B"}
+{"version":3,"file":"copy.d.ts","sourceRoot":"","sources":["../../../src/commands/feature/copy.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,IAAK,SAAQ,WAAW,CAAC,OAAO,IAAI,CAAC;IACxD,MAAM,CAAC,OAAO,SAAuC;IACrD,MAAM,CAAC,WAAW,SAGmC;IAErD,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;;;MAsBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAoBnB,WAAW;CA2B1B"}

package/dist/commands/feature/copy.js

@@ -1,8 +1,6 @@
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, getRefseqId, localhostToAddress, } from '../../utils.js';
 export default class Copy extends BaseCommand {
     static summary = 'Copy a feature to another location';
     static description = 'The feature may be copied to the same or to a different assembly. \
@@ -41,27 +39,17 @@ the database or by name and assembly or by identifier.';
         if (flags.start <= 0) {
             this.error('Start coordinate must be greater than 0');
         }
-        const access = await this.getAccess();
-        const res = await getFeatureById(access.address, access.accessToken, flags['feature-id']);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        const feature = (await res.json());
-        const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
+        const feature = await this.getFeatureById(flags['feature-id']);
+        const refseqIds = await this.getRefseqId(flags.refseq, flags.assembly);
         if (refseqIds.length === 0) {
             this.error('No reference sequence found');
         }
         const [refseq] = refseqIds;
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, refseq);
+        const assembly = await this.getAssemblyFromRefseq(refseq);
         const newId = new ObjectId().toHexString();
-        const rescopy = await this.copyFeature(access.address, access.accessToken, feature, refseq, flags.start, assembly, newId);
-        if (!rescopy.ok) {
-            const errorMessage = await createFetchErrorMessage(rescopy, 'Copy feature failed');
-            throw new Error(errorMessage);
-        }
+        await this.copyFeature(feature, refseq, flags.start, assembly, newId);
     }
-    async copyFeature(address, accessToken, feature, refseq, min, assembly, newId) {
+    async copyFeature(feature, refseq, min, assembly, newId) {
         const featureLen = feature.max - feature.min;
         const change = {
             typeName: 'AddFeatureChange',
@@ -79,21 +67,7 @@ the database or by name and assembly or by identifier.';
             copyFeature: true,
             allIds: [newId],
         };
-        const url = new URL(localhostToAddress(`${address}/changes`));
-        const auth = {
-            method: 'POST',
-            body: JSON.stringify(change),
-            headers: {
-                authorization: `Bearer ${accessToken}`,
-                'Content-Type': 'application/json',
-            },
-        };
-        const res = await fetch(url, auth);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'copyFeature failed');
-            throw new Error(errorMessage);
-        }
-        return res;
+        await this.post('changes', JSON.stringify(change));
     }
 }
 //# sourceMappingURL=copy.js.map

package/dist/commands/feature/copy.js.map

@@ -1 +1 @@
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