@apollo-annotation/cli 1.1.1 → 1.1.2

package/dist/ApolloConf.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ApolloConf.d.ts","sourceRoot":"","sources":["../src/ApolloConf.ts"],"names":[],"mappings":"AAIA,OAAO,IAAI,MAAM,MAAM,CAAA;AAMvB,qBAAa,WAAY,SAAQ,KAAK;CAAG;AAEzC,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,UAAU,eAAe;IACzB,WAAW,gBAAgB;IAC3B,YAAY,iBAAiB;CAC9B;AA4CD,wBAAgB,UAAU,IAAI,MAAM,EAAE,CAMrC;AAED,qBAAa,UAAW,SAAQ,IAAI;gBACtB,UAAU,EAAE,MAAM;IA2B9B,IAAI,KAAK,4BAOR;IAED,IAAI,KAAK,CAAC,QAAQ,yBAAA,EAMjB;IAEM,eAAe,IAAI,MAAM,EAAE;IAI3B,aAAa,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM;IAO/C,SAAS,CAAC,WAAW,EAAE,MAAM;;;;CAoB3C"}
+{"version":3,"file":"ApolloConf.d.ts","sourceRoot":"","sources":["../src/ApolloConf.ts"],"names":[],"mappings":"AAIA,OAAO,IAAI,MAAM,MAAM,CAAA;AAOvB,qBAAa,WAAY,SAAQ,KAAK;CAAG;AAEzC,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,UAAU,eAAe;IACzB,WAAW,gBAAgB;IAC3B,YAAY,iBAAiB;CAC9B;AA4CD,wBAAgB,UAAU,IAAI,MAAM,EAAE,CAMrC;AAED,qBAAa,UAAW,SAAQ,IAAI;gBACtB,UAAU,EAAE,MAAM;IA2B9B,IAAI,KAAK,4BAOR;IAED,IAAI,KAAK,CAAC,QAAQ,yBAAA,EAMjB;IAEM,eAAe,IAAI,MAAM,EAAE;IAI3B,aAAa,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM;IAO/C,SAAS,CAAC,WAAW,EAAE,MAAM;;;;CA+B3C"}

package/dist/ApolloConf.js

@@ -3,8 +3,9 @@ import fs from 'node:fs';
 import path from 'node:path';
 import Conf from 'conf';
 import Joi from 'joi';
+import { fetch } from 'undici';
 import YAML from 'yaml';
-import { checkProfileExists, queryApollo } from './utils.js';
+import { createFetchErrorMessage, localhostToAddress } from './utils.js';
 export class ConfigError extends Error {
 }
 export var KEYS;
@@ -108,7 +109,6 @@ export class ApolloConf extends Conf {
         this.set(`${profileName}.accessType`, accessType);
     }
     async getAccess(profileName) {
-        checkProfileExists(profileName, this);
         const address = this.get(`${profileName}.address`);
         if (address.trim() === '') {
             throw new ConfigError(`Profile "${profileName}" has no address. Please run "apollo config" to set it up.`);
@@ -117,7 +117,18 @@ export class ApolloConf extends Conf {
         if (accessToken.trim() === '') {
             throw new ConfigError(`Profile "${profileName}" has no access token. Please run "apollo login" to set it up.`);
         }
-        await queryApollo(address, accessToken, 'assemblies');
+        const auth = {
+            headers: {
+                Authorization: `Bearer ${accessToken}`,
+                'Content-Type': 'application/json',
+            },
+        };
+        const url = new URL(localhostToAddress(`${address}/assemblies`));
+        const response = await fetch(url, auth);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, 'getAccess failed');
+            throw new ConfigError(errorMessage);
+        }
         return { address, accessToken };
     }
 }

package/dist/ApolloConf.js.map

@@ -1 +1 @@
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package/dist/baseCommand.d.ts

@@ -1,22 +1,58 @@
 import { Command, type Interfaces } from '@oclif/core';
+import { Agent, type RequestInit, type Response, type BodyInit } from 'undici';
+import { ApolloConf } from './ApolloConf.js';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import type { SerializedAddAssemblyAndFeaturesFromFileChange, SerializedAddAssemblyFromExternalChange, SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
+interface AssemblyResponse {
+    _id: string;
+    name: string;
+    aliases?: string[];
+}
+export declare class CheckError extends Error {
+}
 export type Flags<T extends typeof Command> = Interfaces.InferredFlags<(typeof BaseCommand)['baseFlags'] & T['flags']>;
 export type Args<T extends typeof Command> = Interfaces.InferredArgs<T['args']>;
 export declare abstract class BaseCommand<T extends typeof Command> extends Command {
     static baseFlags: {
         profile: Interfaces.OptionFlag<string | undefined, Interfaces.CustomOptions>;
         'config-file': Interfaces.OptionFlag<string | undefined, Interfaces.CustomOptions>;
+        timeout: Interfaces.OptionFlag<string, Interfaces.CustomOptions>;
     };
     protected flags: Flags<T>;
     protected args: Args<T>;
+    protected apolloConfig: ApolloConf;
     init(): Promise<void>;
-    private getConfig;
+    protected getConfig(): ApolloConf;
     getAccess(): Promise<{
         address: string;
         accessToken: string;
     }>;
+    getDispatcher(): Agent;
+    private getURL;
+    private getHeaders;
+    check(response: Response): Promise<Response>;
+    fetchWithoutCheck(endpoint: string, requestInit?: RequestInit, opts?: {
+        json?: boolean;
+    }): Promise<Response>;
+    fetch(endpoint: string, requestInit?: RequestInit, opts?: {
+        json?: boolean;
+    }): Promise<Response>;
+    post(endpoint: string, body: BodyInit, requestInit?: RequestInit): Promise<unknown>;
+    get(endpoint: string, requestInit?: RequestInit): Promise<unknown>;
     protected catch(err: Error & {
         exitCode?: number;
     }): Promise<unknown>;
     protected finally(_: Error | undefined): Promise<unknown>;
+    assemblyNameToIdDict(): Promise<Record<string, string | undefined>>;
+    convertAssemblyNameToId(namesOrIds: string[], verbose?: boolean, removeDuplicates?: boolean): Promise<string[]>;
+    getAssembly(assemblyNameOrId: string): Promise<AssemblyResponse>;
+    getRefseqId(refseqNameOrId?: string, inAssemblyNameOrId?: string): Promise<string[]>;
+    getFeatureById(id: string): Promise<AnnotationFeatureSnapshot>;
+    deleteAssembly(assemblyId: string): Promise<void>;
+    submitAssembly(body: SerializedAddAssemblyFromFileChange | SerializedAddAssemblyFromExternalChange | SerializedAddAssemblyAndFeaturesFromFileChange, force: boolean): Promise<object>;
+    checkNameToIdDict(): Promise<Record<string, string | undefined>>;
+    convertCheckNameToId(namesOrIds: string[]): Promise<string[]>;
+    getAssemblyFromRefseq(refSeq: string): Promise<string>;
 }
+export {};
 //# sourceMappingURL=baseCommand.d.ts.map

package/dist/baseCommand.d.ts.map

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package/dist/baseCommand.js

@@ -1,7 +1,13 @@
 import path from 'node:path';
+import { stderr } from 'node:process';
 import { Command, Flags } from '@oclif/core';
-import { ApolloConf } from './ApolloConf.js';
-import { checkConfigfileExists } from './utils.js';
+import { ObjectId } from 'bson';
+import ms, {} from 'ms';
+import { Agent, fetch, Headers, } from 'undici';
+import { ApolloConf, ConfigError } from './ApolloConf.js';
+import { createFetchErrorMessage, filterJsonList, localhostToAddress, } from './utils.js';
+export class CheckError extends Error {
+}
 export class BaseCommand extends Command {
     static baseFlags = {
         profile: Flags.string({
@@ -10,9 +16,14 @@ export class BaseCommand extends Command {
         'config-file': Flags.string({
             description: 'Use this config file (mostly for testing)',
         }),
+        timeout: Flags.string({
+            description: 'Timeout for each request to the server',
+            default: '1h',
+        }),
     };
     flags;
     args;
+    apolloConfig;
     async init() {
         await super.init();
         const { args, flags } = await this.parse({
@@ -23,19 +34,82 @@ export class BaseCommand extends Command {
         });
         this.flags = flags;
         this.args = args;
-    }
-    getConfig(configFile) {
+        let { 'config-file': configFile } = this.flags;
         configFile ??= path.join(this.config.configDir, 'config.yml');
-        checkConfigfileExists(configFile);
-        const config = new ApolloConf(configFile);
-        return config;
+        const apolloConfig = new ApolloConf(configFile);
+        const { profile } = this.flags;
+        const profileName = process.env.APOLLO_PROFILE ?? profile ?? 'default';
+        if (this.id !== 'config' &&
+            !apolloConfig.getProfileNames().includes(profileName)) {
+            throw new ConfigError(`Profile "${profileName}" does not exist. Please run "apollo config" to set this profile up or choose a different profile`);
+        }
+        this.apolloConfig = apolloConfig;
+    }
+    getConfig() {
+        return this.apolloConfig;
     }
     async getAccess() {
-        const { 'config-file': configFile, profile } = this.flags;
-        const config = this.getConfig(configFile);
+        const { profile } = this.flags;
+        const config = this.getConfig();
         const profileName = process.env.APOLLO_PROFILE ?? profile ?? 'default';
         return config.getAccess(profileName);
     }
+    getDispatcher() {
+        const { timeout } = this.flags;
+        const timeoutMs = ms(timeout);
+        return new Agent({ headersTimeout: timeoutMs });
+    }
+    async getURL(endpoint) {
+        const { address } = await this.getAccess();
+        return new URL(endpoint, localhostToAddress(address));
+    }
+    async getHeaders(options, json = false) {
+        const { accessToken } = await this.getAccess();
+        const headers = new Headers(options?.headers);
+        headers.set('authorization', `Bearer ${accessToken}`);
+        if (json) {
+            headers.set('Content-Type', 'application/json');
+        }
+        return headers;
+    }
+    async check(response) {
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, `Request to "${response.url}" failed`);
+            throw new Error(errorMessage);
+        }
+        return response;
+    }
+    async fetchWithoutCheck(endpoint, requestInit, opts) {
+        const url = await this.getURL(endpoint);
+        const headers = await this.getHeaders(requestInit, opts?.json);
+        const dispatcher = this.getDispatcher();
+        const optionsWithAuth = {
+            ...requestInit,
+            dispatcher,
+            headers,
+        };
+        return fetch(url, optionsWithAuth);
+    }
+    async fetch(endpoint, requestInit, opts) {
+        return this.check(await this.fetchWithoutCheck(endpoint, requestInit, opts));
+    }
+    async post(endpoint, body, requestInit) {
+        const optionsWithAuth = {
+            ...requestInit,
+            body,
+            method: 'POST',
+        };
+        const response = await this.fetch(endpoint, optionsWithAuth, { json: true });
+        return response.json();
+    }
+    async get(endpoint, requestInit) {
+        const optionsWithAuth = {
+            ...requestInit,
+            method: 'GET',
+        };
+        const response = await this.fetch(endpoint, optionsWithAuth, { json: true });
+        return response.json();
+    }
     async catch(err) {
         if (err.cause instanceof Error) {
             console.error(err.cause);
@@ -46,5 +120,148 @@ export class BaseCommand extends Command {
         // called after run and catch regardless of whether or not the command errored
         return super.finally(_);
     }
+    async assemblyNameToIdDict() {
+        const ja = (await this.get('assemblies'));
+        const nameToId = {};
+        for (const x of ja) {
+            nameToId[x['name']] = x['_id'];
+        }
+        return nameToId;
+    }
+    async convertAssemblyNameToId(namesOrIds, verbose = true, removeDuplicates = true) {
+        const nameToId = await this.assemblyNameToIdDict();
+        let ids = [];
+        for (const x of namesOrIds) {
+            if (nameToId[x] !== undefined) {
+                ids.push(nameToId[x]);
+            }
+            else if (Object.values(nameToId).includes(x)) {
+                ids.push(x);
+            }
+            else if (verbose) {
+                stderr.write(`Warning: Omitting unknown assembly: "${x}"\n`);
+            }
+        }
+        if (removeDuplicates) {
+            ids = [...new Set(ids)];
+        }
+        return ids;
+    }
+    async getAssembly(assemblyNameOrId) {
+        if (ObjectId.isValid(assemblyNameOrId)) {
+            return this.get(`assemblies/${assemblyNameOrId}`);
+        }
+        const assemblies = (await this.get('assemblies'));
+        for (const assembly of assemblies) {
+            if (assembly.name === assemblyNameOrId ||
+                assembly.aliases?.includes(assemblyNameOrId)) {
+                return assembly;
+            }
+        }
+        throw new Error(`Could not find assembly: "${assemblyNameOrId}"`);
+    }
+    async getRefseqId(refseqNameOrId, inAssemblyNameOrId) {
+        if (refseqNameOrId === undefined && inAssemblyNameOrId === undefined) {
+            throw new Error('Please provide refseq and/or assembly');
+        }
+        inAssemblyNameOrId ??= '';
+        let assemblyId = [];
+        if (inAssemblyNameOrId !== '') {
+            assemblyId = await this.convertAssemblyNameToId([inAssemblyNameOrId]);
+            if (assemblyId.length !== 1) {
+                throw new Error(`Assembly name or assembly id returned ${assemblyId.length} assemblies instead of just one`);
+            }
+        }
+        const refSeqs = (await this.get('refSeqs'));
+        const refseqIds = [];
+        const nAssemblies = new Set();
+        for (const x of refSeqs) {
+            const aid = x['assembly'];
+            const rid = x['_id'];
+            const rname = x['name'];
+            if (refseqNameOrId === rid ||
+                refseqNameOrId === rname ||
+                refseqNameOrId === undefined) {
+                if (inAssemblyNameOrId === '' || assemblyId.includes(aid)) {
+                    refseqIds.push(rid);
+                    nAssemblies.add(aid);
+                }
+                else {
+                    //
+                }
+            }
+            if (nAssemblies.size > 1) {
+                throw new Error(`Sequence name "${refseqNameOrId}" found in more than one assembly`);
+            }
+        }
+        return refseqIds;
+    }
+    async getFeatureById(id) {
+        return this.get(`features/${id}`);
+    }
+    async deleteAssembly(assemblyId) {
+        const body = {
+            typeName: 'DeleteAssemblyChange',
+            assembly: assemblyId,
+        };
+        await this.post('changes', JSON.stringify(body));
+    }
+    async submitAssembly(body, force) {
+        let assemblies = (await this.get('assemblies'));
+        for (const x of assemblies) {
+            const addedAssemblies = 'changes' in body ? body.changes : [body];
+            for (const addedAssembly of addedAssemblies) {
+                if (x.name === addedAssembly.assemblyName) {
+                    if (force) {
+                        await this.deleteAssembly(x._id);
+                    }
+                    else {
+                        throw new Error(`Error: Assembly "${addedAssembly.assemblyName}" already exists`);
+                    }
+                }
+            }
+        }
+        await this.post('changes', JSON.stringify(body));
+        assemblies = (await this.get('assemblies'));
+        for (const x of assemblies) {
+            const addedAssemblies = 'changes' in body ? body.changes : [body];
+            for (const addedAssembly of addedAssemblies) {
+                if (x.name === addedAssembly.assemblyName) {
+                    return x;
+                }
+            }
+        }
+        throw new Error(`Failed to retrieve assembly from ${body.assembly}`);
+    }
+    async checkNameToIdDict() {
+        const ja = (await this.get('checks/types')); // Not sure if CheckResultSnapshot is the right interface
+        const nameToId = {};
+        for (const x of ja) {
+            const { _id, name } = x; // x['name' as keyof typeof x]
+            nameToId[name] = _id; // x['_id' as keyof typeof x]
+        }
+        return nameToId;
+    }
+    async convertCheckNameToId(namesOrIds) {
+        const nameToId = await this.checkNameToIdDict();
+        const ids = [];
+        for (const x of namesOrIds) {
+            if (nameToId[x] !== undefined) {
+                ids.push(nameToId[x]);
+            }
+            else if (Object.values(nameToId).includes(x)) {
+                ids.push(x);
+            }
+            else {
+                throw new CheckError(`Check name or id "${x}" not found`);
+            }
+        }
+        return ids;
+    }
+    async getAssemblyFromRefseq(refSeq) {
+        const refSeqs = (await this.get('refSeqs'));
+        const refJson = filterJsonList(refSeqs, [refSeq], '_id');
+        return refJson[0]['assembly'];
+    }
 }
 //# sourceMappingURL=baseCommand.js.map

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@@ -1 +1 @@
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package/dist/commands/assembly/add-from-fasta.d.ts

@@ -7,16 +7,16 @@ export default class AddFasta extends FileCommand {
         command: string;
     }[];
     static args: {
-        input: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        input: import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        editable: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        fai: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        gzi: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        gzip: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        decompressed: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        force: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        editable: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        fai: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        gzi: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        gzip: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        decompressed: import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/assembly/add-from-fasta.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"add-from-fasta.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-fasta.ts"],"names":[],"mappings":"AAWA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,QAAS,SAAQ,WAAW;IAC/C,MAAM,CAAC,OAAO,SAAwC;IACtD,MAAM,CAAC,WAAW,SAGiC;IAEnD,MAAM,CAAC,QAAQ;;;QAiBd;IAED,MAAM,CAAC,IAAI;;MAUV;IAED,MAAM,CAAC,KAAK;;;;;;;;MAkCX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkGlC"}

package/dist/commands/assembly/add-from-fasta.js

@@ -4,7 +4,6 @@ import path from 'node:path';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { FileCommand } from '../../fileCommand.js';
-import { isFileId, submitAssembly } from '../../utils.js';
 export default class AddFasta extends FileCommand {
     static summary = 'Add a new assembly from fasta input';
     static description = `Add new assembly. The input fasta may be:
@@ -69,9 +68,8 @@ often has unintended side effects.',
     };
     async run() {
         const { args, flags } = await this.parse(AddFasta);
-        const access = await this.getAccess();
         const assemblyName = flags.assembly ?? path.basename(args.input);
-        const fastaIsFileId = await isFileId(args.input, access.address, access.accessToken);
+        const fastaIsFileId = await this.isFileId(args.input);
         const isExternal = isValidHttpUrl(args.input);
         let body;
         if (isExternal) {
@@ -79,14 +77,20 @@ often has unintended side effects.',
                 this.error(`External fasta files are not editable. The -e/--editable has been set with an external input file.`);
             }
             const fai = flags.fai ?? `${args.input}.fai`;
-            const faiExists = await fetch(fai);
-            if (!faiExists.ok) {
-                this.error(`Index file ${fai} does not exist`);
+            const faiResponse = await this.fetchWithoutCheck(fai, { method: 'HEAD' });
+            if (faiResponse.status === 404) {
+                this.error(`Index file does not exist: ${fai}`);
+            }
+            else if (!faiResponse.ok) {
+                this.error(`Could not access index file ${fai}`);
             }
             const gzi = flags.gzi ?? `${args.input}.gzi`;
-            const gziExists = await fetch(gzi);
-            if (!gziExists.ok) {
-                this.error(`Index file ${gzi} does not exist`);
+            const gziResponse = await this.fetchWithoutCheck(gzi, { method: 'HEAD' });
+            if (gziResponse.status === 404) {
+                this.error(`Index file does not exist: ${gzi}`);
+            }
+            else if (!gziResponse.ok) {
+                this.error(`Could not access index file ${gzi}`);
             }
             body = {
                 assemblyName,
@@ -108,7 +112,7 @@ often has unintended side effects.',
             }
             const fileId = fastaIsFileId
                 ? args.input
-                : await this.uploadFile(access.address, access.accessToken, args.input, 'text/x-fasta', isGzip);
+                : await this.uploadFile(args.input, 'text/x-fasta', isGzip);
             body = {
                 assemblyName,
                 fileIds: { fa: fileId },
@@ -119,8 +123,8 @@ often has unintended side effects.',
         else {
             const gzi = flags.gzi ?? `${args.input}.gzi`;
             const fai = flags.fai ?? `${args.input}.fai`;
-            const gziIsFileId = await isFileId(gzi, access.address, access.accessToken);
-            const faiIsFileId = await isFileId(fai, access.address, access.accessToken);
+            const gziIsFileId = await this.isFileId(gzi);
+            const faiIsFileId = await this.isFileId(fai);
             if (!fs.existsSync(gzi) && !gziIsFileId && !flags.editable) {
                 this.error(`Only bgzip'd and indexed fasta files are supported unless option -e/--editable is set. "${gzi}" is neither a file or a file id`);
             }
@@ -129,13 +133,13 @@ often has unintended side effects.',
             }
             const faId = fastaIsFileId
                 ? args.input
-                : await this.uploadFile(access.address, access.accessToken, args.input, 'application/x-bgzip-fasta', true);
+                : await this.uploadFile(args.input, 'application/x-bgzip-fasta', true);
             const faiId = faiIsFileId
                 ? fai
-                : await this.uploadFile(access.address, access.accessToken, fai, 'text/x-fai', false);
+                : await this.uploadFile(fai, 'text/x-fai', false);
             const gziId = gziIsFileId
                 ? gzi
-                : await this.uploadFile(access.address, access.accessToken, gzi, 'application/x-gzi', false);
+                : await this.uploadFile(gzi, 'application/x-gzi', false);
             body = {
                 assemblyName,
                 typeName: 'AddAssemblyFromFileChange',
@@ -143,7 +147,7 @@ often has unintended side effects.',
                 assembly: new ObjectId().toHexString(),
             };
         }
-        const rec = await submitAssembly(access.address, access.accessToken, body, flags.force);
+        const rec = await this.submitAssembly(body, flags.force);
         this.log(JSON.stringify(rec, null, 2));
     }
 }

package/dist/commands/assembly/add-from-fasta.js.map

@@ -1 +1 @@
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package/dist/commands/assembly/add-from-gff.d.ts

@@ -7,13 +7,13 @@ export default class AddGff extends FileCommand {
         command: string;
     }[];
     static args: {
-        'input-file': import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        'input-file': import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        'omit-features': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        'no-strict': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        'omit-features': import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        force: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        'no-strict': import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/assembly/add-from-gff.d.ts.map

@@ -1 +1 @@
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