@apollo-annotation/cli 0.1.18 → 0.1.20

package/bin/dev.js

@@ -2,8 +2,8 @@
 
 // eslint-disable-next-line node/shebang
 async function main() {
-  const {execute} = await import('@oclif/core')
-  await execute({development: true, dir: import.meta.url})
+  const { execute } = await import('@oclif/core')
+  await execute({ development: true, dir: import.meta.url })
 }
 
 await main()

package/bin/run.js

@@ -1,8 +1,8 @@
 #!/usr/bin/env node
 
 async function main() {
-  const {execute} = await import('@oclif/core')
-  await execute({dir: import.meta.url})
+  const { execute } = await import('@oclif/core')
+  await execute({ dir: import.meta.url })
 }
 
 await main()

package/dist/ApolloConf.js

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-enum-comparison */
 import fs from 'node:fs';
 import path from 'node:path';
 import Conf from 'conf';

package/dist/baseCommand.d.ts

@@ -10,7 +10,7 @@ export declare abstract class BaseCommand<T extends typeof Command> extends Comm
     protected args: Args<T>;
     init(): Promise<void>;
     private getConfig;
-    getAccess(configFile: string | undefined, profileName: string | undefined): Promise<{
+    getAccess(): Promise<{
         address: string;
         accessToken: string;
     }>;

package/dist/baseCommand.js

@@ -26,22 +26,22 @@ export class BaseCommand extends Command {
     }
     getConfig(configFile) {
         if (configFile === undefined) {
-            configFile = path.join(this.config.configDir, 'config.yaml');
+            configFile = path.join(this.config.configDir, 'config.yml');
         }
         checkConfigfileExists(configFile);
         const config = new ApolloConf(configFile);
         return config;
     }
-    async getAccess(configFile, profileName) {
+    async getAccess() {
+        const { 'config-file': configFile, profile } = this.flags;
         const config = this.getConfig(configFile);
-        if (profileName === undefined) {
-            profileName = process.env.APOLLO_PROFILE ?? 'default';
-        }
+        const profileName = process.env.APOLLO_PROFILE ?? profile ?? 'default';
         return config.getAccess(profileName);
     }
     async catch(err) {
-        // add any custom logic to handle errors from the command
-        // or simply return the parent class error handling
+        if (err.cause instanceof Error) {
+            console.error(err.cause);
+        }
         return super.catch(err);
     }
     async finally(_) {

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

@@ -0,0 +1,23 @@
+import { FileCommand } from '../../fileCommand.js';
+export default class AddFasta extends FileCommand {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static args: {
+        input: import("@oclif/core/lib/interfaces/parser.js").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>;
+        index: 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>;
+        'not-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>;
+    };
+    run(): Promise<void>;
+}

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

@@ -0,0 +1,165 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import { Args, Flags } from '@oclif/core';
+import { ObjectId } from 'bson';
+import { FileCommand } from '../../fileCommand.js';
+import { queryApollo, 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:
+    * A local file 
+    * An external fasta file
+    * The id of a file previously uploaded to Apollo`;
+    static examples = [
+        {
+            description: 'From local file:',
+            command: '<%= config.bin %> <%= command.id %> genome.fa -a myAssembly',
+        },
+        {
+            description: 'From external source we also need the URL of the index:',
+            command: '<%= config.bin %> <%= command.id %> https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly',
+        },
+    ];
+    static args = {
+        input: Args.string({
+            description: 'Input fasta file, local or remote, or id of a previously uploaded file',
+            required: true,
+        }),
+    };
+    static flags = {
+        assembly: Flags.string({
+            char: 'a',
+            description: 'Name for this assembly. Use the file name if omitted',
+        }),
+        index: Flags.string({
+            char: 'x',
+            description: 'URL of the index. Required if input is an external source',
+        }),
+        force: Flags.boolean({
+            char: 'f',
+            description: 'Delete existing assembly, if it exists',
+        }),
+        'not-editable': Flags.boolean({
+            char: 'n',
+            description: "The fasta sequence is not editable. Apollo will not load it into \
+the database and instead use the provided indexes to query it. This option assumes \
+the fasta file is bgzip'd with `bgzip` and indexed with `samtools faidx`. \
+Indexes should be named <my.fasta.gz>.gzi and <my.fasta.gz>.fai unless options --fai and --gzi are set",
+        }),
+        fai: Flags.string({
+            description: 'Fasta index of the (not-editable) fasta file',
+        }),
+        gzi: Flags.string({
+            description: 'Gzi index of the (not-editable) fasta file',
+        }),
+        gzip: Flags.boolean({
+            char: 'z',
+            description: 'For local file input: Override autodetection and instruct that input is gzip compressed',
+            exclusive: ['decompressed'],
+        }),
+        decompressed: Flags.boolean({
+            char: 'd',
+            description: 'For local file input: Override autodetection and instruct that input is decompressed',
+            exclusive: ['gzip'],
+        }),
+    };
+    async run() {
+        const { args } = await this.parse(AddFasta);
+        const { 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 isExternal = isValidHttpUrl(args.input);
+        let body;
+        if (isExternal) {
+            if (flags.index === undefined) {
+                this.error('Please provide the URL to the index of the external fasta file');
+            }
+            body = {
+                assemblyName,
+                typeName: 'AddAssemblyFromExternalChange',
+                externalLocation: {
+                    fa: args.input,
+                    fai: flags.index,
+                },
+            };
+        }
+        else if (flags['not-editable']) {
+            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);
+            if (!fs.existsSync(gzi) && !gziIsFileId) {
+                this.error(`Only bgzip'd and indexed fasta files are supported at the moment. "${gzi}" is neither a file or a file id`);
+            }
+            if (!fs.existsSync(fai) && !faiIsFileId) {
+                this.error(`Only bgzip'd and indexed fasta files are supported at the moment. "${fai}" is neither a file or a file id`);
+            }
+            const faId = fastaIsFileId
+                ? args.input
+                : await this.uploadFile(access.address, access.accessToken, args.input, 'application/x-bgzip-fasta', true);
+            const faiId = faiIsFileId
+                ? fai
+                : await this.uploadFile(access.address, access.accessToken, fai, 'text/x-fai', false);
+            const gziId = gziIsFileId
+                ? gzi
+                : await this.uploadFile(access.address, access.accessToken, gzi, 'application/x-gzi', false);
+            body = {
+                assemblyName,
+                typeName: 'AddAssemblyFromFileChange',
+                fileIds: {
+                    fa: faId,
+                    fai: faiId,
+                    gzi: gziId,
+                },
+            };
+        }
+        else {
+            if (!isExternal && !fs.existsSync(args.input) && !fastaIsFileId) {
+                this.error(`Input "${args.input}" is not valid`);
+            }
+            let isGzip = args.input.endsWith('.gz');
+            if (flags.gzip) {
+                isGzip = true;
+            }
+            if (flags.decompressed) {
+                isGzip = false;
+            }
+            const fileId = fastaIsFileId
+                ? args.input
+                : await this.uploadFile(access.address, access.accessToken, args.input, 'text/x-fasta', isGzip);
+            body = {
+                assemblyName,
+                fileIds: { fa: fileId },
+                typeName: 'AddAssemblyFromFileChange',
+                assembly: new ObjectId().toHexString(),
+            };
+        }
+        const rec = await submitAssembly(access.address, access.accessToken, body, flags.force);
+        this.log(JSON.stringify(rec, null, 2));
+    }
+}
+function isValidHttpUrl(x) {
+    let url;
+    try {
+        url = new URL(x);
+    }
+    catch {
+        return false;
+    }
+    return url.protocol === 'http:' || url.protocol === 'https:';
+}
+async function isFileId(x, address, accessToken) {
+    if (x.length != 24) {
+        return false;
+    }
+    const files = await queryApollo(address, accessToken, 'files');
+    const json = (await files.json());
+    for (const fileDoc of json) {
+        if (fileDoc['_id'] === x) {
+            return true;
+        }
+    }
+    return false;
+}

package/dist/commands/assembly/{add-gff.d.ts → add-from-gff.d.ts}

@@ -1,13 +1,15 @@
-import { BaseCommand } from '../../baseCommand.js';
-export default class AddGff extends BaseCommand<typeof AddGff> {
+import { FileCommand } from '../../fileCommand.js';
+export default class AddGff extends FileCommand {
     static summary: string;
     static description: string;
     static examples: {
         description: string;
         command: string;
     }[];
+    static args: {
+        'input-file': import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
     static flags: {
-        'input-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, 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>;
         'omit-features': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
         force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;

package/dist/commands/assembly/{add-gff.js → add-from-gff.js}

@@ -1,12 +1,12 @@
 import * as fs from 'node:fs';
 import * as path from 'node:path';
-import { Flags } from '@oclif/core';
+import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
-import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, submitAssembly, uploadFile, wrapLines, } from '../../utils.js';
-export default class AddGff extends BaseCommand {
+import { FileCommand } from '../../fileCommand.js';
+import { submitAssembly } from '../../utils.js';
+export default class AddGff extends FileCommand {
     static summary = 'Add new assembly from gff or gft file';
-    static description = wrapLines('The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.');
+    static description = 'The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.';
     static examples = [
         {
             description: 'Import sequences and features:',
@@ -14,15 +14,16 @@ export default class AddGff extends BaseCommand {
         },
         {
             description: 'Import sequences only:',
-            command: '<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly -o',
+            command: '<%= config.bin %> <%= command.id %> genome.gff -a myAssembly -o',
         },
     ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
-            description: 'Input gff or gtf file',
+    static args = {
+        'input-file': Args.string({
+            description: 'Input gff file',
             required: true,
         }),
+    };
+    static flags = {
         assembly: Flags.string({
             char: 'a',
             description: 'Name for this assembly. Use the file name if omitted',
@@ -37,28 +38,25 @@ export default class AddGff extends BaseCommand {
         }),
     };
     async run() {
+        const { args } = await this.parse(AddGff);
         const { flags } = await this.parse(AddGff);
-        if (!fs.existsSync(flags['input-file'])) {
-            this.error(`File ${flags['input-file']} does not exist`);
+        if (!fs.existsSync(args['input-file'])) {
+            this.error(`File ${args['input-file']} does not exist`);
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
-        const fileId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3');
+        const access = await this.getAccess();
+        const fileId = await this.uploadFile(access.address, access.accessToken, args['input-file'], 'text/x-gff3', args['input-file'].endsWith('.gz'));
         let typeName = 'AddAssemblyAndFeaturesFromFileChange';
         if (flags['omit-features']) {
             typeName = 'AddAssemblyFromFileChange';
         }
-        const assemblyName = flags.assembly ?? path.basename(flags['input-file']);
+        const assemblyName = flags.assembly ?? path.basename(args['input-file']);
         const body = {
             assemblyName,
-            fileId,
+            fileIds: { fa: fileId },
             typeName,
             assembly: new ObjectId().toHexString(),
         };
-        const res = await submitAssembly(access.address, access.accessToken, body, flags.force);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-        this.exit(0);
+        const rec = await submitAssembly(access.address, access.accessToken, body, flags.force);
+        this.log(JSON.stringify(rec, null, 2));
     }
 }

package/dist/commands/assembly/check.js

@@ -1,7 +1,7 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, } from '../../utils.js';
 async function setChecks(address, accessToken, assembly, checkId) {
     const check = {
         _id: assembly,
@@ -54,8 +54,9 @@ function getCheckTypesForAssembly(checkTypes, assembly) {
 }
 export default class Check extends BaseCommand {
     static summary = 'Add, view, or delete checks to assembly';
-    static description = wrapLines('Manage checks, i.e. the rules ensuring features in an assembly are plausible. \
-    This command only sets the checks to apply, to retrieve features flagged by these checks use `apollo feature check`.');
+    static description = 'Manage checks, i.e. the rules ensuring features in an assembly are plausible. \
+This command only sets the checks to apply, to retrieve features flagged by \
+these checks use `apollo feature check`.';
     static examples = [
         {
             description: 'View available check types:',
@@ -91,7 +92,7 @@ export default class Check extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Check);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const checkTypes = await getCheckTypes(access.address, access.accessToken);
         if (flags.check === undefined && flags.assembly === undefined) {
             this.log(JSON.stringify(checkTypes, null, 2));
@@ -100,11 +101,8 @@ export default class Check extends BaseCommand {
         if (flags.assembly === undefined) {
             this.error('Please specify the assembly to manage for checks');
         }
-        const asm = idReader([flags.assembly]);
+        const asm = await idReader([flags.assembly]);
         const assembly = await getAssembly(access.address, access.accessToken, asm[0]);
-        if (Object.keys(assembly).length === 0) {
-            this.error(`Assembly ${flags.assembly} not found`);
-        }
         const currentChecks = getCheckTypesForAssembly(checkTypes, assembly);
         if (flags.check === undefined) {
             this.log(JSON.stringify(currentChecks, null, 2));
@@ -132,6 +130,8 @@ export default class Check extends BaseCommand {
                 newChecks.add(chk['_id']);
             }
         }
-        await setChecks(access.address, access.accessToken, assembly['_id'], [...newChecks.values()]);
+        await setChecks(access.address, access.accessToken, assembly._id, [
+            ...newChecks.values(),
+        ]);
     }
 }

package/dist/commands/assembly/delete.js

@@ -1,9 +1,9 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, deleteAssembly, getAssembly, idReader, wrapLines, } from '../../utils.js';
+import { convertAssemblyNameToId, deleteAssembly, getAssembly, idReader, } from '../../utils.js';
 export default class Delete extends BaseCommand {
     static summary = 'Delete assemblies';
-    static description = wrapLines('Assemblies to delete may be names or IDs');
+    static description = 'Assemblies to delete may be names or IDs';
     static examples = [
         {
             description: 'Delete multiple assemblies using name or ID:',
@@ -24,8 +24,8 @@ export default class Delete extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Delete);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
-        const assembly = idReader(flags.assembly);
+        const access = await this.getAccess();
+        const assembly = await idReader(flags.assembly);
         const deleteIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
         let i = 0;
         const deleted = [];

package/dist/commands/assembly/get.js

@@ -1,9 +1,9 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, idReader, queryApollo, wrapLines, } from '../../utils.js';
+import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get available assemblies';
-    static description = wrapLines('Print to stdout the list of assemblies in json format');
+    static description = 'Print to stdout the list of assemblies in json format';
     static flags = {
         assembly: Flags.string({
             char: 'a',
@@ -13,11 +13,11 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const assemblies = await queryApollo(access.address, access.accessToken, 'assemblies');
         let assemblyIds = [];
         if (flags.assembly !== undefined) {
-            const assembly = idReader(flags.assembly);
+            const assembly = await idReader(flags.assembly);
             assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
         }
         const json = (await assemblies.json());

package/dist/commands/assembly/get.test.js

@@ -7,7 +7,7 @@ import { CONFIG_FILE, TEST_DATA_DIR, VERBOSE, copyFile, } from '../../test/fixtu
 const __dirname = fileURLToPath(new URL('.', import.meta.url));
 describe.skip('apollo assembly get: Fail without token', () => {
     before(() => {
-        copyFile(`${TEST_DATA_DIR}/guest.yaml`, CONFIG_FILE, VERBOSE);
+        copyFile(`${TEST_DATA_DIR}/guest.yml`, CONFIG_FILE, VERBOSE);
     });
     after(() => {
         fs.rmSync(CONFIG_FILE);
@@ -24,7 +24,7 @@ describe.skip('apollo assembly get: Fail without token', () => {
 // TODO: Need valid token
 describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
     before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yaml`, CONFIG_FILE, VERBOSE);
+        copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE);
     });
     after(() => {
         fs.rmSync(CONFIG_FILE);
@@ -38,7 +38,7 @@ describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
     });
 });
 describe.skip('apollo assembly get: Test nock', () => {
-    const cmd = ['assembly:get', '--config-file', 'tmp.yaml'];
+    const cmd = ['assembly:get', '--config-file', 'tmp.yml'];
     test
         .stdout()
         .nock('http://127.0.0.1:3999', (api) => api.persist().get('/assemblies').reply(200, { stuff: 'foo' }))

package/dist/commands/assembly/sequence.js

@@ -1,9 +1,8 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
+import { Agent, fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getRefseqId, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getRefseqId, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
 async function getSequence(address, accessToken, refSeq, start, end) {
     const url = new URL(localhostToAddress(`${address}/sequence`));
     const searchParams = new URLSearchParams({
@@ -13,15 +12,11 @@ async function getSequence(address, accessToken, refSeq, start, end) {
     });
     url.search = searchParams.toString();
     const uri = url.toString();
-    const controller = new AbortController();
-    setTimeout(() => {
-        controller.abort();
-    }, 24 * 60 * 60 * 1000);
     const auth = {
         headers: {
             authorization: `Bearer ${accessToken}`,
         },
-        signal: controller.signal,
+        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
     };
     const response = await fetch(uri, auth);
     if (!response.ok) {
@@ -32,7 +27,7 @@ async function getSequence(address, accessToken, refSeq, start, end) {
 }
 export default class ApolloCmd extends BaseCommand {
     static summary = 'Get reference sequence in fasta format';
-    static description = wrapLines('Return the reference sequence for a given assembly and coordinates');
+    static description = 'Return the reference sequence for a given assembly and coordinates';
     static examples = [
         {
             description: 'Get all sequences in myAssembly:',
@@ -68,11 +63,11 @@ export default class ApolloCmd extends BaseCommand {
         if (flags.start <= 0 || endCoord <= 0) {
             this.error('Start and end coordinates must be greater than 0.');
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         let assembly = undefined;
         if (flags.assembly !== undefined) {
             ;
-            [assembly] = idReader([flags.assembly]);
+            [assembly] = await idReader([flags.assembly]);
         }
         let refseqIds = [];
         refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
@@ -87,8 +82,8 @@ export default class ApolloCmd extends BaseCommand {
             const seq = new TextDecoder().decode(seqObj?.value);
             let header = '';
             for (const x of refSeqs) {
-                if (x['_id'] === rid) {
-                    const rname = x['name'];
+                if (x._id === rid) {
+                    const rname = x.name;
                     header = `>${rname}:${flags.start}..${flags.start + seq.length - 1}`;
                     break;
                 }
@@ -96,7 +91,6 @@ export default class ApolloCmd extends BaseCommand {
             this.log(header);
             this.log(splitStringIntoChunks(seq, 80).join('\n'));
         }
-        this.exit(0);
     }
 }
 function splitStringIntoChunks(input, chunkSize) {

package/dist/commands/change/get.js

@@ -1,12 +1,12 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, idReader, queryApollo, wrapLines, } from '../../utils.js';
+import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get list of changes';
-    static description = wrapLines('Return the change log in json format. Note \
-  that when an assembly is deleted the link between common name and ID is lost \
-  (it can still be recovered by inspecting the change log but at present this task is left to the user). \
-  In such cases you need to use the assembly ID.');
+    static description = 'Return the change log in json format. Note \
+that when an assembly is deleted the link between common name and ID is lost \
+(it can still be recovered by inspecting the change log but at present this task is left to the user). \
+In such cases you need to use the assembly ID.';
     static flags = {
         assembly: Flags.string({
             char: 'a',
@@ -16,13 +16,13 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const changes = await queryApollo(access.address, access.accessToken, 'changes');
         const json = (await changes.json());
         let keep = json;
         if (flags.assembly !== undefined) {
             keep = [];
-            const assembly = idReader(flags.assembly);
+            const assembly = await idReader(flags.assembly);
             const assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
             for (const x of json) {
                 if (assemblyIds.includes(x['assembly'])) {

package/dist/commands/change/get.test.js

@@ -7,7 +7,7 @@ const __dirname = fileURLToPath(new URL('.', import.meta.url));
 // TODO: Need valid token
 describe.skip('apollo change get: Get changes as YAML string', () => {
     before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yaml`, CONFIG_FILE, VERBOSE);
+        copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE);
     });
     after(() => {
         fs.rmSync(CONFIG_FILE);

package/dist/commands/config.js

@@ -7,13 +7,12 @@ import { Args, Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { ApolloConf, KEYS, optionDesc } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress, wrapLines, } from '../utils.js';
+import { createFetchErrorMessage, localhostToAddress } from '../utils.js';
 export default class ApolloConfig extends BaseCommand {
     static summary = 'Get or set apollo configuration options';
-    static description = wrapLines(`Use this command to create or edit a user profile with credentials to access Apollo. \
-     Configuration options are:
+    static description = `Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:
 
-     ${optionDesc().join('\n\n')}`);
+     ${optionDesc().join('\n\n')}`;
     static args = {
         key: Args.string({
             name: 'key',
@@ -53,7 +52,7 @@ export default class ApolloConfig extends BaseCommand {
         let configFile = flags['config-file'];
         configFile =
             configFile === undefined
-                ? path.join(this.config.configDir, 'config.yaml')
+                ? path.join(this.config.configDir, 'config.yml')
                 : path.resolve(configFile);
         if (flags['get-config-file']) {
             this.log(configFile);