@apollo-annotation/cli 0.1.19 → 0.1.21

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

@@ -32,11 +32,10 @@ export class BaseCommand extends Command {
         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) {

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

@@ -0,0 +1,22 @@
+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>;
+        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>;
+    };
+    run(): Promise<void>;
+}

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

@@ -0,0 +1,157 @@
+/* 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. For local or remote files, it is assumed the file is bgzip'd with \
+`bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at \
+<my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are \
+provided.",
+            required: true,
+        }),
+    };
+    static flags = {
+        assembly: Flags.string({
+            char: 'a',
+            description: 'Name for this assembly. Use the file name if omitted',
+        }),
+        force: Flags.boolean({
+            char: 'f',
+            description: 'Delete existing assembly, if it exists',
+        }),
+        editable: Flags.boolean({
+            char: 'e',
+            description: 'Instead of using indexed fasta lookup, the sequence is loaded into \
+the Apollo database and is editable. Use with caution, as editing the sequence \
+often has unintended side effects.',
+        }),
+        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, 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) {
+            const fai = flags.fai ?? `${args.input}.fai`;
+            const gzi = flags.gzi ?? `${args.input}.gzi`;
+            body = {
+                assemblyName,
+                typeName: 'AddAssemblyFromExternalChange',
+                externalLocation: { fa: args.input, fai, gzi },
+                assembly: new ObjectId().toHexString(),
+            };
+        }
+        else if (flags.editable) {
+            if (!isExternal && !fs.existsSync(args.input) && !fastaIsFileId) {
+                this.error(`Input "${args.input}" is not valid`);
+            }
+            let isGzip = args.input.endsWith('.gz');
+            if (flags.gzip) {
+                isGzip = true;
+            }
+            if (flags.decompressed) {
+                isGzip = false;
+            }
+            const fileId = fastaIsFileId
+                ? args.input
+                : await this.uploadFile(access.address, access.accessToken, args.input, 'text/x-fasta', isGzip);
+            body = {
+                assemblyName,
+                fileIds: { fa: fileId },
+                typeName: 'AddAssemblyFromFileChange',
+                assembly: new ObjectId().toHexString(),
+            };
+        }
+        else {
+            const gzi = flags.gzi ?? `${args.input}.gzi`;
+            const fai = flags.fai ?? `${args.input}.fai`;
+            const gziIsFileId = await isFileId(gzi, access.address, access.accessToken);
+            const faiIsFileId = await isFileId(fai, access.address, access.accessToken);
+            if (!fs.existsSync(gzi) && !gziIsFileId) {
+                this.error(`Only bgzip'd and indexed fasta files are supported at the moment. "${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 },
+                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-from-gff.js

@@ -0,0 +1,64 @@
+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 { submitAssembly } from '../../utils.js';
+export default class AddGff extends FileCommand {
+    static summary = 'Add new assembly from gff or gft file';
+    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:',
+            command: '<%= config.bin %> <%= command.id %> genome.gff -a myAssembly',
+        },
+        {
+            description: 'Import sequences only:',
+            command: '<%= config.bin %> <%= command.id %> genome.gff -a myAssembly -o',
+        },
+    ];
+    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',
+        }),
+        'omit-features': Flags.boolean({
+            char: 'o',
+            description: 'Do not import features, only upload the sequences',
+        }),
+        force: Flags.boolean({
+            char: 'f',
+            description: 'Delete existing assembly, if it exists',
+        }),
+    };
+    async run() {
+        const { args, flags } = await this.parse(AddGff);
+        if (!fs.existsSync(args['input-file'])) {
+            this.error(`File ${args['input-file']} does not exist`);
+        }
+        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'));
+        const assemblyName = flags.assembly ?? path.basename(args['input-file']);
+        const body = flags['omit-features']
+            ? {
+                assemblyName,
+                fileIds: { fa: fileId },
+                typeName: 'AddAssemblyFromFileChange',
+                assembly: new ObjectId().toHexString(),
+            }
+            : {
+                assemblyName,
+                fileIds: { fa: fileId },
+                typeName: 'AddAssemblyAndFeaturesFromFileChange',
+                assembly: new ObjectId().toHexString(),
+            };
+        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/sequence.js

@@ -2,7 +2,7 @@
 import { Flags } from '@oclif/core';
 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({
@@ -27,7 +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:',
@@ -63,11 +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);

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/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',
@@ -48,8 +47,7 @@ export default class ApolloConfig extends BaseCommand {
         },
     ];
     async run() {
-        const { args } = await this.parse(ApolloConfig);
-        const { flags } = await this.parse(ApolloConfig);
+        const { args, flags } = await this.parse(ApolloConfig);
         let configFile = flags['config-file'];
         configFile =
             configFile === undefined

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

@@ -4,14 +4,15 @@ import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, queryApollo, } 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 = wrapLines('See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature with attributes.');
+    static description = 'See the other commands under `apollo feature` \
+to retrive the parent ID of interest and to populate the child feature with attributes.';
     static examples = [
         {
             description: 'Add an exon at genomic coordinates 10..20 to this feature ID:',
-            command: '<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20',
+            command: '<%= config.bin %> <%= command.id %> -i 660...73f -t exon -s 10 -e 20',
         },
     ];
     static flags = {
@@ -44,12 +45,12 @@ export default class Get extends BaseCommand {
         if (flags.start <= 0) {
             this.error('Coordinates must be greater than 0');
         }
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const res = await getFeatureById(access.address, access.accessToken, featureId);
         if (!res.ok) {
             const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');

package/dist/commands/feature/check.js

@@ -1,11 +1,11 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
 export default class Check extends BaseCommand {
     static summary = 'Get check results';
-    static description = wrapLines('Use this command to view which features fail checks along with the reason for failing.\
-    Use `apollo assembly check` for managing which checks should be applied to an assembly');
+    static description = 'Use this command to view which features fail checks along with the reason for failing.\
+Use `apollo assembly check` for managing which checks should be applied to an assembly';
     static examples = [
         {
             description: 'Get all check results in the database:',
@@ -29,10 +29,10 @@ 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();
         let keepFeatures = new Set();
         if (flags['feature-id'] !== undefined) {
-            keepFeatures = new Set(idReader(flags['feature-id']));
+            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');
@@ -75,7 +75,7 @@ async function keepAssemblies(address, accessToken, assembly) {
         }
     }
     else {
-        const ids = idReader([assembly]);
+        const ids = await idReader([assembly]);
         keepAssembly = await convertAssemblyNameToId(address, accessToken, ids);
     }
     return keepAssembly;

package/dist/commands/feature/copy.js

@@ -2,11 +2,12 @@ import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, getRefseqId, localhostToAddress, wrapLines, } from '../../utils.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 = wrapLines('The feature may be copied to the same or to a different assembly. \
-    he destination reference sequence may be selected by name only if unique in the database or by name and assembly or by identifier.');
+    static description = 'The feature may be copied to the same or to a different assembly. \
+The destination reference sequence may be selected by name only if unique in \
+the database or by name and assembly or by identifier.';
     static examples = [
         {
             description: 'Copy this feature ID to chr1:100 in assembly hg38:',
@@ -40,7 +41,7 @@ export default class Copy extends BaseCommand {
         if (flags.start <= 0) {
             this.error('Start coordinate must be greater than 0');
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        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');

package/dist/commands/feature/delete.js

@@ -1,7 +1,7 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 async function deleteFeature(address, accessToken, feature) {
     const changeJson = {
         typeName: 'DeleteFeatureChange',
@@ -34,7 +34,7 @@ async function deleteFeature(address, accessToken, feature) {
 }
 export default class Delete extends BaseCommand {
     static summary = 'Delete one or more features by ID';
-    static description = wrapLines('Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.');
+    static description = 'Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.';
     static flags = {
         'feature-id': Flags.string({
             char: 'i',
@@ -53,12 +53,12 @@ export default class Delete extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Delete);
-        const tmpIds = idReader(flags['feature-id']);
+        const tmpIds = await idReader(flags['feature-id']);
         const featureIds = new Set();
         for (const x of tmpIds) {
             featureIds.add(x);
         }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         for (const featureId of featureIds) {
             const res = await getFeatureById(access.address, access.accessToken, featureId);
             if (res.status === 404 && flags.force) {

package/dist/commands/feature/edit-attribute.js

@@ -1,11 +1,12 @@
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { createFetchErrorMessage, getAssemblyFromRefseq, getFeatureById, idReader, localhostToAddress, } from '../../utils.js';
 export default class EditAttibute extends BaseCommand {
     static summary = 'Add, edit, or view a feature attribute';
-    static description = wrapLines('Be aware that there is no checking whether attributes names and values are valid. \
-    For example, you can create non-unique ID attributes or you can set gene ontology terms to non-existing terms');
+    static description = 'Be aware that there is no checking whether attributes names and values are valid. \
+For example, you can create non-unique ID attributes or you can set gene ontology \
+terms to non-existing terms';
     static examples = [
         {
             description: 'Add attribute "domains" with a list of values:',
@@ -46,12 +47,12 @@ export default class EditAttibute extends BaseCommand {
         if (flags.delete && flags.value) {
             this.error('Error: Options --delete and --value are mutually exclusive');
         }
-        const ff = idReader([flags['feature-id']]);
+        const ff = await idReader([flags['feature-id']]);
         if (ff.length !== 1) {
             this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
-        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const access = await this.getAccess();
         const response = await getFeatureById(access.address, access.accessToken, featureId);
         if (!response.ok) {
             const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');