@apollo-annotation/cli 0.1.17 → 0.1.19

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

@@ -1,11 +1,10 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { BaseCommand } from '../../baseCommand.js';
-import { submitAssembly, uploadFile, wrapLines } from '../../utils.js';
+import { createFetchErrorMessage, submitAssembly, uploadFile, wrapLines, } from '../../utils.js';
 export default class Get extends BaseCommand {
     static description = 'Add new assembly from local or external fasta file';
     static examples = [
@@ -42,11 +41,10 @@ export default class Get extends BaseCommand {
         const access = await this.getAccess(flags['config-file'], flags.profile);
         const assemblyName = flags.assembly ?? path.basename(flags['input-file']);
         const isExternal = isValidHttpUrl(flags['input-file']);
-        let response;
+        let res;
         if (isExternal) {
             if (flags.index === undefined) {
-                this.logToStderr('Please provide the URL to the index of the external fasta file');
-                this.exit(1);
+                this.error('Please provide the URL to the index of the external fasta file');
             }
             const body = {
                 assemblyName,
@@ -56,34 +54,25 @@ export default class Get extends BaseCommand {
                     fai: flags.index,
                 },
             };
-            response = (await submitAssembly(access.address, access.accessToken, body, flags.force));
+            res = (await submitAssembly(access.address, access.accessToken, body, flags.force));
         }
         else {
             if (!isExternal && !fs.existsSync(flags['input-file'])) {
-                this.logToStderr(`File ${flags['input-file']} does not exist`);
-                this.exit(1);
-            }
-            try {
-                const fileId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-fasta');
-                const body = {
-                    assemblyName,
-                    fileId,
-                    typeName: 'AddAssemblyFromFileChange',
-                    assembly: new ObjectId().toHexString(),
-                };
-                response = (await submitAssembly(access.address, access.accessToken, body, flags.force));
-            }
-            catch (error) {
-                this.logToStderr(error.message);
-                this.exit(1);
+                this.error(`File ${flags['input-file']} does not exist`);
             }
+            const fileId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-fasta');
+            const body = {
+                assemblyName,
+                fileId,
+                typeName: 'AddAssemblyFromFileChange',
+                assembly: new ObjectId().toHexString(),
+            };
+            res = (await submitAssembly(access.address, access.accessToken, body, flags.force));
         }
-        if (!response.ok) {
-            const json = JSON.parse(await response.text());
-            this.logToStderr(JSON.stringify(json, null, 2));
-            this.exit(1);
+        if (!res.ok) {
+            const errorMessage = await createFetchErrorMessage(res, 'Submit assembly failed');
+            throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }
 function isValidHttpUrl(x) {

package/dist/commands/assembly/add-gff.js

@@ -1,11 +1,9 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { BaseCommand } from '../../baseCommand.js';
-import { submitAssembly, uploadFile, wrapLines } from '../../utils.js';
+import { createFetchErrorMessage, submitAssembly, uploadFile, wrapLines, } from '../../utils.js';
 export default class AddGff extends BaseCommand {
     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.');
@@ -41,8 +39,7 @@ export default class AddGff extends BaseCommand {
     async run() {
         const { flags } = await this.parse(AddGff);
         if (!fs.existsSync(flags['input-file'])) {
-            this.logToStderr(`File ${flags['input-file']} does not exist`);
-            this.exit(1);
+            this.error(`File ${flags['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');
@@ -51,26 +48,16 @@ export default class AddGff extends BaseCommand {
             typeName = 'AddAssemblyFromFileChange';
         }
         const assemblyName = flags.assembly ?? path.basename(flags['input-file']);
-        let res;
-        try {
-            const body = {
-                assemblyName,
-                fileId,
-                typeName,
-                assembly: new ObjectId().toHexString(),
-            };
-            res = await submitAssembly(access.address, access.accessToken, body, flags.force);
-        }
-        catch (error) {
-            this.logToStderr(error.message);
-            this.exit(1);
-        }
+        const body = {
+            assemblyName,
+            fileId,
+            typeName,
+            assembly: new ObjectId().toHexString(),
+        };
+        const res = await submitAssembly(access.address, access.accessToken, body, flags.force);
         if (!res.ok) {
-            const json = JSON.parse(await res.text());
-            const message = json['message'];
-            this.logToStderr(message);
-            this.exit(1);
+            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
+            throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

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 { CheckError, convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
+import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, wrapLines, } from '../../utils.js';
 async function setChecks(address, accessToken, assembly, checkId) {
     const check = {
         _id: assembly,
@@ -55,7 +55,7 @@ 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 check to apply, to retrieve features flagged by these checks use `apollo feature check`.');
+    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:',
@@ -95,33 +95,23 @@ export default class Check extends BaseCommand {
         const checkTypes = await getCheckTypes(access.address, access.accessToken);
         if (flags.check === undefined && flags.assembly === undefined) {
             this.log(JSON.stringify(checkTypes, null, 2));
-            this.exit(0);
+            return;
         }
         if (flags.assembly === undefined) {
-            this.logToStderr('Please specify the assembly to manage for checks');
-            this.exit(1);
+            this.error('Please specify the assembly to manage for checks');
         }
         const asm = idReader([flags.assembly]);
         const assembly = await getAssembly(access.address, access.accessToken, asm[0]);
         if (Object.keys(assembly).length === 0) {
-            this.logToStderr(`Assembly ${flags.assembly} not found`);
-            this.exit(1);
+            this.error(`Assembly ${flags.assembly} not found`);
         }
         const currentChecks = getCheckTypesForAssembly(checkTypes, assembly);
         if (flags.check === undefined) {
             this.log(JSON.stringify(currentChecks, null, 2));
-            this.exit(0);
+            return;
         }
         let inputCheckIds = [];
-        try {
-            inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
-        }
-        catch (error) {
-            if (error instanceof CheckError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-        }
+        inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
         const newChecks = new Set();
         if (flags.delete) {
             const currentCheckIds = new Set();
@@ -143,6 +133,5 @@ export default class Check extends BaseCommand {
             }
         }
         await setChecks(access.address, access.accessToken, assembly['_id'], [...newChecks.values()]);
-        this.exit(0);
     }
 }

package/dist/commands/assembly/delete.js

@@ -38,6 +38,6 @@ export default class Delete extends BaseCommand {
         if (flags.verbose) {
             this.log(JSON.stringify(deleted, null, 2));
         }
-        this.logToStderr(`${i} assemblies deleted`);
+        this.logToStderr(`${i} assemblies deleted`); // Keep as logToStderr
     }
 }

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

@@ -1,7 +1,6 @@
 /* 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';
 async function getSequence(address, accessToken, refSeq, start, end) {
@@ -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) {
@@ -66,8 +61,7 @@ export default class ApolloCmd extends BaseCommand {
         const { flags } = await this.parse(ApolloCmd);
         const endCoord = flags.end ?? Number.MAX_SAFE_INTEGER;
         if (flags.start <= 0 || endCoord <= 0) {
-            this.logToStderr('Start and end coordinates must be greater than 0.');
-            this.exit(1);
+            this.error('Start and end coordinates must be greater than 0.');
         }
         const access = await this.getAccess(flags['config-file'], flags.profile);
         let assembly = undefined;
@@ -76,16 +70,9 @@ export default class ApolloCmd extends BaseCommand {
             [assembly] = idReader([flags.assembly]);
         }
         let refseqIds = [];
-        try {
-            refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
-        }
-        catch (error) {
-            this.logToStderr(error.message);
-            this.exit(1);
-        }
+        refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
         if (refseqIds.length === 0) {
-            this.logToStderr('No reference sequence found');
-            this.exit(1);
+            this.error('No reference sequence found');
         }
         const refs = await queryApollo(access.address, access.accessToken, 'refSeqs');
         const refSeqs = (await refs.json());
@@ -95,8 +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;
                 }
@@ -104,7 +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.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

@@ -5,8 +5,8 @@ import password from '@inquirer/password';
 import select from '@inquirer/select';
 import { Args, Flags } from '@oclif/core';
 import { fetch } from 'undici';
+import { ApolloConf, KEYS, optionDesc } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { Config, ConfigError, KEYS, optionDesc } from '../Config.js';
 import { createFetchErrorMessage, localhostToAddress, wrapLines, } from '../utils.js';
 export default class ApolloConfig extends BaseCommand {
     static summary = 'Get or set apollo configuration options';
@@ -53,13 +53,13 @@ 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);
-            this.exit(0);
+            return;
         }
-        const config = new Config(configFile);
+        const config = new ApolloConf(configFile);
         if (args.key === undefined) {
             await this.interactiveSetup(config, flags.profile);
         }
@@ -71,33 +71,16 @@ export default class ApolloConfig extends BaseCommand {
             if (flags.profile !== undefined) {
                 profileName = flags.profile;
             }
-            try {
-                if (args.value === undefined) {
-                    const currentValue = config.get(args.key, profileName);
-                    this.log(currentValue);
-                }
-                else {
-                    config.set(args.key, args.value, profileName);
-                }
+            if (args.value === undefined) {
+                const currentValue = config.get(`${profileName}.${args.key}`);
+                this.log(currentValue);
+                return;
             }
-            catch (error) {
-                if (error instanceof Error) {
-                    this.logToStderr(error.message);
-                }
-                this.exit(1);
+            if (args.key === 'accessType') {
+                config.setAccessType(profileName, args.value);
             }
-        }
-        const v = config.validate().error?.message;
-        if (v) {
-            this.logToStderr(v);
-        }
-        try {
-            config.writeConfigFile();
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
+            else {
+                config.set(`${profileName}.${args.key}`, args.value);
             }
         }
     }
@@ -107,34 +90,19 @@ export default class ApolloConfig extends BaseCommand {
         }
         let setMe = true;
         while (setMe) {
-            const address = await this.askAddress(config.get(KEYS[KEYS.address], profileName));
-            try {
-                config.set('address', address, profileName);
-                setMe = false;
-            }
-            catch (error) {
-                if (error instanceof ConfigError) {
-                    this.logToStderr(error.message);
-                }
-            }
+            const address = await this.askAddress(config.get(`${profileName}.${KEYS[KEYS.address]}`));
+            config.set(`${profileName}.${KEYS[KEYS.address]}`, address);
+            setMe = false;
         }
-        const address = config.get(KEYS[KEYS.address], profileName);
+        const address = config.get(`${profileName}.${KEYS[KEYS.address]}`);
         let accessType = '';
-        try {
-            accessType = await this.selectAccessType(address);
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-        }
-        config.set(KEYS[KEYS.accessType], accessType, profileName);
+        accessType = await this.selectAccessType(address);
+        config.setAccessType(profileName, accessType);
         if (accessType === 'root') {
-            const username = await this.askUsername(config.get(KEYS.rootCredentials_username, profileName));
-            config.set('rootCredentials.username', username, profileName);
+            const username = await this.askUsername(config.get(`${profileName}.${KEYS.rootCredentials_username}`));
+            config.set(`${profileName}.rootCredentials.username`, username);
             const password = await this.askPassword();
-            config.set('rootCredentials.password', password, profileName);
+            config.set(`${profileName}.rootCredentials.password`, password);
         }
     }
     async askProfileName(currentProfiles) {

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

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/restrict-plus-operands */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
@@ -42,44 +39,38 @@ export default class Get extends BaseCommand {
     async run() {
         const { flags } = await this.parse(Get);
         if (flags.end < flags.start) {
-            this.logToStderr('Error: End coordinate is lower than the start coordinate');
-            this.exit(1);
+            this.error('Error: End coordinate is lower than the start coordinate');
         }
         if (flags.start <= 0) {
-            this.logToStderr('Coordinates must be greater than 0');
-            this.exit(1);
+            this.error('Coordinates must be greater than 0');
         }
         const ff = idReader([flags['feature-id']]);
         if (ff.length !== 1) {
-            this.logToStderr(`Expected only one feature identifier. Got ${ff.length}`);
+            this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
         const access = await this.getAccess(flags['config-file'], flags.profile);
-        const response = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
+        const res = await getFeatureById(access.address, access.accessToken, featureId);
+        if (!res.ok) {
+            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
-        const feature = JSON.parse(await response.text());
+        const feature = JSON.parse(await res.text());
         const childRes = await this.addChild(access.address, access.accessToken, feature, flags.start - 1, flags.end, flags.type);
         if (!childRes.ok) {
-            const obj = JSON.parse(await response.text());
-            const message = obj['message'];
-            this.logToStderr(message);
-            this.exit(1);
+            const errorMessage = await createFetchErrorMessage(childRes, 'Add child failed');
+            throw new Error(errorMessage);
         }
-        this.exit(0);
     }
-    async addChild(address, accessToken, parentFeature, start, end, type) {
-        const pStart = parentFeature['start'];
-        const pEnd = parentFeature['end'];
-        if (start < pStart || end > pEnd) {
-            this.logToStderr(`Error: Child feature coordinates (${start + 1}-${end}) cannot extend beyond parent coordinates (${pStart + 1}-${pEnd})`);
-            this.exit(1);
+    async addChild(address, accessToken, parentFeature, min, max, type) {
+        const pMin = parentFeature.min;
+        const pMax = parentFeature.max;
+        if (min < pMin || max > pMax) {
+            this.error(`Error: Child feature coordinates (${min + 1}-${max}) cannot extend beyond parent coordinates (${pMin + 1}-${pMax})`);
         }
         const res = await queryApollo(address, accessToken, 'refSeqs');
         const refSeqs = (await res.json());
-        const refSeq = parentFeature['refSeq'];
+        const { refSeq } = parentFeature;
         let assembly = '';
         for (const x of refSeqs) {
             if (x['_id'] === refSeq) {
@@ -89,17 +80,18 @@ export default class Get extends BaseCommand {
         }
         const change = {
             typeName: 'AddFeatureChange',
-            changedIds: [parentFeature['_id']],
+            // eslint-disable-next-line unicorn/consistent-destructuring
+            changedIds: [parentFeature._id],
             assembly,
             addedFeature: {
                 _id: new ObjectId().toHexString(),
-                gffId: '',
                 refSeq,
-                start,
-                end,
+                min,
+                max,
                 type,
             },
-            parentFeatureId: parentFeature['_id'],
+            // eslint-disable-next-line unicorn/consistent-destructuring
+            parentFeatureId: parentFeature._id,
         };
         const url = new URL(localhostToAddress(`${address}/changes`));
         const auth = {

package/dist/commands/feature/check.js

@@ -50,15 +50,15 @@ export default class Check extends BaseCommand {
             if (flags['feature-id'] === undefined) {
                 keep = true;
             }
-            else {
-                for (const x of chk['ids']) {
-                    if (keepFeatures.has(x)) {
+            else if (chk.ids !== undefined) {
+                for (const x of chk.ids) {
+                    if (x !== undefined && keepFeatures.has(x.toString())) {
                         keep = true;
                         break;
                     }
                 }
             }
-            if (keep && refseqId.has(chk['refSeq'])) {
+            if (keep && refseqId.has(chk.refSeq)) {
                 results.push(chk);
             }
         }
@@ -71,7 +71,7 @@ async function keepAssemblies(address, accessToken, assembly) {
         const res = await queryApollo(address, accessToken, 'assemblies');
         const asm = (await res.json());
         for (const x of asm) {
-            keepAssembly.push(x['_id']);
+            keepAssembly.push(x._id);
         }
     }
     else {

package/dist/commands/feature/copy.js

@@ -38,42 +38,31 @@ export default class Copy extends BaseCommand {
     async run() {
         const { flags } = await this.parse(Copy);
         if (flags.start <= 0) {
-            this.logToStderr('Start coordinate must be greater than 0');
-            this.exit(1);
+            this.error('Start coordinate must be greater than 0');
         }
         const access = await this.getAccess(flags['config-file'], flags.profile);
-        const response = await getFeatureById(access.address, access.accessToken, flags['feature-id']);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
+        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 response.json());
+        const feature = (await res.json());
         let refseqIds = [];
-        try {
-            refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
-        }
-        catch (error) {
-            this.logToStderr(error.message);
-            this.exit(1);
-        }
+        refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
         if (refseqIds.length === 0) {
-            this.logToStderr('No reference sequence found');
-            this.exit(1);
+            this.error('No reference sequence found');
         }
         const [refseq] = refseqIds;
         const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, 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 message = feature['message'];
-            this.logToStderr(message);
-            this.exit(1);
+            const errorMessage = await createFetchErrorMessage(rescopy, 'Copy feature failed');
+            throw new Error(errorMessage);
         }
-        this.exit(0);
     }
-    async copyFeature(address, accessToken, feature, refseq, start, assembly, newId) {
-        const featureLen = feature['end'] -
-            feature['start'];
+    async copyFeature(address, accessToken, feature, refseq, min, assembly, newId) {
+        const featureLen = feature.max - feature.min;
         const change = {
             typeName: 'AddFeatureChange',
             changedIds: [newId],
@@ -81,12 +70,11 @@ export default class Copy extends BaseCommand {
             addedFeature: {
                 _id: newId,
                 refSeq: refseq,
-                start: start - 1,
-                end: start + featureLen - 1,
-                type: feature['type'],
-                attributes: feature['attributes'],
-                discontinuousLocations: feature['discontinuousLocations'],
-                strand: feature['strand'],
+                min: min - 1,
+                max: min + featureLen - 1,
+                type: feature.type,
+                attributes: feature.attributes,
+                strand: feature.strand,
             },
             copyFeature: true,
             allIds: [newId],
@@ -100,11 +88,11 @@ export default class Copy extends BaseCommand {
                 'Content-Type': 'application/json',
             },
         };
-        const response = await fetch(url, auth);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'copyFeature failed');
+        const res = await fetch(url, auth);
+        if (!res.ok) {
+            const errorMessage = await createFetchErrorMessage(res, 'copyFeature failed');
             throw new Error(errorMessage);
         }
-        return response;
+        return res;
     }
 }