@apollo-annotation/cli 0.1.18 → 0.1.19

package/README.md

@@ -1,56 +1,61 @@
 # Table of contents
 
 <!-- toc -->
-* [Table of contents](#table-of-contents)
-* [Usage](#usage)
-* [Commands](#commands)
+
+- [Table of contents](#table-of-contents)
+- [Usage](#usage)
+- [Commands](#commands)
 <!-- tocstop -->
 
 # Usage
 
 <!-- usage -->
+
 ```sh-session
 $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.18 linux-x64 node-v18.20.3
+@apollo-annotation/cli/0.1.19 linux-x64 node-v20.14.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
 ...
 ```
+
 <!-- usagestop -->
 
 # Commands
 
 <!-- commands -->
-* [`apollo assembly add-fasta`](#apollo-assembly-add-fasta)
-* [`apollo assembly add-gff`](#apollo-assembly-add-gff)
-* [`apollo assembly check`](#apollo-assembly-check)
-* [`apollo assembly delete`](#apollo-assembly-delete)
-* [`apollo assembly get`](#apollo-assembly-get)
-* [`apollo assembly sequence`](#apollo-assembly-sequence)
-* [`apollo change get`](#apollo-change-get)
-* [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
-* [`apollo feature add-child`](#apollo-feature-add-child)
-* [`apollo feature check`](#apollo-feature-check)
-* [`apollo feature copy`](#apollo-feature-copy)
-* [`apollo feature delete`](#apollo-feature-delete)
-* [`apollo feature edit`](#apollo-feature-edit)
-* [`apollo feature edit-attribute`](#apollo-feature-edit-attribute)
-* [`apollo feature edit-coords`](#apollo-feature-edit-coords)
-* [`apollo feature edit-type`](#apollo-feature-edit-type)
-* [`apollo feature get`](#apollo-feature-get)
-* [`apollo feature get-id`](#apollo-feature-get-id)
-* [`apollo feature import`](#apollo-feature-import)
-* [`apollo feature search`](#apollo-feature-search)
-* [`apollo help [COMMANDS]`](#apollo-help-commands)
-* [`apollo login`](#apollo-login)
-* [`apollo logout`](#apollo-logout)
-* [`apollo refseq get`](#apollo-refseq-get)
-* [`apollo status`](#apollo-status)
-* [`apollo user get`](#apollo-user-get)
+
+- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta)
+- [`apollo assembly add-gff`](#apollo-assembly-add-gff)
+- [`apollo assembly check`](#apollo-assembly-check)
+- [`apollo assembly delete`](#apollo-assembly-delete)
+- [`apollo assembly get`](#apollo-assembly-get)
+- [`apollo assembly sequence`](#apollo-assembly-sequence)
+- [`apollo change get`](#apollo-change-get)
+- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
+- [`apollo feature add-child`](#apollo-feature-add-child)
+- [`apollo feature check`](#apollo-feature-check)
+- [`apollo feature copy`](#apollo-feature-copy)
+- [`apollo feature delete`](#apollo-feature-delete)
+- [`apollo feature edit`](#apollo-feature-edit)
+- [`apollo feature edit-attribute`](#apollo-feature-edit-attribute)
+- [`apollo feature edit-coords`](#apollo-feature-edit-coords)
+- [`apollo feature edit-type`](#apollo-feature-edit-type)
+- [`apollo feature get`](#apollo-feature-get)
+- [`apollo feature get-id`](#apollo-feature-get-id)
+- [`apollo feature import`](#apollo-feature-import)
+- [`apollo feature search`](#apollo-feature-search)
+- [`apollo help [COMMANDS]`](#apollo-help-commands)
+- [`apollo login`](#apollo-login)
+- [`apollo logout`](#apollo-logout)
+- [`apollo refseq add-alias`](#apollo-refseq-add-alias)
+- [`apollo refseq get`](#apollo-refseq-get)
+- [`apollo status`](#apollo-status)
+- [`apollo user get`](#apollo-user-get)
 
 ## `apollo assembly add-fasta`
 
@@ -82,7 +87,8 @@ EXAMPLES
     $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
 ```
 
-_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
+_See code:
+[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
 
 ## `apollo assembly add-gff`
 
@@ -116,7 +122,8 @@ EXAMPLES
     $ apollo assembly add-gff -i genome.gff -a myAssembly -o
 ```
 
-_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
+_See code:
+[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -158,7 +165,8 @@ EXAMPLES
     $ apollo assembly check -a hg19 -c CDSCheck --delete
 ```
 
-_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/check.ts)_
+_See code:
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -185,7 +193,8 @@ EXAMPLES
     $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f
 ```
 
-_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/delete.ts)_
+_See code:
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -206,7 +215,8 @@ DESCRIPTION
   Print to stdout the list of assemblies in json format
 ```
 
-_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/get.ts)_
+_See code:
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -240,7 +250,8 @@ EXAMPLES
     $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000
 ```
 
-_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+_See code:
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -264,7 +275,8 @@ DESCRIPTION
   need to use the assembly ID.
 ```
 
-_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/change/get.ts)_
+_See code:
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -319,7 +331,8 @@ EXAMPLES
     $ apollo config address
 ```
 
-_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/config.ts)_
+_See code:
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo feature add-child`
 
@@ -349,7 +362,8 @@ EXAMPLES
     $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20
 ```
 
-_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/add-child.ts)_
+_See code:
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -382,7 +396,8 @@ EXAMPLES
     $ apollo feature check -a hg19
 ```
 
-_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/check.ts)_
+_See code:
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -413,7 +428,8 @@ EXAMPLES
     $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38
 ```
 
-_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/copy.ts)_
+_See code:
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -437,7 +453,8 @@ DESCRIPTION
   error unless you set -f/--force.
 ```
 
-_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/delete.ts)_
+_See code:
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -479,7 +496,8 @@ EXAMPLES
     echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -
 ```
 
-_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit.ts)_
+_See code:
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -519,7 +537,8 @@ EXAMPLES
     $ apollo feature edit-attribute -i 66...3f -a domains -d
 ```
 
-_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+_See code:
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -553,7 +572,8 @@ EXAMPLES
     $ apollo feature edit-coords -i abc...xyz -e 2000
 ```
 
-_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+_See code:
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -576,7 +596,8 @@ DESCRIPTION
   term although but the valifdity of the new term is not checked.
 ```
 
-_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+_See code:
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -609,7 +630,8 @@ EXAMPLES
     $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000
 ```
 
-_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/get.ts)_
+_See code:
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -638,7 +660,8 @@ EXAMPLES
     $ apollo feature get-id -i abc...zyz def...foo
 ```
 
-_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/get-id.ts)_
+_See code:
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import`
 
@@ -666,7 +689,8 @@ EXAMPLES
     $ apollo feature import -d -i features.gff3 -a myAssembly
 ```
 
-_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/import.ts)_
+_See code:
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -717,7 +741,8 @@ EXAMPLES
     $ apollo feature search -a mm9 mm10 -t bac
 ```
 
-_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/search.ts)_
+_See code:
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -737,7 +762,8 @@ DESCRIPTION
   Display help for apollo.
 ```
 
-_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
+_See code:
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
 
 ## `apollo login`
 
@@ -777,7 +803,8 @@ EXAMPLES
     $ apollo login --profile my-profile
 ```
 
-_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/login.ts)_
+_See code:
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -806,7 +833,38 @@ EXAMPLES
     $ apollo logout --profile my-profile
 ```
 
-_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/logout.ts)_
+_See code:
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_
+
+## `apollo refseq add-alias`
+
+Add reference name aliases from a file
+
+```
+USAGE
+  $ apollo refseq add-alias -i <value> -a <value> [--profile <value>] [--config-file <value>]
+
+FLAGS
+  -a, --assembly=<value>     (required) Name for this assembly.
+  -i, --input-file=<value>   (required) Input refname alias file
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add reference name aliases from a file
+
+  Reference name aliasing is a process to make chromosomes that are named slightly
+  differently but which refer to the same thing render properly. This command
+  reads a file with reference name aliases and adds them to the database.
+
+EXAMPLES
+  Add reference name aliases:
+
+    $ apollo refseq add-alias -i alias.txt -a myAssembly
+```
+
+_See code:
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -838,7 +896,8 @@ EXAMPLES
     $ apollo refseq get -a mm9 mm10
 ```
 
-_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/refseq/get.ts)_
+_See code:
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -860,7 +919,8 @@ DESCRIPTION
   not check the validity of the access token.
 ```
 
-_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/status.ts)_
+_See code:
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -895,5 +955,7 @@ EXAMPLES
     $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'
 ```
 
-_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/user/get.ts)_
+_See code:
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_
+
 <!-- commandsstop -->

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.js

@@ -26,7 +26,7 @@ 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);
@@ -40,8 +40,9 @@ export class BaseCommand extends Command {
         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-fasta.js

@@ -73,7 +73,6 @@ export default class Get extends BaseCommand {
             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

@@ -59,6 +59,5 @@ export default class AddGff extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

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 ${accessToken}`,
         },
-        signal: controller.signal,
+        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
     };
     const response = await fetch(uri, auth);
     if (!response.ok) {
@@ -87,8 +82,8 @@ export default class ApolloCmd extends BaseCommand {
             const seq = new TextDecoder().decode(seqObj?.value);
             let header = '';
             for (const x of refSeqs) {
-                if (x['_id'] === rid) {
-                    const rname = x['name'];
+                if (x._id === rid) {
+                    const rname = x.name;
                     header = `>${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.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

@@ -53,7 +53,7 @@ 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);

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

@@ -1,5 +1,3 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/restrict-plus-operands */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
@@ -63,17 +61,16 @@ export default class Get extends BaseCommand {
             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.error(`Error: Child feature coordinates (${start + 1}-${end}) cannot extend beyond parent coordinates (${pStart + 1}-${pEnd})`);
+    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) {
@@ -83,17 +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

@@ -60,11 +60,9 @@ export default class Copy extends BaseCommand {
             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],
@@ -72,12 +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],