@apollo-annotation/cli 0.1.16 → 0.1.18

package/README.md

@@ -14,7 +14,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.16 linux-x64 node-v18.20.3
+@apollo-annotation/cli/0.1.18 linux-x64 node-v18.20.3
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -82,7 +82,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
+_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
 
 ## `apollo assembly add-gff`
 
@@ -116,7 +116,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
+_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -137,8 +137,8 @@ DESCRIPTION
   Add, view, or delete checks to assembly
 
   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`.
 
 EXAMPLES
   View available check types:
@@ -158,7 +158,7 @@ EXAMPLES
     $ apollo assembly check -a hg19 -c CDSCheck --delete
 ```
 
-_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/assembly/check.ts)_
+_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -185,7 +185,7 @@ EXAMPLES
     $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f
 ```
 
-_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/assembly/delete.ts)_
+_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -206,7 +206,7 @@ DESCRIPTION
   Print to stdout the list of assemblies in json format
 ```
 
-_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/assembly/get.ts)_
+_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -240,7 +240,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -264,7 +264,7 @@ DESCRIPTION
   need to use the assembly ID.
 ```
 
-_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/change/get.ts)_
+_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -319,7 +319,7 @@ EXAMPLES
     $ apollo config address
 ```
 
-_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/config.ts)_
+_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo feature add-child`
 
@@ -349,7 +349,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/feature/add-child.ts)_
+_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -382,7 +382,7 @@ EXAMPLES
     $ apollo feature check -a hg19
 ```
 
-_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/check.ts)_
+_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -413,7 +413,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/feature/copy.ts)_
+_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -437,7 +437,7 @@ DESCRIPTION
   error unless you set -f/--force.
 ```
 
-_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/delete.ts)_
+_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -479,7 +479,7 @@ EXAMPLES
     echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -
 ```
 
-_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/edit.ts)_
+_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -519,7 +519,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -553,7 +553,7 @@ EXAMPLES
     $ apollo feature edit-coords -i abc...xyz -e 2000
 ```
 
-_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -576,7 +576,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -609,7 +609,7 @@ 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/v0.1.16/packages/apollo-cli/src/commands/feature/get.ts)_
+_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -638,7 +638,7 @@ EXAMPLES
     $ apollo feature get-id -i abc...zyz def...foo
 ```
 
-_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/get-id.ts)_
+_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import`
 
@@ -666,7 +666,7 @@ EXAMPLES
     $ apollo feature import -d -i features.gff3 -a myAssembly
 ```
 
-_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/import.ts)_
+_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -717,7 +717,7 @@ EXAMPLES
     $ apollo feature search -a mm9 mm10 -t bac
 ```
 
-_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/feature/search.ts)_
+_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -777,7 +777,7 @@ EXAMPLES
     $ apollo login --profile my-profile
 ```
 
-_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/login.ts)_
+_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -806,7 +806,7 @@ EXAMPLES
     $ apollo logout --profile my-profile
 ```
 
-_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/logout.ts)_
+_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq get`
 
@@ -838,7 +838,7 @@ EXAMPLES
     $ apollo refseq get -a mm9 mm10
 ```
 
-_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/refseq/get.ts)_
+_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -860,7 +860,7 @@ DESCRIPTION
   not check the validity of the access token.
 ```
 
-_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/status.ts)_
+_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -895,5 +895,5 @@ EXAMPLES
     $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'
 ```
 
-_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.16/packages/apollo-cli/src/commands/user/get.ts)_
+_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.18/packages/apollo-cli/src/commands/user/get.ts)_
 <!-- commandsstop -->

package/dist/ApolloConf.d.ts

@@ -0,0 +1,22 @@
+import Conf from 'conf';
+export declare class ConfigError extends Error {
+}
+export declare enum KEYS {
+    address = "address",
+    accessType = "accessType",
+    accessToken = "accessToken",
+    rootCredentials_username = "rootCredentials.username",
+    rootCredentials_password = "rootCredentials.password"
+}
+export declare function optionDesc(): string[];
+export declare class ApolloConf extends Conf {
+    constructor(configFile: string);
+    get store(): Record<string, unknown>;
+    set store(newStore: Record<string, unknown>);
+    getProfileNames(): string[];
+    setAccessType(profileName: string, accessType: string): void;
+    getAccess(profileName: string): Promise<{
+        address: string;
+        accessToken: string;
+    }>;
+}

package/dist/ApolloConf.js

@@ -0,0 +1,143 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import Conf from 'conf';
+import Joi from 'joi';
+import YAML from 'yaml';
+import { checkProfileExists, queryApollo } from './utils.js';
+export class ConfigError extends Error {
+}
+export var KEYS;
+(function (KEYS) {
+    KEYS["address"] = "address";
+    KEYS["accessType"] = "accessType";
+    KEYS["accessToken"] = "accessToken";
+    KEYS["rootCredentials_username"] = "rootCredentials.username";
+    KEYS["rootCredentials_password"] = "rootCredentials.password";
+})(KEYS || (KEYS = {}));
+function optionDocs() {
+    const docs = [];
+    for (const v of Object.values(KEYS)) {
+        switch (v) {
+            case 'address': {
+                docs.push({
+                    key: v,
+                    description: 'Address and port e.g http://localhost:3999',
+                });
+                break;
+            }
+            case 'accessType': {
+                docs.push({
+                    key: v,
+                    description: 'How to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your Apollo setup',
+                });
+                break;
+            }
+            case 'accessToken': {
+                docs.push({
+                    key: v,
+                    description: 'Access token. Usually inserted by `apollo login`',
+                });
+                break;
+            }
+            case 'rootCredentials.username': {
+                docs.push({
+                    key: v,
+                    description: 'Username of root account. Only set this for "root" access type',
+                });
+                break;
+            }
+            case 'rootCredentials.password': {
+                docs.push({
+                    key: v,
+                    description: 'Password for root account. Only set this for "root" access type',
+                });
+                break;
+            }
+            default: {
+                throw new ConfigError(`Unexpected key: ${v}`);
+            }
+        }
+    }
+    return docs;
+}
+export function optionDesc() {
+    const docs = [];
+    for (const x of optionDocs()) {
+        docs.push(`- ${x.key}:\n${x.description}`);
+    }
+    return docs;
+}
+export class ApolloConf extends Conf {
+    constructor(configFile) {
+        let APOLLO_DISABLE_CONFIG_CREATE = false;
+        if (process.env.APOLLO_DISABLE_CONFIG_CREATE !== undefined &&
+            process.env.APOLLO_DISABLE_CONFIG_CREATE !== '0') {
+            APOLLO_DISABLE_CONFIG_CREATE = true;
+        }
+        if (APOLLO_DISABLE_CONFIG_CREATE && !fs.existsSync(configFile)) {
+            throw new ConfigError('Configuration file does not exist yet, please create it as an empty file first.');
+        }
+        super({
+            projectName: 'apollo-cli',
+            fileExtension: path.parse(configFile).ext.replace(/^\./, ''),
+            configName: path.parse(configFile).name,
+            cwd: path.dirname(configFile),
+            serialize: YAML.stringify,
+            deserialize: YAML.parse,
+        });
+        const v = configSchema.validate(this.store);
+        if (v.error?.message !== undefined) {
+            throw new Error(`Invalid setting: ${v.error.message}`);
+        }
+    }
+    get store() {
+        const superStore = super.store;
+        const v = configSchema.validate(superStore);
+        if (v.error?.message !== undefined) {
+            throw new ConfigError(`Invalid key: ${v.error.message}`);
+        }
+        return superStore;
+    }
+    set store(newStore) {
+        const v = configSchema.validate(newStore);
+        if (v.error?.message !== undefined) {
+            throw new ConfigError(`Invalid setting: ${v.error.message}`);
+        }
+        super.store = newStore;
+    }
+    getProfileNames() {
+        return Object.keys(this.store);
+    }
+    setAccessType(profileName, accessType) {
+        if (accessType != 'root') {
+            this.delete(`${profileName}.rootCredentials`);
+        }
+        this.set(`${profileName}.accessType`, accessType);
+    }
+    async getAccess(profileName) {
+        checkProfileExists(profileName, this);
+        const address = this.get(`${profileName}.address`);
+        if (address.trim() === '') {
+            throw new ConfigError(`Profile "${profileName}" has no address. Please run "apollo config" to set it up.`);
+        }
+        const accessToken = this.get(`${profileName}.accessToken`);
+        if (accessToken.trim() === '') {
+            throw new ConfigError(`Profile "${profileName}" has no access token. Please run "apollo login" to set it up.`);
+        }
+        await queryApollo(address, accessToken, 'assemblies');
+        return { address, accessToken };
+    }
+}
+const profileSchema = Joi.object({
+    address: Joi.string().uri({ scheme: /https?/ }),
+    accessType: Joi.string().valid('google', 'microsoft', 'root', 'guest'),
+    accessToken: Joi.string(),
+    rootCredentials: Joi.object({
+        username: Joi.string(),
+        password: Joi.string(),
+    }).when('accessType', {
+        is: Joi.string().valid('root'),
+        otherwise: Joi.forbidden(),
+    }),
+});
+const configSchema = Joi.object().pattern(Joi.string(), profileSchema);

package/dist/baseCommand.js

@@ -1,6 +1,6 @@
 import path from 'node:path';
 import { Command, Flags } from '@oclif/core';
-import { Config, ConfigError } from './Config.js';
+import { ApolloConf } from './ApolloConf.js';
 import { checkConfigfileExists } from './utils.js';
 export class BaseCommand extends Command {
     static baseFlags = {
@@ -29,7 +29,7 @@ export class BaseCommand extends Command {
             configFile = path.join(this.config.configDir, 'config.yaml');
         }
         checkConfigfileExists(configFile);
-        const config = new Config(configFile);
+        const config = new ApolloConf(configFile);
         return config;
     }
     async getAccess(configFile, profileName) {
@@ -37,18 +37,7 @@ export class BaseCommand extends Command {
         if (profileName === undefined) {
             profileName = process.env.APOLLO_PROFILE ?? 'default';
         }
-        try {
-            return await config.getAccess(profileName);
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-            else {
-                throw error;
-            }
-        }
+        return config.getAccess(profileName);
     }
     async catch(err) {
         // add any custom logic to handle errors from the command

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,
@@ -56,32 +54,24 @@ 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);
     }

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');
@@ -51,25 +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
     }
 }