@apollo-annotation/cli 0.1.17 → 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/0.1.17 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/v0.1.17/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/v0.1.17/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`
 
@@ -137,8 +144,8 @@ 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 +165,8 @@ EXAMPLES
     $ apollo assembly check -a hg19 -c CDSCheck --delete
 ```
 
-_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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/v0.1.17/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.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 +1,144 @@
+/* eslint-disable @typescript-eslint/no-unsafe-enum-comparison */
+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 = {
@@ -26,10 +26,10 @@ 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 Config(configFile);
+        const config = new ApolloConf(configFile);
         return config;
     }
     async getAccess(configFile, profileName) {
@@ -37,22 +37,12 @@ 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
-        // or simply return the parent class error handling
+        if (err.cause instanceof Error) {
+            console.error(err.cause);
+        }
         return super.catch(err);
     }
     async finally(_) {