@apollo-annotation/cli 0.1.17 → 0.1.19

package/dist/commands/refseq/add-alias.js

@@ -0,0 +1,72 @@
+import * as fs from 'node:fs';
+import { Agent, fetch } from 'undici';
+import { Flags } from '@oclif/core';
+import { BaseCommand } from '../../baseCommand.js';
+import { createFetchErrorMessage, localhostToAddress, queryApollo, wrapLines, } from '../../utils.js';
+import { ConfigError } from '../../ApolloConf.js';
+export default class AddRefNameAlias extends BaseCommand {
+    static summary = 'Add reference name aliases from a file';
+    static description = wrapLines('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.');
+    static examples = [
+        {
+            description: 'Add reference name aliases:',
+            command: '<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly',
+        },
+    ];
+    static flags = {
+        'input-file': Flags.string({
+            char: 'i',
+            description: 'Input refname alias file',
+            required: true,
+        }),
+        assembly: Flags.string({
+            char: 'a',
+            description: 'Name for this assembly.',
+            required: true,
+        }),
+    };
+    async run() {
+        const { flags } = await this.parse(AddRefNameAlias);
+        if (!fs.existsSync(flags['input-file'])) {
+            this.error(`File ${flags['input-file']} does not exist`);
+        }
+        const access = await this.getAccess(flags['config-file'], flags.profile);
+        const filehandle = await fs.promises.open(flags['input-file']);
+        const fileContent = await filehandle.readFile({ encoding: 'utf8' });
+        await filehandle.close();
+        const lines = fileContent.split('\n');
+        const refNameAliases = [];
+        for (const line of lines) {
+            const [refName, ...aliases] = line.split('\t');
+            refNameAliases.push({ refName, aliases });
+        }
+        const assemblies = await queryApollo(access.address, access.accessToken, 'assemblies');
+        const json = (await assemblies.json());
+        const assembly = json.find((x) => 'name' in x && x.name === flags.assembly);
+        const assemblyId = assembly && '_id' in assembly ? assembly._id : undefined;
+        if (!assemblyId) {
+            this.error(`Assembly ${flags.assembly} not found`);
+        }
+        const change = {
+            typeName: 'AddRefSeqAliasesChange',
+            assembly: assemblyId,
+            refSeqAliases: refNameAliases,
+        };
+        const auth = {
+            method: 'POST',
+            body: JSON.stringify(change),
+            headers: {
+                Authorization: `Bearer ${access.accessToken}`,
+                'Content-Type': 'application/json',
+            },
+            dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
+        };
+        const url = new URL(localhostToAddress(`${access.address}/changes`));
+        const response = await fetch(url, auth);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, 'Failed to add reference name aliases');
+            throw new ConfigError(errorMessage);
+        }
+        this.log(`Reference name aliases added successfully to assembly ${flags.assembly}`);
+    }
+}

package/dist/commands/status.js

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import path from 'node:path';
+import { ApolloConf, KEYS } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { Config, ConfigError, KEYS } from '../Config.js';
 import { basicCheckConfig, wrapLines } from '../utils.js';
 export default class Status extends BaseCommand {
     static summary = 'View authentication status';
@@ -15,19 +15,11 @@ export default class Status extends BaseCommand {
         }
         let configFile = flags['config-file'];
         if (configFile === undefined) {
-            configFile = path.join(this.config.configDir, 'config.yaml');
+            configFile = path.join(this.config.configDir, 'config.yml');
         }
-        try {
-            basicCheckConfig(configFile, profileName);
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-        }
-        const config = new Config(configFile);
-        const accessToken = config.get(KEYS.accessToken, profileName);
+        basicCheckConfig(configFile, profileName);
+        const config = new ApolloConf(configFile);
+        const accessToken = config.get(`${profileName}.${KEYS.accessToken}`);
         if (accessToken === undefined || accessToken.trim() === '') {
             this.log(`${profileName}: Logged out`);
         }

package/dist/commands/user/get.test.js

@@ -7,7 +7,7 @@ const __dirname = fileURLToPath(new URL('.', import.meta.url));
 // TODO: Need valid token
 describe.skip('apollo user get: Get users 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/test/fixtures.js

@@ -4,8 +4,8 @@ import path from 'node:path';
 export const TEST_DATA_DIR = path.resolve('test_data');
 export const VERBOSE = false;
 export const CONFIG_DIR = path.join(os.homedir(), '.config', 'apollo-cli');
-export const CONFIG_FILE = path.join(CONFIG_DIR, 'config.yaml');
-const CONFIG_BAK = path.join(TEST_DATA_DIR, 'original.config.yaml.bak');
+export const CONFIG_FILE = path.join(CONFIG_DIR, 'config.yml');
+const CONFIG_BAK = path.join(TEST_DATA_DIR, 'original.config.yml.bak');
 function renameFile(src, dest, verbose = true) {
     if (fs.existsSync(dest)) {
         throw new Error(`File ${dest} already exists`);

package/dist/utils.d.ts

@@ -1,6 +1,6 @@
 import EventEmitter from 'node:events';
 import { Response } from 'undici';
-import { Config } from './Config.js';
+import { ApolloConf } from './ApolloConf.js';
 export declare const CLI_SERVER_ADDRESS = "http://127.0.0.1:5657";
 export declare const CLI_SERVER_ADDRESS_CALLBACK = "http://127.0.0.1:5657/auth/callback";
 export declare class CheckError extends Error {
@@ -10,7 +10,7 @@ export interface UserCredentials {
 }
 export declare function createFetchErrorMessage(response: Response, additionalText?: string): Promise<string>;
 export declare function checkConfigfileExists(configFile: string): void;
-export declare function checkProfileExists(profileName: string, config: Config): void;
+export declare function checkProfileExists(profileName: string, config: ApolloConf): void;
 export declare function basicCheckConfig(configFile: string, profileName: string): void;
 /**
  * @deprecated Use this function while we wait to resolve the TypeError when using localhost in fetch.
@@ -48,7 +48,7 @@ interface bodyExternalFile {
     };
 }
 export declare function submitAssembly(address: string, accessToken: string, body: bodyLocalFile | bodyExternalFile, force: boolean): Promise<Response>;
-export declare function uploadFile(address: string, accessToken: string, file: string, type: string): Promise<string>;
+export declare function uploadFile(address: string, accessToken: string, file: string, type: string): Promise<never>;
 export declare function wrapLines(s: string, length?: number): string;
 export declare function idReader(input: string[], removeDuplicates?: boolean): string[];
 export {};

package/dist/utils.js

@@ -7,8 +7,10 @@ import * as crypto from 'node:crypto';
 import * as fs from 'node:fs';
 import * as os from 'node:os';
 import * as path from 'node:path';
-import { Agent, FormData, Response, fetch } from 'undici';
-import { Config, ConfigError } from './Config.js';
+import { Transform, pipeline, } from 'node:stream';
+import { SingleBar } from 'cli-progress';
+import { Agent, fetch } from 'undici';
+import { ApolloConf, ConfigError } from './ApolloConf.js';
 const CONFIG_PATH = path.resolve(os.homedir(), '.clirc');
 export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';
 export const CLI_SERVER_ADDRESS_CALLBACK = `${CLI_SERVER_ADDRESS}/auth/callback`;
@@ -37,7 +39,7 @@ export function checkProfileExists(profileName, config) {
 }
 export function basicCheckConfig(configFile, profileName) {
     checkConfigfileExists(configFile);
-    const config = new Config(configFile);
+    const config = new ApolloConf(configFile);
     checkProfileExists(profileName, config);
 }
 /**
@@ -61,6 +63,7 @@ export async function deleteAssembly(address, accessToken, assemblyId) {
             Authorization: `Bearer ${accessToken}`,
             'Content-Type': 'application/json',
         },
+        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
     };
     const url = new URL(localhostToAddress(`${address}/changes`));
     const response = await fetch(url, auth);
@@ -78,7 +81,7 @@ export async function getAssembly(address, accessToken, assemblyNameOrId) {
     const assemblies = (await res.json());
     let assemblyObj = {};
     for (const x of assemblies) {
-        if (x['_id'] === assemblyId[0]) {
+        if (x._id === assemblyId[0]) {
             assemblyObj = JSON.parse(JSON.stringify(x));
             break;
         }
@@ -128,11 +131,11 @@ export async function getRefseqId(address, accessToken, refseqNameOrId, inAssemb
 }
 async function checkNameToIdDict(address, accessToken) {
     const asm = await queryApollo(address, accessToken, 'checks/types');
-    const ja = (await asm.json());
+    const ja = (await asm.json()); // Not sure if CheckResultSnapshot is the right interface
     const nameToId = {};
     for (const x of ja) {
-        const name = x['name'];
-        nameToId[name] = x['_id'];
+        const { _id, name } = x; // x['name' as keyof typeof x]
+        nameToId[name] = _id; // x['_id' as keyof typeof x]
     }
     return nameToId;
 }
@@ -267,10 +270,6 @@ export async function submitAssembly(address, accessToken, body, force) {
             }
         }
     }
-    const controller = new AbortController();
-    setTimeout(() => {
-        controller.abort();
-    }, 24 * 60 * 60 * 1000);
     const auth = {
         method: 'POST',
         body: JSON.stringify(body),
@@ -278,7 +277,7 @@ export async function submitAssembly(address, accessToken, body, force) {
             Authorization: `Bearer ${accessToken}`,
             'Content-Type': 'application/json',
         },
-        signal: controller.signal,
+        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
     };
     const url = new URL(localhostToAddress(`${address}/changes`));
     const response = await fetch(url, auth);
@@ -288,27 +287,50 @@ export async function submitAssembly(address, accessToken, body, force) {
     }
     return response;
 }
+class ProgressTransform extends Transform {
+    size = 0;
+    progressBar;
+    constructor(opts) {
+        super(opts);
+        this.progressBar = opts.progressBar;
+    }
+    _transform(chunk, _encoding, callback) {
+        this.size += chunk.length;
+        this.progressBar.update(this.size);
+        callback(null, chunk);
+    }
+}
 export async function uploadFile(address, accessToken, file, type) {
-    const stream = fs.createReadStream(file, 'utf8');
-    const fileStream = new Response(stream);
-    const fileBlob = await fileStream.blob();
-    const formData = new FormData();
-    formData.append('type', type);
-    formData.append('file', fileBlob);
-    const auth = {
+    const filehandle = await fs.promises.open(file);
+    const { size } = await filehandle.stat();
+    const stream = filehandle.createReadStream();
+    const progressBar = new SingleBar({ etaBuffer: 100_000_000 });
+    const progressTransform = new ProgressTransform({ progressBar });
+    const body = pipeline(stream, progressTransform, (error) => {
+        if (error) {
+            progressBar.stop();
+            console.error('Error processing file.', error);
+            throw error;
+        }
+    });
+    const init = {
         method: 'POST',
-        body: formData,
+        body,
+        duplex: 'half',
         headers: {
             Authorization: `Bearer ${accessToken}`,
+            'Content-Type': type,
+            'Content-Length': String(size),
         },
-        dispatcher: new Agent({
-            keepAliveTimeout: 10 * 60 * 1000,
-            keepAliveMaxTimeout: 10 * 60 * 1000, // 10 minutes
-        }),
+        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
     };
+    const fileName = path.basename(file);
     const url = new URL(localhostToAddress(`${address}/files`));
+    url.searchParams.set('name', fileName);
+    url.searchParams.set('type', type);
+    progressBar.start(size, 0);
     try {
-        const response = await fetch(url, auth);
+        const response = await fetch(url, init);
         if (!response.ok) {
             const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
             throw new ConfigError(errorMessage);
@@ -320,6 +342,9 @@ export async function uploadFile(address, accessToken, file, type) {
         console.error(error);
         throw error;
     }
+    finally {
+        progressBar.stop();
+    }
 }
 /* Wrap text to max `length` per line */
 export function wrapLines(s, length) {

package/oclif.manifest.json

@@ -395,7 +395,7 @@
     "assembly:check": {
       "aliases": [],
       "args": {},
-      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the check to apply, to retrieve features flagged by these\nchecks use `apollo feature check`.",
+      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the checks to apply, to retrieve features flagged by\nthese checks use `apollo feature check`.",
       "examples": [
         {
           "description": "View available check types:",
@@ -654,106 +654,6 @@
         "sequence.js"
       ]
     },
-    "change:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed to use the assembly ID.",
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "change:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get list of changes",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "change",
-        "get.js"
-      ]
-    },
-    "refseq:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
-      "examples": [
-        {
-          "description": "All sequences in the database:",
-          "command": "<%= config.bin %> <%= command.id %>"
-        },
-        {
-          "description": "Only sequences for these assemblies:",
-          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "refseq:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get reference sequences",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "refseq",
-        "get.js"
-      ]
-    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1560,6 +1460,167 @@
         "search.js"
       ]
     },
+    "change:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed to use the assembly ID.",
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "change:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of changes",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "change",
+        "get.js"
+      ]
+    },
+    "refseq:add-alias": {
+      "aliases": [],
+      "args": {},
+      "description": "Reference name aliasing is a process to make chromosomes that are named slightly\ndifferently but which refer to the same thing render properly. This command\nreads a file with reference name aliases and adds them to the database.",
+      "examples": [
+        {
+          "description": "Add reference name aliases:",
+          "command": "<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "input-file": {
+          "char": "i",
+          "description": "Input refname alias file",
+          "name": "input-file",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name for this assembly.",
+          "name": "assembly",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:add-alias",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add reference name aliases from a file",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "add-alias.js"
+      ]
+    },
+    "refseq:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
+      "examples": [
+        {
+          "description": "All sequences in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Only sequences for these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get reference sequences",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "get.js"
+      ]
+    },
     "user:get": {
       "aliases": [],
       "args": {},
@@ -1628,5 +1689,5 @@
       ]
     }
   },
-  "version": "0.1.17"
+  "version": "0.1.19"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@apollo-annotation/cli",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.17",
+  "version": "0.1.19",
   "author": "Apollo Team",
   "repository": {
     "type": "git",
@@ -28,7 +28,7 @@
     "dev": "tsx bin/dev.js",
     "postpack": "shx rm -f oclif.manifest.json",
     "posttest": "yarn lint",
-    "prepack": "yarn build && oclif manifest && oclif readme",
+    "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
     "prepare": "yarn build",
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
@@ -41,6 +41,8 @@
     "@oclif/core": "^3.18.2",
     "@oclif/plugin-help": "^6.0.8",
     "bson": "^6.3.0",
+    "cli-progress": "^3.12.0",
+    "conf": "^12.0.0",
     "joi": "^17.7.0",
     "open": "^10.1.0",
     "tslib": "^2.3.1",
@@ -48,10 +50,13 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
+    "@apollo-annotation/mst": "^0.1.19",
+    "@apollo-annotation/shared": "^0.1.19",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
     "@types/chai": "^4",
+    "@types/cli-progress": "^3",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
     "@types/node": "^18.14.2",
@@ -59,10 +64,13 @@
     "mocha": "^10.2.0",
     "nyc": "^15.1.0",
     "oclif": "^4.4.2",
+    "prettier": "^3.3.2",
+    "react-dom": "^18.2.0",
+    "rxjs": "^7.4.0",
     "shx": "^0.3.3",
     "ts-node": "^10.3.0",
     "tsx": "^4.6.2",
-    "typescript": "^5.1.6"
+    "typescript": "^5.5.3"
   },
   "oclif": {
     "helpOptions": {