@apollo-annotation/cli 0.1.18 → 0.1.19

package/dist/commands/feature/delete.js

@@ -1,5 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
@@ -7,18 +5,15 @@ import { createFetchErrorMessage, getFeatureById, idReader, localhostToAddress,
 async function deleteFeature(address, accessToken, feature) {
     const changeJson = {
         typeName: 'DeleteFeatureChange',
-        changedIds: [feature],
-        assembly: feature['assembly'],
+        changedIds: [feature._id],
+        assembly: '111222333444555666777888', // Use a placeholder objectId (i.e. some 24 chars)
         deletedFeature: {
-            _id: feature['_id'],
-            gffId: feature['gffId'],
-            refSeq: feature['refSeq'],
-            type: feature['type'],
-            start: feature['start'],
-            end: feature['end'],
-            discontinuousLocations: feature['discontinuousLocations'],
-            score: feature['score'],
-            attributes: feature['attributes'],
+            _id: feature._id,
+            refSeq: feature.refSeq,
+            type: feature.type,
+            min: feature.min,
+            max: feature.max,
+            attributes: feature.attributes,
         },
     };
     const url = new URL(localhostToAddress(`${address}/changes`));
@@ -75,7 +70,7 @@ export default class Delete extends BaseCommand {
             }
             const feature = JSON.parse(await res.text());
             if (flags['dry-run']) {
-                this.log(feature);
+                this.log(JSON.stringify(feature, null, 2));
             }
             else {
                 const delFet = await deleteFeature(access.address, access.accessToken, feature);
@@ -85,6 +80,5 @@ export default class Delete extends BaseCommand {
                 }
             }
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit-attribute.js

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
@@ -61,6 +58,9 @@ export default class EditAttibute extends BaseCommand {
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
+        if (featureJson.attributes === undefined) {
+            featureJson.attributes = {};
+        }
         if (flags.value === undefined && !flags.delete) {
             this.log(JSON.stringify(featureJson.attributes[flags.attribute]));
             return;
@@ -72,13 +72,20 @@ export default class EditAttibute extends BaseCommand {
         else {
             featureJson.attributes[flags.attribute] = flags.value;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const attrs = {};
+        for (const [key, val] of Object.entries(featureJson.attributes)) {
+            if (!val) {
+                continue;
+            }
+            attrs[key] = [...val];
+        }
         const changeJson = {
             typeName: 'FeatureAttributeChange',
             changedIds: [featureId],
             assembly,
             featureId,
-            attributes: featureJson.attributes,
+            attributes: attrs,
         };
         const url = new URL(localhostToAddress(`${access.address}/changes`));
         const auth = {
@@ -94,6 +101,5 @@ export default class EditAttibute extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(res, 'edit-attribute failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit-coords.js

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
@@ -62,15 +59,15 @@ export default class Get extends BaseCommand {
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await res.text());
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
-        const currentEnd = featureJson['end'];
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const currentEnd = featureJson.max;
         let edit = ['Start', 'End'];
         if (flags.start !== undefined && flags.start > currentEnd) {
-            // Edit End first so you avoid an intermediate start > end
+            // Edit End (Max) first so you avoid an intermediate start > end
             edit = ['End', 'Start'];
         }
         for (const coord of edit) {
-            const currentStart = featureJson['start'];
+            const currentStart = featureJson.min;
             if (coord === 'Start' &&
                 (flags.start === undefined || flags.start === currentStart)) {
                 continue;
@@ -79,18 +76,36 @@ export default class Get extends BaseCommand {
                 (flags.end === undefined || flags.end === currentEnd)) {
                 continue;
             }
-            const changeJson = {
-                typeName: `Location${coord}Change`,
-                changedIds: [featureId],
-                assembly,
-                featureId,
-                [`old${coord}`]: featureJson[coord.toLowerCase()],
-                [`new${coord}`]: flags[coord.toLowerCase()],
-            };
+            let body;
+            if (coord === 'Start' && flags.start !== undefined) {
+                const oldCoord = featureJson.min;
+                body = {
+                    typeName: 'LocationStartChange',
+                    changedIds: [featureId],
+                    assembly,
+                    featureId,
+                    ['oldStart']: oldCoord,
+                    ['newStart']: flags.start,
+                };
+            }
+            else if (coord === 'End' && flags.end !== undefined) {
+                const oldCoord = featureJson.max;
+                body = {
+                    typeName: 'LocationEndChange',
+                    changedIds: [featureId],
+                    assembly,
+                    featureId,
+                    ['oldEnd']: oldCoord,
+                    ['newEnd']: flags.end,
+                };
+            }
+            else {
+                throw new Error(`Unexpected coordinate name: "${coord}"`);
+            }
             const url = new URL(localhostToAddress(`${access.address}/changes`));
             const auth = {
                 method: 'POST',
-                body: JSON.stringify(changeJson),
+                body: JSON.stringify(body),
                 headers: {
                     authorization: `Bearer ${access.accessToken}`,
                     'Content-Type': 'application/json',

package/dist/commands/feature/edit-type.js

@@ -1,6 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
@@ -34,7 +31,7 @@ export default class Get extends BaseCommand {
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
-        const currentType = featureJson['type'];
+        const currentType = featureJson.type;
         if (flags.type === undefined) {
             this.log(currentType);
             return;
@@ -43,7 +40,7 @@ export default class Get extends BaseCommand {
             this.logToStderr(`NOTE: Feature ${featureId} is already of type "${flags.type}"`);
             return;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
         const changeJson = {
             typeName: 'TypeChange',
             changedIds: [featureId],
@@ -66,6 +63,5 @@ export default class Get extends BaseCommand {
             const errorMessage = await createFetchErrorMessage(res, 'edit-type failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/edit.js

@@ -64,6 +64,5 @@ export default class Get extends BaseCommand {
                 throw new Error(errorMessage);
             }
         }
-        this.exit(0);
     }
 }

package/dist/commands/feature/get-id.js

@@ -33,7 +33,6 @@ export default class Get extends BaseCommand {
             results.push(res);
         }
         this.log(JSON.stringify(results, null, 2));
-        this.exit(0);
     }
     async getFeatureId(address, token, featureId) {
         const url = new URL(localhostToAddress(`${address}/features/${featureId}`));

package/dist/commands/feature/get.js

@@ -50,7 +50,6 @@ export default class Get extends BaseCommand {
             }
         }
         this.log(JSON.stringify(results, null, 2));
-        this.exit(0);
     }
     async getFeatures(address, token, refSeq, start, end) {
         const url = new URL(localhostToAddress(`${address}/features/getFeatures`));

package/dist/commands/feature/import.js

@@ -1,6 +1,6 @@
 import * as fs from 'node:fs';
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
+import { Agent, fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
 import { convertAssemblyNameToId, createFetchErrorMessage, localhostToAddress, uploadFile, } from '../../utils.js';
 export default class Import extends BaseCommand {
@@ -39,39 +39,26 @@ export default class Import extends BaseCommand {
             this.error(`Assembly "${flags.assembly}" does not exist. Perhaps you want to create this assembly first`);
         }
         const uploadId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3');
-        const res = await importFeatures(access.address, access.accessToken, assembly[0], uploadId, flags['delete-existing']);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'Import features failed');
+        const body = {
+            typeName: 'AddFeaturesFromFileChange',
+            assembly: assembly[0],
+            fileId: uploadId,
+            deleteExistingFeatures: flags['delete-existing'],
+        };
+        const auth = {
+            method: 'POST',
+            body: JSON.stringify(body),
+            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, 'importFeatures failed');
             throw new Error(errorMessage);
         }
-        this.exit(0);
     }
 }
-async function importFeatures(address, accessToken, assembly, fileId, deleteExistingFeatures) {
-    const body = {
-        typeName: 'AddFeaturesFromFileChange',
-        assembly,
-        fileId,
-        deleteExistingFeatures,
-    };
-    const controller = new AbortController();
-    setTimeout(() => {
-        controller.abort();
-    }, 24 * 60 * 60 * 1000);
-    const auth = {
-        method: 'POST',
-        body: JSON.stringify(body),
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-        signal: controller.signal,
-    };
-    const url = new URL(localhostToAddress(`${address}/changes`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'importFeatures failed');
-        throw new Error(errorMessage);
-    }
-    return response;
-}

package/dist/commands/feature/search.js

@@ -73,7 +73,7 @@ export default class Search extends BaseCommand {
         if (flags.assembly === undefined) {
             const asm = await queryApollo(access.address, access.accessToken, 'assemblies');
             for (const x of (await asm.json())) {
-                assemblyIds.push(x['_id']);
+                assemblyIds.push(x._id);
             }
         }
         else {

package/dist/commands/login.js

@@ -55,7 +55,7 @@ export default class Login extends BaseCommand {
         const { flags } = await this.parse(Login);
         let configFile = flags['config-file'];
         if (configFile === undefined) {
-            configFile = path.join(this.config.configDir, 'config.yaml');
+            configFile = path.join(this.config.configDir, 'config.yml');
         }
         let profileName = flags.profile;
         if (profileName === undefined) {

package/dist/commands/logout.js

@@ -23,7 +23,7 @@ export default class Logout 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');
         }
         basicCheckConfig(configFile, profileName);
         const config = new ApolloConf(configFile);

package/dist/commands/refseq/add-alias.d.ts

@@ -0,0 +1,14 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class AddRefNameAlias extends BaseCommand<typeof AddRefNameAlias> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        'input-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    run(): Promise<void>;
+}

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

@@ -15,7 +15,7 @@ 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');
         }
         basicCheckConfig(configFile, profileName);
         const config = new ApolloConf(configFile);

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

@@ -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

@@ -7,7 +7,9 @@ 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 { 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';
@@ -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);
@@ -288,32 +287,64 @@ 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`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
-        throw new ConfigError(errorMessage);
+    url.searchParams.set('name', fileName);
+    url.searchParams.set('type', type);
+    progressBar.start(size, 0);
+    try {
+        const response = await fetch(url, init);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
+            throw new ConfigError(errorMessage);
+        }
+        const json = (await response.json());
+        return json['_id'];
+    }
+    catch (error) {
+        console.error(error);
+        throw error;
+    }
+    finally {
+        progressBar.stop();
     }
-    const json = (await response.json());
-    return json['_id'];
 }
 /* Wrap text to max `length` per line */
 export function wrapLines(s, length) {