@apollo-annotation/cli 0.1.17 → 0.1.19

package/dist/commands/feature/delete.js

@@ -1,7 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* 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';
@@ -9,18 +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`));
@@ -67,33 +60,25 @@ export default class Delete extends BaseCommand {
         }
         const access = await this.getAccess(flags['config-file'], flags.profile);
         for (const featureId of featureIds) {
-            const response = await getFeatureById(access.address, access.accessToken, featureId);
-            if (response.status === 404 && flags.force) {
+            const res = await getFeatureById(access.address, access.accessToken, featureId);
+            if (res.status === 404 && flags.force) {
                 continue;
             }
-            if (!response.ok) {
-                const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
+            if (!res.ok) {
+                const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
                 throw new Error(errorMessage);
             }
-            const feature = JSON.parse(await response.text());
-            if (!response.ok) {
-                const message = feature['message'];
-                this.logToStderr(message);
-                this.exit(1);
-            }
+            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);
                 if (!delFet.ok) {
-                    const json = (await delFet.json());
-                    const message = json['message'];
-                    this.logToStderr(message);
-                    this.exit(1);
+                    const errorMessage = await createFetchErrorMessage(delFet, 'Delete feature failed');
+                    throw new Error(errorMessage);
                 }
             }
         }
-        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';
@@ -47,12 +44,11 @@ export default class EditAttibute extends BaseCommand {
     async run() {
         const { flags } = await this.parse(EditAttibute);
         if (flags.delete && flags.value) {
-            this.logToStderr('Error: Options --delete and --value are mutually exclusive');
-            this.exit(1);
+            this.error('Error: Options --delete and --value are mutually exclusive');
         }
         const ff = idReader([flags['feature-id']]);
         if (ff.length !== 1) {
-            this.logToStderr(`Expected only one feature identifier. Got ${ff.length}`);
+            this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
         const access = await this.getAccess(flags['config-file'], flags.profile);
@@ -62,9 +58,12 @@ export default class EditAttibute extends BaseCommand {
             throw new Error(errorMessage);
         }
         const featureJson = JSON.parse(await response.text());
+        if (featureJson.attributes === undefined) {
+            featureJson.attributes = {};
+        }
         if (flags.value === undefined && !flags.delete) {
             this.log(JSON.stringify(featureJson.attributes[flags.attribute]));
-            this.exit(0);
+            return;
         }
         if (flags.delete) {
             // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
@@ -73,13 +72,20 @@ export default class EditAttibute extends BaseCommand {
         else {
             featureJson.attributes[flags.attribute] = flags.value;
         }
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const attrs = {};
+        for (const [key, val] of Object.entries(featureJson.attributes)) {
+            if (!val) {
+                continue;
+            }
+            attrs[key] = [...val];
+        }
         const changeJson = {
             typeName: 'FeatureAttributeChange',
             changedIds: [featureId],
             assembly,
             featureId,
-            attributes: featureJson.attributes,
+            attributes: attrs,
         };
         const url = new URL(localhostToAddress(`${access.address}/changes`));
         const auth = {
@@ -95,6 +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';
@@ -37,43 +34,40 @@ export default class Get extends BaseCommand {
     async run() {
         const { flags } = await this.parse(Get);
         if (flags.start === undefined && flags.end === undefined) {
-            this.logToStderr('Please provide new start and/or end coordinates to edit');
-            this.exit(1);
+            this.error('Please provide new start and/or end coordinates to edit');
         }
         if (flags.start !== undefined && flags.start <= 0) {
-            this.logToStderr('Coordinates must be greater than 0');
-            this.exit(1);
+            this.error('Coordinates must be greater than 0');
         }
         if (flags.start !== undefined &&
             flags.end !== undefined &&
             flags.end < flags.start) {
-            this.logToStderr('Error: The new end coordinate is lower than the new start coordinate');
-            this.exit(1);
+            this.error('Error: The new end coordinate is lower than the new start coordinate');
         }
         if (flags.start !== undefined) {
             flags.start -= 1;
         }
         const ff = idReader([flags['feature-id']]);
         if (ff.length !== 1) {
-            this.logToStderr(`Expected only one feature identifier. Got ${ff.length}`);
+            this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
         const access = await this.getAccess(flags['config-file'], flags.profile);
-        const response = await getFeatureById(access.address, access.accessToken, featureId);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'getFeatureById failed');
+        const res = await getFeatureById(access.address, access.accessToken, featureId);
+        if (!res.ok) {
+            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
             throw new Error(errorMessage);
         }
-        const featureJson = JSON.parse(await response.text());
-        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson['refSeq']);
-        const currentEnd = featureJson['end'];
+        const featureJson = JSON.parse(await res.text());
+        const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
+        const currentEnd = featureJson.max;
         let edit = ['Start', 'End'];
         if (flags.start !== undefined && flags.start > currentEnd) {
-            // Edit End first so you avoid an intermediate start > end
+            // Edit End (Max) first so you avoid an intermediate start > end
             edit = ['End', 'Start'];
         }
         for (const coord of edit) {
-            const currentStart = featureJson['start'];
+            const currentStart = featureJson.min;
             if (coord === 'Start' &&
                 (flags.start === undefined || flags.start === currentStart)) {
                 continue;
@@ -82,18 +76,36 @@ export default class Get extends BaseCommand {
                 (flags.end === undefined || flags.end === currentEnd)) {
                 continue;
             }
-            const changeJson = {
-                typeName: `Location${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';
@@ -24,7 +21,7 @@ export default class Get extends BaseCommand {
         const { flags } = await this.parse(Get);
         const ff = idReader([flags['feature-id']]);
         if (ff.length !== 1) {
-            this.logToStderr(`Expected only one feature identifier. Got ${ff.length}`);
+            this.error(`Expected only one feature identifier. Got ${ff.length}`);
         }
         const [featureId] = ff;
         const access = await this.getAccess(flags['config-file'], flags.profile);
@@ -34,16 +31,16 @@ 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);
-            this.exit(0);
+            return;
         }
         if (flags.type === currentType) {
             this.logToStderr(`NOTE: Feature ${featureId} is already of type "${flags.type}"`);
-            this.exit(0);
+            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],

package/dist/commands/feature/edit.js

@@ -42,21 +42,9 @@ export default class Get extends BaseCommand {
         else if (fs.existsSync(flags['json-input'])) {
             jsonStr = fs.readFileSync(flags['json-input']).toString();
         }
-        let json;
-        try {
-            json = JSON.parse(jsonStr);
-            if (!Array.isArray(json)) {
-                json = [json];
-            }
-        }
-        catch (error) {
-            if (error instanceof Error) {
-                this.logToStderr(`Error parsing json input:\n${error.message}`);
-                this.exit(1);
-            }
-            else {
-                throw error;
-            }
+        let json = JSON.parse(jsonStr);
+        if (!Array.isArray(json)) {
+            json = [json];
         }
         const access = await this.getAccess(flags['config-file'], flags.profile);
         for (const change of json) {
@@ -76,6 +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

@@ -37,21 +37,10 @@ export default class Get extends BaseCommand {
         const { flags } = await this.parse(Get);
         const endCoord = flags.end ?? Number.MAX_SAFE_INTEGER;
         if (flags.start <= 0 || endCoord <= 0) {
-            this.logToStderr('Start and end coordinates must be greater than 0.');
-            this.exit(1);
+            this.error('Start and end coordinates must be greater than 0.');
         }
         const access = await this.getAccess(flags['config-file'], flags.profile);
-        let refseqIds = [];
-        try {
-            refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
-        }
-        catch (error) {
-            this.logToStderr(error.message);
-            this.exit(1);
-        }
-        if (refseqIds.length === 0) {
-            this.logToStderr('No reference sequence found');
-        }
+        const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, flags.assembly);
         const results = [];
         for (const refseq of refseqIds) {
             const features = await this.getFeatures(access.address, access.accessToken, refseq, flags.start, endCoord);
@@ -61,7 +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`));
@@ -77,11 +65,11 @@ export default class Get extends BaseCommand {
                 'Content-Type': 'application/json',
             },
         };
-        const response = await fetch(url, auth);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
+        const res = await fetch(url, auth);
+        if (!res.ok) {
+            const errorMessage = await createFetchErrorMessage(res, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
             throw new Error(errorMessage);
         }
-        return response;
+        return res;
     }
 }

package/dist/commands/feature/import.js

@@ -1,8 +1,6 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 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 {
@@ -33,51 +31,34 @@ export default class Import extends BaseCommand {
     async run() {
         const { flags } = await this.parse(Import);
         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 assembly = await convertAssemblyNameToId(access.address, access.accessToken, [flags.assembly]);
         if (assembly.length === 0) {
-            this.logToStderr(`Assembly "${flags.assembly}" does not exist. Perhaps you want to create this assembly first`);
-            this.exit(1);
+            this.error(`Assembly "${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 response = await importFeatures(access.address, access.accessToken, assembly[0], uploadId, flags['delete-existing']);
+        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 json = JSON.parse(await response.text());
-            const message = json['message'];
-            this.logToStderr(message);
-            this.exit(1);
+            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

@@ -8,8 +8,8 @@ import * as querystring from 'node:querystring';
 import { Errors, Flags, ux } from '@oclif/core';
 import open from 'open';
 import { fetch } from 'undici';
+import { ApolloConf } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { Config, ConfigError } from '../Config.js';
 import { basicCheckConfig, createFetchErrorMessage, getUserCredentials, localhostToAddress, waitFor, wrapLines, } from '../utils.js';
 export default class Login extends BaseCommand {
     static summary = 'Login to Apollo';
@@ -55,27 +55,18 @@ 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) {
             profileName = process.env.APOLLO_PROFILE ?? 'default';
         }
-        try {
-            basicCheckConfig(configFile, profileName);
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-        }
-        const config = new Config(configFile);
-        const accessType = config.get('accessType', profileName);
-        const address = flags.address ?? config.get('address', profileName);
+        basicCheckConfig(configFile, profileName);
+        const config = new ApolloConf(configFile);
+        const accessType = config.get(`${profileName}.accessType`);
+        const address = flags.address ?? config.get(`${profileName}.address`);
         if (address === undefined) {
-            this.logToStderr('Address to apollo must be set');
-            this.exit(1);
+            this.error('Address to apollo must be set');
         }
         let userCredentials = { accessToken: '' };
         try {
@@ -83,11 +74,12 @@ export default class Login extends BaseCommand {
                 await this.checkUserAlreadyLoggedIn();
             }
             if (accessType === 'root' || flags.username !== undefined) {
-                const username = flags.username ?? config.get('rootCredentials.username', profileName);
-                const password = flags.password ?? config.get('rootCredentials.password', profileName);
+                const username = flags.username ??
+                    config.get(`${profileName}.rootCredentials.username`);
+                const password = flags.password ??
+                    config.get(`${profileName}.rootCredentials.password`);
                 if (username === undefined || password === undefined) {
-                    this.logToStderr('Username and password must be set');
-                    this.exit(1);
+                    this.error('Username and password must be set');
                 }
                 userCredentials = await this.startRootLogin(address, username, password);
             }
@@ -95,8 +87,7 @@ export default class Login extends BaseCommand {
                 userCredentials = await this.startGuestLogin(address);
             }
             else if (accessType === undefined) {
-                this.logToStderr('Undefined access type');
-                this.exit(1);
+                this.error('Undefined access type');
             }
             else {
                 userCredentials = await this.startAuthorizationCodeFlow(address, accessType, flags.port);
@@ -105,16 +96,13 @@ export default class Login extends BaseCommand {
         catch (error) {
             if ((error instanceof Errors.CLIError && error.message === 'ctrl-c') ||
                 error instanceof Errors.ExitError) {
-                this.exit(0);
+                return;
             }
-            else if (error instanceof Error) {
-                this.logToStderr(error.stack);
-                ux.action.stop(error.message);
-                this.exit(1);
+            if (error instanceof Error) {
+                throw error;
             }
         }
-        config.set('accessToken', userCredentials.accessToken, profileName);
-        config.writeConfigFile();
+        config.set(`${profileName}.accessToken`, userCredentials.accessToken);
     }
     async checkUserAlreadyLoggedIn() {
         const userCredentials = getUserCredentials();

package/dist/commands/logout.js

@@ -1,6 +1,6 @@
 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 Logout extends BaseCommand {
     static summary = 'Logout of Apollo';
@@ -23,19 +23,10 @@ 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');
         }
-        try {
-            basicCheckConfig(configFile, profileName);
-        }
-        catch (error) {
-            if (error instanceof ConfigError) {
-                this.logToStderr(error.message);
-                this.exit(1);
-            }
-        }
-        const config = new Config(configFile);
-        config.set(KEYS.accessToken, '', profileName);
-        config.writeConfigFile();
+        basicCheckConfig(configFile, profileName);
+        const config = new ApolloConf(configFile);
+        config.delete(`${profileName}.${KEYS.accessToken}`);
     }
 }

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>;
+}