@apollo-annotation/cli 1.1.0 → 1.1.2

package/dist/commands/jbrowse/get-config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"get-config.js","sourceRoot":"","sources":["../../../src/commands/jbrowse/get-config.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAA6B;IAClE,MAAM,CAAC,OAAO,GAAG,uCAAuC,CAAA;IACxD,MAAM,CAAC,WAAW,GAChB,sEAAsE,CAAA;IAExE,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,4BAA4B;YACzC,OAAO,EAAE,mDAAmD;SAC7D;KACF,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,qBAAqB,CAAC,CAAW,CAAA;QAC9D,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACzC,CAAC"}

package/dist/commands/jbrowse/set-config.d.ts

@@ -7,7 +7,7 @@ export default class SetConfig extends BaseCommand<typeof SetConfig> {
         command: string;
     }[];
     static args: {
-        inputFile: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        inputFile: import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     run(): Promise<void>;
 }

package/dist/commands/jbrowse/set-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"set-config.d.ts","sourceRoot":"","sources":["../../../src/commands/jbrowse/set-config.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAAW,CAAC,OAAO,SAAS,CAAC;IAClE,MAAM,CAAC,OAAO,SAA8B;IAC5C,MAAM,CAAC,WAAW,SAC0C;IAE5D,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAEK,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkB3B"}

package/dist/commands/jbrowse/set-config.js

@@ -1,9 +1,6 @@
 import * as fs from 'node:fs';
 import { Args } from '@oclif/core';
-import { Agent, fetch } from 'undici';
-import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress } from '../../utils.js';
 export default class SetConfig extends BaseCommand {
     static summary = 'Set JBrowse configuration';
     static description = 'Set JBrowse configuration in Apollo collaboration server';
@@ -24,7 +21,6 @@ export default class SetConfig extends BaseCommand {
         if (!fs.existsSync(args.inputFile)) {
             this.error(`File ${args.inputFile} does not exist`);
         }
-        const access = await this.getAccess();
         const filehandle = await fs.promises.open(args.inputFile);
         const fileContent = await filehandle.readFile({ encoding: 'utf8' });
         await filehandle.close();
@@ -32,21 +28,7 @@ export default class SetConfig extends BaseCommand {
             typeName: 'ImportJBrowseConfigChange',
             newJBrowseConfig: JSON.parse(fileContent),
         };
-        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 JBrowse configuration');
-            throw new ConfigError(errorMessage);
-        }
+        await this.post('changes', JSON.stringify(change));
     }
 }
 //# sourceMappingURL=set-config.js.map

package/dist/commands/jbrowse/set-config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"set-config.js","sourceRoot":"","sources":["../../../src/commands/jbrowse/set-config.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAM7B,OAAO,EAAE,IAAI,EAAE,MAAM,aAAa,CAAA;AAElC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAA6B;IAClE,MAAM,CAAC,OAAO,GAAG,2BAA2B,CAAA;IAC5C,MAAM,CAAC,WAAW,GAChB,0DAA0D,CAAA;IAE5D,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,4BAA4B;YACzC,OAAO,EAAE,iDAAiD;SAC3D;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,SAAS,EAAE,IAAI,CAAC,MAAM,CAAC;YACrB,WAAW,EAAE,4BAA4B;YACzC,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,KAAK,CAAC,GAAG;QACP,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;QAE5C,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;YACnC,IAAI,CAAC,KAAK,CAAC,QAAQ,IAAI,CAAC,SAAS,iBAAiB,CAAC,CAAA;QACrD,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACzD,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAA;QACnE,MAAM,UAAU,CAAC,KAAK,EAAE,CAAA;QAExB,MAAM,MAAM,GAAwC;YAClD,QAAQ,EAAE,2BAA2B;YACrC,gBAAgB,EAAE,IAAI,CAAC,KAAK,CAAC,WAAW,CAAkB;SAC3D,CAAA;QAED,MAAM,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAA;IACpD,CAAC"}

package/dist/commands/login.d.ts

@@ -7,11 +7,11 @@ export default class Login extends BaseCommand<typeof Login> {
         command: string;
     }[];
     static flags: {
-        address: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        username: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        password: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        force: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
-        port: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        address: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        username: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        password: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        force: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        port: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
     private checkUserAlreadyLoggedIn;

package/dist/commands/login.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"login.d.ts","sourceRoot":"","sources":["../../src/commands/login.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAY/C,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAAoB;IAClC,MAAM,CAAC,WAAW,SAGwF;IAE1G,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,KAAK;;;;;;MAyBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAkDnB,wBAAwB;YAmBxB,cAAc;YAwBd,eAAe;YAmBf,0BAA0B;CAwDzC"}

package/dist/commands/login.js

@@ -3,14 +3,14 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import EventEmitter from 'node:events';
 import * as http from 'node:http';
-import path from 'node:path';
 import * as querystring from 'node:querystring';
+import { confirm } from '@inquirer/prompts';
 import { Errors, Flags, ux } from '@oclif/core';
 import open from 'open';
 import { fetch } from 'undici';
-import { ApolloConf, KEYS } from '../ApolloConf.js';
+import { KEYS } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { basicCheckConfig, createFetchErrorMessage, localhostToAddress, waitFor, } from '../utils.js';
+import { createFetchErrorMessage, localhostToAddress, waitFor, } from '../utils.js';
 export default class Login extends BaseCommand {
     static summary = 'Login to Apollo';
     static description = 'Use the provided credentials to obtain and save the token to access Apollo. \
@@ -53,10 +53,8 @@ need to execute this command again unless the token has expired. To setup a new
     };
     async run() {
         const { flags } = await this.parse(Login);
-        const configFile = flags['config-file'] ?? path.join(this.config.configDir, 'config.yml');
         const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default';
-        basicCheckConfig(configFile, profileName);
-        const config = new ApolloConf(configFile);
+        const config = this.getConfig();
         const accessType = config.get(`${profileName}.accessType`);
         const address = flags.address ?? config.get(`${profileName}.address`);
         if (address === undefined) {
@@ -101,7 +99,10 @@ need to execute this command again unless the token has expired. To setup a new
         if (!accessToken) {
             return;
         }
-        const reAuthenticate = await ux.confirm("You're already logged. Do you want to re-authenticate? (y/n)");
+        const reAuthenticate = await confirm({
+            message: "You're already logged in. Do you want to re-authenticate?",
+            default: true,
+        });
         if (!reAuthenticate) {
             this.exit(0);
         }

package/dist/commands/login.js.map

@@ -1 +1 @@
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package/dist/commands/logout.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"logout.d.ts","sourceRoot":"","sources":["../../src/commands/logout.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAqB;IACnC,MAAM,CAAC,WAAW,SAC+C;IAEjE,MAAM,CAAC,QAAQ;;;QASd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAWlC"}
+{"version":3,"file":"logout.d.ts","sourceRoot":"","sources":["../../src/commands/logout.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAqB;IACnC,MAAM,CAAC,WAAW,SAC+C;IAEjE,MAAM,CAAC,QAAQ;;;QASd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAQlC"}

package/dist/commands/logout.js

@@ -1,7 +1,5 @@
-import path from 'node:path';
-import { ApolloConf, KEYS } from '../ApolloConf.js';
+import { KEYS } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { basicCheckConfig } from '../utils.js';
 export default class Logout extends BaseCommand {
     static summary = 'Logout of Apollo';
     static description = 'Logout by removing the access token from the selected profile';
@@ -18,9 +16,7 @@ export default class Logout extends BaseCommand {
     async run() {
         const { flags } = await this.parse(Logout);
         const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default';
-        const configFile = flags['config-file'] ?? path.join(this.config.configDir, 'config.yml');
-        basicCheckConfig(configFile, profileName);
-        const config = new ApolloConf(configFile);
+        const config = this.getConfig();
         config.delete(`${profileName}.${KEYS.accessToken}`);
     }
 }

package/dist/commands/logout.js.map

@@ -1 +1 @@
-{"version":3,"file":"logout.js","sourceRoot":"","sources":["../../src/commands/logout.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAA;AAE5B,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAC/C,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAE9C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAA0B;IAC5D,MAAM,CAAC,OAAO,GAAG,kBAAkB,CAAA;IACnC,MAAM,CAAC,WAAW,GAChB,+DAA+D,CAAA;IAEjE,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,yBAAyB;YACtC,OAAO,EAAE,qCAAqC;SAC/C;QACD;YACE,WAAW,EAAE,yBAAyB;YACtC,OAAO,EAAE,0DAA0D;SACpE;KACF,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE1C,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,cAAc,IAAI,SAAS,CAAA;QAE5E,MAAM,UAAU,GACd,KAAK,CAAC,aAAa,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACxE,gBAAgB,CAAC,UAAU,EAAE,WAAW,CAAC,CAAA;QACzC,MAAM,MAAM,GAAe,IAAI,UAAU,CAAC,UAAU,CAAC,CAAA;QACrD,MAAM,CAAC,MAAM,CAAC,GAAG,WAAW,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;IACrD,CAAC"}
+{"version":3,"file":"logout.js","sourceRoot":"","sources":["../../src/commands/logout.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AACvC,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAA0B;IAC5D,MAAM,CAAC,OAAO,GAAG,kBAAkB,CAAA;IACnC,MAAM,CAAC,WAAW,GAChB,+DAA+D,CAAA;IAEjE,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,yBAAyB;YACtC,OAAO,EAAE,qCAAqC;SAC/C;QACD;YACE,WAAW,EAAE,yBAAyB;YACtC,OAAO,EAAE,0DAA0D;SACpE;KACF,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE1C,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,cAAc,IAAI,SAAS,CAAA;QAE5E,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,EAAE,CAAA;QAC/B,MAAM,CAAC,MAAM,CAAC,GAAG,WAAW,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;IACrD,CAAC"}

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

@@ -7,10 +7,10 @@ export default class AddRefNameAlias extends BaseCommand<typeof AddRefNameAlias>
         command: string;
     }[];
     static args: {
-        'input-file': import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        'input-file': import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

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

@@ -1 +1 @@
-{"version":3,"file":"add-alias.d.ts","sourceRoot":"","sources":["../../../src/commands/refseq/add-alias.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAOlD,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,WAAW,CACtD,OAAO,eAAe,CACvB;IACC,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACsN;IAExO,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;MAMX;IAEK,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA4D3B"}
+{"version":3,"file":"add-alias.d.ts","sourceRoot":"","sources":["../../../src/commands/refseq/add-alias.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,WAAW,CACtD,OAAO,eAAe,CACvB;IACC,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACsN;IAExO,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;MAMX;IAEK,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAqC3B"}

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

@@ -1,9 +1,6 @@
 import * as fs from 'node:fs';
 import { Args, Flags } from '@oclif/core';
-import { Agent, fetch } from 'undici';
-import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress, queryApollo, } from '../../utils.js';
 export default class AddRefNameAlias extends BaseCommand {
     static summary = 'Add reference name aliases from a file';
     static description = '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.';
@@ -31,7 +28,6 @@ export default class AddRefNameAlias extends BaseCommand {
         if (!fs.existsSync(args['input-file'])) {
             this.error(`File ${args['input-file']} does not exist`);
         }
-        const access = await this.getAccess();
         const filehandle = await fs.promises.open(args['input-file']);
         const fileContent = await filehandle.readFile({ encoding: 'utf8' });
         await filehandle.close();
@@ -41,8 +37,7 @@ export default class AddRefNameAlias extends BaseCommand {
             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 json = (await this.get('assemblies'));
         const assembly = json.find((x) => 'name' in x && x.name === flags.assembly);
         const assemblyId = assembly && '_id' in assembly ? assembly._id : undefined;
         if (!assemblyId) {
@@ -53,21 +48,7 @@ export default class AddRefNameAlias extends BaseCommand {
             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);
-        }
+        await this.post('changes', JSON.stringify(change));
         this.log(`Reference name aliases added successfully to assembly ${flags.assembly}`);
     }
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"add-alias.js","sourceRoot":"","sources":["../../../src/commands/refseq/add-alias.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAG7B,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEzC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,WAE5C;IACC,MAAM,CAAC,OAAO,GAAG,wCAAwC,CAAA;IACzD,MAAM,CAAC,WAAW,GAChB,sOAAsO,CAAA;IAExO,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,6BAA6B;YAC1C,OAAO,EAAE,6DAA6D;SACvE;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,YAAY,EAAE,IAAI,CAAC,MAAM,CAAC;YACxB,WAAW,EAAE,0BAA0B;YACvC,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,yBAAyB;YACtC,QAAQ,EAAE,IAAI;SACf,CAAC;KACH,CAAA;IAED,KAAK,CAAC,GAAG;QACP,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,eAAe,CAAC,CAAA;QAEzD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC;YACvC,IAAI,CAAC,KAAK,CAAC,QAAQ,IAAI,CAAC,YAAY,CAAC,iBAAiB,CAAC,CAAA;QACzD,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAA;QAC7D,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAA;QACnE,MAAM,UAAU,CAAC,KAAK,EAAE,CAAA;QACxB,MAAM,KAAK,GAAG,WAAW,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAErC,MAAM,cAAc,GAAG,EAAE,CAAA;QACzB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,MAAM,CAAC,OAAO,EAAE,GAAG,OAAO,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC9C,cAAc,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,CAAA;QAC3C,CAAC;QAED,MAAM,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAa,CAAA;QACvD,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAA;QAC3E,MAAM,UAAU,GAAG,QAAQ,IAAI,KAAK,IAAI,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;QAE3E,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,IAAI,CAAC,KAAK,CAAC,YAAY,KAAK,CAAC,QAAQ,YAAY,CAAC,CAAA;QACpD,CAAC;QAED,MAAM,MAAM,GAAkC;YAC5C,QAAQ,EAAE,wBAAwB;YAClC,QAAQ,EAAE,UAAoB;YAC9B,aAAa,EAAE,cAAc;SAC9B,CAAA;QAED,MAAM,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,CACN,yDAAyD,KAAK,CAAC,QAAQ,EAAE,CAC1E,CAAA;IACH,CAAC"}

package/dist/commands/refseq/get.d.ts

@@ -7,7 +7,7 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/refseq/get.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/refseq/get.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA4B;IAC1C,MAAM,CAAC,WAAW,SAGc;IAEhC,MAAM,CAAC,QAAQ;;;QASd;IAED,MAAM,CAAC,KAAK;;MAOX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA6BlC"}
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/refseq/get.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAA4B;IAC1C,MAAM,CAAC,WAAW,SAGc;IAEhC,MAAM,CAAC,QAAQ;;;QASd;IAED,MAAM,CAAC,KAAK;;MAOX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkBlC"}

package/dist/commands/refseq/get.js

@@ -1,6 +1,6 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, idReader, queryApollo } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get reference sequences';
     static description = 'Output the reference sequences in one or more assemblies in json format. \
@@ -25,14 +25,12 @@ Use `assembly sequence` for that.';
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess();
-        const refSeqs = await queryApollo(access.address, access.accessToken, 'refSeqs');
-        const json = (await refSeqs.json());
+        const json = (await this.get('refSeqs'));
         let keep = json;
         if (flags.assembly !== undefined) {
             keep = [];
             const assembly = await idReader(flags.assembly);
-            const assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
+            const assemblyIds = await this.convertAssemblyNameToId(assembly);
             for (const x of json) {
                 if (assemblyIds.includes(x['assembly'])) {
                     keep.push(x);

package/dist/commands/refseq/get.js.map

@@ -1 +1 @@
-{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/refseq/get.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAGnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,uBAAuB,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAA;AAE/E,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,yBAAyB,CAAA;IAC1C,MAAM,CAAC,WAAW,GAChB;;kCAE8B,CAAA;IAEhC,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,gCAAgC;YAC7C,OAAO,EAAE,qCAAqC;SAC/C;QACD;YACE,WAAW,EAAE,sCAAsC;YACnD,OAAO,EAAE,iDAAiD;SAC3D;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,QAAQ,EAAE,IAAI;YACd,WAAW,EACT,sFAAsF;SACzF,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAErC,MAAM,OAAO,GAAa,MAAM,WAAW,CACzC,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,SAAS,CACV,CAAA;QACD,MAAM,IAAI,GAAG,CAAC,MAAM,OAAO,CAAC,IAAI,EAAE,CAAa,CAAA;QAE/C,IAAI,IAAI,GAAG,IAAI,CAAA;QACf,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YACjC,IAAI,GAAG,EAAE,CAAA;YACT,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;YAC/C,MAAM,WAAW,GAAG,MAAM,uBAAuB,CAC/C,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,QAAQ,CACT,CAAA;YACD,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;gBACrB,IAAI,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,UAA4B,CAAC,CAAC,EAAE,CAAC;oBAC1D,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACd,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACzC,CAAC"}
+{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/refseq/get.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,yBAAyB,CAAA;IAC1C,MAAM,CAAC,WAAW,GAChB;;kCAE8B,CAAA;IAEhC,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,gCAAgC;YAC7C,OAAO,EAAE,qCAAqC;SAC/C;QACD;YACE,WAAW,EAAE,sCAAsC;YACnD,OAAO,EAAE,iDAAiD;SAC3D;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,QAAQ,EAAE,IAAI;YACd,WAAW,EACT,sFAAsF;SACzF,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAa,CAAA;QAEpD,IAAI,IAAI,GAAG,IAAI,CAAA;QACf,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YACjC,IAAI,GAAG,EAAE,CAAA;YACT,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;YAC/C,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,QAAQ,CAAC,CAAA;YAChE,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;gBACrB,IAAI,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,UAA4B,CAAC,CAAC,EAAE,CAAC;oBAC1D,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBACd,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACzC,CAAC"}

package/dist/commands/status.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/commands/status.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAA+B;IAC7C,MAAM,CAAC,WAAW,SAGoD;IAEzD,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAmBlC"}
+{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/commands/status.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAA+B;IAC7C,MAAM,CAAC,WAAW,SAGoD;IAEzD,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAelC"}

package/dist/commands/status.js

@@ -1,8 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import path from 'node:path';
-import { ApolloConf, KEYS } from '../ApolloConf.js';
+import { KEYS } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
-import { basicCheckConfig } from '../utils.js';
 export default class Status extends BaseCommand {
     static summary = 'View authentication status';
     static description = 'This command returns "<profile>: Logged in" if the selected profile \
@@ -11,9 +9,7 @@ Note that this command does not check the validity of the access token.';
     async run() {
         const { flags } = await this.parse(Status);
         const profileName = flags.profile ?? process.env.APOLLO_PROFILE ?? 'default';
-        const configFile = flags['config-file'] ?? path.join(this.config.configDir, 'config.yml');
-        basicCheckConfig(configFile, profileName);
-        const config = new ApolloConf(configFile);
+        const config = this.getConfig();
         const accessToken = config.get(`${profileName}.${KEYS.accessToken}`);
         if (accessToken === undefined || accessToken.trim() === '') {
             this.log(`${profileName}: Logged out`);

package/dist/commands/status.js.map

@@ -1 +1 @@
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+{"version":3,"file":"status.js","sourceRoot":"","sources":["../../src/commands/status.ts"],"names":[],"mappings":"AAAA,gEAAgE;AAChE,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AACvC,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAE/C,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAA0B;IAC5D,MAAM,CAAC,OAAO,GAAG,4BAA4B,CAAA;IAC7C,MAAM,CAAC,WAAW,GAChB;;wEAEoE,CAAA;IAE/D,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE1C,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,IAAI,OAAO,CAAC,GAAG,CAAC,cAAc,IAAI,SAAS,CAAA;QAE5E,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,EAAE,CAAA;QAC/B,MAAM,WAAW,GAAW,MAAM,CAAC,GAAG,CACpC,GAAG,WAAW,IAAI,IAAI,CAAC,WAAW,EAAE,CAC3B,CAAA;QACX,IAAI,WAAW,KAAK,SAAS,IAAI,WAAW,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YAC3D,IAAI,CAAC,GAAG,CAAC,GAAG,WAAW,cAAc,CAAC,CAAA;QACxC,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,GAAG,CAAC,GAAG,WAAW,aAAa,CAAC,CAAA;QACvC,CAAC;IACH,CAAC"}

package/dist/commands/user/get.d.ts

@@ -7,8 +7,8 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static flags: {
-        username: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        role: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        username: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        role: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/user/get.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/user/get.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAC6D;IAE/E,MAAM,CAAC,QAAQ;;;QAcd;IAED,MAAM,CAAC,KAAK;;;MASX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAwBlC"}
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/user/get.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAC6D;IAE/E,MAAM,CAAC,QAAQ;;;QAcd;IAED,MAAM,CAAC,KAAK;;;MASX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAgBlC"}

package/dist/commands/user/get.js

@@ -1,6 +1,5 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { queryApollo } from '../../utils.js';
 export default class Get extends BaseCommand {
     static summary = 'Get list of users';
     static description = 'If set, filters username and role must be both satisfied to return an entry';
@@ -30,9 +29,7 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess();
-        const users = await queryApollo(access.address, access.accessToken, 'users');
-        const json = (await users.json());
+        const json = (await this.get('users'));
         const out = [];
         for (const x of json) {
             if ((flags.username === undefined ||

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

@@ -1 +1 @@
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+{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/user/get.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAuB;IACtD,MAAM,CAAC,OAAO,GAAG,mBAAmB,CAAA;IACpC,MAAM,CAAC,WAAW,GAChB,6EAA6E,CAAA;IAE/E,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,cAAc;YAC3B,OAAO,EAAE,8CAA8C;SACxD;QACD;YACE,WAAW,EAAE,UAAU;YACvB,OAAO,EAAE,8CAA8C;SACxD;QACD;YACE,WAAW,EAAE,0BAA0B;YACvC,OAAO,EACL,sFAAsF;SACzF;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,oBAAoB;SAClC,CAAC;QACF,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC;YACjB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,0BAA0B;SACxC,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,IAAI,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAa,CAAA;QAClD,MAAM,GAAG,GAAa,EAAE,CAAA;QACxB,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;YACrB,IACE,CAAC,KAAK,CAAC,QAAQ,KAAK,SAAS;gBAC3B,CAAC,CAAC,UAA4B,CAAC,KAAK,KAAK,CAAC,QAAQ,CAAC;gBACrD,CAAC,KAAK,CAAC,IAAI,KAAK,SAAS,IAAI,CAAC,CAAC,MAAwB,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,EACxE,CAAC;gBACD,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACxC,CAAC"}

package/dist/fileCommand.d.ts

@@ -1,6 +1,7 @@
 import { BaseCommand } from './baseCommand.js';
 export declare abstract class FileCommand extends BaseCommand<typeof FileCommand> {
     init(): Promise<void>;
-    uploadFile(address: string, accessToken: string, file: string, type: string, isGzip: boolean): Promise<string>;
+    uploadFile(file: string, type: string, isGzip: boolean): Promise<string>;
+    isFileId(x: string): Promise<boolean>;
 }
 //# sourceMappingURL=fileCommand.d.ts.map

package/dist/fileCommand.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"fileCommand.d.ts","sourceRoot":"","sources":["../src/fileCommand.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AA4B9C,8BAAsB,WAAY,SAAQ,WAAW,CAAC,OAAO,WAAW,CAAC;IAC1D,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAIrB,UAAU,CACrB,OAAO,EAAE,MAAM,EACf,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,MAAM,CAAC;CAsDnB"}
+{"version":3,"file":"fileCommand.d.ts","sourceRoot":"","sources":["../src/fileCommand.ts"],"names":[],"mappings":"AAYA,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AA4B9C,8BAAsB,WAAY,SAAQ,WAAW,CAAC,OAAO,WAAW,CAAC;IAC1D,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAIrB,UAAU,CACrB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,MAAM,CAAC;IAsDZ,QAAQ,CAAC,CAAC,EAAE,MAAM;CAYzB"}

package/dist/fileCommand.js

@@ -2,10 +2,9 @@ import * as fs from 'node:fs';
 import path from 'node:path';
 import { Transform, pipeline, } from 'node:stream';
 import { SingleBar } from 'cli-progress';
-import { Agent, fetch } from 'undici';
-import { ConfigError } from './ApolloConf.js';
+import { Headers } from 'undici';
 import { BaseCommand } from './baseCommand.js';
-import { createFetchErrorMessage, localhostToAddress } from './utils.js';
+import { createFetchErrorMessage } from './utils.js';
 class ProgressTransform extends Transform {
     size = 0;
     progressBar;
@@ -23,7 +22,7 @@ export class FileCommand extends BaseCommand {
     async init() {
         await super.init();
     }
-    async uploadFile(address, accessToken, file, type, isGzip) {
+    async uploadFile(file, type, isGzip) {
         const filehandle = await fs.promises.open(file);
         const { size } = await filehandle.stat();
         const stream = filehandle.createReadStream();
@@ -37,7 +36,6 @@ export class FileCommand extends BaseCommand {
             }
         });
         const headers = new Headers({
-            Authorization: `Bearer ${accessToken}`,
             'Content-Type': type,
             'Content-Length': String(size),
         });
@@ -48,19 +46,16 @@ export class FileCommand extends BaseCommand {
             method: 'POST',
             body,
             duplex: 'half',
-            dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
             headers,
         };
         const fileName = path.basename(file);
-        const url = new URL(localhostToAddress(`${address}/files`));
-        url.searchParams.set('name', fileName);
-        url.searchParams.set('type', type);
+        const searchParams = new URLSearchParams({ name: fileName, type });
         progressBar.start(size, 0);
         try {
-            const response = await fetch(url, init);
+            const response = await this.fetch(`files?${searchParams.toString()}`, init);
             if (!response.ok) {
                 const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
-                throw new ConfigError(errorMessage);
+                throw new Error(errorMessage);
             }
             const json = (await response.json());
             return json['_id'];
@@ -73,5 +68,17 @@ export class FileCommand extends BaseCommand {
             progressBar.stop();
         }
     }
+    async isFileId(x) {
+        if (x.length != 24) {
+            return false;
+        }
+        const json = (await this.get('files'));
+        for (const fileDoc of json) {
+            if (fileDoc['_id'] === x) {
+                return true;
+            }
+        }
+        return false;
+    }
 }
 //# sourceMappingURL=fileCommand.js.map

package/dist/fileCommand.js.map

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