@apollo-annotation/cli 1.1.1 → 1.1.2

package/dist/commands/assembly/add-from-gff.js

@@ -3,7 +3,6 @@ import path from 'node:path';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { FileCommand } from '../../fileCommand.js';
-import { submitAssembly } from '../../utils.js';
 export default class AddGff extends FileCommand {
     static summary = 'Add new assembly from gff or gft file';
     static description = 'The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.';
@@ -45,8 +44,7 @@ export default class AddGff extends FileCommand {
         if (!fs.existsSync(args['input-file'])) {
             this.error(`File ${args['input-file']} does not exist`);
         }
-        const access = await this.getAccess();
-        const fileId = await this.uploadFile(access.address, access.accessToken, args['input-file'], 'text/x-gff3', args['input-file'].endsWith('.gz'));
+        const fileId = await this.uploadFile(args['input-file'], 'text/x-gff3', args['input-file'].endsWith('.gz'));
         const assemblyName = flags.assembly ?? path.basename(args['input-file']);
         const body = flags['omit-features']
             ? {
@@ -62,7 +60,7 @@ export default class AddGff extends FileCommand {
                 assembly: new ObjectId().toHexString(),
                 parseOptions: { strict: !flags['no-strict'] },
             };
-        const rec = await submitAssembly(access.address, access.accessToken, body, flags.force);
+        const rec = await this.submitAssembly(body, flags.force);
         this.log(JSON.stringify(rec, null, 2));
     }
 }

package/dist/commands/assembly/add-from-gff.js.map

@@ -1 +1 @@
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+{"version":3,"file":"add-from-gff.js","sourceRoot":"","sources":["../../../src/commands/assembly/add-from-gff.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAA;AAC7B,OAAO,IAAI,MAAM,WAAW,CAAA;AAO5B,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,aAAa,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,MAAM,CAAA;AAE/B,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW;IAC7C,MAAM,CAAC,OAAO,GAAG,uCAAuC,CAAA;IACxD,MAAM,CAAC,WAAW,GAChB,iHAAiH,CAAA;IAEnH,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,gCAAgC;YAC7C,OAAO,EAAE,8DAA8D;SACxE;QACD;YACE,WAAW,EAAE,wBAAwB;YACrC,OAAO,EACL,iEAAiE;SACpE;KACF,CAAA;IAED,MAAM,CAAC,IAAI,GAAG;QACZ,YAAY,EAAE,IAAI,CAAC,MAAM,CAAC;YACxB,WAAW,EAAE,gBAAgB;YAC7B,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,sDAAsD;SACpE,CAAC;QACF,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC;YAC7B,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,mDAAmD;SACjE,CAAC;QACF,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,wCAAwC;SACtD,CAAC;QACF,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC;YACzB,WAAW,EACT,+FAA+F;SAClG,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAEhD,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,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAClC,IAAI,CAAC,YAAY,CAAC,EAClB,aAAa,EACb,IAAI,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CACnC,CAAA;QAED,MAAM,YAAY,GAAG,KAAK,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAA;QAExE,MAAM,IAAI,GAG2C,KAAK,CAAC,eAAe,CAAC;YACzE,CAAC,CAAC;gBACE,YAAY;gBACZ,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,QAAQ,EAAE,2BAA2B;gBACrC,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;aACvC;YACH,CAAC,CAAC;gBACE,YAAY;gBACZ,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,QAAQ,EAAE,sCAAsC;gBAChD,QAAQ,EAAE,IAAI,QAAQ,EAAE,CAAC,WAAW,EAAE;gBACtC,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC,KAAK,CAAC,WAAW,CAAC,EAAE;aAC9C,CAAA;QACL,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,CAAA;QACxD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAA;IACxC,CAAC"}

package/dist/commands/assembly/check.d.ts

@@ -7,9 +7,9 @@ export default class Check extends BaseCommand<typeof Check> {
         command: string;
     }[];
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        check: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        delete: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        check: import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        delete: import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/assembly/check.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/check.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAkBlD,MAAM,CAAC,OAAO,OAAO,KAAM,SAAQ,WAAW,CAAC,OAAO,KAAK,CAAC;IAC1D,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAGqB;IAEvC,MAAM,CAAC,QAAQ;;;QAkBd;IAED,MAAM,CAAC,KAAK;;;;MAeX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAwDlC"}

package/dist/commands/assembly/check.js

@@ -1,46 +1,6 @@
 import { Flags } from '@oclif/core';
-import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertCheckNameToId, createFetchErrorMessage, getAssembly, idReader, localhostToAddress, } from '../../utils.js';
-async function setChecks(address, accessToken, assembly, checkId) {
-    const check = {
-        _id: assembly,
-        checks: checkId,
-        name: '',
-    };
-    const auth = {
-        method: 'POST',
-        body: JSON.stringify(check),
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-    };
-    const url = new URL(localhostToAddress(`${address}/assemblies/checks`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'setChecks failed');
-        throw new Error(errorMessage);
-    }
-    return response;
-}
-async function getCheckTypes(address, accessToken) {
-    const auth = {
-        method: 'GET',
-        headers: {
-            Authorization: `Bearer ${accessToken}`,
-            'Content-Type': 'application/json',
-        },
-    };
-    const url = new URL(localhostToAddress(`${address}/checks/types`));
-    const response = await fetch(url, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'getCheckTypes failed');
-        throw new Error(errorMessage);
-    }
-    const chk = (await response.json());
-    return chk;
-}
+import { idReader } from '../../utils.js';
 function getCheckTypesForAssembly(checkTypes, assembly) {
     const checks = [];
     for (const chkType of checkTypes) {
@@ -92,8 +52,7 @@ these checks use `apollo feature check`.';
     };
     async run() {
         const { flags } = await this.parse(Check);
-        const access = await this.getAccess();
-        const checkTypes = await getCheckTypes(access.address, access.accessToken);
+        const checkTypes = (await this.get('checks/types'));
         if (flags.check === undefined && flags.assembly === undefined) {
             this.log(JSON.stringify(checkTypes, null, 2));
             return;
@@ -102,13 +61,13 @@ these checks use `apollo feature check`.';
             this.error('Please specify the assembly to manage for checks');
         }
         const asm = await idReader([flags.assembly]);
-        const assembly = await getAssembly(access.address, access.accessToken, asm[0]);
+        const assembly = await this.getAssembly(asm[0]);
         const currentChecks = getCheckTypesForAssembly(checkTypes, assembly);
         if (flags.check === undefined) {
             this.log(JSON.stringify(currentChecks, null, 2));
             return;
         }
-        const inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
+        const inputCheckIds = await this.convertCheckNameToId(flags.check);
         const newChecks = new Set();
         if (flags.delete) {
             for (const chk of currentChecks) {
@@ -126,9 +85,12 @@ these checks use `apollo feature check`.';
                 newChecks.add(chk['_id']);
             }
         }
-        await setChecks(access.address, access.accessToken, assembly._id, [
-            ...newChecks.values(),
-        ]);
+        const check = {
+            _id: assembly._id,
+            checks: [...newChecks.values()],
+            name: '',
+        };
+        await this.fetch('assemblies/checks', { method: 'POST', body: JSON.stringify(check) }, { json: true });
     }
 }
 //# sourceMappingURL=check.js.map

package/dist/commands/assembly/check.js.map

@@ -1 +1 @@
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package/dist/commands/assembly/delete.d.ts

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

package/dist/commands/assembly/delete.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"delete.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/delete.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAQlD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAA6C;IAC/D,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAwBlC"}
+{"version":3,"file":"delete.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/delete.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,MAAO,SAAQ,WAAW,CAAC,OAAO,MAAM,CAAC;IAC5D,MAAM,CAAC,OAAO,SAAsB;IACpC,MAAM,CAAC,WAAW,SAA6C;IAC/D,MAAM,CAAC,QAAQ;;;QAMd;IAED,MAAM,CAAC,KAAK;;;MAWX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkBlC"}

package/dist/commands/assembly/delete.js

@@ -1,6 +1,6 @@
 import { Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
-import { convertAssemblyNameToId, deleteAssembly, getAssembly, idReader, } from '../../utils.js';
+import { idReader } from '../../utils.js';
 export default class Delete extends BaseCommand {
     static summary = 'Delete assemblies';
     static description = 'Assemblies to delete may be names or IDs';
@@ -24,14 +24,13 @@ export default class Delete extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Delete);
-        const access = await this.getAccess();
         const assembly = await idReader(flags.assembly);
-        const deleteIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
+        const deleteIds = await this.convertAssemblyNameToId(assembly);
         let i = 0;
         const deleted = [];
         for (const x of deleteIds) {
-            const asm = await getAssembly(access.address, access.accessToken, x);
-            await deleteAssembly(access.address, access.accessToken, x);
+            const asm = await this.getAssembly(x);
+            await this.deleteAssembly(x);
             deleted.push(asm);
             i += 1;
         }

package/dist/commands/assembly/delete.js.map

@@ -1 +1 @@
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package/dist/commands/assembly/get.d.ts

@@ -3,7 +3,7 @@ export default class Get extends BaseCommand<typeof Get> {
     static summary: string;
     static description: 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/assembly/get.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/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,SAA6B;IAC3C,MAAM,CAAC,WAAW,SAA0D;IAE5E,MAAM,CAAC,KAAK;;MAMX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAiClC"}
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/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,SAA6B;IAC3C,MAAM,CAAC,WAAW,SAA0D;IAE5E,MAAM,CAAC,KAAK;;MAMX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAsBlC"}

package/dist/commands/assembly/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 available assemblies';
     static description = 'Print to stdout the list of assemblies in json format';
@@ -13,14 +13,12 @@ export default class Get extends BaseCommand {
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess();
-        const assemblies = await queryApollo(access.address, access.accessToken, 'assemblies');
+        const json = (await this.get('assemblies'));
         let assemblyIds = [];
         if (flags.assembly !== undefined) {
             const assembly = await idReader(flags.assembly);
-            assemblyIds = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
+            assemblyIds = await this.convertAssemblyNameToId(assembly);
         }
-        const json = (await assemblies.json());
         const keep = [];
         for (const x of json) {
             if (flags.assembly === undefined ||

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

@@ -1 +1 @@
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+{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/assembly/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,0BAA0B,CAAA;IAC3C,MAAM,CAAC,WAAW,GAAG,uDAAuD,CAAA;IAE5E,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,6CAA6C;YAC1D,QAAQ,EAAE,IAAI;SACf,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,YAAY,CAAC,CAAa,CAAA;QAEvD,IAAI,WAAW,GAAa,EAAE,CAAA;QAC9B,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YACjC,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAA;YAC/C,WAAW,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,QAAQ,CAAC,CAAA;QAC5D,CAAC;QAED,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,MAAM,CAAC,IAAI,IAAI,EAAE,CAAC;YACrB,IACE,KAAK,CAAC,QAAQ,KAAK,SAAS;gBAC5B,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAuB,CAAC,CAAC,EAChD,CAAC;gBACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACd,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/assembly/sequence.d.ts

@@ -7,10 +7,10 @@ export default class ApolloCmd extends BaseCommand<typeof ApolloCmd> {
         command: string;
     }[];
     static flags: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        refseq: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        start: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        end: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        assembly: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        refseq: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        start: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
+        end: import("@oclif/core/interfaces").OptionFlag<number | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/assembly/sequence.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sequence.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/sequence.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AA0ClD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAAW,CAAC,OAAO,SAAS,CAAC;IAClE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACoD;IAEtE,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,KAAK;;;;;MAkBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAsDlC"}
+{"version":3,"file":"sequence.d.ts","sourceRoot":"","sources":["../../../src/commands/assembly/sequence.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,WAAW,CAAC,OAAO,SAAS,CAAC;IAClE,MAAM,CAAC,OAAO,SAA2C;IACzD,MAAM,CAAC,WAAW,SACoD;IAEtE,MAAM,CAAC,QAAQ;;;QAUd;IAED,MAAM,CAAC,KAAK;;;;;MAkBX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAyClC"}

package/dist/commands/assembly/sequence.js

@@ -1,30 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 import { Flags } from '@oclif/core';
-import { Agent, fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, getRefseqId, idReader, localhostToAddress, queryApollo, } from '../../utils.js';
-async function getSequence(address, accessToken, refSeq, start, end) {
-    const url = new URL(localhostToAddress(`${address}/sequence`));
-    const searchParams = new URLSearchParams({
-        refSeq,
-        start: start.toString(),
-        end: end.toString(),
-    });
-    url.search = searchParams.toString();
-    const uri = url.toString();
-    const auth = {
-        headers: {
-            authorization: `Bearer ${accessToken}`,
-        },
-        dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
-    };
-    const response = await fetch(uri, auth);
-    if (!response.ok) {
-        const errorMessage = await createFetchErrorMessage(response, 'getSequence failed');
-        throw new Error(errorMessage);
-    }
-    return response;
-}
+import { idReader } from '../../utils.js';
 export default class ApolloCmd extends BaseCommand {
     static summary = 'Get reference sequence in fasta format';
     static description = 'Return the reference sequence for a given assembly and coordinates';
@@ -63,20 +40,23 @@ export default class ApolloCmd extends BaseCommand {
         if (flags.start <= 0 || endCoord <= 0) {
             this.error('Start and end coordinates must be greater than 0.');
         }
-        const access = await this.getAccess();
         let assembly = undefined;
         if (flags.assembly !== undefined) {
             ;
             [assembly] = await idReader([flags.assembly]);
         }
-        const refseqIds = await getRefseqId(access.address, access.accessToken, flags.refseq, assembly);
+        const refseqIds = await this.getRefseqId(flags.refseq, assembly);
         if (refseqIds.length === 0) {
             this.error('No reference sequence found');
         }
-        const refs = await queryApollo(access.address, access.accessToken, 'refSeqs');
-        const refSeqs = (await refs.json());
+        const refSeqs = (await this.get('refSeqs'));
         for (const rid of refseqIds) {
-            const res = await getSequence(access.address, access.accessToken, rid, flags.start - 1, endCoord);
+            const searchParams = new URLSearchParams({
+                refSeq: rid,
+                start: (flags.start - 1).toString(),
+                end: endCoord.toString(),
+            });
+            const res = await this.fetch(`sequence?${searchParams.toString()}`);
             const seqObj = await res.body?.getReader().read();
             const seq = new TextDecoder().decode(seqObj?.value);
             let header = '';

package/dist/commands/assembly/sequence.js.map

@@ -1 +1 @@
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+{"version":3,"file":"sequence.js","sourceRoot":"","sources":["../../../src/commands/assembly/sequence.ts"],"names":[],"mappings":"AAAA,0DAA0D;AAG1D,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,SAAU,SAAQ,WAA6B;IAClE,MAAM,CAAC,OAAO,GAAG,wCAAwC,CAAA;IACzD,MAAM,CAAC,WAAW,GAChB,oEAAoE,CAAA;IAEtE,MAAM,CAAC,QAAQ,GAAG;QAChB;YACE,WAAW,EAAE,kCAAkC;YAC/C,OAAO,EAAE,mDAAmD;SAC7D;QACD;YACE,WAAW,EAAE,2CAA2C;YACxD,OAAO,EACL,wEAAwE;SAC3E;KACF,CAAA;IAED,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,gDAAgD;SAC9D,CAAC;QACF,MAAM,EAAE,KAAK,CAAC,MAAM,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,iDAAiD;SAC/D,CAAC;QACF,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC;YACnB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,4BAA4B;YACzC,OAAO,EAAE,CAAC;SACX,CAAC;QACF,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC;YACjB,IAAI,EAAE,GAAG;YACT,WAAW,EAAE,gBAAgB;SAC9B,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;QAE7C,MAAM,QAAQ,GAAW,KAAK,CAAC,GAAG,IAAI,MAAM,CAAC,gBAAgB,CAAA;QAC7D,IAAI,KAAK,CAAC,KAAK,IAAI,CAAC,IAAI,QAAQ,IAAI,CAAC,EAAE,CAAC;YACtC,IAAI,CAAC,KAAK,CAAC,mDAAmD,CAAC,CAAA;QACjE,CAAC;QAED,IAAI,QAAQ,GAAG,SAAS,CAAA;QACxB,IAAI,KAAK,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YACjC,CAAC;YAAA,CAAC,QAAQ,CAAC,GAAG,MAAM,QAAQ,CAAC,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAA;QAChD,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;QAChE,IAAI,SAAS,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC3B,IAAI,CAAC,KAAK,CAAC,6BAA6B,CAAC,CAAA;QAC3C,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAA2B,CAAA;QACrE,KAAK,MAAM,GAAG,IAAI,SAAS,EAAE,CAAC;YAC5B,MAAM,YAAY,GAAG,IAAI,eAAe,CAAC;gBACvC,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE;gBACnC,GAAG,EAAE,QAAQ,CAAC,QAAQ,EAAE;aACzB,CAAC,CAAA;YACF,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,YAAY,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;YAEnE,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,SAAS,EAAE,CAAC,IAAI,EAAE,CAAA;YACjD,MAAM,GAAG,GAAW,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;YAC3D,IAAI,MAAM,GAAG,EAAE,CAAA;YACf,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,IAAI,CAAC,CAAC,GAAG,KAAK,GAAG,EAAE,CAAC;oBAClB,MAAM,KAAK,GAAG,CAAC,CAAC,IAAI,CAAA;oBACpB,MAAM,GAAG,IAAI,KAAK,IAAI,KAAK,CAAC,KAAK,KAAK,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAA;oBACpE,MAAK;gBACP,CAAC;YACH,CAAC;YACD,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YAChB,IAAI,CAAC,GAAG,CAAC,qBAAqB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;QACrD,CAAC;IACH,CAAC;;AAGH,SAAS,qBAAqB,CAAC,KAAa,EAAE,SAAiB;IAC7D,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QAC3C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC"}

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

@@ -3,7 +3,7 @@ export default class Get extends BaseCommand<typeof Get> {
     static summary: string;
     static description: 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/change/get.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/change/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,SAAwB;IACtC,MAAM,CAAC,WAAW,SAI2B;IAE7C,MAAM,CAAC,KAAK;;MAOX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CA6BlC"}
+{"version":3,"file":"get.d.ts","sourceRoot":"","sources":["../../../src/commands/change/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,SAAwB;IACtC,MAAM,CAAC,WAAW,SAI2B;IAE7C,MAAM,CAAC,KAAK;;MAOX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkBlC"}

package/dist/commands/change/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 list of changes';
     static description = 'Return the change log in json format. Note \
@@ -16,14 +16,12 @@ In such cases you need to use the assembly ID.';
     };
     async run() {
         const { flags } = await this.parse(Get);
-        const access = await this.getAccess();
-        const response = await queryApollo(access.address, access.accessToken, 'changes');
-        const { changes } = (await response.json());
+        const { changes } = (await this.get('changes'));
         let keep = changes;
         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 changes) {
                 if (assemblyIds.includes(x['assembly'])) {
                     keep.push(x);

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

@@ -1 +1 @@
-{"version":3,"file":"get.js","sourceRoot":"","sources":["../../../src/commands/change/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,qBAAqB,CAAA;IACtC,MAAM,CAAC,WAAW,GAChB;;;+CAG2C,CAAA;IAE7C,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,QAAQ,EAAE,IAAI;YACd,WAAW,EACT,wEAAwE;SAC3E,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,QAAQ,GAAa,MAAM,WAAW,CAC1C,MAAM,CAAC,OAAO,EACd,MAAM,CAAC,WAAW,EAClB,SAAS,CACV,CAAA;QACD,MAAM,EAAE,OAAO,EAAE,GAAG,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAA0B,CAAA;QAEpE,IAAI,IAAI,GAAG,OAAO,CAAA;QAClB,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,OAAO,EAAE,CAAC;gBACxB,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/change/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,qBAAqB,CAAA;IACtC,MAAM,CAAC,WAAW,GAChB;;;+CAG2C,CAAA;IAE7C,MAAM,CAAC,KAAK,GAAG;QACb,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC;YACrB,IAAI,EAAE,GAAG;YACT,QAAQ,EAAE,IAAI;YACd,WAAW,EACT,wEAAwE;SAC3E,CAAC;KACH,CAAA;IAEM,KAAK,CAAC,GAAG;QACd,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAEvC,MAAM,EAAE,OAAO,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAA0B,CAAA;QAExE,IAAI,IAAI,GAAG,OAAO,CAAA;QAClB,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,OAAO,EAAE,CAAC;gBACxB,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/config.d.ts

@@ -3,12 +3,12 @@ export default class ApolloConfig extends BaseCommand<typeof ApolloConfig> {
     static summary: string;
     static description: string;
     static args: {
-        key: import("@oclif/core/lib/interfaces/parser.js").Arg<string | undefined, Record<string, unknown>>;
-        value: import("@oclif/core/lib/interfaces/parser.js").Arg<string | undefined, Record<string, unknown>>;
+        key: import("@oclif/core/interfaces").Arg<string | undefined, Record<string, unknown>>;
+        value: import("@oclif/core/interfaces").Arg<string | undefined, Record<string, unknown>>;
     };
     static flags: {
-        profile: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        'get-config-file': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        profile: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        'get-config-file': import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     static examples: {
         description: string;

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

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/commands/config.ts"],"names":[],"mappings":"AAUA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAEc;IAEhC,MAAM,CAAC,IAAI;;;MASV;IAED,MAAM,CAAC,KAAK;;;MASX;IAED,MAAM,CAAC,QAAQ;;;QAcd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YAqCnB,gBAAgB;YA0BhB,cAAc;YAuBd,WAAW;YAYX,WAAW;YAaX,UAAU;YAaV,gBAAgB;YAahB,aAAa;CAe5B"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/commands/config.ts"],"names":[],"mappings":"AAaA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAA;AAG/C,MAAM,CAAC,OAAO,OAAO,YAAa,SAAQ,WAAW,CAAC,OAAO,YAAY,CAAC;IACxE,MAAM,CAAC,OAAO,SAA4C;IAC1D,MAAM,CAAC,WAAW,SAEc;IAEhC,MAAM,CAAC,IAAI;;;MASV;IAED,MAAM,CAAC,KAAK;;;MASX;IAED,MAAM,CAAC,QAAQ;;;QAcd;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;YA0CnB,gBAAgB;YA0BhB,cAAc;YAkBd,WAAW;YAYX,WAAW;YAaX,UAAU;YAaV,gBAAgB;YAUhB,aAAa;CAiB5B"}

package/dist/commands/config.js

@@ -1,11 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import path from 'node:path';
-import input from '@inquirer/input';
-import password from '@inquirer/password';
-import select from '@inquirer/select';
+import { input, password, select } from '@inquirer/prompts';
 import { Args, Flags } from '@oclif/core';
 import { fetch } from 'undici';
-import { ApolloConf, KEYS, optionDesc } from '../ApolloConf.js';
+import { ConfigError, KEYS, optionDesc, } from '../ApolloConf.js';
 import { BaseCommand } from '../baseCommand.js';
 import { createFetchErrorMessage, localhostToAddress } from '../utils.js';
 export default class ApolloConfig extends BaseCommand {
@@ -57,7 +55,7 @@ export default class ApolloConfig extends BaseCommand {
             this.log(configFile);
             return;
         }
-        const config = new ApolloConf(configFile);
+        const config = this.getConfig();
         if (args.key === undefined) {
             await this.interactiveSetup(config, flags.profile);
         }
@@ -67,6 +65,9 @@ export default class ApolloConfig extends BaseCommand {
                 profileName = flags.profile;
             }
             if (args.value === undefined) {
+                if (!config.getProfileNames().includes(profileName)) {
+                    throw new ConfigError(`Profile "${profileName}" does not exist. Please run "apollo config" to set this profile up or choose a different profile`);
+                }
                 const currentValue = config.get(`${profileName}.${args.key}`);
                 this.log(currentValue);
                 return;
@@ -98,16 +99,11 @@ export default class ApolloConfig extends BaseCommand {
     async askProfileName(currentProfiles) {
         const newProfile = '<New profile>';
         currentProfiles.push(newProfile);
-        const xchoices = [];
-        for (const profileName of currentProfiles) {
-            xchoices.push({ name: profileName, value: profileName });
-        }
+        const choices = currentProfiles.map((p) => ({ name: p, value: p }));
+        const message = 'Select profile to edit or create a new one:';
         let answer = newProfile;
         if (currentProfiles.length > 1) {
-            answer = await select({
-                message: 'Select profile to edit or create a new one:',
-                choices: xchoices,
-            });
+            answer = await select({ message, choices });
         }
         if (answer === newProfile) {
             answer = await input({
@@ -149,15 +145,12 @@ export default class ApolloConfig extends BaseCommand {
         return answer.trim();
     }
     async selectAccessType(address) {
-        const xchoices = [{ name: 'root', value: 'root' }];
+        const choices = [{ name: 'root', value: 'root' }];
         const types = await this.getLoginTypes(address);
         for (const type of types) {
-            xchoices.push({ name: type, value: type });
+            choices.push({ name: type.name, value: type.name });
         }
-        const answer = await select({
-            message: 'Select login type',
-            choices: xchoices,
-        });
+        const answer = await select({ message: 'Select login type', choices });
         return answer;
     }
     async getLoginTypes(address) {

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package/dist/commands/export/gff3.d.ts

@@ -6,10 +6,10 @@ export default class Get extends BaseCommand<typeof Get> {
         command: string;
     }[];
     static args: {
-        assembly: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+        assembly: import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
     };
     static flags: {
-        'include-fasta': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'include-fasta': import("@oclif/core/interfaces").BooleanFlag<boolean>;
     };
     run(): Promise<void>;
 }

package/dist/commands/export/gff3.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gff3.d.ts","sourceRoot":"","sources":["../../../src/commands/export/gff3.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAQlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,WAAW,SAC0C;IAE5D,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;MAKX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAgElC"}
+{"version":3,"file":"gff3.d.ts","sourceRoot":"","sources":["../../../src/commands/export/gff3.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,WAAW,CAAC,OAAO,GAAG,CAAC;IACtD,MAAM,CAAC,WAAW,SAC0C;IAE5D,MAAM,CAAC,QAAQ;;;QAKd;IAED,MAAM,CAAC,IAAI;;MAKV;IAED,MAAM,CAAC,KAAK;;MAKX;IAEY,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAkClC"}