@apollo-annotation/cli 0.1.20 → 0.1.21

package/dist/commands/feature/import.js

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs';
-import { Flags } from '@oclif/core';
+import { Args, Flags } from '@oclif/core';
 import { Agent, fetch } from 'undici';
 import { FileCommand } from '../../fileCommand.js';
 import { convertAssemblyNameToId, createFetchErrorMessage, localhostToAddress, } from '../../utils.js';
@@ -9,15 +9,16 @@ export default class Import extends FileCommand {
     static examples = [
         {
             description: 'Delete features in myAssembly and then import features.gff3:',
-            command: '<%= config.bin %> <%= command.id %> -d -i features.gff3 -a myAssembly',
+            command: '<%= config.bin %> <%= command.id %> features.gff3 -d -a myAssembly',
         },
     ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
+    static args = {
+        'input-file': Args.string({
             description: 'Input gff file',
             required: true,
         }),
+    };
+    static flags = {
         assembly: Flags.string({
             char: 'a',
             description: 'Import into this assembly name or assembly ID',
@@ -29,16 +30,16 @@ export default class Import extends FileCommand {
         }),
     };
     async run() {
-        const { flags } = await this.parse(Import);
-        if (!fs.existsSync(flags['input-file'])) {
-            this.error(`File "${flags['input-file']}" does not exist`);
+        const { args, flags } = await this.parse(Import);
+        if (!fs.existsSync(args['input-file'])) {
+            this.error(`File "${args['input-file']}" does not exist`);
         }
         const access = await this.getAccess();
         const assembly = await convertAssemblyNameToId(access.address, access.accessToken, [flags.assembly]);
         if (assembly.length === 0) {
             this.error(`Assembly "${flags.assembly}" does not exist. Perhaps you want to create this assembly first`);
         }
-        const uploadId = await this.uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3', false);
+        const uploadId = await this.uploadFile(access.address, access.accessToken, args['input-file'], 'text/x-gff3', false);
         const body = {
             typeName: 'AddFeaturesFromFileChange',
             assembly: assembly[0],

package/dist/commands/file/upload.d.ts

@@ -6,8 +6,10 @@ export default class Upload extends FileCommand {
         description: string;
         command: string;
     }[];
+    static args: {
+        'input-file': import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
     static flags: {
-        'input-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
         type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
         gzip: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
         decompressed: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;

package/dist/commands/file/upload.js

@@ -1,4 +1,4 @@
-import { Flags } from '@oclif/core';
+import { Args, Flags } from '@oclif/core';
 import { FileCommand } from '../../fileCommand.js';
 import { filterJsonList, queryApollo } from '../../utils.js';
 export default class Upload extends FileCommand {
@@ -9,15 +9,16 @@ export default class Upload extends FileCommand {
     static examples = [
         {
             description: 'Upload local file, type auto-detected:',
-            command: '<%= config.bin %> <%= command.id %> -i genome.fa > file.json',
+            command: '<%= config.bin %> <%= command.id %> genome.fa > file.json',
         },
     ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
+    static args = {
+        'input-file': Args.string({
             description: 'Local file to upload',
             required: true,
         }),
+    };
+    static flags = {
         type: Flags.string({
             char: 't',
             description: 'Set file type or autodetected it if not set.\n\
@@ -42,14 +43,14 @@ export default class Upload extends FileCommand {
         }),
     };
     async run() {
-        const { flags } = await this.parse(Upload);
+        const { args, flags } = await this.parse(Upload);
         const access = await this.getAccess();
         let { type } = flags;
         if (type === undefined) {
-            const hasGzipExt = flags['input-file'].endsWith('.gz');
-            const infile = flags['input-file'].replace(/\.gz$/, '');
+            const hasGzipExt = args['input-file'].endsWith('.gz');
+            const infile = args['input-file'].replace(/\.gz$/, '');
             if (/\.fasta$|\.fas$|\.fa$|\.fna$/.test(infile) && hasGzipExt) {
-                this.error(`Unable to auto-detect file type for "${flags['input-file']}" since it may be gzip or bgzip compressed. Please set the -t/--type option`);
+                this.error(`Unable to auto-detect file type for "${args['input-file']}" since it may be gzip or bgzip compressed. Please set the -t/--type option`);
             }
             else if (/\.fasta$|\.fas$|\.fa$|\.fna$/.test(infile)) {
                 type = 'text/x-fasta';
@@ -64,10 +65,10 @@ export default class Upload extends FileCommand {
                 type = 'application/x-gzi';
             }
             else {
-                this.error(`Unable to auto-detect the type of file "${flags['input-file']}". Please set the --type/-t option.`);
+                this.error(`Unable to auto-detect the type of file "${args['input-file']}". Please set the --type/-t option.`);
             }
         }
-        let isGzip = flags['input-file'].endsWith('.gz');
+        let isGzip = args['input-file'].endsWith('.gz');
         // eslint-disable-next-line unicorn/consistent-destructuring
         if (flags.gzip) {
             isGzip = true;
@@ -77,7 +78,7 @@ export default class Upload extends FileCommand {
             isGzip = false;
         }
         this.logToStderr(`Input is gzip'd: ${isGzip}`);
-        const fileId = await this.uploadFile(access.address, access.accessToken, flags['input-file'], type, isGzip);
+        const fileId = await this.uploadFile(access.address, access.accessToken, args['input-file'], type, isGzip);
         const res = await queryApollo(access.address, access.accessToken, 'files');
         // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
         const json = JSON.parse(await res.text());

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

@@ -6,8 +6,10 @@ export default class AddRefNameAlias extends BaseCommand<typeof AddRefNameAlias>
         description: string;
         command: string;
     }[];
+    static args: {
+        'input-file': import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
     static flags: {
-        'input-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
         assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
     };
     run(): Promise<void>;

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

@@ -1,6 +1,6 @@
 import * as fs from 'node:fs';
 import { Agent, fetch } from 'undici';
-import { Flags } from '@oclif/core';
+import { Args, Flags } from '@oclif/core';
 import { BaseCommand } from '../../baseCommand.js';
 import { createFetchErrorMessage, localhostToAddress, queryApollo, } from '../../utils.js';
 import { ConfigError } from '../../ApolloConf.js';
@@ -10,15 +10,16 @@ export default class AddRefNameAlias extends BaseCommand {
     static examples = [
         {
             description: 'Add reference name aliases:',
-            command: '<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly',
+            command: '<%= config.bin %> <%= command.id %> alias.txt -a myAssembly',
         },
     ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
+    static args = {
+        'input-file': Args.string({
             description: 'Input refname alias file',
             required: true,
         }),
+    };
+    static flags = {
         assembly: Flags.string({
             char: 'a',
             description: 'Name for this assembly.',
@@ -26,12 +27,12 @@ export default class AddRefNameAlias extends BaseCommand {
         }),
     };
     async run() {
-        const { flags } = await this.parse(AddRefNameAlias);
-        if (!fs.existsSync(flags['input-file'])) {
-            this.error(`File ${flags['input-file']} does not exist`);
+        const { args, flags } = await this.parse(AddRefNameAlias);
+        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(flags['input-file']);
+        const filehandle = await fs.promises.open(args['input-file']);
         const fileContent = await filehandle.readFile({ encoding: 'utf8' });
         await filehandle.close();
         const lines = fileContent.split('\n');

package/dist/utils.d.ts

@@ -1,4 +1,5 @@
 import EventEmitter from 'node:events';
+import type { SerializedAddAssemblyAndFeaturesFromFileChange, SerializedAddAssemblyFromExternalChange, SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
 import { Response } from 'undici';
 import { ApolloConf } from './ApolloConf.js';
 import { ApolloAssemblySnapshot } from '@apollo-annotation/mst';
@@ -34,32 +35,6 @@ export declare const generatePkceChallenge: () => {
     codeChallenge: string;
 };
 export declare const waitFor: <T>(eventName: string, emitter: EventEmitter) => Promise<T>;
-interface bodyFastaFile {
-    assemblyName: string;
-    typeName: string;
-    fileIds: {
-        fa: string;
-    };
-    assembly: string;
-}
-interface bodyIndexedFiles {
-    assemblyName: string;
-    typeName: string;
-    fileIds: {
-        fa: string;
-        fai: string;
-        gzi: string;
-    };
-}
-interface bodyExternalFile {
-    assemblyName: string;
-    typeName: string;
-    externalLocation: {
-        fa: string;
-        fai: string;
-    };
-}
-export declare function submitAssembly(address: string, accessToken: string, body: bodyFastaFile | bodyExternalFile | bodyIndexedFiles, force: boolean): Promise<object>;
+export declare function submitAssembly(address: string, accessToken: string, body: SerializedAddAssemblyFromFileChange | SerializedAddAssemblyFromExternalChange | SerializedAddAssemblyAndFeaturesFromFileChange, force: boolean): Promise<object>;
 export declare function readStdin(): Promise<string>;
 export declare function idReader(input: string[], removeDuplicates?: boolean): Promise<string[]>;
-export {};

package/dist/utils.js

@@ -241,12 +241,15 @@ export const waitFor = (eventName, emitter) => {
 export async function submitAssembly(address, accessToken, body, force) {
     let assemblies = await queryApollo(address, accessToken, 'assemblies');
     for (const x of (await assemblies.json())) {
-        if (x['name'] === body.assemblyName) {
-            if (force) {
-                await deleteAssembly(address, accessToken, x['_id']);
-            }
-            else {
-                throw new Error(`Error: Assembly "${body.assemblyName}" already exists`);
+        const addedAssemblies = 'changes' in body ? body.changes : [body];
+        for (const addedAssembly of addedAssemblies) {
+            if (x.name === addedAssembly.assemblyName) {
+                if (force) {
+                    await deleteAssembly(address, accessToken, x._id);
+                }
+                else {
+                    throw new Error(`Error: Assembly "${addedAssembly.assemblyName}" already exists`);
+                }
             }
         }
     }
@@ -267,11 +270,14 @@ export async function submitAssembly(address, accessToken, body, force) {
     }
     assemblies = await queryApollo(address, accessToken, 'assemblies');
     for (const x of (await assemblies.json())) {
-        if (x['name'] === body.assemblyName) {
-            return x;
+        const addedAssemblies = 'changes' in body ? body.changes : [body];
+        for (const addedAssembly of addedAssemblies) {
+            if (x.name === addedAssembly.assemblyName) {
+                return x;
+            }
         }
     }
-    throw new Error(`Failed to retrieve assembly ${body.assemblyName}`);
+    throw new Error(`Failed to retrieve assembly from ${body.assembly}`);
 }
 export async function readStdin() {
     const chunks = [];