@apollo-annotation/cli 0.1.19 → 0.1.21

package/package.json

@@ -1,22 +1,19 @@
 {
   "name": "@apollo-annotation/cli",
+  "version": "0.1.21",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.19",
-  "author": "Apollo Team",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
     "directory": "packages/apollo-cli"
   },
-  "bin": {
-    "apollo": "./bin/run.js"
-  },
+  "author": "Apollo Team",
   "type": "module",
+  "exports": "./dist/index.js",
   "main": "",
   "types": "dist/index.d.ts",
-  "exports": "./dist/index.js",
-  "engines": {
-    "node": ">=18.0.0"
+  "bin": {
+    "apollo": "./bin/run.js"
   },
   "files": [
     "/bin",
@@ -26,13 +23,50 @@
   "scripts": {
     "build": "shx rm -rf dist && tsc -b",
     "dev": "tsx bin/dev.js",
-    "postpack": "shx rm -f oclif.manifest.json",
-    "posttest": "yarn lint",
     "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
+    "postpack": "shx rm -f oclif.manifest.json",
     "prepare": "yarn build",
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
+    "posttest": "yarn lint",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
-    "version": "oclif readme && git add README.md"
+    "version": "oclif readme --multi --dir ../website/docs/cli/ && oclif readme && git add README.md"
+  },
+  "oclif": {
+    "bin": "apollo",
+    "commands": "./dist/commands",
+    "dirname": "apollo-cli",
+    "helpOptions": {
+      "flagSortOrder": "none",
+      "maxWidth": 80
+    },
+    "plugins": [
+      "@oclif/plugin-help"
+    ],
+    "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
+    "topicSeparator": " ",
+    "topics": {
+      "assembly": {
+        "description": "Commands to manage assemblies"
+      },
+      "change": {
+        "description": "Commands to manage the change log"
+      },
+      "feature": {
+        "description": "Commands to manage features"
+      },
+      "file": {
+        "description": "Commands to manage files"
+      },
+      "jbrowse": {
+        "description": "Commands to manage the JBrowse configuration"
+      },
+      "refseq": {
+        "description": "Commands to manage reference sequences"
+      },
+      "user": {
+        "description": "Commands to manage users"
+      }
+    }
   },
   "dependencies": {
     "@inquirer/input": "^1.2.14",
@@ -50,12 +84,12 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.1.19",
-    "@apollo-annotation/shared": "^0.1.19",
+    "@apollo-annotation/mst": "^0.1.21",
+    "@apollo-annotation/shared": "^0.1.21",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
-    "@types/chai": "^4",
+    "@types/chai": "^4.3.19",
     "@types/cli-progress": "^3",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
@@ -72,35 +106,8 @@
     "tsx": "^4.6.2",
     "typescript": "^5.5.3"
   },
-  "oclif": {
-    "helpOptions": {
-      "flagSortOrder": "none"
-    },
-    "bin": "apollo",
-    "dirname": "apollo-cli",
-    "commands": "./dist/commands",
-    "plugins": [
-      "@oclif/plugin-help"
-    ],
-    "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
-    "topicSeparator": " ",
-    "topics": {
-      "assembly": {
-        "description": "Commands to handle assemblies"
-      },
-      "change": {
-        "description": "Commands to handle the log of changes made to the database"
-      },
-      "feature": {
-        "description": "Commands to handle features"
-      },
-      "refseq": {
-        "description": "Commands to handle reference sequences"
-      },
-      "user": {
-        "description": "Commands to handle users"
-      }
-    }
+  "engines": {
+    "node": ">=18.0.0"
   },
   "publishConfig": {
     "access": "public"

package/dist/commands/assembly/add-fasta.d.ts

@@ -1,15 +0,0 @@
-import { BaseCommand } from '../../baseCommand.js';
-export default class Get extends BaseCommand<typeof Get> {
-    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 | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
-        index: 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>;
-    };
-    run(): Promise<void>;
-}

package/dist/commands/assembly/add-fasta.js

@@ -1,87 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import * as fs from 'node:fs';
-import * as path from 'node:path';
-import { Flags } from '@oclif/core';
-import { ObjectId } from 'bson';
-import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, submitAssembly, uploadFile, wrapLines, } from '../../utils.js';
-export default class Get extends BaseCommand {
-    static description = 'Add new assembly from local or external fasta file';
-    static examples = [
-        {
-            description: wrapLines('From local file:'),
-            command: '<%= config.bin %> <%= command.id %> -i genome.fa -a myAssembly',
-        },
-        {
-            description: wrapLines('From external source we also need the URL of the index:'),
-            command: '<%= config.bin %> <%= command.id %> -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly',
-        },
-    ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
-            description: 'Input fasta file',
-            required: true,
-        }),
-        assembly: Flags.string({
-            char: 'a',
-            description: 'Name for this assembly. Use the file name if omitted',
-        }),
-        index: Flags.string({
-            char: 'x',
-            description: 'URL of the index. Required if input is an external source and ignored if input is a local file',
-        }),
-        force: Flags.boolean({
-            char: 'f',
-            description: 'Delete existing assembly, if it exists',
-        }),
-    };
-    async run() {
-        const { flags } = await this.parse(Get);
-        const access = await this.getAccess(flags['config-file'], flags.profile);
-        const assemblyName = flags.assembly ?? path.basename(flags['input-file']);
-        const isExternal = isValidHttpUrl(flags['input-file']);
-        let res;
-        if (isExternal) {
-            if (flags.index === undefined) {
-                this.error('Please provide the URL to the index of the external fasta file');
-            }
-            const body = {
-                assemblyName,
-                typeName: 'AddAssemblyFromExternalChange',
-                externalLocation: {
-                    fa: flags['input-file'],
-                    fai: flags.index,
-                },
-            };
-            res = (await submitAssembly(access.address, access.accessToken, body, flags.force));
-        }
-        else {
-            if (!isExternal && !fs.existsSync(flags['input-file'])) {
-                this.error(`File ${flags['input-file']} does not exist`);
-            }
-            const fileId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-fasta');
-            const body = {
-                assemblyName,
-                fileId,
-                typeName: 'AddAssemblyFromFileChange',
-                assembly: new ObjectId().toHexString(),
-            };
-            res = (await submitAssembly(access.address, access.accessToken, body, flags.force));
-        }
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'Submit assembly failed');
-            throw new Error(errorMessage);
-        }
-    }
-}
-function isValidHttpUrl(x) {
-    let url;
-    try {
-        url = new URL(x);
-    }
-    catch {
-        return false;
-    }
-    return url.protocol === 'http:' || url.protocol === 'https:';
-}

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

@@ -1,63 +0,0 @@
-import * as fs from 'node:fs';
-import * as path from 'node:path';
-import { Flags } from '@oclif/core';
-import { ObjectId } from 'bson';
-import { BaseCommand } from '../../baseCommand.js';
-import { createFetchErrorMessage, submitAssembly, uploadFile, wrapLines, } from '../../utils.js';
-export default class AddGff extends BaseCommand {
-    static summary = 'Add new assembly from gff or gft file';
-    static description = wrapLines('The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.');
-    static examples = [
-        {
-            description: 'Import sequences and features:',
-            command: '<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly',
-        },
-        {
-            description: 'Import sequences only:',
-            command: '<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly -o',
-        },
-    ];
-    static flags = {
-        'input-file': Flags.string({
-            char: 'i',
-            description: 'Input gff or gtf file',
-            required: true,
-        }),
-        assembly: Flags.string({
-            char: 'a',
-            description: 'Name for this assembly. Use the file name if omitted',
-        }),
-        'omit-features': Flags.boolean({
-            char: 'o',
-            description: 'Do not import features, only upload the sequences',
-        }),
-        force: Flags.boolean({
-            char: 'f',
-            description: 'Delete existing assembly, if it exists',
-        }),
-    };
-    async run() {
-        const { flags } = await this.parse(AddGff);
-        if (!fs.existsSync(flags['input-file'])) {
-            this.error(`File ${flags['input-file']} does not exist`);
-        }
-        const access = await this.getAccess(flags['config-file'], flags.profile);
-        const fileId = await uploadFile(access.address, access.accessToken, flags['input-file'], 'text/x-gff3');
-        let typeName = 'AddAssemblyAndFeaturesFromFileChange';
-        if (flags['omit-features']) {
-            typeName = 'AddAssemblyFromFileChange';
-        }
-        const assemblyName = flags.assembly ?? path.basename(flags['input-file']);
-        const body = {
-            assemblyName,
-            fileId,
-            typeName,
-            assembly: new ObjectId().toHexString(),
-        };
-        const res = await submitAssembly(access.address, access.accessToken, body, flags.force);
-        if (!res.ok) {
-            const errorMessage = await createFetchErrorMessage(res, 'getFeatureById failed');
-            throw new Error(errorMessage);
-        }
-    }
-}