@apollo-annotation/cli 0.3.11 → 0.3.12

package/dist/utils.js.map

@@ -0,0 +1 @@
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package/oclif.manifest.json

@@ -404,6 +404,12 @@
           "name": "force",
           "allowNo": false,
           "type": "boolean"
+        },
+        "no-strict": {
+          "description": "If any feature lines in the GFF3 can't be processed, skip them instead of aborting the import",
+          "name": "no-strict",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
@@ -684,10 +690,22 @@
         "sequence.js"
       ]
     },
-    "change:get": {
+    "export:gff3": {
       "aliases": [],
-      "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
+      "args": {
+        "assembly": {
+          "description": "Export annotations for this assembly name or id",
+          "name": "assembly",
+          "required": true
+        }
+      },
+      "description": "Export the annotations for an assembly to stdout as gff3",
+      "examples": [
+        {
+          "description": "Export annotations for myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -703,48 +721,33 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
+        "include-fasta": {
+          "description": "Include fasta sequence in output",
+          "name": "include-fasta",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "change:get",
+      "id": "export:gff3",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "change",
-        "get.js"
+        "export",
+        "gff3.js"
       ]
     },
-    "export:gff3": {
+    "change:get": {
       "aliases": [],
-      "args": {
-        "assembly": {
-          "description": "Export annotations for this assembly name or id",
-          "name": "assembly",
-          "required": true
-        }
-      },
-      "description": "Export the annotations for an assembly to stdout as gff3",
-      "examples": [
-        {
-          "description": "Export annotations for myAssembly:",
-          "command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
-        }
-      ],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -760,27 +763,30 @@
           "multiple": false,
           "type": "option"
         },
-        "include-fasta": {
-          "description": "Include fasta sequence in output",
-          "name": "include-fasta",
-          "allowNo": false,
-          "type": "boolean"
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "export:gff3",
+      "id": "change:get",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
+      "summary": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "export",
-        "gff3.js"
+        "change",
+        "get.js"
       ]
     },
     "feature:add-child": {
@@ -1710,6 +1716,12 @@
           "name": "delete-existing",
           "allowNo": false,
           "type": "boolean"
+        },
+        "no-strict": {
+          "description": "If any lines in the GFF3 can't be processed, skip them instead of aborting the import",
+          "name": "no-strict",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
@@ -2399,5 +2411,5 @@
       ]
     }
   },
-  "version": "0.3.11"
+  "version": "0.3.12"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.11",
+  "version": "0.3.12",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -10,7 +10,6 @@
   "author": "Apollo Team",
   "type": "module",
   "exports": "./dist/index.js",
-  "main": "",
   "types": "dist/index.d.ts",
   "bin": {
     "apollo": "./bin/run.js"
@@ -26,10 +25,8 @@
     "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'",
-    "test:cli": "yarn tsx src/test/test.ts",
+    "test": "yarn tsx src/test/test.ts",
+    "test:ci": "yarn tsx src/test/test.ts",
     "version": "oclif readme --multi --dir ../website/docs/03-guides/04-cli/ && oclif readme && git add README.md"
   },
   "oclif": {
@@ -89,8 +86,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.11",
-    "@apollo-annotation/shared": "^0.3.11",
+    "@apollo-annotation/mst": "^0.3.12",
+    "@apollo-annotation/shared": "^0.3.12",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
@@ -98,11 +95,9 @@
     "@types/cli-progress": "^3",
     "@types/cross-spawn": "^6.0.6",
     "@types/inquirer": "^9.0.7",
-    "@types/mocha": "^10",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "babel-plugin-istanbul": "^6.1.1",
     "cross-spawn": "^7.0.3",
-    "mocha": "^10.2.0",
     "mongodb": "^4.7.0",
     "nyc": "^15.1.0",
     "oclif": "^4.4.2",
@@ -116,7 +111,7 @@
     "typescript": "^5.5.3"
   },
   "engines": {
-    "node": ">=18.0.0"
+    "node": ">=20.0.0"
   },
   "publishConfig": {
     "access": "public"

package/dist/commands/assembly/get.test.d.ts

@@ -1 +0,0 @@
-export {};

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

@@ -1,50 +0,0 @@
-import fs from 'node:fs';
-import path from 'node:path';
-import { fileURLToPath } from 'node:url';
-import { expect, test } from '@oclif/test';
-import { CONFIG_FILE, TEST_DATA_DIR, VERBOSE, copyFile, } from '../../test/fixtures.js';
-// import nock from 'nock'
-const __dirname = fileURLToPath(new URL('.', import.meta.url));
-describe.skip('apollo assembly get: Fail without token', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/guest.yml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    const cmd = ['assembly:get'];
-    test
-        .stderr()
-        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-        .exit(1)
-        .do((output) => expect(output.stderr).to.contain('Profile "default" has no access token'))
-        .do((output) => expect(output.stderr).to.not.contain(' at async ')) // Don't print error stack
-        .it(cmd.join(' '));
-});
-// TODO: Need valid token
-describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    const cmd = ['assembly:get'];
-    test
-        .stdout()
-        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-        .it(cmd.join(' '), (output) => {
-        JSON.parse(output.stdout);
-    });
-});
-describe.skip('apollo assembly get: Test nock', () => {
-    const cmd = ['assembly:get', '--config-file', 'tmp.yml'];
-    test
-        .stdout()
-        .nock('http://127.0.0.1:3999', (api) => api.persist().get('/assemblies').reply(200, { stuff: 'foo' }))
-        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-        .it(cmd.join(' '), (output) => {
-        console.error(output.stdout);
-        // const out = JSON.parse(output.stdout)
-    });
-});

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

@@ -1 +0,0 @@
-export {};

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

@@ -1,22 +0,0 @@
-import fs from 'node:fs';
-import path from 'node:path';
-import { fileURLToPath } from 'node:url';
-import { test } from '@oclif/test';
-import { CONFIG_FILE, TEST_DATA_DIR, VERBOSE, copyFile, } from '../../test/fixtures.js';
-const __dirname = fileURLToPath(new URL('.', import.meta.url));
-// TODO: Need valid token
-describe.skip('apollo change get: Get changes as YAML string', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    const cmd = ['change:get'];
-    test
-        .stdout()
-        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-        .it(cmd.join(' '), (output) => {
-        JSON.parse(output.stdout);
-    });
-});

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

@@ -1 +0,0 @@
-export {};

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

@@ -1,23 +0,0 @@
-import fs from 'node:fs';
-import path from 'node:path';
-import { fileURLToPath } from 'node:url';
-import { expect, test } from '@oclif/test';
-import { CONFIG_FILE, TEST_DATA_DIR, VERBOSE, copyFile, } from '../../test/fixtures.js';
-const __dirname = fileURLToPath(new URL('.', import.meta.url));
-// TODO: Need valid token
-describe.skip('apollo user get: Get users as YAML string', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    const cmd = ['user:get'];
-    test
-        .stdout()
-        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-        .it(cmd.join(' '), (output) => {
-        const str = JSON.stringify(JSON.parse(output.stdout));
-        expect(str).contain('username');
-    });
-});

package/dist/test/fixtures.d.ts

@@ -1,7 +0,0 @@
-export declare const TEST_DATA_DIR: string;
-export declare const VERBOSE = false;
-export declare const CONFIG_DIR: string;
-export declare const CONFIG_FILE: string;
-export declare function copyFile(src: string, dest: string, verbose: boolean): void;
-export declare function mochaGlobalSetup(): void;
-export declare function mochaGlobalTeardown(): void;

package/dist/test/fixtures.js

@@ -1,40 +0,0 @@
-import fs from 'node:fs';
-import os from 'node:os';
-import path from 'node:path';
-export const TEST_DATA_DIR = path.resolve('test_data');
-export const VERBOSE = false;
-export const CONFIG_DIR = path.join(os.homedir(), '.config', 'apollo-cli');
-export const CONFIG_FILE = path.join(CONFIG_DIR, 'config.yml');
-const CONFIG_BAK = path.join(TEST_DATA_DIR, 'original.config.yml.bak');
-function renameFile(src, dest, verbose = true) {
-    if (fs.existsSync(dest)) {
-        throw new Error(`File ${dest} already exists`);
-    }
-    let msg = '';
-    if (fs.existsSync(src)) {
-        fs.renameSync(src, dest);
-        msg = `mv ${src} ${dest}`;
-    }
-    else {
-        msg = `${src} does not exist`;
-    }
-    if (verbose) {
-        process.stdout.write(`${msg}\n`);
-    }
-}
-export function copyFile(src, dest, verbose) {
-    fs.mkdirSync(path.dirname(dest), { recursive: true });
-    fs.copyFileSync(src, dest);
-    if (verbose) {
-        const msg = `cp ${src} ${dest}`;
-        process.stdout.write(`${msg} # Copied: ${fs.existsSync(dest)}\n`);
-    }
-}
-export function mochaGlobalSetup() {
-    process.stdout.write(`Temporarily remove config file ${CONFIG_FILE} if any`);
-    renameFile(CONFIG_FILE, CONFIG_BAK, VERBOSE);
-}
-export function mochaGlobalTeardown() {
-    process.stdout.write(`Putting back config file ${CONFIG_FILE} if any\n`);
-    renameFile(CONFIG_BAK, CONFIG_FILE, VERBOSE);
-}