@apollo-annotation/cli 0.3.10 → 0.3.12

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,
@@ -862,6 +868,146 @@
         "add-child.js"
       ]
     },
+    "feature:add": {
+      "aliases": [],
+      "args": {
+        "feature-json": {
+          "description": "Inline JSON describing the feature(s) to add. Can also be provided via stdin.",
+          "name": "feature-json"
+        }
+      },
+      "description": "A single simple feature can be added using the --min, --max, etc. flags.\n\nTo add multiple features, features with more details, or features with children, you can pass in JSON via argument or stdin or use the --feature-json-file options.\n",
+      "examples": [
+        {
+          "description": "Add a single feature by specifying its location and type",
+          "command": "<%= config.bin %> <%= command.id %> --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark"
+        },
+        {
+          "description": "Add a single feature from inline JSON",
+          "command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"}'"
+        },
+        {
+          "description": "Add mutilple features from stdin JSON",
+          "command": "echo '[{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"},{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":101,\"max\":200,\"type\":\"<featureType>\"}]' | <%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Add a feature with children from inline JSON",
+          "command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\",\"children\":[{\"min\":1,\"max\":50,\"type\":\"<featureType>\"}]}'"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "refSeq": {
+          "char": "r",
+          "dependsOn": [
+            "min",
+            "max",
+            "type"
+          ],
+          "description": "Name or ID of target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "refSeq",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "min": {
+          "char": "s",
+          "dependsOn": [
+            "refSeq",
+            "max",
+            "type"
+          ],
+          "description": "Start position in target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "min",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "max": {
+          "char": "e",
+          "dependsOn": [
+            "refSeq",
+            "min",
+            "type"
+          ],
+          "description": "End position in target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "max",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "dependsOn": [
+            "refSeq",
+            "min",
+            "max"
+          ],
+          "description": "Type of child feature",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "type",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "feature-json-file": {
+          "char": "F",
+          "description": "File with JSON describing the feature(s) to add",
+          "name": "feature-json-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:add",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add one or more features to Apollo",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "add.js"
+      ]
+    },
     "feature:check": {
       "aliases": [],
       "args": {},
@@ -1570,6 +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,
@@ -2259,5 +2411,5 @@
       ]
     }
   },
-  "version": "0.3.10"
+  "version": "0.3.12"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.10",
+  "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": "^0.3.10",
-    "@apollo-annotation/shared": "^0.3.10",
+    "@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);
-}