@apollo-annotation/cli 0.1.21 → 0.2.1

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.21 linux-x64 node-v18.20.4
+@apollo-annotation/cli/0.2.1 linux-x64 node-v18.20.5
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -108,7 +108,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -144,7 +144,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -186,7 +186,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -214,7 +214,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -236,7 +236,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -271,7 +271,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -295,7 +295,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -350,7 +350,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo feature add-child`
 
@@ -381,7 +381,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -414,7 +414,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -445,7 +445,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -469,7 +469,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -511,7 +511,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -551,7 +551,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -585,7 +585,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -609,7 +609,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -643,7 +643,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -671,7 +671,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -702,7 +702,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -753,7 +753,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -780,7 +780,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -808,7 +808,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -835,7 +835,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -872,7 +872,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -919,7 +919,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -948,7 +948,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -987,7 +987,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1017,7 +1017,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1048,7 +1048,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1080,7 +1080,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1102,7 +1102,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1138,6 +1138,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.21/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.1/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

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

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import * as fs from 'node:fs';
-import * as path from 'node:path';
+import path from 'node:path';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { FileCommand } from '../../fileCommand.js';

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

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs';
-import * as path from 'node:path';
+import path from 'node:path';
 import { Args, Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { FileCommand } from '../../fileCommand.js';

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

@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { dirname } from 'node:path';
+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';
@@ -15,7 +15,7 @@ describe.skip('apollo assembly get: Fail without token', () => {
     const cmd = ['assembly:get'];
     test
         .stderr()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
+        .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
@@ -32,7 +32,7 @@ describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
     const cmd = ['assembly:get'];
     test
         .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
+        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
         .it(cmd.join(' '), (output) => {
         JSON.parse(output.stdout);
     });
@@ -42,7 +42,7 @@ describe.skip('apollo assembly get: Test nock', () => {
     test
         .stdout()
         .nock('http://127.0.0.1:3999', (api) => api.persist().get('/assemblies').reply(200, { stuff: 'foo' }))
-        .command(cmd, { root: dirname(dirname(__dirname)) })
+        .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.js

@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { dirname } from 'node:path';
+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';
@@ -15,7 +15,7 @@ describe.skip('apollo change get: Get changes as YAML string', () => {
     const cmd = ['change:get'];
     test
         .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
+        .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
         .it(cmd.join(' '), (output) => {
         JSON.parse(output.stdout);
     });

package/dist/commands/feature/add-child.js

@@ -71,7 +71,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
         }
         const res = await queryApollo(address, accessToken, 'refSeqs');
         const refSeqs = (await res.json());
-        const { refSeq } = parentFeature;
+        const { refSeq, _id } = parentFeature;
         let assembly = '';
         for (const x of refSeqs) {
             if (x['_id'] === refSeq) {
@@ -81,8 +81,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
         }
         const change = {
             typeName: 'AddFeatureChange',
-            // eslint-disable-next-line unicorn/consistent-destructuring
-            changedIds: [parentFeature._id],
+            changedIds: [_id],
             assembly,
             addedFeature: {
                 _id: new ObjectId().toHexString(),
@@ -91,8 +90,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
                 max,
                 type,
             },
-            // eslint-disable-next-line unicorn/consistent-destructuring
-            parentFeatureId: parentFeature._id,
+            parentFeatureId: _id,
         };
         const url = new URL(localhostToAddress(`${address}/changes`));
         const auth = {

package/dist/commands/file/upload.js

@@ -46,6 +46,7 @@ export default class Upload extends FileCommand {
         const { args, flags } = await this.parse(Upload);
         const access = await this.getAccess();
         let { type } = flags;
+        const { gzip, decompressed } = flags;
         if (type === undefined) {
             const hasGzipExt = args['input-file'].endsWith('.gz');
             const infile = args['input-file'].replace(/\.gz$/, '');
@@ -69,12 +70,10 @@ export default class Upload extends FileCommand {
             }
         }
         let isGzip = args['input-file'].endsWith('.gz');
-        // eslint-disable-next-line unicorn/consistent-destructuring
-        if (flags.gzip) {
+        if (gzip) {
             isGzip = true;
         }
-        // eslint-disable-next-line unicorn/consistent-destructuring
-        if (flags.decompressed) {
+        if (decompressed) {
             isGzip = false;
         }
         this.logToStderr(`Input is gzip'd: ${isGzip}`);

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

@@ -1,5 +1,5 @@
 import fs from 'node:fs';
-import { dirname } from 'node:path';
+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';
@@ -15,7 +15,7 @@ describe.skip('apollo user get: Get users as YAML string', () => {
     const cmd = ['user:get'];
     test
         .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
+        .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/fileCommand.js

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs';
-import * as path from 'node:path';
+import path from 'node:path';
 import { Transform, pipeline, } from 'node:stream';
 import { SingleBar } from 'cli-progress';
 import { Agent, fetch } from 'undici';

package/dist/utils.js

@@ -231,7 +231,12 @@ export const generatePkceChallenge = () => {
 export const waitFor = (eventName, emitter) => {
     const promise = new Promise((resolve, reject) => {
         const handleEvent = (eventData) => {
-            eventData instanceof Error ? reject(eventData) : resolve(eventData);
+            if (eventData instanceof Error) {
+                reject(eventData);
+            }
+            else {
+                resolve(eventData);
+            }
             emitter.removeListener(eventName, handleEvent);
         };
         emitter.addListener(eventName, handleEvent);

package/oclif.manifest.json

@@ -2048,5 +2048,5 @@
       ]
     }
   },
-  "version": "0.1.21"
+  "version": "0.2.1"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.1.21",
+  "version": "0.2.1",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -84,8 +84,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.1.21",
-    "@apollo-annotation/shared": "^0.1.21",
+    "@apollo-annotation/mst": "^0.2.1",
+    "@apollo-annotation/shared": "^0.2.1",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",