@apollo-annotation/cli 0.3.4 → 0.3.6

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.4 linux-x64 node-v18.20.7
+@apollo-annotation/cli/0.3.6 linux-x64 node-v18.20.8
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -114,7 +114,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -150,7 +150,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -192,7 +192,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -220,7 +220,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -242,7 +242,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -277,7 +277,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -301,7 +301,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -353,7 +353,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -381,7 +381,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -412,7 +412,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -445,7 +445,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -476,7 +476,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -500,7 +500,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -542,7 +542,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -582,7 +582,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -616,7 +616,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -640,7 +640,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -674,7 +674,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -702,7 +702,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -733,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -784,7 +784,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -811,7 +811,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -839,7 +839,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -866,7 +866,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -903,7 +903,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -950,7 +950,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -979,7 +979,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1018,7 +1018,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1048,7 +1048,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1079,7 +1079,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1111,7 +1111,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1133,7 +1133,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1169,6 +1169,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.4/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/baseCommand.d.ts

@@ -1,4 +1,4 @@
-import { Command, Interfaces } from '@oclif/core';
+import { Command, type Interfaces } from '@oclif/core';
 export type Flags<T extends typeof Command> = Interfaces.InferredFlags<(typeof BaseCommand)['baseFlags'] & T['flags']>;
 export type Args<T extends typeof Command> = Interfaces.InferredArgs<T['args']>;
 export declare abstract class BaseCommand<T extends typeof Command> extends Command {

package/dist/commands/export/gff3.js

@@ -1,8 +1,8 @@
+import { Readable } from 'node:stream';
 import { Args, Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';
 import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
-import { Readable } from 'node:stream';
 export default class Get extends BaseCommand {
     static description = 'Export the annotations for an assembly to stdout as gff3';
     static examples = [

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

@@ -1,5 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { ObjectId } from 'bson';
 import { fetch } from 'undici';

package/dist/commands/feature/check.js

@@ -62,6 +62,7 @@ Use `apollo assembly check` for managing which checks should be applied to an as
                 results.push(chk);
             }
         }
+        results.sort((a, b) => (a.start < b.start ? -1 : 1));
         this.log(JSON.stringify(results, null, 2));
     }
 }

package/dist/commands/feature/search.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { Flags } from '@oclif/core';
 import { fetch } from 'undici';
 import { BaseCommand } from '../../baseCommand.js';

package/dist/commands/jbrowse/set-config.js

@@ -3,7 +3,7 @@ import { Args } from '@oclif/core';
 import { Agent, fetch } from 'undici';
 import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
-import { localhostToAddress, createFetchErrorMessage } from '../../utils.js';
+import { createFetchErrorMessage, localhostToAddress } from '../../utils.js';
 export default class SetConfig extends BaseCommand {
     static summary = 'Set JBrowse configuration';
     static description = 'Set JBrowse configuration in Apollo collaboration server';

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

@@ -1,9 +1,9 @@
 import * as fs from 'node:fs';
-import { Agent, fetch } from 'undici';
 import { Args, Flags } from '@oclif/core';
+import { Agent, fetch } from 'undici';
+import { ConfigError } from '../../ApolloConf.js';
 import { BaseCommand } from '../../baseCommand.js';
 import { createFetchErrorMessage, localhostToAddress, queryApollo, } from '../../utils.js';
-import { ConfigError } from '../../ApolloConf.js';
 export default class AddRefNameAlias extends BaseCommand {
     static summary = 'Add reference name aliases from a file';
     static description = 'Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.';

package/dist/test/test.js

@@ -16,11 +16,10 @@
  * yarn test:cli --test-name-pattern='Print help|Feature get'
  */
 import assert from 'node:assert';
-import { before, beforeEach, afterEach, describe } from 'node:test';
-import { Shell } from './utils.js';
-import fs from 'node:fs';
 import * as crypto from 'node:crypto';
-import path from 'node:path';
+import fs from 'node:fs';
+import { afterEach, before, beforeEach, describe } from 'node:test';
+import { Shell } from './utils.js';
 const apollo = 'yarn dev';
 const P = '--profile testAdmin';
 let configFile = '';
@@ -28,7 +27,7 @@ let configFileBak = '';
 void describe('Test CLI', () => {
     before(() => {
         configFile = new Shell(`${apollo} config --get-config-file`).stdout.trim();
-        configFileBak = `${path.basename(configFile)}.bak`;
+        configFileBak = `${configFile}.bak`;
         if (fs.existsSync(configFileBak)) {
             throw new Error(`Backup config file ${configFileBak} already exists. If safe to do so, delete it before testing`);
         }
@@ -114,7 +113,7 @@ void describe('Test CLI', () => {
         assert.ok(p.stdout.includes('vv2'));
         assert.ok(p.stdout.includes('vv3') == false);
         const out = JSON.parse(p.stdout);
-        const aid = out.filter((x) => x.name === 'vv1').at(0)._id;
+        const aid = out.find((x) => x.name === 'vv1')._id;
         p = new Shell(`${apollo} assembly get ${P} -a ${aid} vv2`);
         assert.ok(p.stdout.includes('vv1'));
         assert.ok(p.stdout.includes('vv2'));
@@ -202,7 +201,7 @@ void describe('Test CLI', () => {
         p = new Shell(`${apollo} refseq get ${P}`);
         const refseq = JSON.parse(p.stdout.trim());
         const vv1ref = refseq.filter((x) => x.assembly === asm_id);
-        const refseq_id = vv1ref.filter((x) => x.name === 'ctgA').at(0)._id;
+        const refseq_id = vv1ref.find((x) => x.name === 'ctgA')._id;
         p = new Shell(`${apollo} feature get ${P} -r ${refseq_id}`);
         const ff = JSON.parse(p.stdout);
         assert.deepStrictEqual(ff, []);
@@ -226,7 +225,7 @@ void describe('Test CLI', () => {
         new Shell(`${apollo} assembly add-from-fasta ${P} test_data/tmp.fa -a test -e -f`, true, 60_000);
         fs.unlinkSync('test_data/tmp.fa');
     });
-    void globalThis.itName('FIXME Checks are triggered and resolved', () => {
+    void globalThis.itName('Checks are triggered and resolved', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/checks.gff -f`);
         let p = new Shell(`${apollo} feature get ${P} -a checks.gff`);
         const out = JSON.parse(p.stdout);
@@ -241,15 +240,42 @@ void describe('Test CLI', () => {
         new Shell(`${apollo} feature edit-coords ${P} -i ${cds_id} --start 4 --end 24`);
         p = new Shell(`${apollo} feature check ${P} -a checks.gff`);
         const checks = JSON.parse(p.stdout);
-        // FIXME: There should be 2 failing checks, not 3
-        assert.strictEqual(checks.length, 3);
-        assert.ok(p.stdout.includes('InternalStopCodonCheck'));
-        assert.ok(p.stdout.includes('MissingStopCodonCheck'));
+        assert.strictEqual(checks.length, 2);
+        assert.ok(p.stdout.includes('InternalStopCodon'));
+        assert.ok(p.stdout.includes('MissingStopCodon'));
         // Problems fixed
         new Shell(`${apollo} feature edit-coords ${P} -i ${cds_id} --start 16 --end 27`);
         p = new Shell(`${apollo} feature check ${P} -a checks.gff`);
-        // FIXME: After fixing, how many warnings do we expect?
-        assert.deepStrictEqual(JSON.parse(p.stdout).length, 4);
+        assert.deepStrictEqual(JSON.parse(p.stdout).length, 0);
+    });
+    void globalThis.itName('FIXME: Checks stay after invalid operation', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/checks.gff -f`);
+        let p = new Shell(`${apollo} feature get ${P} -a checks.gff`);
+        const out = JSON.parse(p.stdout);
+        p = new Shell(`${apollo} feature check ${P} -a checks.gff`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]'); // No failing check
+        // Get the ID of the CDS. We need need it to modify the CDS coordinates
+        const gene = out.filter((x) => JSON.stringify(x.attributes.gff_id) === JSON.stringify(['gene01']));
+        const mrna = Object.values(gene.at(0).children).at(0);
+        const cds = Object.values(mrna.children).find((x) => x.attributes.gff_id.at(0) === 'cds01');
+        const cds_id = cds._id;
+        // Introduce problems
+        new Shell(`${apollo} feature edit-coords ${P} -i ${cds_id} --start 4 --end 24`);
+        p = new Shell(`${apollo} feature check ${P} -a checks.gff`);
+        let checks = JSON.parse(p.stdout);
+        assert.strictEqual(checks.length, 2);
+        assert.ok(p.stdout.includes('InternalStopCodon'));
+        assert.ok(p.stdout.includes('MissingStopCodon'));
+        // Do something invalid: extend CDS beyond parent
+        p = new Shell(`${apollo} feature edit-coords ${P} -i ${cds_id} --end 30`, false);
+        assert.ok(p.returncode != 0);
+        assert.ok(p.stderr.includes('exceeds the bounds of its parent'));
+        // FIXME: Checks should be the same as before the invalid edit
+        p = new Shell(`${apollo} feature check ${P} -a checks.gff`);
+        checks = JSON.parse(p.stdout);
+        //assert.strictEqual(checks.length, 2)
+        //assert.ok(p.stdout.includes('InternalStopCodon'))
+        //assert.ok(p.stdout.includes('MissingStopCodon'))
     });
     void globalThis.itName('Add assembly from local fasta', () => {
         let p = new Shell(`${apollo} assembly add-from-fasta ${P} test_data/tiny.fasta -a vv1 -e -f`);
@@ -281,12 +307,12 @@ void describe('Test CLI', () => {
         assert.ok(p.returncode != 0);
     });
     void globalThis.itName('Detect missing external index', () => {
-        const p = new Shell(`${apollo} assembly add-from-fasta ${P} -a vv1 -f https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta`, false);
+        const p = new Shell(`${apollo} assembly add-from-fasta ${P} -a vv1 -f http://localhost:3131/tiny.fasta`, false);
         assert.ok(p.returncode != 0);
         assert.ok(p.stderr.includes('Index file') && p.stderr.includes('does not exist'));
     });
     void globalThis.itName('Editable sequence not allowed with external source', () => {
-        const cmd = `${apollo} assembly add-from-fasta ${P} -a vv1 -f https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta.gz`;
+        const cmd = `${apollo} assembly add-from-fasta ${P} -a vv1 -f http://localhost:3131/tiny.fasta.gz`;
         new Shell(cmd);
         const p = new Shell(`${cmd} -e`, false);
         assert.ok(p.returncode != 0);
@@ -377,9 +403,7 @@ void describe('Test CLI', () => {
         // Edit a feature by extending beyond the boundary of its parent and
         // check it throws a meaningful error message
         // let eden_gene = undefined
-        const eden_gene = features
-            .filter((x) => x.type === 'gene' && x.attributes.gff_name.at(0) === 'EDEN')
-            .at(0);
+        const eden_gene = features.find((x) => x.type === 'gene' && x.attributes.gff_name.at(0) === 'EDEN');
         assert.ok(eden_gene);
         const mrna_id = Object.keys(eden_gene.children).at(0);
         p = new Shell(`${apollo} feature edit-coords ${P} -i ${mrna_id} -s 1`, false);
@@ -545,9 +569,7 @@ void describe('Test CLI', () => {
         assert.strictEqual(out.max, 50);
         // RefSeq id does not need assembly
         p = new Shell(`${apollo} refseq get ${P} -a dest2`);
-        const destRefSeq = JSON.parse(p.stdout)
-            .filter((x) => x.name === 'ctgA')
-            .at(0)._id;
+        const destRefSeq = JSON.parse(p.stdout).find((x) => x.name === 'ctgA')._id;
         p = new Shell(`${apollo} feature copy ${P} -i ${fid} -r ${destRefSeq} -s 2`);
         p = new Shell(`${apollo} feature search ${P} -a dest2 -t contig`);
         out = JSON.parse(p.stdout).at(0);
@@ -643,7 +665,7 @@ void describe('Test CLI', () => {
         let p = new Shell(`${apollo} assembly check ${P}`);
         let out = JSON.parse(p.stdout);
         assert.ok(p.stdout.includes('CDSCheck'));
-        const cdsCheckId = out.filter((x) => x.name === 'CDSCheck').at(0)._id;
+        const cdsCheckId = out.find((x) => x.name === 'CDSCheck')._id;
         // Test view checks set for assembly
         p = new Shell(`${apollo} assembly check ${P} -a v1`);
         out = JSON.parse(p.stdout);
@@ -682,14 +704,14 @@ void describe('Test CLI', () => {
         let p = new Shell(`${apollo} feature check ${P} -a v1`);
         const out = JSON.parse(p.stdout);
         assert.ok(out.length > 1);
-        assert.ok(p.stdout.includes('InternalStopCodonCheck'));
+        assert.ok(p.stdout.includes('InternalStopCodon'));
         // Ids with checks
         const ids = out.map((x) => x.ids);
         assert.ok(new Set(ids).size > 1);
         // Retrieve by feature id
         const xid = [...ids].join(' ');
         p = new Shell(`${apollo} feature check ${P} -i ${xid}`);
-        assert.ok(p.stdout.includes('InternalStopCodonCheck'));
+        assert.ok(p.stdout.includes('InternalStopCodon'));
     });
     void globalThis.itName('Feature checks indexed', () => {
         new Shell(`${apollo} assembly add-from-fasta ${P} -a v1 test_data/tiny.fasta.gz -f`);
@@ -698,14 +720,14 @@ void describe('Test CLI', () => {
         let p = new Shell(`${apollo} feature check ${P} -a v1`);
         const out = JSON.parse(p.stdout);
         assert.ok(out.length > 1);
-        assert.ok(p.stdout.includes('InternalStopCodonCheck'));
+        assert.ok(p.stdout.includes('InternalStopCodon'));
         // Ids with checks
         const ids = out.map((x) => x.ids);
         assert.ok(new Set(ids).size > 1);
         // Retrieve by feature id
         const xid = [...ids].join(' ');
         p = new Shell(`${apollo} feature check ${P} -i ${xid}`);
-        assert.ok(p.stdout.includes('InternalStopCodonCheck'));
+        assert.ok(p.stdout.includes('InternalStopCodon'));
     });
     void globalThis.itName('User', () => {
         let p = new Shell(`${apollo} user get ${P}`);
@@ -932,7 +954,7 @@ void describe('Test CLI', () => {
         assert.ok(gff.startsWith('##gff-version 3'));
         assert.ok(gff.includes('multivalue=val1,val2,val3'));
         assert.ok(gff.includes('##FASTA\n'));
-        assert.deepStrictEqual(gff.slice(-6, gff.length), 'taccc\n');
+        assert.deepStrictEqual(gff.slice(-6), 'taccc\n');
         p = new Shell(`${apollo} export gff3 ${P} vv1`);
         gff = p.stdout;
         assert.ok(gff.startsWith('##gff-version 3'));
@@ -952,7 +974,7 @@ void describe('Test CLI', () => {
         assert.ok(gff.includes('multivalue=val1,val2,val3'));
         assert.ok(gff.includes('##FASTA\n'));
         // We end with two newlines because the test data does have an extra newline at the end.
-        assert.deepStrictEqual(gff.slice(-7, gff.length), 'taccc\n\n');
+        assert.deepStrictEqual(gff.slice(-7), 'taccc\n\n');
         p = new Shell(`${apollo} export gff3 ${P} vv1`);
         gff = p.stdout;
         assert.ok(gff.startsWith('##gff-version 3'));
@@ -960,7 +982,7 @@ void describe('Test CLI', () => {
         assert.ok(!gff.includes('##FASTA\n'));
     });
     void globalThis.itName('Export gff3 from external assembly', () => {
-        new Shell(`${apollo} assembly add-from-fasta ${P} https://raw.githubusercontent.com/GMOD/Apollo3/refs/heads/main/packages/apollo-cli/test_data/tiny.fasta.gz -a vv1 -f`);
+        new Shell(`${apollo} assembly add-from-fasta ${P} http://localhost:3131/tiny.fasta.gz -a vv1 -f`);
         new Shell(`${apollo} feature import ${P} test_data/tiny.fasta.gff3 -a vv1`);
         let p = new Shell(`${apollo} export gff3 ${P} vv1 --include-fasta`);
         let gff = p.stdout;
@@ -968,11 +990,75 @@ void describe('Test CLI', () => {
         assert.ok(gff.includes('multivalue=val1,val2,val3'));
         assert.ok(gff.includes('##FASTA\n'));
         // We end with two newlines because the test data does have an extra newline at the end.
-        assert.deepStrictEqual(gff.slice(-7, gff.length), 'taccc\n\n');
+        assert.deepStrictEqual(gff.slice(-7), 'taccc\n\n');
         p = new Shell(`${apollo} export gff3 ${P} vv1`);
         gff = p.stdout;
         assert.ok(gff.startsWith('##gff-version 3'));
         assert.ok(gff.includes('multivalue=val1,val2,val3'));
         assert.ok(!gff.includes('##FASTA\n'));
     });
+    void globalThis.itName('Position of internal stop codon warning in forward', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/warningPositionForward.gff -a vv1 -f`);
+        const p = new Shell(`${apollo} feature check ${P} -a vv1`);
+        const out = JSON.parse(p.stdout);
+        assert.deepStrictEqual(out.length, 2);
+        assert.deepStrictEqual(out.at(0).cause, 'InternalStopCodon');
+        assert.deepStrictEqual(out.at(0).start, 9);
+        assert.deepStrictEqual(out.at(0).end, 15);
+        assert.deepStrictEqual(out.at(1).cause, 'InternalStopCodon');
+        assert.deepStrictEqual(out.at(1).start, 21);
+        assert.deepStrictEqual(out.at(1).end, 24);
+    });
+    void globalThis.itName('Position of internal stop codon warning in reverse', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/warningPositionReverse.gff -a vv1 -f`);
+        const p = new Shell(`${apollo} feature check ${P} -a vv1`);
+        const out = JSON.parse(p.stdout);
+        assert.deepStrictEqual(out.length, 2);
+        assert.deepStrictEqual(out.at(0).cause, 'InternalStopCodon');
+        assert.deepStrictEqual(out.at(0).start, 3);
+        assert.deepStrictEqual(out.at(0).end, 18);
+        assert.deepStrictEqual(out.at(1).cause, 'InternalStopCodon');
+        assert.deepStrictEqual(out.at(1).start, 18);
+        assert.deepStrictEqual(out.at(1).end, 21);
+    });
+    void globalThis.itName('Detect missing start codon forward', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/missingStartCodonForward.gff3 -a m1 -f`);
+        const p = new Shell(`${apollo} feature check ${P} -a m1`);
+        const out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.deepStrictEqual(out.at(0).cause, 'MissingStartCodon');
+        assert.deepStrictEqual(out.at(0).start, 3);
+        assert.deepStrictEqual(out.at(0).end, 3);
+        assert.ok(out.at(0).message.includes('TTG'));
+    });
+    void globalThis.itName('Detect missing start codon reverse', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/missingStartCodonReverse.gff3 -a m1 -f`);
+        const p = new Shell(`${apollo} feature check ${P} -a m1`);
+        const out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.deepStrictEqual(out.at(0).cause, 'MissingStartCodon');
+        assert.deepStrictEqual(out.at(0).start, 23);
+        assert.deepStrictEqual(out.at(0).end, 23);
+        assert.ok(out.at(0).message.includes('agC'));
+    });
+    void globalThis.itName('Edit exon inferred from CDS', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/cdsWithoutExon.gff3 -f`);
+        let p = new Shell(`${apollo} feature search ${P} -t mrna01 -a cdsWithoutExon.gff3`);
+        let out = JSON.parse(p.stdout);
+        const gene = out.at(0);
+        const mrna = Object.values(gene.children).at(0);
+        const cdsExon = Object.values(mrna.children);
+        const exon = cdsExon.filter((x) => x.type === 'exon');
+        assert.deepStrictEqual(exon.length, 1);
+        const exon_id = exon[0]._id;
+        // Before edit
+        p = new Shell(`${apollo} feature get-id ${P} -i ${exon_id}`);
+        out = JSON.parse(p.stdout);
+        assert.deepStrictEqual(out.at(0)?.max, 20);
+        // After edit
+        new Shell(`${apollo} feature edit-coords ${P} -i ${exon_id} -e 30`);
+        p = new Shell(`${apollo} feature get-id ${P} -i ${exon_id}`);
+        out = JSON.parse(p.stdout);
+        assert.deepStrictEqual(out.at(0)?.max, 30);
+    });
 });

package/dist/test/test_docker.js

@@ -1,8 +1,8 @@
 import assert from 'node:assert';
-import { after, before, describe } from 'node:test';
-import { Shell } from './utils.js';
 import fs from 'node:fs';
 import path from 'node:path';
+import { after, before, describe } from 'node:test';
+import { Shell } from './utils.js';
 const hostTmpDir = path.resolve('tmpTestDocker');
 const hostDataDir = path.resolve('test_data');
 const apollo = `docker run --network host -v ${hostTmpDir}:/root/.config/apollo-cli -v ${hostDataDir}:/data apollo`;

package/dist/utils.d.ts

@@ -1,8 +1,8 @@
-import EventEmitter from 'node:events';
-import type { SerializedAddAssemblyAndFeaturesFromFileChange, SerializedAddAssemblyFromExternalChange, SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
-import { Response } from 'undici';
+import type EventEmitter from 'node:events';
+import { type ApolloAssemblySnapshot } from '@apollo-annotation/mst';
+import { type SerializedAddAssemblyAndFeaturesFromFileChange, type SerializedAddAssemblyFromExternalChange, type SerializedAddAssemblyFromFileChange } from '@apollo-annotation/shared';
+import { type Response } from 'undici';
 import { ApolloConf } from './ApolloConf.js';
-import { ApolloAssemblySnapshot } from '@apollo-annotation/mst';
 export declare const CLI_SERVER_ADDRESS = "http://127.0.0.1:5657";
 export declare const CLI_SERVER_ADDRESS_CALLBACK = "http://127.0.0.1:5657/auth/callback";
 export declare class CheckError extends Error {

package/dist/utils.js

@@ -1,6 +1,6 @@
 import * as crypto from 'node:crypto';
 import * as fs from 'node:fs';
-import { stdin, stderr } from 'node:process';
+import { stderr, stdin } from 'node:process';
 import { Agent, fetch } from 'undici';
 import { ApolloConf, ConfigError } from './ApolloConf.js';
 export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';
@@ -72,6 +72,7 @@ export async function getAssembly(address, accessToken, assemblyNameOrId) {
     const assemblies = (await res.json());
     for (const x of assemblies) {
         if (x._id === assemblyId[0]) {
+            // eslint-disable-next-line unicorn/prefer-structured-clone
             return JSON.parse(JSON.stringify(x));
         }
     }

package/oclif.manifest.json

@@ -2106,5 +2106,5 @@
       ]
     }
   },
-  "version": "0.3.4"
+  "version": "0.3.6"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.4",
+  "version": "0.3.6",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -88,8 +88,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.4",
-    "@apollo-annotation/shared": "^0.3.4",
+    "@apollo-annotation/mst": "^0.3.6",
+    "@apollo-annotation/shared": "^0.3.6",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
@@ -107,6 +107,7 @@
     "prettier": "^3.3.2",
     "react-dom": "^18.2.0",
     "rxjs": "^7.4.0",
+    "serve": "^14.0.1",
     "shx": "^0.3.3",
     "ts-node": "^10.3.0",
     "tsx": "^4.6.2",