@apollo-annotation/cli 0.3.8 → 0.3.10

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.8 linux-x64 node-v20.19.5
+@apollo-annotation/cli/0.3.10 linux-x64 node-v24.11.1
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -48,6 +48,7 @@ USAGE
 - [`apollo feature edit-type`](#apollo-feature-edit-type)
 - [`apollo feature get`](#apollo-feature-get)
 - [`apollo feature get-id`](#apollo-feature-get-id)
+- [`apollo feature get-indexed-id ID`](#apollo-feature-get-indexed-id-id)
 - [`apollo feature import INPUT-FILE`](#apollo-feature-import-input-file)
 - [`apollo feature search`](#apollo-feature-search)
 - [`apollo file delete`](#apollo-file-delete)
@@ -115,7 +116,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -151,7 +152,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -193,7 +194,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -221,7 +222,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -243,7 +244,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -278,7 +279,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -302,7 +303,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -354,7 +355,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -382,7 +383,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -413,7 +414,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -446,7 +447,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -477,7 +478,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -501,7 +502,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -543,7 +544,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -583,7 +584,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -617,7 +618,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -641,7 +642,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -675,7 +676,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -703,7 +704,39 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-id.ts)_
+
+## `apollo feature get-indexed-id ID`
+
+Get features given an indexed identifier
+
+```
+USAGE
+  $ apollo feature get-indexed-id ID [--profile <value>] [--config-file <value>] [-a <value>] [--topLevel]
+
+ARGUMENTS
+  ID  Indexed identifier to search for
+
+FLAGS
+  -a, --assembly=<value>...  Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
+                             assemblies
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+      --topLevel             Return the top-level parent of the feature instead of the feature itself
+
+DESCRIPTION
+  Get features given an indexed identifier
+
+  Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file
+
+EXAMPLES
+  Get features for this indexed identifier:
+
+    $ apollo feature get-indexed-id -i abc...zyz def...foo
+```
+
+_See code:
+[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -734,7 +767,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -785,7 +818,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -812,7 +845,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -840,7 +873,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -867,7 +900,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -904,7 +937,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -970,7 +1003,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
 
 ## `apollo jbrowse get-config`
 
@@ -996,7 +1029,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -1025,7 +1058,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1064,7 +1097,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1094,7 +1127,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1125,7 +1158,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1157,7 +1190,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1179,7 +1212,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1215,6 +1248,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.8/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/commands/feature/get-indexed-id.d.ts

@@ -0,0 +1,17 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Get extends BaseCommand<typeof Get> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static args: {
+        id: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
+    static flags: {
+        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string[] | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        topLevel: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/feature/get-indexed-id.js

@@ -0,0 +1,66 @@
+import { Args, Flags } from '@oclif/core';
+import { fetch } from 'undici';
+import { BaseCommand } from '../../baseCommand.js';
+import { convertAssemblyNameToId, createFetchErrorMessage, idReader, localhostToAddress, } from '../../utils.js';
+export default class Get extends BaseCommand {
+    static summary = 'Get features given an indexed identifier';
+    static description = 'Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file';
+    static examples = [
+        {
+            description: 'Get features for this indexed identifier:',
+            command: '<%= config.bin %> <%= command.id %> -i abc...zyz def...foo',
+        },
+    ];
+    static args = {
+        id: Args.string({
+            description: 'Indexed identifier to search for',
+            required: true,
+        }),
+    };
+    static flags = {
+        assembly: Flags.string({
+            char: 'a',
+            multiple: true,
+            description: 'Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all assemblies',
+        }),
+        topLevel: Flags.boolean({
+            description: 'Return the top-level parent of the feature instead of the feature itself',
+        }),
+    };
+    async run() {
+        const { args, flags } = await this.parse(Get);
+        const access = await this.getAccess();
+        const { topLevel } = flags;
+        const { id } = args;
+        const assembly = flags.assembly && (await idReader(flags.assembly));
+        const assemblyIds = assembly &&
+            (await convertAssemblyNameToId(access.address, access.accessToken, assembly));
+        if (assemblyIds?.length === 0) {
+            this.log(JSON.stringify([], null, 2));
+            this.exit(0);
+        }
+        const url = new URL(localhostToAddress(`${access.address}/features/getByIndexedId`));
+        const searchParams = new URLSearchParams({ id });
+        if (assemblyIds) {
+            searchParams.append('assemblies', assemblyIds.join(','));
+        }
+        if (topLevel) {
+            searchParams.append('topLevel', 'true');
+        }
+        url.search = searchParams.toString();
+        const uri = url.toString();
+        const auth = {
+            headers: {
+                authorization: `Bearer ${access.accessToken}`,
+                'Content-Type': 'application/json',
+            },
+        };
+        const response = await fetch(uri, auth);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, 'Failed to access Apollo with the current address and/or access token\nThe server returned:\n');
+            throw new Error(errorMessage);
+        }
+        const results = (await response.json());
+        this.log(JSON.stringify(results, null, 2));
+    }
+}

package/dist/test/test.js

@@ -18,14 +18,19 @@
 import assert from 'node:assert';
 import * as crypto from 'node:crypto';
 import fs from 'node:fs';
-import { afterEach, before, beforeEach, describe } from 'node:test';
+import { after, afterEach, before, beforeEach, describe } from 'node:test';
+import { MongoClient } from 'mongodb';
 import { Shell, deleteAllChecks } from './utils.js';
 const apollo = 'yarn dev';
 const P = '--profile testAdmin';
+// let client = MongoClient
+let client;
 let configFile = '';
 let configFileBak = '';
 void describe('Test CLI', () => {
     before(() => {
+        const uri = 'mongodb://localhost:27017/apolloTestCliDb?directConnection=true';
+        client = new MongoClient(uri);
         configFile = new Shell(`${apollo} config --get-config-file`).stdout.trim();
         configFileBak = `${configFile}.bak`;
         if (fs.existsSync(configFileBak)) {
@@ -36,11 +41,24 @@ void describe('Test CLI', () => {
         new Shell(`${apollo} config ${P} rootPassword pass`);
         new Shell(`${apollo} login ${P} -f`);
     });
+    after(async () => {
+        await client.close();
+    });
     beforeEach(() => {
         // Backup starting config file
         fs.copyFileSync(configFile, configFileBak);
     });
-    afterEach(() => {
+    afterEach(async () => {
+        const database = client.db('apolloTestCliDb');
+        await Promise.all([
+            'assemblies',
+            'changes',
+            'counters',
+            'features',
+            'files',
+            'refseqchunks',
+            'refseqs',
+        ].map((collectionName) => database.collection(collectionName).deleteMany({})));
         // Put back starting config file
         fs.renameSync(configFileBak, configFile);
     });
@@ -501,6 +519,42 @@ void describe('Test CLI', () => {
         p = new Shell(`${apollo} feature search ${P} -a vv1 -t Q`);
         assert.ok(p.stdout.includes('"Q"'));
     });
+    void globalThis.itName('Get feature by indexed ID', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`);
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv2 -f`);
+        // Search multiple assemblies
+        let p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene -a vv1 vv2`);
+        let out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 2);
+        assert.ok(p.stdout.includes('MyGene'));
+        // Specifying no assembly defaults to searching all assemblies
+        p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 2);
+        assert.ok(p.stdout.includes('MyGene'));
+        // Search single assembly
+        p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(p.stdout.includes('MyGene'));
+        // Warn on unknown assembly
+        p = new Shell(`${apollo} feature get-indexed-id ${P} EDEN -a foobar`);
+        assert.strictEqual('[]', p.stdout.trim());
+        assert.ok(p.stderr.includes('Warning'));
+        // Return empty array with no matches
+        p = new Shell(`${apollo} feature get-indexed-id ${P} foobarspam -a vv1`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]');
+        // Gets subfeature
+        p = new Shell(`${apollo} feature get-indexed-id ${P} myCDS.1 -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(out.at(0)?.type === 'CDS');
+        // Gets top-level feature from subfeature id
+        p = new Shell(`${apollo} feature get-indexed-id ${P} myCDS.1 -a vv1 --topLevel`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(out.at(0)?.type === 'gene');
+    });
     void globalThis.itName('Delete features', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`);
         let p = new Shell(`${apollo} feature search ${P} -a vv1 -t EDEN`);

package/oclif.manifest.json

@@ -684,10 +684,22 @@
         "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 +715,33 @@
           "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 +757,30 @@
           "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": {
@@ -1382,6 +1382,69 @@
         "get-id.js"
       ]
     },
+    "feature:get-indexed-id": {
+      "aliases": [],
+      "args": {
+        "id": {
+          "description": "Indexed identifier to search for",
+          "name": "id",
+          "required": true
+        }
+      },
+      "description": "Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file",
+      "examples": [
+        {
+          "description": "Get features for this indexed identifier:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
+        }
+      ],
+      "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": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "topLevel": {
+          "description": "Return the top-level parent of the feature instead of the feature itself",
+          "name": "topLevel",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:get-indexed-id",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get features given an indexed identifier",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "get-indexed-id.js"
+      ]
+    },
     "feature:get": {
       "aliases": [],
       "args": {},
@@ -2196,5 +2259,5 @@
       ]
     }
   },
-  "version": "0.3.8"
+  "version": "0.3.10"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.8",
+  "version": "0.3.10",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -30,7 +30,7 @@
     "posttest": "yarn lint",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
     "test:cli": "yarn tsx src/test/test.ts",
-    "version": "oclif readme --multi --dir ../website/docs/admin/cli/ && oclif readme && git add README.md"
+    "version": "oclif readme --multi --dir ../website/docs/03-guides/04-cli/ && oclif readme && git add README.md"
   },
   "oclif": {
     "bin": "apollo",
@@ -89,8 +89,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.8",
-    "@apollo-annotation/shared": "^0.3.8",
+    "@apollo-annotation/mst": "^0.3.10",
+    "@apollo-annotation/shared": "^0.3.10",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
@@ -99,10 +99,11 @@
     "@types/cross-spawn": "^6.0.6",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
-    "@types/node": "^18.14.2",
+    "@types/node": "^20.19.15",
     "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",
     "prettier": "^3.3.2",