@apollo-annotation/cli 0.3.1 → 0.3.2

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.1 linux-x64 node-v18.20.5
+@apollo-annotation/cli/0.3.2 linux-x64 node-v18.20.6
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -37,6 +37,7 @@ USAGE
 - [`apollo assembly sequence`](#apollo-assembly-sequence)
 - [`apollo change get`](#apollo-change-get)
 - [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
+- [`apollo export gff3 ASSEMBLY`](#apollo-export-gff3-assembly)
 - [`apollo feature add-child`](#apollo-feature-add-child)
 - [`apollo feature check`](#apollo-feature-check)
 - [`apollo feature copy`](#apollo-feature-copy)
@@ -75,7 +76,8 @@ USAGE
 ARGUMENTS
   INPUT  Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is
          assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at
-         <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided.
+         <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided. A local file can be
+         uncompressed if the flag -e/--editable is set (but see below about using -e)
 
 FLAGS
   -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
@@ -93,22 +95,26 @@ DESCRIPTION
   Add a new assembly from fasta input
 
   Add new assembly. The input fasta may be:
-  * A local file
-  * An external fasta file
+  * A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e)
+  * An external fasta file bgzip'd and indexed
   * The id of a file previously uploaded to Apollo
 
 EXAMPLES
-  From local file:
+  From local file assuming indexes genome.gz.fai and genome.gz.gzi are present:
+
+    $ apollo assembly add-from-fasta genome.fa.gz -a myAssembly
+
+  Local file with editable sequence does not require compression and indexing:
 
     $ apollo assembly add-from-fasta genome.fa -a myAssembly
 
-  From external source we also need the URL of the index:
+  From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi:
 
-    $ apollo assembly add-from-fasta https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
+    $ apollo assembly add-from-fasta https://.../genome.fa.gz -a myAssembly
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -144,7 +150,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -186,7 +192,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -214,7 +220,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -236,7 +242,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -271,7 +277,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -295,7 +301,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -347,7 +353,35 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/config.ts)_
+
+## `apollo export gff3 ASSEMBLY`
+
+Export the annotations for an assembly to stdout as gff3
+
+```
+USAGE
+  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--include-fasta]
+
+ARGUMENTS
+  ASSEMBLY  Export annotations for this assembly name or id
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --include-fasta        Include fasta sequence in output
+  --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Export the annotations for an assembly to stdout as gff3
+
+EXAMPLES
+  Export annotations for myAssembly:
+
+    $ apollo export gff3 myAssembly > out.gff3
+```
+
+_See code:
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -378,7 +412,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -411,7 +445,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -442,7 +476,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -466,7 +500,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -508,7 +542,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -548,7 +582,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -582,7 +616,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -606,7 +640,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -640,7 +674,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -668,7 +702,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -699,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -750,7 +784,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -777,7 +811,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -805,7 +839,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -832,7 +866,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -869,7 +903,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -916,7 +950,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -945,7 +979,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -984,7 +1018,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1014,7 +1048,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1045,7 +1079,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1077,7 +1111,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1099,7 +1133,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1135,6 +1169,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.1/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.2/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

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

@@ -8,17 +8,21 @@ import { queryApollo, submitAssembly } from '../../utils.js';
 export default class AddFasta extends FileCommand {
     static summary = 'Add a new assembly from fasta input';
     static description = `Add new assembly. The input fasta may be:
-    * A local file
-    * An external fasta file
+    * A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e)
+    * An external fasta file bgzip'd and indexed
     * The id of a file previously uploaded to Apollo`;
     static examples = [
         {
-            description: 'From local file:',
+            description: 'From local file assuming indexes genome.gz.fai and genome.gz.gzi are present:',
+            command: '<%= config.bin %> <%= command.id %> genome.fa.gz -a myAssembly',
+        },
+        {
+            description: 'Local file with editable sequence does not require compression and indexing:',
             command: '<%= config.bin %> <%= command.id %> genome.fa -a myAssembly',
         },
         {
-            description: 'From external source we also need the URL of the index:',
-            command: '<%= config.bin %> <%= command.id %> https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly',
+            description: 'From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi:',
+            command: '<%= config.bin %> <%= command.id %> https://.../genome.fa.gz -a myAssembly',
         },
     ];
     static args = {
@@ -27,7 +31,7 @@ export default class AddFasta extends FileCommand {
 file. For local or remote files, it is assumed the file is bgzip'd with \
 `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at \
 <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are \
-provided.",
+provided. A local file can be uncompressed if the flag -e/--editable is set (but see below about using -e)",
             required: true,
         }),
     };
@@ -71,8 +75,19 @@ often has unintended side effects.',
         const isExternal = isValidHttpUrl(args.input);
         let body;
         if (isExternal) {
+            if (flags.editable) {
+                this.error(`External fasta files are not editable. The -e/--editable has been set with an external input file.`);
+            }
             const fai = flags.fai ?? `${args.input}.fai`;
+            const faiExists = await fetch(fai);
+            if (!faiExists.ok) {
+                this.error(`Index file ${fai} does not exist`);
+            }
             const gzi = flags.gzi ?? `${args.input}.gzi`;
+            const gziExists = await fetch(gzi);
+            if (!gziExists.ok) {
+                this.error(`Index file ${gzi} does not exist`);
+            }
             body = {
                 assemblyName,
                 typeName: 'AddAssemblyFromExternalChange',
@@ -106,8 +121,8 @@ often has unintended side effects.',
             const fai = flags.fai ?? `${args.input}.fai`;
             const gziIsFileId = await isFileId(gzi, access.address, access.accessToken);
             const faiIsFileId = await isFileId(fai, access.address, access.accessToken);
-            if (!fs.existsSync(gzi) && !gziIsFileId) {
-                this.error(`Only bgzip'd and indexed fasta files are supported at the moment. "${gzi}" is neither a file or a file id`);
+            if (!fs.existsSync(gzi) && !gziIsFileId && !flags.editable) {
+                this.error(`Only bgzip'd and indexed fasta files are supported unless option -e/--editable is set. "${gzi}" is neither a file or a file id`);
             }
             if (!fs.existsSync(fai) && !faiIsFileId) {
                 this.error(`Only bgzip'd and indexed fasta files are supported at the moment. "${fai}" is neither a file or a file id`);

package/dist/commands/export/gff3.d.ts

@@ -0,0 +1,15 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Get extends BaseCommand<typeof Get> {
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static args: {
+        assembly: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
+    static flags: {
+        'include-fasta': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/export/gff3.js

@@ -0,0 +1,74 @@
+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 = [
+        {
+            description: 'Export annotations for myAssembly:',
+            command: '<%= config.bin %> <%= command.id %> myAssembly > out.gff3',
+        },
+    ];
+    static args = {
+        assembly: Args.string({
+            description: 'Export annotations for this assembly name or id',
+            required: true,
+        }),
+    };
+    static flags = {
+        'include-fasta': Flags.boolean({
+            description: 'Include fasta sequence in output',
+            default: false,
+        }),
+    };
+    async run() {
+        const { args } = await this.parse(Get);
+        const access = await this.getAccess();
+        const assembly = await idReader([args.assembly]);
+        const [assemblyId] = await convertAssemblyNameToId(access.address, access.accessToken, assembly);
+        if (!assemblyId) {
+            this.error(`Invalid assembly name or id: ${args.assembly}`);
+        }
+        const url = new URL(localhostToAddress(`${access.address}/export/getID`));
+        const searchParams = new URLSearchParams({
+            assembly: assemblyId,
+        });
+        url.search = searchParams.toString();
+        const uri = url.toString();
+        const auth = {
+            headers: {
+                authorization: `Bearer ${access.accessToken}`,
+            },
+        };
+        const response = await fetch(uri, auth);
+        if (!response.ok) {
+            const newErrorMessage = await createFetchErrorMessage(response, 'Error when exporting ID');
+            throw new Error(newErrorMessage);
+        }
+        const { exportID } = (await response.json());
+        const exportURL = new URL(localhostToAddress(`${access.address}/export`));
+        const params = {
+            exportID,
+            assemblyId,
+            includeFASTA: this.flags['include-fasta'] ? 'true' : 'false',
+        };
+        const exportSearchParams = new URLSearchParams(params);
+        exportURL.search = exportSearchParams.toString();
+        const exportUri = exportURL.toString();
+        const responseExport = await fetch(exportUri, auth);
+        if (!responseExport.ok) {
+            const newErrorMessage = await createFetchErrorMessage(responseExport, 'Error when exporting gff');
+            throw new Error(newErrorMessage);
+        }
+        const { body } = responseExport;
+        if (body) {
+            const readable = Readable.from(body);
+            readable.pipe(process.stdout);
+        }
+        else {
+            this.error('Failed to export gff3');
+        }
+    }
+}

package/dist/test/test.d.ts

@@ -0,0 +1,11 @@
+/**
+ * USAGE
+ * From package root directory (`packages/apollo-cli`). Run all tests:
+ *
+ * yarn test:cli
+ *
+ * Run only matching pattern:
+ *
+ * yarn test:cli --test-name-pattern='Print help|Feature get'
+ */
+export {};