@apollo-annotation/cli 0.3.7 → 0.3.9

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.7 linux-x64 node-v20.19.3
+@apollo-annotation/cli/0.3.9 linux-x64 node-v24.11.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -55,6 +55,7 @@ USAGE
 - [`apollo file get`](#apollo-file-get)
 - [`apollo file upload INPUT-FILE`](#apollo-file-upload-input-file)
 - [`apollo help [COMMANDS]`](#apollo-help-commands)
+- [`apollo jbrowse desktop JBROWSEFILE`](#apollo-jbrowse-desktop-jbrowsefile)
 - [`apollo jbrowse get-config`](#apollo-jbrowse-get-config)
 - [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile)
 - [`apollo login`](#apollo-login)
@@ -114,7 +115,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -150,7 +151,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -192,7 +193,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -220,7 +221,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -242,7 +243,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -277,7 +278,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -301,7 +302,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -353,7 +354,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -381,7 +382,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -412,7 +413,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -445,7 +446,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -476,7 +477,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -500,7 +501,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -542,7 +543,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -582,7 +583,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -616,7 +617,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -640,7 +641,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -674,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -702,7 +703,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -733,7 +734,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -784,7 +785,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -811,7 +812,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -839,7 +840,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -866,7 +867,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -903,7 +904,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -926,6 +927,51 @@ DESCRIPTION
 _See code:
 [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
 
+## `apollo jbrowse desktop JBROWSEFILE`
+
+Generate JBrowse file for use with desktop client
+
+```
+USAGE
+  $ apollo jbrowse desktop JBROWSEFILE [--profile <value>] [--config-file <value>] [-o | -w <value>] [-f <value>]
+
+ARGUMENTS
+  JBROWSEFILE  Generated JBrowse file
+
+FLAGS
+  -f, --gff3-file=<value>    generated session will open the specified file
+  -o, --open                 open generated file
+  -w, --open-with=<value>    open generated file with specified application
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Generate JBrowse file for use with desktop client
+
+  Generates a file that can be opened with JBrowse Desktop. This file has Apollo already configured and, optionally, a
+  GFF3 for local editing configured as well.
+
+EXAMPLES
+  Generate JBrowse file:
+
+    $ apollo jbrowse desktop apollo.jbrowse
+
+  Generate JBrowse file and open with default handler:
+
+    $ apollo jbrowse desktop apollo.jbrowse --open
+
+  Generate JBrowse file and open with specified application:
+
+    $ apollo jbrowse desktop apollo.jbrowse --open-with=path/to/jbrowse.AppImage
+
+  Generate JBrowse file opening specified gff3 file:
+
+    $ apollo jbrowse desktop apollo.jbrowse --gff3-file=path/to/file.gff3
+```
+
+_See code:
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+
 ## `apollo jbrowse get-config`
 
 Get JBrowse configuration from Apollo
@@ -950,7 +996,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -979,7 +1025,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1018,7 +1064,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1048,7 +1094,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1079,7 +1125,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1111,7 +1157,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1133,7 +1179,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1169,6 +1215,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/commands/assembly/check.js

@@ -112,13 +112,10 @@ these checks use `apollo feature check`.';
         inputCheckIds = await convertCheckNameToId(access.address, access.accessToken, flags.check);
         const newChecks = new Set();
         if (flags.delete) {
-            const currentCheckIds = new Set();
             for (const chk of currentChecks) {
-                currentCheckIds.add(chk['_id']);
-            }
-            for (const id of inputCheckIds) {
-                if (!currentCheckIds.has(id)) {
-                    newChecks.add(id);
+                const chkId = chk['_id'];
+                if (!inputCheckIds.includes(chkId)) {
+                    newChecks.add(chkId);
                 }
             }
         }

package/dist/commands/jbrowse/desktop.d.ts

@@ -0,0 +1,18 @@
+import { BaseCommand } from '../../baseCommand.js';
+export default class Desktop extends BaseCommand<typeof Desktop> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static args: {
+        jbrowseFile: import("@oclif/core/lib/interfaces/parser.js").Arg<string, Record<string, unknown>>;
+    };
+    static flags: {
+        open: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'open-with': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'gff3-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    run(): Promise<void>;
+}

package/dist/commands/jbrowse/desktop.js

@@ -0,0 +1,163 @@
+import fsPromises from 'node:fs/promises';
+import path from 'node:path';
+import { Args, Flags } from '@oclif/core';
+import { nanoid } from 'nanoid';
+import open from 'open';
+import { BaseCommand } from '../../baseCommand.js';
+class Gff3File {
+    filepath;
+    stem;
+    uid;
+    constructor(filepath) {
+        this.stem = path.basename(filepath, path.extname(filepath));
+        this.uid = `${this.stem}-${path.basename(filepath)}-${nanoid(8)}`;
+        this.filepath = path.resolve(filepath);
+    }
+    assemblyConfig() {
+        return {
+            name: this.uid,
+            aliases: [this.stem],
+            sequence: {
+                type: 'ReferenceSequenceTrack',
+                trackId: `sequenceConfigId-${this.stem}`,
+                adapter: {
+                    type: 'ApolloSequenceAdapter',
+                    assemblyId: this.uid,
+                },
+                metadata: {
+                    apollo: true,
+                    file: this.filepath,
+                },
+            },
+            displayName: this.stem,
+        };
+    }
+    trackConfig() {
+        return {
+            type: 'ApolloTrack',
+            trackId: this.uid,
+            name: `Annotations (${this.stem})`,
+            assemblyNames: [this.uid],
+        };
+    }
+}
+export default class Desktop extends BaseCommand {
+    static summary = 'Generate JBrowse file for use with desktop client';
+    static description = 'Generates a file that can be opened with JBrowse Desktop. This file has Apollo already configured and, optionally, a GFF3 for local editing configured as well.';
+    static examples = [
+        {
+            description: 'Generate JBrowse file:',
+            command: '<%= config.bin %> <%= command.id %> apollo.jbrowse',
+        },
+        {
+            description: 'Generate JBrowse file and open with default handler:',
+            command: '<%= config.bin %> <%= command.id %> apollo.jbrowse --open',
+        },
+        {
+            description: 'Generate JBrowse file and open with specified application:',
+            command: '<%= config.bin %> <%= command.id %> apollo.jbrowse --open-with=path/to/jbrowse.AppImage',
+        },
+        {
+            description: 'Generate JBrowse file opening specified gff3 file:',
+            command: '<%= config.bin %> <%= command.id %> apollo.jbrowse --gff3-file=path/to/file.gff3',
+        },
+    ];
+    static args = {
+        jbrowseFile: Args.string({
+            description: 'Generated JBrowse file',
+            required: true,
+        }),
+    };
+    static flags = {
+        open: Flags.boolean({
+            char: 'o',
+            description: 'open generated file',
+            exclusive: ['open-with'],
+        }),
+        'open-with': Flags.string({
+            char: 'w',
+            description: 'open generated file with specified application',
+            exclusive: ['open'],
+        }),
+        'gff3-file': Flags.string({
+            char: 'f',
+            description: 'generated session will open the specified file',
+        }),
+    };
+    async run() {
+        const { args, flags } = await this.parse(Desktop);
+        const jbrowseFileContent = {
+            plugins: [
+                {
+                    name: 'Apollo',
+                    umdUrl: 'https://cdn.jsdelivr.net/npm/@apollo-annotation/jbrowse-plugin-apollo/dist/jbrowse-plugin-apollo.umd.production.min.js',
+                },
+            ],
+            assemblies: [],
+            tracks: [],
+            configuration: {
+                theme: {
+                    palette: {
+                        primary: {
+                            main: '#0c4f4b',
+                        },
+                        secondary: {
+                            main: '#1AA39B',
+                        },
+                        tertiary: {
+                            main: '#4f0c10',
+                        },
+                        quaternary: {
+                            main: '#571AA3',
+                        },
+                        framesCDS: [
+                            null,
+                            {
+                                main: 'rgb(204,121,167)',
+                            },
+                            {
+                                main: 'rgb(230,159,0)',
+                            },
+                            {
+                                main: 'rgb(240,228,66)',
+                            },
+                            {
+                                main: 'rgb(86,180,233)',
+                            },
+                            {
+                                main: 'rgb(0,114,178)',
+                            },
+                            {
+                                main: 'rgb(0,158,115)',
+                            },
+                        ],
+                    },
+                },
+                ApolloPlugin: {
+                    ontologies: [
+                        {
+                            name: 'Sequence Ontology',
+                            source: {
+                                uri: 'https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/refs/heads/master/Ontology_Files/so.json',
+                                locationType: 'UriLocation',
+                            },
+                        },
+                    ],
+                },
+            },
+        };
+        if (flags['gff3-file']) {
+            const gff3 = new Gff3File(flags['gff3-file']);
+            jbrowseFileContent.assemblies.push(gff3.assemblyConfig());
+            jbrowseFileContent.tracks.push(gff3.trackConfig());
+        }
+        await fsPromises.writeFile(args.jbrowseFile, JSON.stringify(jbrowseFileContent));
+        if (flags.open || flags['open-with']) {
+            let options = {};
+            if (flags['open-with']) {
+                options = { app: { name: flags['open-with'] } };
+            }
+            await open(args.jbrowseFile, options);
+        }
+    }
+}

package/dist/test/test.js

@@ -19,7 +19,7 @@ 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 { Shell } from './utils.js';
+import { Shell, deleteAllChecks } from './utils.js';
 const apollo = 'yarn dev';
 const P = '--profile testAdmin';
 let configFile = '';
@@ -665,11 +665,12 @@ void describe('Test CLI', () => {
         let p = new Shell(`${apollo} assembly check ${P}`);
         let out = JSON.parse(p.stdout);
         assert.ok(p.stdout.includes('CDSCheck'));
+        assert.ok(p.stdout.includes('TranscriptCheck'));
         const cdsCheckId = out.find((x) => x.name === 'CDSCheck')._id;
         // Test view checks set for assembly
         p = new Shell(`${apollo} assembly check ${P} -a v1`);
         out = JSON.parse(p.stdout);
-        assert.strictEqual(out.length, 1);
+        assert.strictEqual(out.length, 2);
         // Test non-existant assembly
         p = new Shell(`${apollo} assembly check ${P} -a non-existant`, false);
         assert.strictEqual(p.returncode, 1);
@@ -683,20 +684,22 @@ void describe('Test CLI', () => {
         new Shell(`${apollo} assembly check ${P} -a v1 -c CDSCheck CDSCheck`);
         p = new Shell(`${apollo} assembly check ${P} -a v1`);
         out = JSON.parse(p.stdout);
-        assert.strictEqual(out.length, 1);
+        assert.strictEqual(out.length, 2);
         assert.deepStrictEqual(out.at(0).name, 'CDSCheck');
         // Works also with check id
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a v2 -f`);
         new Shell(`${apollo} assembly check ${P} -a v2 -c ${cdsCheckId}`);
         p = new Shell(`${apollo} assembly check ${P} -a v2`);
         out = JSON.parse(p.stdout);
-        assert.strictEqual(out.length, 1);
+        assert.strictEqual(out.length, 2);
         assert.deepStrictEqual(out.at(0).name, 'CDSCheck');
         // Delete check
         new Shell(`${apollo} assembly check ${P} -a v1 -d -c CDSCheck`);
         p = new Shell(`${apollo} assembly check ${P} -a v1`);
         out = JSON.parse(p.stdout);
-        assert.deepStrictEqual(p.stdout.trim(), '[]');
+        assert.strictEqual(out.length, 1);
+        assert.ok(!p.stdout.includes('CDSCheck'));
+        assert.ok(p.stdout.includes('TranscriptCheck'));
     });
     void globalThis.itName('Feature checks', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a v1 -f`);
@@ -729,6 +732,25 @@ void describe('Test CLI', () => {
         p = new Shell(`${apollo} feature check ${P} -i ${xid}`);
         assert.ok(p.stdout.includes('InternalStopCodon'));
     });
+    void globalThis.itName('Delete check results when unregistering a check', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a v1 -f`);
+        let p = new Shell(`${apollo} feature check ${P} -a v1`);
+        let checkResults = JSON.parse(p.stdout);
+        assert.ok(checkResults.length > 1);
+        // Delete all checks and consequently delete all check results
+        p = new Shell(`${apollo} assembly check ${P} -a v1`);
+        const checkNames = JSON.parse(p.stdout).map((x) => x.name);
+        new Shell(`${apollo} assembly check ${P} -a v1 -d -c ${checkNames.join(' ')}`);
+        p = new Shell(`${apollo} feature check ${P} -a v1`);
+        checkResults = JSON.parse(p.stdout);
+        assert.deepEqual(checkResults.length, 0);
+        // Put one check back
+        new Shell(`${apollo} assembly check ${P} -a v1 -c CDSCheck`);
+        p = new Shell(`${apollo} feature check ${P} -a v1`);
+        checkResults = JSON.parse(p.stdout);
+        assert.ok(checkResults.length > 0);
+        assert.deepEqual(checkResults.filter((x) => x.name === 'CDSCheck').length, checkResults.length);
+    });
     void globalThis.itName('User', () => {
         let p = new Shell(`${apollo} user get ${P}`);
         let out = JSON.parse(p.stdout);
@@ -999,6 +1021,8 @@ void describe('Test CLI', () => {
     });
     void globalThis.itName('Position of internal stop codon warning in forward', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/warningPositionForward.gff -a vv1 -f`);
+        deleteAllChecks(apollo, P, 'vv1');
+        new Shell(`${apollo} assembly check ${P} -a vv1 -c CDSCheck`);
         const p = new Shell(`${apollo} feature check ${P} -a vv1`);
         const out = JSON.parse(p.stdout);
         assert.deepStrictEqual(out.length, 2);
@@ -1011,6 +1035,8 @@ void describe('Test CLI', () => {
     });
     void globalThis.itName('Position of internal stop codon warning in reverse', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/warningPositionReverse.gff -a vv1 -f`);
+        deleteAllChecks(apollo, P, 'vv1');
+        new Shell(`${apollo} assembly check ${P} -a vv1 -c CDSCheck`);
         const p = new Shell(`${apollo} feature check ${P} -a vv1`);
         const out = JSON.parse(p.stdout);
         assert.deepStrictEqual(out.length, 2);
@@ -1023,6 +1049,8 @@ void describe('Test CLI', () => {
     });
     void globalThis.itName('Detect missing start codon forward', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/missingStartCodonForward.gff3 -a m1 -f`);
+        deleteAllChecks(apollo, P, 'm1');
+        new Shell(`${apollo} assembly check ${P} -a m1 -c CDSCheck`);
         const p = new Shell(`${apollo} feature check ${P} -a m1`);
         const out = JSON.parse(p.stdout);
         assert.strictEqual(out.length, 1);
@@ -1033,6 +1061,8 @@ void describe('Test CLI', () => {
     });
     void globalThis.itName('Detect missing start codon reverse', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/missingStartCodonReverse.gff3 -a m1 -f`);
+        deleteAllChecks(apollo, P, 'm1');
+        new Shell(`${apollo} assembly check ${P} -a m1 -c CDSCheck`);
         const p = new Shell(`${apollo} feature check ${P} -a m1`);
         const out = JSON.parse(p.stdout);
         assert.strictEqual(out.length, 1);
@@ -1061,4 +1091,62 @@ void describe('Test CLI', () => {
         out = JSON.parse(p.stdout);
         assert.deepStrictEqual(out.at(0)?.max, 30);
     });
+    void globalThis.itName('Check splice site', () => {
+        new Shell(`${apollo} assembly add-from-gff ${P} test_data/checkSplice.fasta.gff3 -f`);
+        deleteAllChecks(apollo, P, 'checkSplice.fasta.gff3');
+        new Shell(`${apollo} assembly check ${P} -a checkSplice.fasta.gff3 -c TranscriptCheck`);
+        let p = new Shell(`${apollo} feature get ${P} -a checkSplice.fasta.gff3`);
+        const features = JSON.parse(p.stdout);
+        const okMrnaId = [];
+        let warnMrnaIdForw;
+        let warnMrnaIdRev;
+        for (const x of features) {
+            const children = Object.values(x.children);
+            for (const child of children) {
+                if (!child.attributes) {
+                    throw new Error('Error getting attributes');
+                }
+                if (JSON.stringify(child.attributes.gff_id) ===
+                    JSON.stringify(['EDEN.1']) ||
+                    JSON.stringify(child.attributes.gff_id) ===
+                        JSON.stringify(['EDEN2.1'])) {
+                    okMrnaId.push(child._id);
+                }
+                if (JSON.stringify(child.attributes.gff_id) === JSON.stringify(['EDEN.2'])) {
+                    warnMrnaIdForw = child._id;
+                }
+                if (JSON.stringify(child.attributes.gff_id) ===
+                    JSON.stringify(['EDEN2.2'])) {
+                    warnMrnaIdRev = child._id;
+                }
+            }
+        }
+        p = new Shell(`${apollo} feature check ${P} -a checkSplice.fasta.gff3 -i ${okMrnaId.join(' ')}`);
+        let out = JSON.parse(p.stdout);
+        assert.deepStrictEqual(out, []);
+        // Check forward transcript
+        p = new Shell(`${apollo} feature check ${P} -a checkSplice.fasta.gff3 -i ${warnMrnaIdForw}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 4);
+        let chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtFivePrime' && x.start === 11);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtFivePrime' && x.start === 31);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtThreePrime' && x.start === 17);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtThreePrime' && x.start === 37);
+        assert.strictEqual(chk.length, 1);
+        // Check reverse transcript
+        p = new Shell(`${apollo} feature check ${P} -a checkSplice.fasta.gff3 -i ${warnMrnaIdRev}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 4);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtThreePrime' && x.start === 11);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtThreePrime' && x.start === 31);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtFivePrime' && x.start === 17);
+        assert.strictEqual(chk.length, 1);
+        chk = out.filter((x) => x.cause === 'NonCanonicalSpliceSiteAtFivePrime' && x.start === 37);
+        assert.strictEqual(chk.length, 1);
+    });
 });

package/dist/test/utils.d.ts

@@ -7,3 +7,4 @@ export declare class Shell {
     stderr: string;
     constructor(cmd: string, strict?: boolean, timeout?: number);
 }
+export declare function deleteAllChecks(apollo: string, profile: string, assembly: string): void;

package/dist/test/utils.js

@@ -26,3 +26,9 @@ export class Shell {
         }
     }
 }
+export function deleteAllChecks(apollo, profile, assembly) {
+    const p = new Shell(`${apollo} assembly check ${profile}`);
+    const out = JSON.parse(p.stdout);
+    const checks = out.map((chk) => chk.name);
+    new Shell(`${apollo} assembly check ${profile} --assembly ${assembly} --delete --check ${checks.join(' ')}`);
+}

package/oclif.manifest.json

@@ -236,6 +236,105 @@
         "status.js"
       ]
     },
+    "change:get": {
+      "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.",
+      "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": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "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",
+        "change",
+        "get.js"
+      ]
+    },
+    "export:gff3": {
+      "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"
+        }
+      ],
+      "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"
+        },
+        "include-fasta": {
+          "description": "Include fasta sequence in output",
+          "name": "include-fasta",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "export:gff3",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "export",
+        "gff3.js"
+      ]
+    },
     "assembly:add-from-fasta": {
       "aliases": [],
       "args": {
@@ -684,105 +783,6 @@
         "sequence.js"
       ]
     },
-    "change:get": {
-      "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.",
-      "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": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "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",
-        "change",
-        "get.js"
-      ]
-    },
-    "export:gff3": {
-      "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"
-        }
-      ],
-      "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"
-        },
-        "include-fasta": {
-          "description": "Include fasta sequence in output",
-          "name": "include-fasta",
-          "allowNo": false,
-          "type": "boolean"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "export:gff3",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "export",
-        "gff3.js"
-      ]
-    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1833,6 +1833,96 @@
         "upload.js"
       ]
     },
+    "jbrowse:desktop": {
+      "aliases": [],
+      "args": {
+        "jbrowseFile": {
+          "description": "Generated JBrowse file",
+          "name": "jbrowseFile",
+          "required": true
+        }
+      },
+      "description": "Generates a file that can be opened with JBrowse Desktop. This file has Apollo already configured and, optionally, a GFF3 for local editing configured as well.",
+      "examples": [
+        {
+          "description": "Generate JBrowse file:",
+          "command": "<%= config.bin %> <%= command.id %> apollo.jbrowse"
+        },
+        {
+          "description": "Generate JBrowse file and open with default handler:",
+          "command": "<%= config.bin %> <%= command.id %> apollo.jbrowse --open"
+        },
+        {
+          "description": "Generate JBrowse file and open with specified application:",
+          "command": "<%= config.bin %> <%= command.id %> apollo.jbrowse --open-with=path/to/jbrowse.AppImage"
+        },
+        {
+          "description": "Generate JBrowse file opening specified gff3 file:",
+          "command": "<%= config.bin %> <%= command.id %> apollo.jbrowse --gff3-file=path/to/file.gff3"
+        }
+      ],
+      "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"
+        },
+        "open": {
+          "char": "o",
+          "description": "open generated file",
+          "exclusive": [
+            "open-with"
+          ],
+          "name": "open",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "open-with": {
+          "char": "w",
+          "description": "open generated file with specified application",
+          "exclusive": [
+            "open"
+          ],
+          "name": "open-with",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "gff3-file": {
+          "char": "f",
+          "description": "generated session will open the specified file",
+          "name": "gff3-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "jbrowse:desktop",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Generate JBrowse file for use with desktop client",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "jbrowse",
+        "desktop.js"
+      ]
+    },
     "jbrowse:get-config": {
       "aliases": [],
       "args": {},
@@ -2106,5 +2196,5 @@
       ]
     }
   },
-  "version": "0.3.7"
+  "version": "0.3.9"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.7",
+  "version": "0.3.9",
   "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",
@@ -82,14 +82,15 @@
     "cli-progress": "^3.12.0",
     "conf": "^12.0.0",
     "joi": "^17.7.0",
+    "nanoid": "^4.0.2",
     "open": "^10.1.0",
     "tslib": "^2.3.1",
     "undici": "^6.7.0",
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.7",
-    "@apollo-annotation/shared": "^0.3.7",
+    "@apollo-annotation/mst": "^0.3.9",
+    "@apollo-annotation/shared": "^0.3.9",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
@@ -98,7 +99,7 @@
     "@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",