@apollo-annotation/cli 0.2.0 → 0.2.2

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.2.0 linux-x64 node-v18.20.5
+@apollo-annotation/cli/0.2.2 linux-x64 node-v18.20.5
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -108,7 +108,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -144,7 +144,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -186,7 +186,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -214,7 +214,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -236,7 +236,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -271,7 +271,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -295,7 +295,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -329,10 +329,7 @@ DESCRIPTION
   - accessToken:
   Access token. Usually inserted by `apollo login`
 
-  - rootCredentials.username:
-  Username of root account. Only set this for "root" access type
-
-  - rootCredentials.password:
+  - rootPassword:
   Password for root account. Only set this for "root" access type
 
 EXAMPLES
@@ -350,7 +347,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo feature add-child`
 
@@ -381,7 +378,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -414,7 +411,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -445,7 +442,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -469,7 +466,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -511,7 +508,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -551,7 +548,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -585,7 +582,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -609,7 +606,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -643,7 +640,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -671,7 +668,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -702,7 +699,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -753,7 +750,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -780,7 +777,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -808,7 +805,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -835,7 +832,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -872,7 +869,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -919,7 +916,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -948,7 +945,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -987,7 +984,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1017,7 +1014,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1048,7 +1045,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1080,7 +1077,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1102,7 +1099,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1138,6 +1135,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.0/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.2.2/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/ApolloConf.d.ts

@@ -5,8 +5,7 @@ export declare enum KEYS {
     address = "address",
     accessType = "accessType",
     accessToken = "accessToken",
-    rootCredentials_username = "rootCredentials.username",
-    rootCredentials_password = "rootCredentials.password"
+    rootPassword = "rootPassword"
 }
 export declare function optionDesc(): string[];
 export declare class ApolloConf extends Conf {

package/dist/ApolloConf.js

@@ -12,8 +12,7 @@ export var KEYS;
     KEYS["address"] = "address";
     KEYS["accessType"] = "accessType";
     KEYS["accessToken"] = "accessToken";
-    KEYS["rootCredentials_username"] = "rootCredentials.username";
-    KEYS["rootCredentials_password"] = "rootCredentials.password";
+    KEYS["rootPassword"] = "rootPassword";
 })(KEYS || (KEYS = {}));
 function optionDocs() {
     const docs = [];
@@ -40,14 +39,7 @@ function optionDocs() {
                 });
                 break;
             }
-            case 'rootCredentials.username': {
-                docs.push({
-                    key: v,
-                    description: 'Username of root account. Only set this for "root" access type',
-                });
-                break;
-            }
-            case 'rootCredentials.password': {
+            case 'rootPassword': {
                 docs.push({
                     key: v,
                     description: 'Password for root account. Only set this for "root" access type',
@@ -111,7 +103,7 @@ export class ApolloConf extends Conf {
     }
     setAccessType(profileName, accessType) {
         if (accessType != 'root') {
-            this.delete(`${profileName}.rootCredentials`);
+            this.delete(`${profileName}.rootPassword`);
         }
         this.set(`${profileName}.accessType`, accessType);
     }
@@ -133,10 +125,7 @@ const profileSchema = Joi.object({
     address: Joi.string().uri({ scheme: /https?/ }),
     accessType: Joi.string().valid('google', 'microsoft', 'root', 'guest'),
     accessToken: Joi.string(),
-    rootCredentials: Joi.object({
-        username: Joi.string(),
-        password: Joi.string(),
-    }).when('accessType', {
+    rootPassword: Joi.string().when('accessType', {
         is: Joi.string().valid('root'),
         otherwise: Joi.forbidden(),
     }),

package/dist/commands/config.js

@@ -97,10 +97,8 @@ export default class ApolloConfig extends BaseCommand {
         accessType = await this.selectAccessType(address);
         config.setAccessType(profileName, accessType);
         if (accessType === 'root') {
-            const username = await this.askUsername(config.get(`${profileName}.${KEYS.rootCredentials_username}`));
-            config.set(`${profileName}.rootCredentials.username`, username);
             const password = await this.askPassword();
-            config.set(`${profileName}.rootCredentials.password`, password);
+            config.set(`${profileName}.rootPassword`, password);
         }
     }
     async askProfileName(currentProfiles) {

package/dist/commands/login.js

@@ -74,14 +74,12 @@ need to execute this command again unless the token has expired. To setup a new
                 await this.checkUserAlreadyLoggedIn(config, profileName);
             }
             if (accessType === 'root' || flags.username !== undefined) {
-                const username = flags.username ??
-                    config.get(`${profileName}.rootCredentials.username`);
                 const password = flags.password ??
-                    config.get(`${profileName}.rootCredentials.password`);
-                if (username === undefined || password === undefined) {
+                    config.get(`${profileName}.rootPassword`);
+                if (password === undefined) {
                     this.error('Username and password must be set');
                 }
-                userCredentials = await this.startRootLogin(address, username, password);
+                userCredentials = await this.startRootLogin(address, password);
             }
             else if (accessType === 'guest') {
                 userCredentials = await this.startGuestLogin(address);
@@ -114,12 +112,12 @@ need to execute this command again unless the token has expired. To setup a new
             this.exit(0);
         }
     }
-    async startRootLogin(address, username, password) {
+    async startRootLogin(address, password) {
         const url = localhostToAddress(`${address}/auth/root`);
         const response = await fetch(url, {
             headers: { 'Content-Type': 'application/json' },
             method: 'POST',
-            body: JSON.stringify({ username, password }),
+            body: JSON.stringify({ password }),
         });
         if (!response.ok) {
             const errorMessage = await createFetchErrorMessage(response, 'startRootLogin failed');

package/oclif.manifest.json

@@ -12,7 +12,7 @@
           "name": "value"
         }
       },
-      "description": "Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:\n\n     - address:\nAddress and port e.g http://localhost:3999\n\n- accessType:\nHow to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your Apollo setup\n\n- accessToken:\nAccess token. Usually inserted by `apollo login`\n\n- rootCredentials.username:\nUsername of root account. Only set this for \"root\" access type\n\n- rootCredentials.password:\nPassword for root account. Only set this for \"root\" access type",
+      "description": "Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:\n\n     - address:\nAddress and port e.g http://localhost:3999\n\n- accessType:\nHow to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your Apollo setup\n\n- accessToken:\nAccess token. Usually inserted by `apollo login`\n\n- rootPassword:\nPassword for root account. Only set this for \"root\" access type",
       "examples": [
         {
           "description": "Interactive setup:",
@@ -725,6 +725,254 @@
         "get.js"
       ]
     },
+    "file:delete": {
+      "aliases": [],
+      "args": {},
+      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
+      "examples": [
+        {
+          "description": "Delete file multiple files:",
+          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
+        }
+      ],
+      "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"
+        },
+        "file-id": {
+          "char": "i",
+          "description": "IDs of the files to delete",
+          "name": "file-id",
+          "default": [
+            "-"
+          ],
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:delete",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Delete files from the Apollo server",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "delete.js"
+      ]
+    },
+    "file:download": {
+      "aliases": [],
+      "args": {},
+      "description": "See also `apollo file get` to list the files on the server",
+      "examples": [
+        {
+          "description": "Download file with id xyz",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
+        }
+      ],
+      "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"
+        },
+        "file-id": {
+          "char": "i",
+          "description": "ID of the file to download",
+          "name": "file-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "output": {
+          "char": "o",
+          "description": "Write output to this file or \"-\" for stdout. Default to the name of the uploaded file.",
+          "name": "output",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:download",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Download a file from the Apollo server",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "download.js"
+      ]
+    },
+    "file:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Print to stdout the list of files in json format",
+      "examples": [
+        {
+          "description": "Get files by id:",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
+        }
+      ],
+      "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"
+        },
+        "file-id": {
+          "char": "i",
+          "description": "Get files matching this IDs",
+          "name": "file-id",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of files uploaded to the Apollo server",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "get.js"
+      ]
+    },
+    "file:upload": {
+      "aliases": [],
+      "args": {
+        "input-file": {
+          "description": "Local file to upload",
+          "name": "input-file",
+          "required": true
+        }
+      },
+      "description": "This command only uploads a file and returns the corresponding file id.\n  To add an assembly based on this file or to upload & add an assembly in a single pass   see `apollo assembly add-from-fasta` and `add-from-gff`",
+      "examples": [
+        {
+          "description": "Upload local file, type auto-detected:",
+          "command": "<%= config.bin %> <%= command.id %> genome.fa > file.json"
+        }
+      ],
+      "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"
+        },
+        "type": {
+          "char": "t",
+          "description": "Set file type or autodetected it if not set.\n        NB: There is no check for whether the file complies to this type",
+          "name": "type",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "options": [
+            "text/x-fasta",
+            "text/x-gff3",
+            "application/x-bgzip-fasta",
+            "text/x-fai",
+            "application/x-gzi"
+          ],
+          "type": "option"
+        },
+        "gzip": {
+          "char": "z",
+          "description": "Override autodetection and instruct that input is gzip compressed",
+          "exclusive": [
+            "decompressed"
+          ],
+          "name": "gzip",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "decompressed": {
+          "char": "d",
+          "description": "Override autodetection and instruct that input is decompressed",
+          "exclusive": [
+            "gzip"
+          ],
+          "name": "decompressed",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "file:upload",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Upload a local file to the Apollo server",
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "file",
+        "upload.js"
+      ]
+    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1527,254 +1775,6 @@
         "search.js"
       ]
     },
-    "file:delete": {
-      "aliases": [],
-      "args": {},
-      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
-      "examples": [
-        {
-          "description": "Delete file multiple files:",
-          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
-        }
-      ],
-      "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"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "IDs of the files to delete",
-          "name": "file-id",
-          "default": [
-            "-"
-          ],
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:delete",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Delete files from the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "delete.js"
-      ]
-    },
-    "file:download": {
-      "aliases": [],
-      "args": {},
-      "description": "See also `apollo file get` to list the files on the server",
-      "examples": [
-        {
-          "description": "Download file with id xyz",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
-        }
-      ],
-      "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"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "ID of the file to download",
-          "name": "file-id",
-          "default": "-",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "output": {
-          "char": "o",
-          "description": "Write output to this file or \"-\" for stdout. Default to the name of the uploaded file.",
-          "name": "output",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:download",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Download a file from the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "download.js"
-      ]
-    },
-    "file:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Print to stdout the list of files in json format",
-      "examples": [
-        {
-          "description": "Get files by id:",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
-        }
-      ],
-      "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"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "Get files matching this IDs",
-          "name": "file-id",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get list of files uploaded to the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "get.js"
-      ]
-    },
-    "file:upload": {
-      "aliases": [],
-      "args": {
-        "input-file": {
-          "description": "Local file to upload",
-          "name": "input-file",
-          "required": true
-        }
-      },
-      "description": "This command only uploads a file and returns the corresponding file id.\n  To add an assembly based on this file or to upload & add an assembly in a single pass   see `apollo assembly add-from-fasta` and `add-from-gff`",
-      "examples": [
-        {
-          "description": "Upload local file, type auto-detected:",
-          "command": "<%= config.bin %> <%= command.id %> genome.fa > file.json"
-        }
-      ],
-      "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"
-        },
-        "type": {
-          "char": "t",
-          "description": "Set file type or autodetected it if not set.\n        NB: There is no check for whether the file complies to this type",
-          "name": "type",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "options": [
-            "text/x-fasta",
-            "text/x-gff3",
-            "application/x-bgzip-fasta",
-            "text/x-fai",
-            "application/x-gzi"
-          ],
-          "type": "option"
-        },
-        "gzip": {
-          "char": "z",
-          "description": "Override autodetection and instruct that input is gzip compressed",
-          "exclusive": [
-            "decompressed"
-          ],
-          "name": "gzip",
-          "allowNo": false,
-          "type": "boolean"
-        },
-        "decompressed": {
-          "char": "d",
-          "description": "Override autodetection and instruct that input is decompressed",
-          "exclusive": [
-            "gzip"
-          ],
-          "name": "decompressed",
-          "allowNo": false,
-          "type": "boolean"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:upload",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Upload a local file to the Apollo server",
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "upload.js"
-      ]
-    },
     "jbrowse:get-config": {
       "aliases": [],
       "args": {},
@@ -2048,5 +2048,5 @@
       ]
     }
   },
-  "version": "0.2.0"
+  "version": "0.2.2"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.2.0",
+  "version": "0.2.2",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -84,8 +84,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.2.0",
-    "@apollo-annotation/shared": "^0.2.0",
+    "@apollo-annotation/mst": "^0.2.2",
+    "@apollo-annotation/shared": "^0.2.2",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",