@apollo-annotation/cli 0.3.10 → 0.3.11

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.10 linux-x64 node-v24.11.1
+@apollo-annotation/cli/0.3.11 linux-x64 node-v24.11.1
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -38,6 +38,7 @@ USAGE
 - [`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 [FEATURE-JSON]`](#apollo-feature-add-feature-json)
 - [`apollo feature add-child`](#apollo-feature-add-child)
 - [`apollo feature check`](#apollo-feature-check)
 - [`apollo feature copy`](#apollo-feature-copy)
@@ -116,7 +117,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -152,7 +153,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -194,7 +195,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -222,7 +223,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -244,7 +245,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -279,7 +280,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -303,7 +304,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -355,7 +356,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -383,7 +384,63 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/export/gff3.ts)_
+
+## `apollo feature add [FEATURE-JSON]`
+
+Add one or more features to Apollo
+
+```
+USAGE
+  $ apollo feature add [FEATURE-JSON] [--profile <value>] [--config-file <value>] [-a <value>] [-r <value> -s
+    <value> -e <value> -t <value>] [-F <value>]
+
+ARGUMENTS
+  FEATURE-JSON  Inline JSON describing the feature(s) to add. Can also be provided via stdin.
+
+FLAGS
+  -F, --feature-json-file=<value>  File with JSON describing the feature(s) to add
+  -a, --assembly=<value>           Name or ID of target assembly. Not required if refseq is unique in the database
+  -e, --max=<value>                End position in target reference sequence
+  -r, --refSeq=<value>             Name or ID of target reference sequence
+  -s, --min=<value>                Start position in target reference sequence
+  -t, --type=<value>               Type of child feature
+      --config-file=<value>        Use this config file (mostly for testing)
+      --profile=<value>            Use credentials from this profile
+
+DESCRIPTION
+  Add one or more features to Apollo
+
+  A single simple feature can be added using the --min, --max, etc. flags.
+
+  To add multiple features, features with more details, or features with children, you can pass in JSON via argument or
+  stdin or use the --feature-json-file options.
+
+
+EXAMPLES
+  Add a single feature by specifying its location and type
+
+    $ apollo feature add --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark
+
+  Add a single feature from inline JSON
+
+    $ apollo feature add \
+      '{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"}'
+
+  Add mutilple features from stdin JSON
+
+    echo '[{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"},{" \
+      assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":101,"max":200,"type":"<featureType>"}]' | \
+      apollo feature add
+
+  Add a feature with children from inline JSON
+
+    $ apollo feature add '{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<fe \
+      atureType>","children":[{"min":1,"max":50,"type":"<featureType>"}]}'
+```
+
+_See code:
+[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add.ts)_
 
 ## `apollo feature add-child`
 
@@ -414,7 +471,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -447,7 +504,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -478,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -502,7 +559,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -544,7 +601,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -584,7 +641,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -618,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -642,7 +699,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -676,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -704,7 +761,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature get-indexed-id ID`
 
@@ -736,7 +793,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
+[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -767,7 +824,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -818,7 +875,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -845,7 +902,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -873,7 +930,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -900,7 +957,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -937,7 +994,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -1003,7 +1060,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
+[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
 
 ## `apollo jbrowse get-config`
 
@@ -1029,7 +1086,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -1058,7 +1115,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1097,7 +1154,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1127,7 +1184,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1158,7 +1215,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1190,7 +1247,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1212,7 +1269,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1248,6 +1305,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.10/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/commands/feature/add.d.ts

@@ -0,0 +1,57 @@
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type SerializedAddFeatureChange } from '@apollo-annotation/shared';
+import { type Response } from 'undici';
+import { BaseCommand } from '../../baseCommand.js';
+interface BaseFeatureJSON {
+    min: number;
+    max: number;
+    type: string;
+    children?: BaseFeatureJSON[];
+    [key: string]: unknown;
+}
+interface FeatureJSON extends BaseFeatureJSON {
+    assembly?: string;
+    refSeq: string;
+}
+export default class Add extends BaseCommand<typeof Add> {
+    static summary: string;
+    static description: string;
+    static examples: {
+        description: string;
+        command: string;
+    }[];
+    static flags: {
+        assembly: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        refSeq: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        min: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        max: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        type: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'feature-json-file': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string | undefined, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+    };
+    static args: {
+        'feature-json': import("@oclif/core/lib/interfaces/parser.js").Arg<string | undefined, Record<string, unknown>>;
+    };
+    run(): Promise<void>;
+    addFeatureFromJSON(featureJSONString: string): Promise<void>;
+    makeFeatureSnapshot(details: FeatureJSON, ids: string[]): AnnotationFeatureSnapshot;
+    addFeatureFromFlags(refSeqNameOrId: string, min: number, max: number, type: string, assemblyNameOrId?: string): Promise<void>;
+    getAssemblyAndRefSeqIds(refSeqNameOrId: string, assemblyNameOrId?: string): Promise<[string, string]>;
+    getAssembly(assemblyNameOrId: string): Promise<{
+        _id: string;
+        name: string;
+        aliases?: string[];
+    }>;
+    getRefSeq(refSeqNameOrId: string, assemblyId?: string): Promise<{
+        _id: string;
+        name: string;
+        assembly: string;
+        aliases?: string[];
+    }>;
+    submitChange(change: SerializedAddFeatureChange): Promise<void>;
+    fetch(endpoint: string, options?: {
+        method?: string;
+        body?: string;
+        headers?: Record<string, string>;
+    }): Promise<Response>;
+}
+export {};

package/dist/commands/feature/add.js

@@ -0,0 +1,323 @@
+import { readFile } from 'node:fs/promises';
+import { Args, Flags } from '@oclif/core';
+import { ObjectId } from 'bson';
+import { fetch } from 'undici';
+import { BaseCommand } from '../../baseCommand.js';
+import { createFetchErrorMessage, localhostToAddress } from '../../utils.js';
+export default class Add extends BaseCommand {
+    static summary = 'Add one or more features to Apollo';
+    static description = `A single simple feature can be added using the --min, --max, etc. flags.
+
+To add multiple features, features with more details, or features with children, you can pass in JSON via argument or stdin or use the --feature-json-file options.
+`;
+    static examples = [
+        {
+            description: 'Add a single feature by specifying its location and type',
+            command: '<%= config.bin %> <%= command.id %> --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark',
+        },
+        {
+            description: 'Add a single feature from inline JSON',
+            command: '<%= config.bin %> <%= command.id %> \'{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"}\'',
+        },
+        {
+            description: 'Add mutilple features from stdin JSON',
+            command: 'echo \'[{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"},{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":101,"max":200,"type":"<featureType>"}]\' | <%= config.bin %> <%= command.id %>',
+        },
+        {
+            description: 'Add a feature with children from inline JSON',
+            command: '<%= config.bin %> <%= command.id %> \'{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>","children":[{"min":1,"max":50,"type":"<featureType>"}]}\'',
+        },
+    ];
+    static flags = {
+        assembly: Flags.string({
+            char: 'a',
+            description: 'Name or ID of target assembly. Not required if refseq is unique in the database',
+        }),
+        refSeq: Flags.string({
+            char: 'r',
+            description: 'Name or ID of target reference sequence',
+            dependsOn: ['min', 'max', 'type'],
+            exclusive: ['feature-json-file'],
+        }),
+        min: Flags.integer({
+            char: 's',
+            description: 'Start position in target reference sequence',
+            dependsOn: ['refSeq', 'max', 'type'],
+            exclusive: ['feature-json-file'],
+        }),
+        max: Flags.integer({
+            char: 'e',
+            description: 'End position in target reference sequence',
+            dependsOn: ['refSeq', 'min', 'type'],
+            exclusive: ['feature-json-file'],
+        }),
+        type: Flags.string({
+            char: 't',
+            description: 'Type of child feature',
+            dependsOn: ['refSeq', 'min', 'max'],
+            exclusive: ['feature-json-file'],
+        }),
+        'feature-json-file': Flags.file({
+            char: 'F',
+            description: 'File with JSON describing the feature(s) to add',
+            exists: true,
+        }),
+    };
+    static args = {
+        'feature-json': Args.string({
+            description: 'Inline JSON describing the feature(s) to add. Can also be provided via stdin.',
+        }),
+    };
+    async run() {
+        const { args, flags } = this;
+        const { 'feature-json': featureJSONString } = args;
+        const { assembly, refSeq, min, max, type, 'feature-json-file': featureJSONFile, } = flags;
+        if (featureJSONString) {
+            if (assembly !== undefined ||
+                refSeq !== undefined ||
+                min !== undefined ||
+                max !== undefined ||
+                type !== undefined ||
+                featureJSONFile !== undefined) {
+                this.error('Cannot use the following flags when providing a feature JSON: --assembly, --refSeq, --min, --max, --type, --feature-json-file');
+            }
+            await this.addFeatureFromJSON(featureJSONString);
+            return;
+        }
+        if (featureJSONFile) {
+            const fileText = await readFile(featureJSONFile, 'utf8');
+            await this.addFeatureFromJSON(fileText);
+            return;
+        }
+        if (refSeq === undefined ||
+            min === undefined ||
+            max === undefined ||
+            type === undefined) {
+            this.error('Must provide all of: --refSeq, --min, --max, and --type');
+        }
+        await this.addFeatureFromFlags(refSeq, min, max, type, assembly);
+    }
+    async addFeatureFromJSON(featureJSONString) {
+        let featureJSON;
+        try {
+            featureJSON = parseFeatureJSON(featureJSONString);
+        }
+        catch (error) {
+            this.logToStderr('Error: feature JSON is not valid');
+            if (error instanceof Error || typeof error === 'string') {
+                this.error(error);
+            }
+            throw error;
+        }
+        if (Array.isArray(featureJSON)) {
+            const firstFeature = featureJSON.at(0);
+            if (!firstFeature) {
+                throw new Error('Feature array is empty');
+            }
+            const { assembly, refSeq } = firstFeature;
+            if (!featureJSON.every((feature) => feature.assembly === assembly)) {
+                throw new Error('Cannot add features to multiple assemblies at the same time');
+            }
+            const [assemblyId] = await this.getAssemblyAndRefSeqIds(refSeq, assembly);
+            const changedIds = [];
+            const changes = await Promise.all(featureJSON.map(async (singleFeatureJSON) => {
+                const { children, assembly, refSeq, ...rest } = singleFeatureJSON;
+                const refSeqDocument = await this.getRefSeq(refSeq);
+                return {
+                    addedFeature: this.makeFeatureSnapshot({
+                        assembly: assemblyId,
+                        refSeq: refSeqDocument._id,
+                        ...rest,
+                    }, changedIds),
+                };
+            }));
+            const change = {
+                changedIds,
+                typeName: 'AddFeatureChange',
+                assembly: assemblyId,
+                changes,
+            };
+            return this.submitChange(change);
+        }
+        const { assembly, refSeq, ...rest } = featureJSON;
+        const [assemblyId, refSeqId] = await this.getAssemblyAndRefSeqIds(refSeq, assembly);
+        const changedIds = [];
+        const details = {
+            addedFeature: this.makeFeatureSnapshot({
+                assembly: assemblyId,
+                refSeq: refSeqId,
+                ...rest,
+            }, changedIds),
+        };
+        const change = {
+            changedIds,
+            typeName: 'AddFeatureChange',
+            assembly: assemblyId,
+            ...details,
+        };
+        return this.submitChange(change);
+    }
+    makeFeatureSnapshot(details, ids) {
+        const { children, ...rest } = details;
+        let childrenDetails = undefined;
+        if (children) {
+            childrenDetails = {};
+            const { refSeq } = rest;
+            for (const child of children) {
+                const childDetails = this.makeFeatureSnapshot({ refSeq, ...child }, ids);
+                childrenDetails[childDetails._id] = childDetails;
+            }
+        }
+        const _id = new ObjectId().toHexString();
+        ids.push(_id);
+        return {
+            _id,
+            ...rest,
+            ...(childrenDetails ? { children: childrenDetails } : {}),
+        };
+    }
+    async addFeatureFromFlags(refSeqNameOrId, min, max, type, assemblyNameOrId) {
+        const [assemblyId, refSeqId] = await this.getAssemblyAndRefSeqIds(refSeqNameOrId, assemblyNameOrId);
+        const changedIds = [];
+        const details = {
+            addedFeature: this.makeFeatureSnapshot({ refSeq: refSeqId, min: min - 1, max, type }, changedIds),
+        };
+        const change = {
+            changedIds,
+            typeName: 'AddFeatureChange',
+            assembly: assemblyId,
+            ...details,
+        };
+        return this.submitChange(change);
+    }
+    async getAssemblyAndRefSeqIds(refSeqNameOrId, assemblyNameOrId) {
+        const refSeqIsObjectId = ObjectId.isValid(refSeqNameOrId);
+        const assemblyIsObjectId = assemblyNameOrId
+            ? ObjectId.isValid(assemblyNameOrId)
+            : false;
+        if (assemblyNameOrId && assemblyIsObjectId && refSeqIsObjectId) {
+            return [assemblyNameOrId, refSeqNameOrId];
+        }
+        if (refSeqIsObjectId) {
+            if (assemblyNameOrId) {
+                this.warn('Ignoring provided --assembly because it is not an ID');
+            }
+            const refSeqDocument = await this.getRefSeq(refSeqNameOrId);
+            return [refSeqDocument.assembly, refSeqNameOrId];
+        }
+        if (!assemblyNameOrId) {
+            this.error(`If provided refSeq (${refSeqNameOrId}) is not an ID, assembly must also be provided`);
+        }
+        const assemblyDocument = await this.getAssembly(assemblyNameOrId);
+        const refSeqDocument = await this.getRefSeq(refSeqNameOrId, assemblyDocument._id);
+        return [assemblyDocument._id, refSeqDocument._id];
+    }
+    async getAssembly(assemblyNameOrId) {
+        if (ObjectId.isValid(assemblyNameOrId)) {
+            const response = await this.fetch(`assemblies/${assemblyNameOrId}`);
+            if (!response.ok) {
+                const errorMessage = await createFetchErrorMessage(response, `Could not find assembly: "${assemblyNameOrId}"`);
+                this.error(errorMessage);
+            }
+            return response.json();
+        }
+        const response = await this.fetch('assemblies');
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, `Could not find assembly: "${assemblyNameOrId}"`);
+            this.error(errorMessage);
+        }
+        const assemblies = (await response.json());
+        for (const assembly of assemblies) {
+            if (assembly.name === assemblyNameOrId ||
+                assembly.aliases?.includes(assemblyNameOrId)) {
+                return assembly;
+            }
+        }
+        throw new Error(`Could not find assembly: "${assemblyNameOrId}"`);
+    }
+    async getRefSeq(refSeqNameOrId, assemblyId) {
+        if (ObjectId.isValid(refSeqNameOrId)) {
+            const response = await this.fetch(`refSeqs/${refSeqNameOrId}`);
+            if (!response.ok) {
+                const errorMessage = await createFetchErrorMessage(response, `Could not find refSeq: "${refSeqNameOrId}"`);
+                this.error(errorMessage);
+            }
+            return response.json();
+        }
+        let endpoint = 'refSeqs';
+        if (assemblyId) {
+            const searchParams = new URLSearchParams({ assembly: assemblyId });
+            endpoint = `${endpoint}?${searchParams.toString()}`;
+        }
+        const response = await this.fetch(endpoint);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, `Could not find refSeq: "${refSeqNameOrId}"`);
+            this.error(errorMessage);
+        }
+        const refSeqs = (await response.json());
+        for (const refSeq of refSeqs) {
+            if (refSeq.name === refSeqNameOrId ||
+                refSeq.aliases?.includes(refSeqNameOrId)) {
+                return refSeq;
+            }
+        }
+        throw new Error(`Could not find refSeq: "${refSeqNameOrId}"`);
+    }
+    async submitChange(change) {
+        const options = { method: 'POST', body: JSON.stringify(change) };
+        const response = await this.fetch('changes', options);
+        if (!response.ok) {
+            const errorMessage = await createFetchErrorMessage(response, 'Could not add feature');
+            this.error(errorMessage);
+        }
+        this.log(await response.text());
+    }
+    async fetch(endpoint, options) {
+        const { address, accessToken } = await this.getAccess();
+        const url = new URL(localhostToAddress(`${address}/${endpoint}`));
+        const optionsWithAuth = {
+            ...options,
+            headers: {
+                authorization: `Bearer ${accessToken}`,
+                'Content-Type': 'application/json',
+                ...options?.headers,
+            },
+        };
+        return fetch(url, optionsWithAuth);
+    }
+}
+function parseFeatureJSON(featureJSONString) {
+    const featureJSON = JSON.parse(featureJSONString);
+    if (Array.isArray(featureJSON)) {
+        return featureJSON.map((feature) => {
+            assertFeatureIsValid(feature, true);
+            return feature;
+        });
+    }
+    assertFeatureIsValid(featureJSON, true);
+    return featureJSON;
+}
+function assertFeatureIsValid(feature, topLevel = false) {
+    if (typeof feature !== 'object' ||
+        feature === null ||
+        Array.isArray(feature)) {
+        throw new TypeError(`Feature is not a key-value record: '${JSON.stringify(feature)}'`);
+    }
+    for (const attribute of ['min', 'max', 'type']) {
+        if (!(attribute in feature)) {
+            throw new Error(`Feature does not contain "${attribute}": '${JSON.stringify(feature)}'`);
+        }
+    }
+    if (topLevel && !('refSeq' in feature)) {
+        throw new Error(`Top-level feature does not contain "refSeq": '${JSON.stringify(feature)}'`);
+    }
+    if ('children' in feature) {
+        const { children } = feature;
+        if (!Array.isArray(children)) {
+            throw new TypeError(`"children" is not an array of features '${JSON.stringify(feature)}'`);
+        }
+        for (const child of children) {
+            assertFeatureIsValid(child);
+        }
+    }
+}

package/dist/test/test.js

@@ -554,6 +554,75 @@ void describe('Test CLI', () => {
         out = JSON.parse(p.stdout);
         assert.strictEqual(out.length, 1);
         assert.ok(out.at(0)?.type === 'gene');
+        // Gets feature and child feature that were added manually (not imported)
+        p = new Shell(`${apollo} feature add ${P} <<EOF
+{
+  "assembly": "vv1",
+  "refSeq": "ctgA",
+  "min": 301,
+  "max": 310,
+  "type": "match",
+  "attributes": {"gff_id": ["match1"]},
+  "children": [
+    {
+      "min": 301,
+      "max": 305,
+      "type": "match_part",
+      "attributes": {"gff_id": ["matchPart1"]}
+    }
+  ]
+}
+EOF`);
+        p = new Shell(`${apollo} feature get-indexed-id ${P} match1 -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(p.stdout.includes('match1'));
+        p = new Shell(`${apollo} feature get-indexed-id ${P} matchPart1 -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(p.stdout.includes('matchPart1'));
+        // Doesn't get child feature after it was deleted
+        const idToDelete = out[0]._id;
+        new Shell(`${apollo} feature delete ${P} -i ${idToDelete}`);
+        p = new Shell(`${apollo} feature get-indexed-id ${P} matchPart1 -a vv1`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]');
+        // Gets feature after ID was manually added
+        p = new Shell(`${apollo} feature add ${P} <<EOF
+{
+  "assembly": "vv1",
+  "refSeq": "ctgA",
+  "min": 311,
+  "max": 320,
+  "type": "match"
+}
+EOF`);
+        out = JSON.parse(p.stdout);
+        const { assembly, changes } = out;
+        const { _id, refSeq } = changes[0].addedFeature;
+        new Shell(`${apollo} feature edit-attribute ${P} -i ${_id} -a gff_id -v match2`);
+        p = new Shell(`${apollo} feature get-indexed-id ${P} match2 -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(p.stdout.includes('match2'));
+        // Gets child featuer after it was added with an ID
+        // add-child CLI command doesn't support adding attributes yet, so we'll
+        // manually do it with curl for testing for neow
+        p = new Shell(`${apollo} config ${P} accessToken`);
+        const token = p.stdout.trim();
+        const newChildFeatureID = '69408088d502fc21aea1bb0a';
+        new Shell(`curl -X POST http://127.0.0.1:3999/changes -d '{"typeName":"AddFeatureChange","changedIds":["${newChildFeatureID}"],"assembly":"${assembly}","addedFeature":{"_id":"${newChildFeatureID}","refSeq":"${refSeq}","min":311,"max":315,"type":"match_part","attributes":{"gff_id":["matchPart2"]}},"parentFeatureId":"${_id}"}' -H "Content-Type: application/json" -H "Authorization: Bearer ${token}"`);
+        p = new Shell(`${apollo} feature get-indexed-id ${P} matchPart2 -a vv1`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        assert.ok(p.stdout.includes('matchPart2'));
+        // Doesn't get feature or child after IDs were manually removed
+        new Shell(`${apollo} feature edit-attribute ${P} -i ${_id} -a gff_id -d`);
+        const childId = out[0]._id;
+        new Shell(`${apollo} feature edit-attribute ${P} -i ${childId} -a gff_id -d`);
+        p = new Shell(`${apollo} feature get-indexed-id ${P} match2 -a vv1`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]');
+        p = new Shell(`${apollo} feature get-indexed-id ${P} matchPart2 -a vv1`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]');
     });
     void globalThis.itName('Delete features', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`);
@@ -570,6 +639,75 @@ void describe('Test CLI', () => {
         p = new Shell(`${apollo} feature delete ${P} --force -i ${fid}`);
         assert.strictEqual(p.returncode, 0);
     });
+    void globalThis.itName('Add features', () => {
+        let p = new Shell(`${apollo} assembly add-from-fasta ${P} test_data/tiny.fasta.gz -a tiny -f`);
+        let out = JSON.parse(p.stdout);
+        const assemblyId = out._id;
+        p = new Shell(`${apollo} feature get ${P} -a tiny`);
+        assert.deepStrictEqual(p.stdout.trim(), '[]');
+        // Can add a feature using flags
+        p = new Shell(`${apollo} feature add ${P} -a tiny -r ctgA -s 1 -e 10 -t remark`);
+        out = JSON.parse(p.stdout);
+        p = new Shell(`${apollo} feature get ${P} -a tiny`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 1);
+        const refSeqId = out[0].refSeq;
+        // Can add a feature using assembly and refSeq ids
+        p = new Shell(`${apollo} feature add ${P} -a ${assemblyId} -r ${refSeqId} -s 11 -e 20 -t remark`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 2);
+        // Can add a feature using JSON arg
+        p = new Shell(`${apollo} feature add ${P} '{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":21,"max":30,"type":"remark"}'`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 3);
+        // Can add a feature using JSON from stdin
+        p = new Shell(`${apollo} feature add ${P} <<EOF
+{
+  "assembly": "${assemblyId}",
+  "refSeq": "${refSeqId}",
+  "min": 31,
+  "max": 40,
+  "type": "remark"
+}
+EOF`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 4);
+        // Can add a feature using JSON from a file
+        fs.writeFileSync('test_data/tmp.json', `{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":41,"max":50,"type":"remark"}\n`);
+        p = new Shell(`${apollo} feature add ${P} --feature-json-file test_data/tmp.json`);
+        fs.unlinkSync('test_data/tmp.json');
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 5);
+        // Can add multiple features using JSON
+        p = new Shell(`${apollo} feature add ${P} '[{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":51,"max":60,"type":"remark"},{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":61,"max":70,"type":"remark"}]'`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId}`);
+        out = JSON.parse(p.stdout);
+        assert.strictEqual(out.length, 7);
+        // Can add a feature with children from JSON
+        p = new Shell(`${apollo} feature add ${P} '{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":71,"max":80,"type":"match","children":[{"min":71,"max":75,"type":"match_part"}]}'`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId} -r ${refSeqId} -s 71 -e 80`);
+        out = JSON.parse(p.stdout);
+        let feature = out.at(0);
+        assert.strictEqual(Object.keys(feature?.children).length, 1);
+        // Can add a feature with attributes from JSON
+        p = new Shell(`${apollo} feature add ${P} '{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":81,"max":90,"type":"remark","attributes":{"key1":["val1"]}}'`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId} -r ${refSeqId} -s 81 -e 90`);
+        out = JSON.parse(p.stdout);
+        feature = out.at(0);
+        assert.strictEqual(feature?.attributes?.key1?.[0], 'val1');
+        // Can add a feature with children from JSON
+        p = new Shell(`${apollo} feature add ${P} '{"assembly":"${assemblyId}","refSeq":"${refSeqId}","min":91,"max":100,"type":"match","children":[{"min":91,"max":95,"type":"match_part","attributes":{"key2":["val2"]}}]}'`);
+        p = new Shell(`${apollo} feature get ${P} -a ${assemblyId} -r ${refSeqId} -s 91 -e 100`);
+        out = JSON.parse(p.stdout);
+        feature = out.at(0);
+        const keys = Object.keys(feature?.children);
+        assert.strictEqual(keys.length, 1);
+        assert.strictEqual(feature.children[keys[0]].attributes.key2[0], 'val2');
+    });
     void globalThis.itName('Add child features', () => {
         new Shell(`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`);
         let p = new Shell(`${apollo} feature search ${P} -a vv1 -t contig`);

package/oclif.manifest.json

@@ -684,6 +684,51 @@
         "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": {
@@ -738,10 +783,16 @@
         "gff3.js"
       ]
     },
-    "change:get": {
+    "feature:add-child": {
       "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.",
+      "description": "See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature with attributes.",
+      "examples": [
+        {
+          "description": "Add an exon at genomic coordinates 10..20 to this feature ID:",
+          "command": "<%= config.bin %> <%= command.id %> -i 660...73f -t exon -s 10 -e 20"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -757,40 +808,85 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
+        "feature-id": {
+          "char": "i",
+          "description": "Add a child to this feature ID; use - to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start coordinate of the child feature (1-based)",
+          "name": "start",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "End coordinate of the child feature (1-based)",
+          "name": "end",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Type of child feature",
+          "name": "type",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
           "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "change:get",
+      "id": "feature:add-child",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of changes",
+      "summary": "Add a child feature (e.g. add an exon to an mRNA)",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "change",
-        "get.js"
+        "feature",
+        "add-child.js"
       ]
     },
-    "feature:add-child": {
+    "feature:add": {
       "aliases": [],
-      "args": {},
-      "description": "See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature with attributes.",
+      "args": {
+        "feature-json": {
+          "description": "Inline JSON describing the feature(s) to add. Can also be provided via stdin.",
+          "name": "feature-json"
+        }
+      },
+      "description": "A single simple feature can be added using the --min, --max, etc. flags.\n\nTo add multiple features, features with more details, or features with children, you can pass in JSON via argument or stdin or use the --feature-json-file options.\n",
       "examples": [
         {
-          "description": "Add an exon at genomic coordinates 10..20 to this feature ID:",
-          "command": "<%= config.bin %> <%= command.id %> -i 660...73f -t exon -s 10 -e 20"
+          "description": "Add a single feature by specifying its location and type",
+          "command": "<%= config.bin %> <%= command.id %> --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark"
+        },
+        {
+          "description": "Add a single feature from inline JSON",
+          "command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"}'"
+        },
+        {
+          "description": "Add mutilple features from stdin JSON",
+          "command": "echo '[{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"},{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":101,\"max\":200,\"type\":\"<featureType>\"}]' | <%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Add a feature with children from inline JSON",
+          "command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\",\"children\":[{\"min\":1,\"max\":50,\"type\":\"<featureType>\"}]}'"
         }
       ],
       "flags": {
@@ -808,38 +904,82 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Add a child to this feature ID; use - to read it from stdin",
-          "name": "feature-id",
-          "default": "-",
+        "assembly": {
+          "char": "a",
+          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
+          "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "start": {
+        "refSeq": {
+          "char": "r",
+          "dependsOn": [
+            "min",
+            "max",
+            "type"
+          ],
+          "description": "Name or ID of target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "refSeq",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "min": {
           "char": "s",
-          "description": "Start coordinate of the child feature (1-based)",
-          "name": "start",
-          "required": true,
+          "dependsOn": [
+            "refSeq",
+            "max",
+            "type"
+          ],
+          "description": "Start position in target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "min",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "end": {
+        "max": {
           "char": "e",
-          "description": "End coordinate of the child feature (1-based)",
-          "name": "end",
-          "required": true,
+          "dependsOn": [
+            "refSeq",
+            "min",
+            "type"
+          ],
+          "description": "End position in target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "max",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
         "type": {
           "char": "t",
+          "dependsOn": [
+            "refSeq",
+            "min",
+            "max"
+          ],
           "description": "Type of child feature",
+          "exclusive": [
+            "feature-json-file"
+          ],
           "name": "type",
-          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "feature-json-file": {
+          "char": "F",
+          "description": "File with JSON describing the feature(s) to add",
+          "name": "feature-json-file",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -847,19 +987,19 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:add-child",
+      "id": "feature:add",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Add a child feature (e.g. add an exon to an mRNA)",
+      "summary": "Add one or more features to Apollo",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "add-child.js"
+        "add.js"
       ]
     },
     "feature:check": {
@@ -2259,5 +2399,5 @@
       ]
     }
   },
-  "version": "0.3.10"
+  "version": "0.3.11"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.10",
+  "version": "0.3.11",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -89,8 +89,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.10",
-    "@apollo-annotation/shared": "^0.3.10",
+    "@apollo-annotation/mst": "^0.3.11",
+    "@apollo-annotation/shared": "^0.3.11",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",