@apollo-annotation/cli 0.3.6 → 0.3.7

package/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.6 linux-x64 node-v18.20.8
+@apollo-annotation/cli/0.3.7 linux-x64 node-v20.19.3
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -114,7 +114,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
+[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
 
 ## `apollo assembly add-from-gff INPUT-FILE`
 
@@ -150,7 +150,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
+[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -192,7 +192,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/check.ts)_
+[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -220,7 +220,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/delete.ts)_
+[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -242,7 +242,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/get.ts)_
+[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -277,7 +277,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -301,7 +301,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/change/get.ts)_
+[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -353,7 +353,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/config.ts)_
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo export gff3 ASSEMBLY`
 
@@ -381,7 +381,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/export/gff3.ts)_
+[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/export/gff3.ts)_
 
 ## `apollo feature add-child`
 
@@ -412,7 +412,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/add-child.ts)_
+[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -445,7 +445,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/check.ts)_
+[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -476,7 +476,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/copy.ts)_
+[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -500,7 +500,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/delete.ts)_
+[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -542,7 +542,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit.ts)_
+[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -582,7 +582,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -616,7 +616,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -640,7 +640,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -674,7 +674,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get.ts)_
+[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -702,7 +702,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/get-id.ts)_
+[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import INPUT-FILE`
 
@@ -733,7 +733,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/import.ts)_
+[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -784,7 +784,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/feature/search.ts)_
+[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo file delete`
 
@@ -811,7 +811,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/delete.ts)_
+[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/delete.ts)_
 
 ## `apollo file download`
 
@@ -839,7 +839,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/download.ts)_
+[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/download.ts)_
 
 ## `apollo file get`
 
@@ -866,7 +866,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/get.ts)_
+[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/get.ts)_
 
 ## `apollo file upload INPUT-FILE`
 
@@ -903,7 +903,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/file/upload.ts)_
+[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -950,7 +950,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
+[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
 ## `apollo jbrowse set-config INPUTFILE`
 
@@ -979,7 +979,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
 
 ## `apollo login`
 
@@ -1018,7 +1018,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/login.ts)_
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -1048,7 +1048,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/logout.ts)_
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq add-alias INPUT-FILE`
 
@@ -1079,7 +1079,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
+[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
 
 ## `apollo refseq get`
 
@@ -1111,7 +1111,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/refseq/get.ts)_
+[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -1133,7 +1133,7 @@ DESCRIPTION
 ```
 
 _See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/status.ts)_
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -1169,6 +1169,6 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.6/packages/apollo-cli/src/commands/user/get.ts)_
+[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.7/packages/apollo-cli/src/commands/user/get.ts)_
 
 <!-- commandsstop -->

package/dist/commands/feature/edit-attribute.js

@@ -62,31 +62,39 @@ terms to non-existing terms';
         if (featureJson.attributes === undefined) {
             featureJson.attributes = {};
         }
+        const oldAttributes = {};
+        for (const [key, val] of Object.entries(featureJson.attributes)) {
+            if (!val) {
+                continue;
+            }
+            oldAttributes[key] = [...val];
+        }
         if (flags.value === undefined && !flags.delete) {
-            this.log(JSON.stringify(featureJson.attributes[flags.attribute]));
+            this.log(JSON.stringify(oldAttributes[flags.attribute]));
             return;
         }
+        const newAttributes = {};
+        for (const [key, val] of Object.entries(oldAttributes)) {
+            newAttributes[key] = [...val];
+        }
         if (flags.delete) {
             // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
-            delete featureJson.attributes[flags.attribute];
+            delete newAttributes[flags.attribute];
+        }
+        else if (flags.value) {
+            newAttributes[flags.attribute] = flags.value;
         }
         else {
-            featureJson.attributes[flags.attribute] = flags.value;
+            throw new Error(`Unexpected condition: value is "${flags.value}"`);
         }
         const assembly = await getAssemblyFromRefseq(access.address, access.accessToken, featureJson.refSeq);
-        const attrs = {};
-        for (const [key, val] of Object.entries(featureJson.attributes)) {
-            if (!val) {
-                continue;
-            }
-            attrs[key] = [...val];
-        }
         const changeJson = {
             typeName: 'FeatureAttributeChange',
             changedIds: [featureId],
             assembly,
             featureId,
-            attributes: attrs,
+            oldAttributes,
+            newAttributes,
         };
         const url = new URL(localhostToAddress(`${access.address}/changes`));
         const auth = {

package/dist/test/test.d.ts

@@ -6,6 +6,6 @@
  *
  * Run only matching pattern:
  *
- * yarn test:cli --test-name-pattern='Print help|Feature get'
+ * yarn tsx --test-name-pattern='Print help|Feature get' src/test/test.ts
  */
 export {};

package/dist/test/test.js

@@ -13,7 +13,7 @@
  *
  * Run only matching pattern:
  *
- * yarn test:cli --test-name-pattern='Print help|Feature get'
+ * yarn tsx --test-name-pattern='Print help|Feature get' src/test/test.ts
  */
 import assert from 'node:assert';
 import * as crypto from 'node:crypto';
@@ -421,7 +421,7 @@ void describe('Test CLI', () => {
         p = new Shell(`${apollo} feature get ${P} -r ${refseq} | jq '.[] | select(.type == "contig") | ._id'`);
         const fid = p.stdout.trim();
         // Edit existing attribute value
-        p = new Shell(`${apollo} feature edit-attribute ${P} -i $${fid} -a source -v 'Eggs & Stuff'`);
+        p = new Shell(`${apollo} feature edit-attribute ${P} -i ${fid} -a source -v 'Eggs & Stuff'`);
         p = new Shell(`${apollo} feature edit-attribute ${P} -i ${fid} -a source`);
         let out = JSON.parse(p.stdout);
         assert.deepStrictEqual(out.at(0), `Eggs & Stuff`);

package/oclif.manifest.json

@@ -684,22 +684,10 @@
         "sequence.js"
       ]
     },
-    "export:gff3": {
+    "change:get": {
       "aliases": [],
-      "args": {
-        "assembly": {
-          "description": "Export annotations for this assembly name or id",
-          "name": "assembly",
-          "required": true
-        }
-      },
-      "description": "Export the annotations for an assembly to stdout as gff3",
-      "examples": [
-        {
-          "description": "Export annotations for myAssembly:",
-          "command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
-        }
-      ],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -715,33 +703,48 @@
           "multiple": false,
           "type": "option"
         },
-        "include-fasta": {
-          "description": "Include fasta sequence in output",
-          "name": "include-fasta",
-          "allowNo": false,
-          "type": "boolean"
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "export:gff3",
+      "id": "change:get",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
+      "summary": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "export",
-        "gff3.js"
+        "change",
+        "get.js"
       ]
     },
-    "change:get": {
+    "export:gff3": {
       "aliases": [],
-      "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
+      "args": {
+        "assembly": {
+          "description": "Export annotations for this assembly name or id",
+          "name": "assembly",
+          "required": true
+        }
+      },
+      "description": "Export the annotations for an assembly to stdout as gff3",
+      "examples": [
+        {
+          "description": "Export annotations for myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -757,30 +760,27 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
+        "include-fasta": {
+          "description": "Include fasta sequence in output",
+          "name": "include-fasta",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "change:get",
+      "id": "export:gff3",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "change",
-        "get.js"
+        "export",
+        "gff3.js"
       ]
     },
     "feature:add-child": {
@@ -2106,5 +2106,5 @@
       ]
     }
   },
-  "version": "0.3.6"
+  "version": "0.3.7"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.6",
+  "version": "0.3.7",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -88,8 +88,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.6",
-    "@apollo-annotation/shared": "^0.3.6",
+    "@apollo-annotation/mst": "^0.3.7",
+    "@apollo-annotation/shared": "^0.3.7",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",