@apollo-annotation/cli 0.1.18 → 0.1.19

package/oclif.manifest.json

@@ -654,51 +654,6 @@
         "sequence.js"
       ]
     },
-    "change:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed 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"
-      ]
-    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1505,6 +1460,112 @@
         "search.js"
       ]
     },
+    "change:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed 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"
+      ]
+    },
+    "refseq:add-alias": {
+      "aliases": [],
+      "args": {},
+      "description": "Reference name aliasing is a process to make chromosomes that are named slightly\ndifferently but which refer to the same thing render properly. This command\nreads a file with reference name aliases and adds them to the database.",
+      "examples": [
+        {
+          "description": "Add reference name aliases:",
+          "command": "<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly"
+        }
+      ],
+      "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"
+        },
+        "input-file": {
+          "char": "i",
+          "description": "Input refname alias file",
+          "name": "input-file",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name for this assembly.",
+          "name": "assembly",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:add-alias",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add reference name aliases from a file",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "add-alias.js"
+      ]
+    },
     "refseq:get": {
       "aliases": [],
       "args": {},
@@ -1628,5 +1689,5 @@
       ]
     }
   },
-  "version": "0.1.18"
+  "version": "0.1.19"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@apollo-annotation/cli",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.18",
+  "version": "0.1.19",
   "author": "Apollo Team",
   "repository": {
     "type": "git",
@@ -28,7 +28,7 @@
     "dev": "tsx bin/dev.js",
     "postpack": "shx rm -f oclif.manifest.json",
     "posttest": "yarn lint",
-    "prepack": "yarn build && oclif manifest && oclif readme",
+    "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
     "prepare": "yarn build",
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
@@ -41,6 +41,7 @@
     "@oclif/core": "^3.18.2",
     "@oclif/plugin-help": "^6.0.8",
     "bson": "^6.3.0",
+    "cli-progress": "^3.12.0",
     "conf": "^12.0.0",
     "joi": "^17.7.0",
     "open": "^10.1.0",
@@ -49,10 +50,13 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
+    "@apollo-annotation/mst": "^0.1.19",
+    "@apollo-annotation/shared": "^0.1.19",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
     "@types/chai": "^4",
+    "@types/cli-progress": "^3",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
     "@types/node": "^18.14.2",
@@ -60,10 +64,13 @@
     "mocha": "^10.2.0",
     "nyc": "^15.1.0",
     "oclif": "^4.4.2",
+    "prettier": "^3.3.2",
+    "react-dom": "^18.2.0",
+    "rxjs": "^7.4.0",
     "shx": "^0.3.3",
     "ts-node": "^10.3.0",
     "tsx": "^4.6.2",
-    "typescript": "^5.1.6"
+    "typescript": "^5.5.3"
   },
   "oclif": {
     "helpOptions": {