@apollo-annotation/cli 0.3.1 → 0.3.2

package/oclif.manifest.json

@@ -240,20 +240,24 @@
       "aliases": [],
       "args": {
         "input": {
-          "description": "Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided.",
+          "description": "Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided. A local file can be uncompressed if the flag -e/--editable is set (but see below about using -e)",
           "name": "input",
           "required": true
         }
       },
-      "description": "Add new assembly. The input fasta may be:\n    * A local file\n    * An external fasta file\n    * The id of a file previously uploaded to Apollo",
+      "description": "Add new assembly. The input fasta may be:\n    * A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e)\n    * An external fasta file bgzip'd and indexed\n    * The id of a file previously uploaded to Apollo",
       "examples": [
         {
-          "description": "From local file:",
+          "description": "From local file assuming indexes genome.gz.fai and genome.gz.gzi are present:",
+          "command": "<%= config.bin %> <%= command.id %> genome.fa.gz -a myAssembly"
+        },
+        {
+          "description": "Local file with editable sequence does not require compression and indexing:",
           "command": "<%= config.bin %> <%= command.id %> genome.fa -a myAssembly"
         },
         {
-          "description": "From external source we also need the URL of the index:",
-          "command": "<%= config.bin %> <%= command.id %> https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly"
+          "description": "From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi:",
+          "command": "<%= config.bin %> <%= command.id %> https://.../genome.fa.gz -a myAssembly"
         }
       ],
       "flags": {
@@ -680,113 +684,20 @@
         "sequence.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.",
-      "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"
-        },
+      "args": {
         "assembly": {
-          "char": "a",
-          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "description": "Export annotations for this assembly name or id",
           "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"
-      ]
-    },
-    "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"
+          "required": true
         }
       },
-      "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",
+      "description": "Export the annotations for an assembly to stdout as gff3",
       "examples": [
         {
-          "description": "Download file with id xyz",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
+          "description": "Export annotations for myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
         }
       ],
       "flags": {
@@ -804,51 +715,33 @@
           "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"
+        "include-fasta": {
+          "description": "Include fasta sequence in output",
+          "name": "include-fasta",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:download",
+      "id": "export:gff3",
       "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"
+        "export",
+        "gff3.js"
       ]
     },
-    "file:get": {
+    "change: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"
-        }
-      ],
+      "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",
@@ -864,10 +757,10 @@
           "multiple": false,
           "type": "option"
         },
-        "file-id": {
-          "char": "i",
-          "description": "Get files matching this IDs",
-          "name": "file-id",
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
@@ -875,104 +768,21 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:get",
+      "id": "change:get",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of files uploaded to the Apollo server",
+      "summary": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "file",
+        "change",
         "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": {},
@@ -1775,6 +1585,254 @@
         "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 +2106,5 @@
       ]
     }
   },
-  "version": "0.3.1"
+  "version": "0.3.2"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.3.1",
+  "version": "0.3.2",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -29,6 +29,7 @@
     "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
     "posttest": "yarn lint",
     "test:ci": "nyc mocha 'src/**/*.test.ts'",
+    "test:cli": "yarn tsx src/test/test.ts",
     "version": "oclif readme --multi --dir ../website/docs/admin/cli/ && oclif readme && git add README.md"
   },
   "oclif": {
@@ -51,6 +52,9 @@
       "change": {
         "description": "Commands to manage the change log"
       },
+      "export": {
+        "description": "Commands to export data"
+      },
       "feature": {
         "description": "Commands to manage features"
       },
@@ -84,17 +88,19 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.1",
-    "@apollo-annotation/shared": "^0.3.1",
+    "@apollo-annotation/mst": "^0.3.2",
+    "@apollo-annotation/shared": "^0.3.2",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
     "@types/chai": "^4.3.19",
     "@types/cli-progress": "^3",
+    "@types/cross-spawn": "^6.0.6",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
     "@types/node": "^18.14.2",
     "babel-plugin-istanbul": "^6.1.1",
+    "cross-spawn": "^7.0.3",
     "mocha": "^10.2.0",
     "nyc": "^15.1.0",
     "oclif": "^4.4.2",