@apollo-annotation/cli 0.1.20 → 0.1.21

package/oclif.manifest.json

@@ -240,12 +240,12 @@
       "aliases": [],
       "args": {
         "input": {
-          "description": "Input fasta file, local or remote, or id of a previously uploaded file",
+          "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.",
           "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\n    * An external fasta file\n    * The id of a file previously uploaded to Apollo",
       "examples": [
         {
           "description": "From local file:",
@@ -279,14 +279,6 @@
           "multiple": false,
           "type": "option"
         },
-        "index": {
-          "char": "x",
-          "description": "URL of the index. Required if input is an external source",
-          "name": "index",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "force": {
           "char": "f",
           "description": "Delete existing assembly, if it exists",
@@ -294,10 +286,10 @@
           "allowNo": false,
           "type": "boolean"
         },
-        "not-editable": {
-          "char": "n",
-          "description": "The fasta sequence is not editable. Apollo will not load it into the database and instead use the provided indexes to query it. This option assumes the fasta file is bgzip'd with `bgzip` and indexed with `samtools faidx`. Indexes should be named <my.fasta.gz>.gzi and <my.fasta.gz>.fai unless options --fai and --gzi are set",
-          "name": "not-editable",
+        "editable": {
+          "char": "e",
+          "description": "Instead of using indexed fasta lookup, the sequence is loaded into the Apollo database and is editable. Use with caution, as editing the sequence often has unintended side effects.",
+          "name": "editable",
           "allowNo": false,
           "type": "boolean"
         },
@@ -365,7 +357,7 @@
       "examples": [
         {
           "description": "Import sequences and features:",
-          "command": "<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> genome.gff -a myAssembly"
         },
         {
           "description": "Import sequences only:",
@@ -733,257 +725,6 @@
         "get.js"
       ]
     },
-    "file:delete": {
-      "aliases": [],
-      "args": {},
-      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
-      "examples": [
-        {
-          "description": "Delete file multiple files:",
-          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "IDs of the files to delete",
-          "name": "file-id",
-          "default": [
-            "-"
-          ],
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:delete",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Delete files from the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "delete.js"
-      ]
-    },
-    "file:download": {
-      "aliases": [],
-      "args": {},
-      "description": "See also `apollo file get` to list the files on the server",
-      "examples": [
-        {
-          "description": "Download file with id xyz",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "ID of the file to download",
-          "name": "file-id",
-          "default": "-",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "output": {
-          "char": "o",
-          "description": "Write output to this file or \"-\" for stdout. Default to the name of the uploaded file.",
-          "name": "output",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:download",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Download a file from the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "download.js"
-      ]
-    },
-    "file:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Print to stdout the list of files in json format",
-      "examples": [
-        {
-          "description": "Get files by id:",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "file-id": {
-          "char": "i",
-          "description": "Get files matching this IDs",
-          "name": "file-id",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "file:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get list of files uploaded to the Apollo server",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "file",
-        "get.js"
-      ]
-    },
-    "file:upload": {
-      "aliases": [],
-      "args": {},
-      "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 %> -i 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"
-        },
-        "input-file": {
-          "char": "i",
-          "description": "Local file to upload",
-          "name": "input-file",
-          "required": true,
-          "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": {},
@@ -1664,12 +1405,18 @@
     },
     "feature:import": {
       "aliases": [],
-      "args": {},
+      "args": {
+        "input-file": {
+          "description": "Input gff file",
+          "name": "input-file",
+          "required": true
+        }
+      },
       "description": "By default, features are added to the existing ones.",
       "examples": [
         {
           "description": "Delete features in myAssembly and then import features.gff3:",
-          "command": "<%= config.bin %> <%= command.id %> -d -i features.gff3 -a myAssembly"
+          "command": "<%= config.bin %> <%= command.id %> features.gff3 -d -a myAssembly"
         }
       ],
       "flags": {
@@ -1687,15 +1434,6 @@
           "multiple": false,
           "type": "option"
         },
-        "input-file": {
-          "char": "i",
-          "description": "Input gff file",
-          "name": "input-file",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
         "assembly": {
           "char": "a",
           "description": "Import into this assembly name or assembly ID",
@@ -1789,6 +1527,254 @@
         "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": {},
@@ -1883,12 +1869,18 @@
     },
     "refseq:add-alias": {
       "aliases": [],
-      "args": {},
+      "args": {
+        "input-file": {
+          "description": "Input refname alias file",
+          "name": "input-file",
+          "required": true
+        }
+      },
       "description": "Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads 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"
+          "command": "<%= config.bin %> <%= command.id %> alias.txt -a myAssembly"
         }
       ],
       "flags": {
@@ -1906,15 +1898,6 @@
           "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.",
@@ -2065,5 +2048,5 @@
       ]
     }
   },
-  "version": "0.1.20"
+  "version": "0.1.21"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/cli",
-  "version": "0.1.20",
+  "version": "0.1.21",
   "description": "Command line interface for the Apollo annotation server",
   "repository": {
     "type": "git",
@@ -84,8 +84,8 @@
     "yaml": "^2.3.4"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.1.20",
-    "@apollo-annotation/shared": "^0.1.20",
+    "@apollo-annotation/mst": "^0.1.21",
+    "@apollo-annotation/shared": "^0.1.21",
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",