@apollo-annotation/cli 1.1.1 → 1.1.2

package/oclif.manifest.json

@@ -43,6 +43,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "get-config-file": {
           "description": "Return the path to the config file and exit (this file may not exist yet)",
           "name": "get-config-file",
@@ -95,6 +103,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "address": {
           "char": "a",
           "description": "Address of Apollo server",
@@ -182,6 +198,14 @@
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
+        },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
@@ -218,67 +242,30 @@
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "status",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "View authentication status",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "status.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",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "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",
+      "id": "status",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of changes",
+      "summary": "View authentication status",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "change",
-        "get.js"
+        "status.js"
       ]
     },
     "assembly:add-from-fasta": {
@@ -320,6 +307,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Name for this assembly. Use the file name if omitted",
@@ -428,6 +423,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Name for this assembly. Use the file name if omitted",
@@ -510,6 +513,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Manage checks in this assembly",
@@ -576,6 +587,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Assembly names or IDs to delete",
@@ -629,6 +648,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Get assemblies in this list of names or IDs",
@@ -684,6 +711,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Find input reference sequence in this assembly",
@@ -766,6 +801,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "include-fasta": {
           "description": "Include fasta sequence in output",
           "name": "include-fasta",
@@ -789,16 +832,10 @@
         "gff3.js"
       ]
     },
-    "feature:add-child": {
+    "change:get": {
       "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.",
-      "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": "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",
@@ -814,85 +851,48 @@
           "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": "-",
-          "hasDynamicHelp": false,
-          "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,
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "type": {
-          "char": "t",
-          "description": "Type of child feature",
-          "name": "type",
-          "required": true,
+        "assembly": {
+          "char": "a",
+          "description": "Get changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:add-child",
+      "id": "change:get",
       "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": "Get list of changes",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "add-child.js"
+        "change",
+        "get.js"
       ]
     },
-    "feature:add": {
+    "file:delete": {
       "aliases": [],
-      "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",
+      "args": {},
+      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
       "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>\"}]}'"
+          "description": "Delete file multiple files:",
+          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
         }
       ],
       "flags": {
@@ -910,116 +910,51 @@
           "multiple": false,
           "type": "option"
         },
-        "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"
-        },
-        "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",
-          "dependsOn": [
-            "refSeq",
-            "max",
-            "type"
-          ],
-          "description": "Start position in target reference sequence",
-          "exclusive": [
-            "feature-json-file"
-          ],
-          "name": "min",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "max": {
-          "char": "e",
-          "dependsOn": [
-            "refSeq",
-            "min",
-            "type"
-          ],
-          "description": "End position in target reference sequence",
-          "exclusive": [
-            "feature-json-file"
-          ],
-          "name": "max",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "type": {
-          "char": "t",
-          "dependsOn": [
-            "refSeq",
-            "min",
-            "max"
-          ],
-          "description": "Type of child feature",
-          "exclusive": [
-            "feature-json-file"
+        "file-id": {
+          "char": "i",
+          "description": "IDs of the files to delete",
+          "name": "file-id",
+          "default": [
+            "-"
           ],
-          "name": "type",
-          "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,
+          "multiple": true,
           "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:add",
+      "id": "file:delete",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Add one or more features to Apollo",
+      "summary": "Delete files from the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "add.js"
+        "file",
+        "delete.js"
       ]
     },
-    "feature:check": {
+    "file:download": {
       "aliases": [],
       "args": {},
-      "description": "Use this command to view which features fail checks along with the reason for failing.Use `apollo assembly check` for managing which checks should be applied to an assembly",
+      "description": "See also `apollo file get` to list the files on the server",
       "examples": [
         {
-          "description": "Get all check results in the database:",
-          "command": "<%= config.bin %> <%= command.id %>"
-        },
-        {
-          "description": "Get check results for assembly hg19:",
-          "command": "<%= config.bin %> <%= command.id %> -a hg19"
+          "description": "Download file with id xyz",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
         }
       ],
       "flags": {
@@ -1037,18 +972,27 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "file-id": {
           "char": "i",
-          "description": "Get checks for these feature identifiers",
-          "name": "feature-id",
+          "description": "ID of the file to download",
+          "name": "file-id",
+          "default": "-",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Get checks for this assembly",
-          "name": "assembly",
+        "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"
@@ -1056,29 +1000,29 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:check",
+      "id": "file:download",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get check results",
+      "summary": "Download a file from the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "check.js"
+        "file",
+        "download.js"
       ]
     },
-    "feature:copy": {
+    "file:get": {
       "aliases": [],
       "args": {},
-      "description": "The feature may be copied to the same or to a different assembly. The destination reference sequence may be selected by name only if unique in the database or by name and assembly or by identifier.",
+      "description": "Print to stdout the list of files in json format",
       "examples": [
         {
-          "description": "Copy this feature ID to chr1:100 in assembly hg38:",
-          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38"
+          "description": "Get files by id:",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
         }
       ],
       "flags": {
@@ -1096,64 +1040,56 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Feature ID to copy to; use - to read it from stdin",
-          "name": "feature-id",
-          "default": "-",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "refseq": {
-          "char": "r",
-          "description": "Name or ID of target reference sequence",
-          "name": "refseq",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "start": {
-          "char": "s",
-          "description": "Start position in target reference sequence",
-          "name": "start",
-          "required": true,
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
-          "name": "assembly",
-          "required": false,
+        "file-id": {
+          "char": "i",
+          "description": "Get files matching this IDs",
+          "name": "file-id",
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:copy",
+      "id": "file:get",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Copy a feature to another location",
+      "summary": "Get list of files uploaded to the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "copy.js"
+        "file",
+        "get.js"
       ]
     },
-    "feature:delete": {
+    "file:upload": {
       "aliases": [],
-      "args": {},
-      "description": "Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.",
+      "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",
@@ -1169,65 +1105,74 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Feature IDs to delete",
-          "name": "feature-id",
-          "default": [
-            "-"
-          ],
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
           "type": "option"
         },
-        "force": {
-          "char": "f",
-          "description": "Ignore non-existing features",
-          "name": "force",
+        "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"
         },
-        "dry-run": {
-          "char": "n",
-          "description": "Only show what would be delete",
-          "name": "dry-run",
+        "decompressed": {
+          "char": "d",
+          "description": "Override autodetection and instruct that input is decompressed",
+          "exclusive": [
+            "gzip"
+          ],
+          "name": "decompressed",
           "allowNo": false,
           "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:delete",
+      "id": "file:upload",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Delete one or more features by ID",
-      "enableJsonFlag": false,
+      "summary": "Upload a local file to the Apollo server",
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "delete.js"
+        "file",
+        "upload.js"
       ]
     },
-    "feature:edit-attribute": {
+    "feature:add-child": {
       "aliases": [],
       "args": {},
-      "description": "Be aware that there is no checking whether attributes names and values are valid. For example, you can create non-unique ID attributes or you can set gene ontology terms to non-existing terms",
+      "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 attribute \"domains\" with a list of values:",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -v ABC PLD"
-        },
-        {
-          "description": "Print values in \"domains\" as json array:",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains"
-        },
-        {
-          "description": "Delete attribute \"domains\"",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -d"
+          "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": {
@@ -1245,69 +1190,93 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "feature-id": {
           "char": "i",
-          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "description": "Add a child to this feature ID; use - to read it from stdin",
           "name": "feature-id",
           "default": "-",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "attribute": {
-          "char": "a",
-          "description": "Attribute key to add or edit",
-          "name": "attribute",
+        "start": {
+          "char": "s",
+          "description": "Start coordinate of the child feature (1-based)",
+          "name": "start",
           "required": true,
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "value": {
-          "char": "v",
-          "description": "New attribute value. Separated mutliple values by space to them as a list. If unset return current value",
-          "name": "value",
+        "end": {
+          "char": "e",
+          "description": "End coordinate of the child feature (1-based)",
+          "name": "end",
+          "required": true,
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
           "type": "option"
         },
-        "delete": {
-          "char": "d",
-          "description": "Delete this attribute",
-          "name": "delete",
-          "allowNo": false,
-          "type": "boolean"
+        "type": {
+          "char": "t",
+          "description": "Type of child feature",
+          "name": "type",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit-attribute",
+      "id": "feature:add-child",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Add, edit, or view a feature attribute",
+      "summary": "Add a child feature (e.g. add an exon to an mRNA)",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit-attribute.js"
+        "add-child.js"
       ]
     },
-    "feature:edit-coords": {
+    "feature:add": {
       "aliases": [],
-      "args": {},
-      "description": "If editing a child feature that new coordinates must be within the parent's coordinates.To get the identifier of the feature to edit consider using `apollo feature get` or `apollo feature search`",
+      "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": "Edit start and end:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -s 10 -e 1000"
+          "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": "Edit end and leave start as it is:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -e 2000"
+          "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": {
@@ -1325,27 +1294,90 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Feature ID to edit or \"-\" to read it from stdin",
-          "name": "feature-id",
-          "default": "-",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "start": {
+        "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"
+        },
+        "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": "New start coordinate (1-based)",
-          "name": "start",
+          "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": "New end coordinate (1-based)",
-          "name": "end",
+          "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",
+          "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"
@@ -1353,25 +1385,35 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit-coords",
+      "id": "feature:add",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Edit feature start and/or end coordinates",
+      "summary": "Add one or more features to Apollo",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit-coords.js"
+        "add.js"
       ]
     },
-    "feature:edit-type": {
+    "feature:check": {
       "aliases": [],
       "args": {},
-      "description": "Feature type is column 3 in gff format.It must be a valid sequence ontology term although but the valifdity of the new term is not checked.",
+      "description": "Use this command to view which features fail checks along with the reason for failing.Use `apollo assembly check` for managing which checks should be applied to an assembly",
+      "examples": [
+        {
+          "description": "Get all check results in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Get check results for assembly hg19:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1387,19 +1429,26 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "feature-id": {
           "char": "i",
-          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "description": "Get checks for these feature identifiers",
           "name": "feature-id",
-          "default": "-",
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         },
-        "type": {
-          "char": "t",
-          "description": "Assign feature to this type. If unset return the current type",
-          "name": "type",
+        "assembly": {
+          "char": "a",
+          "description": "Get checks for this assembly",
+          "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -1407,29 +1456,29 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit-type",
+      "id": "feature:check",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Edit or view feature type",
+      "summary": "Get check results",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit-type.js"
+        "check.js"
       ]
     },
-    "feature:edit": {
+    "feature:copy": {
       "aliases": [],
       "args": {},
-      "description": "Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.\n\n    Input may be a json string or a json file and it may be an array of changes. This is an example input for editing feature type:\n\n    {\n      \"typeName\": \"TypeChange\",\n      \"changedIds\": [\n        \"6613f7d22c957525d631b1cc\"\n      ],\n      \"assembly\": \"6613f7d1360321540a11e5ed\",\n      \"featureId\": \"6613f7d22c957525d631b1cc\",\n      \"oldType\": \"BAC\",\n      \"newType\": \"G_quartet\"\n    }",
+      "description": "The feature may be copied to the same or to a different assembly. The destination reference sequence may be selected by name only if unique in the database or by name and assembly or by identifier.",
       "examples": [
         {
-          "description": "Editing by passing a json to stdin:",
-          "command": "echo '{\"typeName\": ... \"newType\": \"G_quartet\"}' | <%= config.bin %> <%= command.id %> -j -"
+          "description": "Copy this feature ID to chr1:100 in assembly hg38:",
+          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38"
         }
       ],
       "flags": {
@@ -1447,43 +1496,72 @@
           "multiple": false,
           "type": "option"
         },
-        "json-input": {
-          "char": "j",
-          "description": "Json string or json file or \"-\" to read json from stdin",
-          "name": "json-input",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to copy to; use - to read it from stdin",
+          "name": "feature-id",
           "default": "-",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
+        },
+        "refseq": {
+          "char": "r",
+          "description": "Name or ID of target reference sequence",
+          "name": "refseq",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start position in target reference sequence",
+          "name": "start",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
+          "name": "assembly",
+          "required": false,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit",
+      "id": "feature:copy",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Edit features using an appropiate json input",
+      "summary": "Copy a feature to another location",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit.js"
-      ]
-    },
-    "feature:get-id": {
-      "aliases": [],
-      "args": {},
-      "description": "Invalid identifiers or identifiers not found in the database will be silently ignored",
-      "examples": [
-        {
-          "description": "Get features for these identifiers:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
-        }
-      ],
+        "copy.js"
+      ]
+    },
+    "feature:delete": {
+      "aliases": [],
+      "args": {},
+      "description": "Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.",
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1499,9 +1577,17 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "feature-id": {
           "char": "i",
-          "description": "Retrieves feature with these IDs. Use \"-\" to read IDs from stdin (one per line)",
+          "description": "Feature IDs to delete",
           "name": "feature-id",
           "default": [
             "-"
@@ -1509,39 +1595,55 @@
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
+        },
+        "force": {
+          "char": "f",
+          "description": "Ignore non-existing features",
+          "name": "force",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "dry-run": {
+          "char": "n",
+          "description": "Only show what would be delete",
+          "name": "dry-run",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:get-id",
+      "id": "feature:delete",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get features given their identifiers",
+      "summary": "Delete one or more features by ID",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "get-id.js"
+        "delete.js"
       ]
     },
-    "feature:get-indexed-id": {
+    "feature:edit-attribute": {
       "aliases": [],
-      "args": {
-        "id": {
-          "description": "Indexed identifier to search for",
-          "name": "id",
-          "required": true
-        }
-      },
-      "description": "Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file",
+      "args": {},
+      "description": "Be aware that there is no checking whether attributes names and values are valid. For example, you can create non-unique ID attributes or you can set gene ontology terms to non-existing terms",
       "examples": [
         {
-          "description": "Get features for this indexed identifier:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
+          "description": "Add attribute \"domains\" with a list of values:",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -v ABC PLD"
+        },
+        {
+          "description": "Print values in \"domains\" as json array:",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains"
+        },
+        {
+          "description": "Delete attribute \"domains\"",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -d"
         }
       ],
       "flags": {
@@ -1559,50 +1661,77 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "attribute": {
           "char": "a",
-          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
-          "name": "assembly",
+          "description": "Attribute key to add or edit",
+          "name": "attribute",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "value": {
+          "char": "v",
+          "description": "New attribute value. Separated mutliple values by space to them as a list. If unset return current value",
+          "name": "value",
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
         },
-        "topLevel": {
-          "description": "Return the top-level parent of the feature instead of the feature itself",
-          "name": "topLevel",
+        "delete": {
+          "char": "d",
+          "description": "Delete this attribute",
+          "name": "delete",
           "allowNo": false,
           "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:get-indexed-id",
+      "id": "feature:edit-attribute",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get features given an indexed identifier",
+      "summary": "Add, edit, or view a feature attribute",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "get-indexed-id.js"
+        "edit-attribute.js"
       ]
     },
-    "feature:get": {
+    "feature:edit-coords": {
       "aliases": [],
       "args": {},
-      "description": "Get features in assembly, reference sequence or genomic window",
+      "description": "If editing a child feature that new coordinates must be within the parent's coordinates.To get the identifier of the feature to edit consider using `apollo feature get` or `apollo feature search`",
       "examples": [
         {
-          "description": "Get all features in myAssembly:",
-          "command": "<%= config.bin %> <%= command.id %> -a myAssembly"
+          "description": "Edit start and end:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -s 10 -e 1000"
         },
         {
-          "description": "Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences named chr1:",
-          "command": "<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000"
+          "description": "Edit end and leave start as it is:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -e 2000"
         }
       ],
       "flags": {
@@ -1620,34 +1749,34 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Find input reference sequence in this assembly",
-          "name": "assembly",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "refseq": {
-          "char": "r",
-          "description": "Reference sequence. If unset, query all sequences",
-          "name": "refseq",
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
         "start": {
           "char": "s",
-          "description": "Start coordinate (1-based)",
+          "description": "New start coordinate (1-based)",
           "name": "start",
-          "default": 1,
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
         "end": {
           "char": "e",
-          "description": "End coordinate",
+          "description": "New end coordinate (1-based)",
           "name": "end",
           "hasDynamicHelp": false,
           "multiple": false,
@@ -1656,34 +1785,91 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:get",
+      "id": "feature:edit-coords",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
+      "summary": "Edit feature start and/or end coordinates",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "get.js"
+        "edit-coords.js"
       ]
     },
-    "feature:import": {
+    "feature:edit-type": {
       "aliases": [],
-      "args": {
-        "input-file": {
-          "description": "Input gff file",
-          "name": "input-file",
-          "required": true
+      "args": {},
+      "description": "Feature type is column 3 in gff format.It must be a valid sequence ontology term although but the valifdity of the new term is not checked.",
+      "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"
+        },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Assign feature to this type. If unset return the current type",
+          "name": "type",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
-      "description": "By default, features are added to the existing ones.",
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:edit-type",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Edit or view feature type",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "edit-type.js"
+      ]
+    },
+    "feature:edit": {
+      "aliases": [],
+      "args": {},
+      "description": "Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very low level command which most users probably do not need.\n\n    Input may be a json string or a json file and it may be an array of changes. This is an example input for editing feature type:\n\n    {\n      \"typeName\": \"TypeChange\",\n      \"changedIds\": [\n        \"6613f7d22c957525d631b1cc\"\n      ],\n      \"assembly\": \"6613f7d1360321540a11e5ed\",\n      \"featureId\": \"6613f7d22c957525d631b1cc\",\n      \"oldType\": \"BAC\",\n      \"newType\": \"G_quartet\"\n    }",
       "examples": [
         {
-          "description": "Delete features in myAssembly and then import features.gff3:",
-          "command": "<%= config.bin %> <%= command.id %> features.gff3 -d -a myAssembly"
+          "description": "Editing by passing a json to stdin:",
+          "command": "echo '{\"typeName\": ... \"newType\": \"G_quartet\"}' | <%= config.bin %> <%= command.id %> -j -"
         }
       ],
       "flags": {
@@ -1701,53 +1887,49 @@
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Import into this assembly name or assembly ID",
-          "name": "assembly",
-          "required": true,
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "delete-existing": {
-          "char": "d",
-          "description": "Delete existing features before importing",
-          "name": "delete-existing",
-          "allowNo": false,
-          "type": "boolean"
-        },
-        "no-strict": {
-          "description": "If any lines in the GFF3 can't be processed, skip them instead of aborting the import",
-          "name": "no-strict",
-          "allowNo": false,
-          "type": "boolean"
+        "json-input": {
+          "char": "j",
+          "description": "Json string or json file or \"-\" to read json from stdin",
+          "name": "json-input",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:import",
+      "id": "feature:edit",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Import features from local gff file",
+      "summary": "Edit features using an appropiate json input",
+      "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "import.js"
+        "edit.js"
       ]
     },
-    "feature:search": {
+    "feature:get-id": {
       "aliases": [],
       "args": {},
-      "description": "Return features matching a query string. This command searches only in:\n\n    - Attribute *values* (not attribute names)\n    - Source field (which in fact is stored as an attribute)\n    - Feature type\n\n    The search mode is:\n\n    - Case insensitive\n    - Match only full words, but not necessarily the full value\n    - Common words are ignored. E.g. \"the\", \"with\"\n\n    For example, given this feature:\n\n    chr1 example SNP 10 30 0.987 . . \"someKey=Fingerprint BAC with reads\"\n\n    Queries \"bac\" or \"mRNA\" return the feature. Instead these queries will NOT match:\n\n    - \"someKey\"\n    - \"with\"\n    - \"Finger\"\n    - \"chr1\"\n    - \"0.987\"",
+      "description": "Invalid identifiers or identifiers not found in the database will be silently ignored",
       "examples": [
         {
-          "description": "Search \"bac\" in these assemblies:",
-          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10 -t bac"
+          "description": "Get features for these identifiers:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
         }
       ],
       "flags": {
@@ -1765,19 +1947,21 @@
           "multiple": false,
           "type": "option"
         },
-        "text": {
-          "char": "t",
-          "description": "Search for this text query",
-          "name": "text",
-          "required": true,
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "assembly": {
-          "char": "a",
-          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
-          "name": "assembly",
+        "feature-id": {
+          "char": "i",
+          "description": "Retrieves feature with these IDs. Use \"-\" to read IDs from stdin (one per line)",
+          "name": "feature-id",
+          "default": [
+            "-"
+          ],
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
@@ -1785,29 +1969,35 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:search",
+      "id": "feature:get-id",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Free text search for feature in one or more assemblies",
+      "summary": "Get features given their identifiers",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "search.js"
+        "get-id.js"
       ]
     },
-    "file:delete": {
+    "feature:get-indexed-id": {
       "aliases": [],
-      "args": {},
-      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
+      "args": {
+        "id": {
+          "description": "Indexed identifier to search for",
+          "name": "id",
+          "required": true
+        }
+      },
+      "description": "Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file",
       "examples": [
         {
-          "description": "Delete file multiple files:",
-          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
+          "description": "Get features for this indexed identifier:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
         }
       ],
       "flags": {
@@ -1825,43 +2015,58 @@
           "multiple": false,
           "type": "option"
         },
-        "file-id": {
-          "char": "i",
-          "description": "IDs of the files to delete",
-          "name": "file-id",
-          "default": [
-            "-"
-          ],
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
+          "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": true,
           "type": "option"
+        },
+        "topLevel": {
+          "description": "Return the top-level parent of the feature instead of the feature itself",
+          "name": "topLevel",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:delete",
+      "id": "feature:get-indexed-id",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Delete files from the Apollo server",
+      "summary": "Get features given an indexed identifier",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "file",
-        "delete.js"
+        "feature",
+        "get-indexed-id.js"
       ]
     },
-    "file:download": {
+    "feature:get": {
       "aliases": [],
       "args": {},
-      "description": "See also `apollo file get` to list the files on the server",
+      "description": "Get features in assembly, reference sequence or genomic window",
       "examples": [
         {
-          "description": "Download file with id xyz",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
+          "description": "Get all features in myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly"
+        },
+        {
+          "description": "Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences named chr1:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000"
         }
       ],
       "flags": {
@@ -1879,19 +2084,43 @@
           "multiple": false,
           "type": "option"
         },
-        "file-id": {
-          "char": "i",
-          "description": "ID of the file to download",
-          "name": "file-id",
-          "default": "-",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "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",
+        "assembly": {
+          "char": "a",
+          "description": "Find input reference sequence in this assembly",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "refseq": {
+          "char": "r",
+          "description": "Reference sequence. If unset, query all sequences",
+          "name": "refseq",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start coordinate (1-based)",
+          "name": "start",
+          "default": 1,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "End coordinate",
+          "name": "end",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -1899,29 +2128,34 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:download",
+      "id": "feature:get",
       "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"
+        "feature",
+        "get.js"
       ]
     },
-    "file:get": {
+    "feature:import": {
       "aliases": [],
-      "args": {},
-      "description": "Print to stdout the list of files in json format",
+      "args": {
+        "input-file": {
+          "description": "Input gff file",
+          "name": "input-file",
+          "required": true
+        }
+      },
+      "description": "By default, features are added to the existing ones.",
       "examples": [
         {
-          "description": "Get files by id:",
-          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
+          "description": "Delete features in myAssembly and then import features.gff3:",
+          "command": "<%= config.bin %> <%= command.id %> features.gff3 -d -a myAssembly"
         }
       ],
       "flags": {
@@ -1939,46 +2173,61 @@
           "multiple": false,
           "type": "option"
         },
-        "file-id": {
-          "char": "i",
-          "description": "Get files matching this IDs",
-          "name": "file-id",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Import into this assembly name or assembly ID",
+          "name": "assembly",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
           "type": "option"
+        },
+        "delete-existing": {
+          "char": "d",
+          "description": "Delete existing features before importing",
+          "name": "delete-existing",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "no-strict": {
+          "description": "If any lines in the GFF3 can't be processed, skip them instead of aborting the import",
+          "name": "no-strict",
+          "allowNo": false,
+          "type": "boolean"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:get",
+      "id": "feature:import",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get list of files uploaded to the Apollo server",
-      "enableJsonFlag": false,
+      "summary": "Import features from local gff file",
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "file",
-        "get.js"
+        "feature",
+        "import.js"
       ]
     },
-    "file:upload": {
+    "feature:search": {
       "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`",
+      "args": {},
+      "description": "Return features matching a query string. This command searches only in:\n\n    - Attribute *values* (not attribute names)\n    - Source field (which in fact is stored as an attribute)\n    - Feature type\n\n    The search mode is:\n\n    - Case insensitive\n    - Match only full words, but not necessarily the full value\n    - Common words are ignored. E.g. \"the\", \"with\"\n\n    For example, given this feature:\n\n    chr1 example SNP 10 30 0.987 . . \"someKey=Fingerprint BAC with reads\"\n\n    Queries \"bac\" or \"mRNA\" return the feature. Instead these queries will NOT match:\n\n    - \"someKey\"\n    - \"with\"\n    - \"Finger\"\n    - \"chr1\"\n    - \"0.987\"",
       "examples": [
         {
-          "description": "Upload local file, type auto-detected:",
-          "command": "<%= config.bin %> <%= command.id %> genome.fa > file.json"
+          "description": "Search \"bac\" in these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10 -t bac"
         }
       ],
       "flags": {
@@ -1996,56 +2245,47 @@
           "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",
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
           "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"
+        "text": {
+          "char": "t",
+          "description": "Search for this text query",
+          "name": "text",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         },
-        "decompressed": {
-          "char": "d",
-          "description": "Override autodetection and instruct that input is decompressed",
-          "exclusive": [
-            "gzip"
-          ],
-          "name": "decompressed",
-          "allowNo": false,
-          "type": "boolean"
+        "assembly": {
+          "char": "a",
+          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "file:upload",
+      "id": "feature:search",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Upload a local file to the Apollo server",
+      "summary": "Free text search for feature in one or more assemblies",
+      "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "file",
-        "upload.js"
+        "feature",
+        "search.js"
       ]
     },
     "jbrowse:desktop": {
@@ -2091,6 +2331,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "open": {
           "char": "o",
           "description": "open generated file",
@@ -2162,6 +2410,14 @@
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
+        },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
@@ -2211,6 +2467,14 @@
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
+        },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
@@ -2261,6 +2525,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Name for this assembly.",
@@ -2317,6 +2589,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "assembly": {
           "char": "a",
           "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
@@ -2376,6 +2656,14 @@
           "multiple": false,
           "type": "option"
         },
+        "timeout": {
+          "description": "Timeout for each request to the server",
+          "name": "timeout",
+          "default": "1h",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
         "username": {
           "char": "u",
           "description": "Find this username",
@@ -2411,5 +2699,5 @@
       ]
     }
   },
-  "version": "1.1.1"
+  "version": "1.1.2"
 }