@apollo-annotation/cli 1.1.0 → 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,
@@ -218,6 +242,14 @@
           "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,
@@ -275,6 +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",
@@ -383,6 +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",
@@ -465,6 +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",
@@ -531,6 +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",
@@ -584,6 +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",
@@ -639,6 +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",
@@ -721,6 +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",
@@ -763,6 +851,14 @@
           "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 changes only for these assembly names or IDs (but see description)",
@@ -789,14 +885,14 @@
         "get.js"
       ]
     },
-    "feature:add-child": {
+    "file:delete": {
       "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.",
+      "description": "Deleted files are printed to stdout. See also `apollo file get` to list the files on the server",
       "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": "Delete file multiple files:",
+          "command": "<%= config.bin %> <%= command.id %> -i 123...abc xyz...789"
         }
       ],
       "flags": {
@@ -814,85 +910,51 @@
           "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,
+        "file-id": {
+          "char": "i",
+          "description": "IDs of the files to delete",
+          "name": "file-id",
+          "default": [
+            "-"
+          ],
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:add-child",
+      "id": "file:delete",
       "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": "Delete files from the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "add-child.js"
+        "file",
+        "delete.js"
       ]
     },
-    "feature:add": {
+    "file:download": {
       "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": "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": "Download file with id xyz",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz -o genome.fa"
         }
       ],
       "flags": {
@@ -910,82 +972,27 @@
           "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"
-          ],
-          "name": "type",
+        "file-id": {
+          "char": "i",
+          "description": "ID of the file to download",
+          "name": "file-id",
+          "default": "-",
           "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",
+        "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"
@@ -993,33 +1000,29 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:add",
+      "id": "file:download",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Add one or more features to Apollo",
+      "summary": "Download a file from the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "add.js"
+        "file",
+        "download.js"
       ]
     },
-    "feature:check": {
+    "file:get": {
       "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": "Print to stdout the list of files in json format",
       "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": "Get files by id:",
+          "command": "<%= config.bin %> <%= command.id %> -i xyz abc"
         }
       ],
       "flags": {
@@ -1037,48 +1040,54 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Get checks for these feature identifiers",
-          "name": "feature-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": "Get checks for this assembly",
-          "name": "assembly",
+        "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:check",
+      "id": "file:get",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Get check results",
+      "summary": "Get list of files uploaded to the Apollo server",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "check.js"
+        "file",
+        "get.js"
       ]
     },
-    "feature:copy": {
+    "file:upload": {
       "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.",
-      "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"
+      "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": {
@@ -1096,64 +1105,76 @@
           "multiple": false,
           "type": "option"
         },
-        "feature-id": {
-          "char": "i",
-          "description": "Feature ID to copy to; use - 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"
         },
-        "refseq": {
-          "char": "r",
-          "description": "Name or ID of target reference sequence",
-          "name": "refseq",
-          "required": true,
+        "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"
         },
-        "start": {
-          "char": "s",
-          "description": "Start position in target reference sequence",
-          "name": "start",
-          "required": true,
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
+        "gzip": {
+          "char": "z",
+          "description": "Override autodetection and instruct that input is gzip compressed",
+          "exclusive": [
+            "decompressed"
+          ],
+          "name": "gzip",
+          "allowNo": false,
+          "type": "boolean"
         },
-        "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"
+        "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:copy",
+      "id": "file:upload",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Copy a feature to another location",
-      "enableJsonFlag": false,
+      "summary": "Upload a local file to the Apollo server",
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
-        "feature",
-        "copy.js"
+        "file",
+        "upload.js"
       ]
     },
-    "feature:delete": {
+    "feature:add-child": {
       "aliases": [],
       "args": {},
-      "description": "Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.",
+      "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"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1169,65 +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 IDs to delete",
+          "description": "Add a child to this feature ID; use - to read it from stdin",
           "name": "feature-id",
-          "default": [
-            "-"
-          ],
+          "default": "-",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
           "type": "option"
         },
-        "force": {
-          "char": "f",
-          "description": "Ignore non-existing features",
-          "name": "force",
-          "allowNo": false,
-          "type": "boolean"
+        "start": {
+          "char": "s",
+          "description": "Start coordinate of the child feature (1-based)",
+          "name": "start",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         },
-        "dry-run": {
-          "char": "n",
-          "description": "Only show what would be delete",
-          "name": "dry-run",
-          "allowNo": false,
-          "type": "boolean"
+        "end": {
+          "char": "e",
+          "description": "End coordinate of the child feature (1-based)",
+          "name": "end",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Type of child feature",
+          "name": "type",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:delete",
+      "id": "feature:add-child",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Delete one or more features by ID",
+      "summary": "Add a child feature (e.g. add an exon to an mRNA)",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "delete.js"
+        "add-child.js"
       ]
     },
-    "feature:edit-attribute": {
+    "feature:add": {
       "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",
+      "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": "Add attribute \"domains\" with a list of values:",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -v ABC PLD"
+          "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": "Print values in \"domains\" as json array:",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains"
+          "description": "Add a single feature from inline JSON",
+          "command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"}'"
         },
         {
-          "description": "Delete attribute \"domains\"",
-          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -d"
+          "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": {
@@ -1245,69 +1294,124 @@
           "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"
         },
-        "attribute": {
+        "assembly": {
           "char": "a",
-          "description": "Attribute key to add or edit",
-          "name": "attribute",
-          "required": true,
+          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
+          "name": "assembly",
           "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",
+        "refSeq": {
+          "char": "r",
+          "dependsOn": [
+            "min",
+            "max",
+            "type"
+          ],
+          "description": "Name or ID of target reference sequence",
+          "exclusive": [
+            "feature-json-file"
+          ],
+          "name": "refSeq",
           "hasDynamicHelp": false,
-          "multiple": true,
+          "multiple": false,
           "type": "option"
         },
-        "delete": {
-          "char": "d",
-          "description": "Delete this attribute",
-          "name": "delete",
-          "allowNo": false,
-          "type": "boolean"
+        "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",
+          "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"
         }
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit-attribute",
+      "id": "feature:add",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Add, edit, or view a feature attribute",
+      "summary": "Add one or more features to Apollo",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit-attribute.js"
+        "add.js"
       ]
     },
-    "feature:edit-coords": {
+    "feature:check": {
       "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`",
+      "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": "Edit start and end:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -s 10 -e 1000"
+          "description": "Get all check results in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
         },
         {
-          "description": "Edit end and leave start as it is:",
-          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -e 2000"
+          "description": "Get check results for assembly hg19:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19"
         }
       ],
       "flags": {
@@ -1325,27 +1429,26 @@
           "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": {
-          "char": "s",
-          "description": "New start coordinate (1-based)",
-          "name": "start",
+        "feature-id": {
+          "char": "i",
+          "description": "Get checks for these feature identifiers",
+          "name": "feature-id",
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         },
-        "end": {
-          "char": "e",
-          "description": "New end coordinate (1-based)",
-          "name": "end",
+        "assembly": {
+          "char": "a",
+          "description": "Get checks for this assembly",
+          "name": "assembly",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -1353,25 +1456,31 @@
       },
       "hasDynamicHelp": false,
       "hiddenAliases": [],
-      "id": "feature:edit-coords",
+      "id": "feature:check",
       "pluginAlias": "@apollo-annotation/cli",
       "pluginName": "@apollo-annotation/cli",
       "pluginType": "core",
       "strict": true,
-      "summary": "Edit feature start and/or end coordinates",
+      "summary": "Get check results",
       "enableJsonFlag": false,
       "isESM": true,
       "relativePath": [
         "dist",
         "commands",
         "feature",
-        "edit-coords.js"
+        "check.js"
       ]
     },
-    "feature:edit-type": {
+    "feature:copy": {
       "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": "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": "Copy this feature ID to chr1:100 in assembly hg38:",
+          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38"
+        }
+      ],
       "flags": {
         "profile": {
           "description": "Use credentials from this profile",
@@ -1387,71 +1496,46 @@
           "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": "Feature ID to copy to; use - 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"
-        }
-      },
-      "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": "Editing by passing a json to stdin:",
-          "command": "echo '{\"typeName\": ... \"newType\": \"G_quartet\"}' | <%= config.bin %> <%= command.id %> -j -"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
+        "refseq": {
+          "char": "r",
+          "description": "Name or ID of target reference sequence",
+          "name": "refseq",
+          "required": true,
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
+        "start": {
+          "char": "s",
+          "description": "Start position in target reference sequence",
+          "name": "start",
+          "required": true,
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
-        "json-input": {
-          "char": "j",
-          "description": "Json string or json file or \"-\" to read json from stdin",
-          "name": "json-input",
-          "default": "-",
+        "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"
@@ -1459,31 +1543,25 @@
       },
       "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": "1.1.0"
+  "version": "1.1.2"
 }