Measurements command

augur/__init__.py

@@ -40,7 +40,8 @@
     "export",
     "validate",
     "version",
-    "import"
+    "import",
+    "measurements",
 ]
 
 COMMANDS = [importlib.import_module('augur.' + c) for c in command_strings]

augur/data/schema-auspice-config-v2.json

@@ -223,7 +223,7 @@
             "minItems": 1,
             "items": {
                 "type": "string",
-                "enum": ["tree", "map", "frequencies", "entropy"]
+                "enum": ["tree", "map", "frequencies", "entropy", "measurements"]
             }
         },
         "vaccine_choices": {

augur/data/schema-export-v2.json

@@ -103,7 +103,7 @@
                     "type": "array",
                     "items": {
                         "type": "string",
-                        "enum": ["tree", "map", "frequencies", "entropy"]
+                        "enum": ["tree", "map", "frequencies", "entropy", "measurements"]
                     },
                     "uniqueItems": true,
                     "minItems": 1

augur/data/schema-measurements-collection-config.json

@@ -0,0 +1,107 @@
+{
+    "$schema": "http://json-schema.org/draft-06/schema#",
+    "$id": "https://nextstrain.org/schemas/dataset/measurements/collection/config",
+    "title": "Collection config file to be supplied to `augur measurements export`",
+    "type": "object",
+    "additionalProperties": false,
+    "required": [],
+    "properties": {
+        "key": {
+            "description": "The short name of the collection that is only used internally within Auspice. Each collection is expected to have a unique key.",
+            "type": "string"
+        },
+        "title": {
+            "description": "The title to display in the collections dropdown and panel title. Optional -- if not provided, then `key` will be used",
+            "type": "string"
+        },
+        "fields": {
+            "description": "Custom field order and display titles. Order of the fields determines the order they are shown in the measurement hover display. Optional -- if not provided, then the key of the field will be displayed in alphabetical order.",
+            "type": "array",
+            "minItems": 1,
+            "items": {
+                "description": "A single field of the measurements",
+                "type": "object",
+                "additionalProperties": false,
+                "required": ["key"],
+                "properties": {
+                    "key": {
+                        "description": "The property name of the field within the measurement object",
+                        "type": "string"
+                    },
+                    "title": {
+                        "description": "The display title for the field. Optional -- if not provided, then `key` will be used",
+                        "type": "string"
+                    }
+                }
+            }
+        },
+        "groupings": {
+            "description": "The available group by fields for measurements. Order of the group by fields determines the order they are shown in the group by dropdown.",
+            "type": "array",
+            "minItems": 1,
+            "items": {
+                "description": "A single group by field for measurements",
+                "type": "object",
+                "additionalProperties": false,
+                "required": ["key"],
+                "properties": {
+                    "key": {
+                        "description": "The property name of the group by field within the measurement object",
+                        "type": "string"
+                    },
+                    "order": {
+                        "description": "A custom order of group by values to customize the display order of the subplots when using group by field",
+                        "type": "array",
+                        "minItems": 1,
+                        "items": {
+                            "description": "A single value of the group by field present in measurements",
+                            "type": ["string", "number", "boolean"]
+                        }
+                    }
+                }
+            }
+        },
+        "filters": {
+            "description": "The available filter options for measurements. Order of the filter options determines the order they are shown in the filter dropdown. Optional -- if not provided, then all fields will be available as filters.",
+            "type": "array",
+            "minItems": 1,
+            "items": {
+                "description": "The property name of the filter field within the measurement object",
+                "type": "string"
+            }
+        },
+        "x_axis_label": {
+            "description": "The short label to display for the x-axis that describes the `value` of the measurements in a collection",
+            "type": "string"
+        },
+        "threshold": {
+            "description": "A numeric measurement threshold to be displayed as a single grey line shared across subplots. Optional -- if not provided, no threshold will be displayed",
+            "type": "number"
+        },
+        "display_defaults": {
+            "description": "Default display options of the collection",
+            "type": "object",
+            "additionalProperties": false,
+            "minProperty": 1,
+            "properties": {
+                "group_by": {
+                    "description": "Default group by field name that must be included as a group by option in the groupings array. Optional -- if not provided, first group by option will be used",
+                    "type": "string"
+                },
+                "measurements_display": {
+                    "description": "Dictates how the measurements are displayed, either as the raw data points or as the means of values grouped by the tree color-by attribute",
+                    "type": "string",
+                    "enum": ["raw", "mean"]
+                },
+                "show_overall_mean": {
+                    "description": "Should the overall mean per group be displayed by default?",
+                    "type": "boolean"
+                },
+                "show_threshold": {
+                    "description": "Should the threshold line be displayed by default? Ignored if no threshold has been provided for collection",
+                    "type": "boolean"
+                }
+            }
+        }
+    }
+}

augur/export_v2.py

@@ -842,7 +842,7 @@ def register_arguments_v2(subparsers):
     config.add_argument('--description', metavar="description.md", help="Markdown file with description of build and/or acknowledgements to be displayed by Auspice")
     config.add_argument('--geo-resolutions', metavar="trait", nargs='+', help="Geographic traits to be displayed on map")
     config.add_argument('--color-by-metadata', metavar="trait", nargs='+', help="Metadata columns to include as coloring options")
-    config.add_argument('--panels', metavar="panels", nargs='+', choices=['tree', 'map', 'entropy', 'frequencies'], help="Restrict panel display in auspice. Options are %(choices)s. Ignore this option to display all available panels.")
+    config.add_argument('--panels', metavar="panels", nargs='+', choices=['tree', 'map', 'entropy', 'frequencies', 'measurements'], help="Restrict panel display in auspice. Options are %(choices)s. Ignore this option to display all available panels.")
 
     optional_inputs = v2.add_argument_group(
         title="OPTIONAL INPUT FILES"