Merge branch 'branch_label_allow'

* branch_label_allow:
  Add "clean" rule to validation tests
  Check branch labels upon v2 dataset JSON validation
  allow config/validate of branch_label display default (v2)

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

@@ -132,6 +132,10 @@
                 "layout": {
                     "type": "string",
                     "enum": ["rect", "radial", "unrooted", "clock"]
+                },
+                "branch_label": {
+                    "type": "string",
+                    "enum": ["clade", "aa", "none"]
                 }
             }
         },

augur/data/schema-export-v2.json

@@ -217,10 +217,14 @@
                           "description": "Default tree layout",
                           "type": "string",
                           "enum": ["rect", "radial", "unrooted", "clock"]
-                      },
+                        },
                         "map_triplicate": {
                             "description": "Should the map be extended / wrapped around. Useful if transmissions are worldwide.",
                             "type": "boolean"
+                        },
+                        "branch_label": {
+                            "description": "What branch label should be displayed by default.",
+                            "type": "string"
                         }
                     }
                 },

augur/export_v2.py

@@ -719,7 +719,8 @@ def set_display_defaults(data_json, config):
         ["color_by", "colorBy"],
         ["distance_measure", "distanceMeasure"],
         ["map_triplicate", "mapTriplicate"],
-        ["layout", "layout"]
+        ["layout", "layout"],
+        ["branch_label", "branch_label"]
     ]
 
     display_defaults = {}

augur/validate_export.py

@@ -57,6 +57,14 @@ def recurse(node):
     genes -= {"nuc"}
     return genes
 
+def collectBranchLabels(root):
+    labels = set()
+    def recurse(node):
+        labels.update(node.get("branch_attrs", {}).get("labels", {}).keys())
+        if "children" in node:
+            [recurse(child) for child in node["children"]]
+    recurse(root)
+    return labels
 
 def verifyMainJSONIsInternallyConsistent(data, ValidateError):
     """
@@ -144,6 +152,12 @@ def warn(msg):
                 if gene not in data["meta"]["genome_annotations"]:
                     warn("The tree defined mutations on gene {} which doesn't appear in the metadata annotations object.".format(gene))
 
+    default_branch_label = data.get("meta").get("display_defaults", {}).get("branch_label")
+    if default_branch_label and default_branch_label.lower() != "none":
+        labels = collectBranchLabels(data['tree'])
+        if not default_branch_label in labels:
+            warn("Default label to display \"{}\" isn't found anywhere on the tree!".format(default_branch_label))
+
     return not warnings
 
 

tests/builds/validation/.gitignore

@@ -0,0 +1 @@
+!/auspice/*

tests/builds/validation/Snakefile

@@ -0,0 +1,9 @@
+rule all:
+  shell:
+    """
+    augur validate export-v2 auspice/v2_zika.json
+    """
+
+rule clean:
+  run:
+    pass