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check colors & geo locations are defined in metadata #192

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Aug 6, 2018
Merged

check colors & geo locations are defined in metadata #192

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27 changes: 24 additions & 3 deletions augur/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,15 +182,28 @@ def warn(msg):
for geoValue in mj["geo"][geoName]:
if geoValue not in treeAttrs[geoName]["values"]:
warn("\"{}\", a value of the geographic resolution \"{}\", does not appear as a value of attr->{} on any tree nodes.".format(geoValue, geoName, geoName))
for geoValue in treeAttrs[geoName]["values"]:
if geoValue not in mj["geo"][geoName]:
error("\"{}\", a value of the geographic resolution \"{}\", appears in the tree but not in the metadata.".format(geoValue, geoName))
error("\tThis will cause transmissions & demes involving this location not to be displayed in Auspice")


if "color_options" in mj:
for colorBy in [x for x in mj["color_options"] if x != "gt"]:
if colorBy not in treeAttrs:
error("The color_option \"{}\" does not appear as an attr on any tree nodes.".format(colorBy))
elif "color_map" in mj["color_options"][colorBy]:
# if there's a color_map, then check that there are no values which aren't seen on the tree
for (value, hex) in mj["color_options"][colorBy]["color_map"]:
if value not in treeAttrs[colorBy]["values"]:
warn("Color option \"{}\" specifies a hex code for \"{}\" but this isn't ever seen on the tree nodes.".format(colorBy, value))
# inversely, check for values on the tree not defined in the color_map
for value in treeAttrs[colorBy]["values"]:
color_map_values = [x[0] for x in mj["color_options"][colorBy]["color_map"]]
if value not in color_map_values:
warn("Color option \"{}\", which contains a color_map, is missing \"{}\"".format(colorBy, value))



if "filters" in mj:
for filter in mj["filters"]:
Expand Down Expand Up @@ -254,6 +267,10 @@ def warn(msg):
for geoValue in data["geographic_info"][geoName]:
if geoValue not in treeTraits[geoName]["values"]:
warn("\"{}\", a value of the geographic resolution \"{}\", does not appear as a value of attr->{} on any tree nodes.".format(geoValue, geoName, geoName))
for geoValue in treeTraits[geoName]["values"]:
if geoValue not in data["geographic_info"][geoName]:
error("\"{}\", a value of the geographic resolution \"{}\", appears in the tree but not in the metadata.".format(geoValue, geoName))
error("\tThis will cause transmissions & demes involving this location not to be displayed in Auspice")
else:
if "map" in data["panels"]:
error("Map panel was requested but no geographic_info was provided")
Expand All @@ -276,8 +293,12 @@ def warn(msg):
if "domain" in data["colorings"][colorBy]:
domain = data["colorings"][colorBy]["domain"]
if data["colorings"][colorBy]["type"] in ["ordinal", "categorical"]:
if len([val for val in domain if val not in treeTraits[colorBy]["values"]]):
warn("Domain for {} defined values which are not present on the tree...".format(colorBy))
inMetaNotInTree = [val for val in domain if val not in treeTraits[colorBy]["values"]]
if len(inMetaNotInTree):
warn("Domain for {} defined the following values which are not present on the tree: {}".format(colorBy, inMetaNotInTree.join(", ")))
inTreeNotInMeta = [val for val in treeTraits[colorBy]["values"] if val not in domain]
if len(inTreeNotInMeta):
warn("Tree defined values for {} which were not in the domain: {}".format(colorBy, inTreeNotInMeta.join(", ")))
elif data["colorings"][colorBy]["type"] == "boolean":
error("Cannot povide a domain for a boolean coloring ({})".format(colorBy))
else:
Expand Down Expand Up @@ -352,7 +373,7 @@ def run(args):
else:
if "main" in datasets:
return_status = verifyMainJSONIsInternallyConsistent(datasets["main"]) | return_status

if not return_status:
print("SUCCESS")

return return_status