def convert_per_cluster_data(clusters):
per_cluster_data_output = {"distributions": [], "country_names": []}
per_cluster_data_output_interp = {"distributions": [], "country_names": []}
for _, cluster in clusters.items():
display_name = cluster['display_name']
build_name = cluster['build_name']
distribution = []
with open(os.path.join(cluster_tables_path, f"{build_name}_data.json"),
"r") as f:
json_input = json.load(f)
for (country, cluster_data) in json_input.items():
per_cluster_data_output["country_names"] = \
sorted(list(set([country] + per_cluster_data_output["country_names"])))
cluster_data_interp = interpolate_per_cluster_data(
cluster_data)
update_per_cluster_distribution(cluster_data_interp, country,
distribution)
per_cluster_data_output["distributions"].append({
'cluster':
display_name,
'distribution':
distribution
})
return per_cluster_data_output, per_cluster_data_output_interp
def convert_per_cluster_data(clusters):
per_cluster_data_output = {"distributions": [], "country_names": []}
per_cluster_data_output_interp = {"distributions": [], "country_names": []}
for _, cluster in clusters.items():
if cluster["type"] == "do_not_display":
continue
display_name = cluster["display_name"]
build_name = cluster["build_name"]
distribution = []
with open(os.path.join(cluster_tables_path, f"{build_name}_data.json"),
"r") as f:
json_input = json.load(f)
for (country, cluster_data) in json_input.items():
per_cluster_data_output["country_names"] = sorted(
list(
set([country] +
per_cluster_data_output["country_names"])))
cluster_data_interp = interpolate_per_cluster_data(
cluster_data)
update_per_cluster_distribution(cluster_data_interp, country,
distribution)
distribution.sort(key=lambda d: d['week'])
per_cluster_data_output["distributions"].append({
"cluster":
display_name,
"distribution":
distribution
})
return per_cluster_data_output, per_cluster_data_output_interp
with open(os.path.join(output_path, "perCountryData.json"), "w") as fh:
json.dump(per_country_data_output, fh, indent=2, sort_keys=True)
params = {
"min_date": min_date,
"max_date": max_date,
}
with open(os.path.join(output_path, "params.json"), "w") as fh:
json.dump(params, fh, indent=2, sort_keys=True)
per_cluster_data_output, per_cluster_data_output_interp = convert_per_cluster_data(
clusters)
with open(os.path.join(output_path, "perClusterData.json"), "w") as fh:
json.dump(per_cluster_data_output, fh, indent=2, sort_keys=True)
clusters = [cluster for _, cluster in clusters.items()]
with open(os.path.join(output_path, "clusters.json"), "w") as fh:
json.dump({'clusters': clusters}, fh, indent=2, sort_keys=True)
mutation_comparison_output = convert_mutation_comparison(
mutation_comparison)
with open(os.path.join(output_path, "mutationComparison.json"), "w") as fh:
json.dump(mutation_comparison_output, fh, indent=2, sort_keys=True)
with open(os.path.join(output_path, "countryStyles.json"), "w") as fh:
json.dump(country_styles_all, fh, indent=2, sort_keys=True)
copyfile(
os.path.join(cluster_tables_path, 'perVariant_countries_toPlot.json'),
os.path.join(output_path, "countriesToPlot.json"))
def filter_clusters(clusters):
return {
k: cluster
for k, cluster in clusters.items() if should_include(cluster)
}