def run(self, user_request):
table = OTUTable(user_request.user_id, user_request.pid)
base, headers, sample_labels = table.get_table_after_filtering_and_aggregation(
user_request)
metadata_vals = table.get_sample_metadata(
).get_metadata_column_table_order(sample_labels, user_request.catvar)
phylogenetic_tree = table.get_phylogenetic_tree()
return self.analyse(user_request, base, headers, sample_labels,
metadata_vals, phylogenetic_tree)
def run(self, user_request):
table = OTUTable(user_request.user_id, user_request.pid)
# No OTUs should be excluded for diversity analysis
otu_table, headers, sample_labels = table.get_table_after_filtering_and_aggregation(user_request)
metadata_values = table.get_sample_metadata().get_metadata_column_table_order(sample_labels, user_request.catvar)
if user_request.get_custom_attr("colorvar") != "None":
color_metadata_values = table.get_sample_metadata().get_metadata_column_table_order(sample_labels, user_request.get_custom_attr("colorvar"))
else:
color_metadata_values = []
strata_values = None
if user_request.get_custom_attr("strata").lower() != "none":
strata_values = table.get_sample_metadata().get_metadata_column_table_order(sample_labels, user_request.get_custom_attr("strata"))
sample_ids_to_metadata_map = table.get_sample_metadata().get_sample_id_to_metadata_map(user_request.catvar)
phylogenetic_tree = table.get_phylogenetic_tree()
if user_request.get_custom_attr("api").lower() == "beta":
return self.analyse(user_request, otu_table, headers, sample_labels, metadata_values, color_metadata_values, sample_ids_to_metadata_map, phylogenetic_tree)
else:
return self.analyse_permanova(user_request, otu_table, headers, sample_labels, metadata_values, strata_values, sample_ids_to_metadata_map)