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Source code for galaxy.tools.parameters.history_query
import logging
log = logging.getLogger(__name__)
[docs]class HistoryQuery(object):
""" An object for describing the collections to pull out of a history,
used by DataCollectionToolParameter.
"""
[docs] def __init__(self, **kwargs):
self.collection_type_descriptions = kwargs.get("collection_type_descriptions", None)
[docs] @staticmethod
def from_parameter(param, collection_type_descriptions):
""" Take in a tool parameter element.
"""
collection_types = param.collection_types
if collection_types:
collection_type_descriptions = [collection_type_descriptions.for_collection_type(t) for t in collection_types]
# Place higher dimension descriptions first so subcollection mapping
# (until we expose it to the user) will default to providing tool as much
# data as possible. So a list:list:paired mapped to a tool that takes
# list,paired,list:paired - will map over list:paired and create a flat list.
collection_type_descriptions = sorted(collection_type_descriptions, key=lambda t: t.dimension, reverse=True)
else:
collection_type_descriptions = None
kwargs = dict(collection_type_descriptions=collection_type_descriptions)
return HistoryQuery(**kwargs)
[docs] def direct_match(self, hdca):
collection_type_descriptions = self.collection_type_descriptions
if collection_type_descriptions is not None:
for collection_type_description in collection_type_descriptions:
if collection_type_description.can_match_type(hdca.collection.collection_type):
return True
return False
return True
[docs] def can_map_over(self, hdca):
collection_type_descriptions = self.collection_type_descriptions
if collection_type_descriptions is None:
return False
hdca_collection_type = hdca.collection.collection_type
for collection_type_description in collection_type_descriptions:
# See note about the way this is sorted above.
if collection_type_description.is_subcollection_of_type(hdca_collection_type):
return collection_type_description
return False