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Source code for galaxy.tools.parameters.dataset_matcher

from logging import getLogger

import galaxy.model

log = getLogger(__name__)

[docs]def set_dataset_matcher_factory(trans, tool): trans.dataset_matcher_factory = DatasetMatcherFactory(trans, tool)
[docs]def unset_dataset_matcher_factory(trans): trans.dataset_matcher_factory = None
[docs]def get_dataset_matcher_factory(trans): dataset_matcher_factory = getattr(trans, "dataset_matcher_factory", None) return dataset_matcher_factory or DatasetMatcherFactory(trans)
class DatasetMatcherFactory: """""" def __init__(self, trans, tool=None): self._trans = trans self._tool = tool self._data_inputs = [] self._matches_format_cache = {} if tool: valid_input_states = tool.valid_input_states else: valid_input_states = galaxy.model.Dataset.valid_input_states self.valid_input_states = valid_input_states can_process_summary = False if tool is not None: for input in tool.inputs.values(): self._collect_data_inputs(input) require_public = self._tool and self._tool.tool_type == 'data_destination' if not require_public and self._data_inputs: can_process_summary = True for data_input in self._data_inputs: if data_input.options: can_process_summary = False break self._can_process_summary = can_process_summary def matches_any_format(self, hda_extension, formats): for format in formats: if self.matches_format(hda_extension, format): return True return False def matches_format(self, hda_extension, format): # cache datatype checking combinations for fast recall if hda_extension not in self._matches_format_cache: self._matches_format_cache[hda_extension] = {} formats = self._matches_format_cache[hda_extension] if format not in formats: datatype = galaxy.model.datatype_for_extension(hda_extension, datatypes_registry=self._trans.app.datatypes_registry) formats[format] = datatype.matches_any([format]) return formats[format] def _collect_data_inputs(self, input): type_name = input.type if type_name == "repeat" or type_name == "upload_dataset" or type_name == "section": for child_input in input.inputs.values(): self._collect_data_inputs(child_input) elif type_name == "conditional": for case in input.cases: for child_input in case.inputs.values(): self._collect_data_inputs(child_input) elif type_name == "data" or type_name == "data_collection": self._data_inputs.append(input) def dataset_matcher(self, param, other_values): return DatasetMatcher(self, self._trans, param, other_values) def dataset_collection_matcher(self, dataset_matcher): if self._can_process_summary: return SummaryDatasetCollectionMatcher(self, self._trans, dataset_matcher) else: return DatasetCollectionMatcher(self._trans, dataset_matcher) class DatasetMatcher: """ Utility class to aid DataToolParameter and similar classes in reasoning about what HDAs could match or are selected for a parameter and value. Goal here is to both encapsulate and reuse logic related to filtering, datatype matching, hiding errored dataset, finding implicit conversions, and permission handling. """ def __init__(self, dataset_matcher_factory, trans, param, other_values): self.dataset_matcher_factory = dataset_matcher_factory self.trans = trans self.param = param self.tool = param.tool filter_values = set() if param.options and other_values: try: for v in param.options.get_options(trans, other_values): filter_values.add(v[0]) except IndexError: pass # no valid options self.filter_values = filter_values def valid_hda_match(self, hda, check_implicit_conversions=True): """ Return False if this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ rval = False formats = self.param.formats direct_match, target_ext, converted_dataset = hda.find_conversion_destination(formats) if direct_match: rval = HdaDirectMatch(hda) else: if not check_implicit_conversions: return False if target_ext: original_hda = hda if converted_dataset: hda = converted_dataset rval = HdaImplicitMatch(hda, target_ext, original_hda) else: return False if self.filter(hda): return False return rval def hda_match(self, hda, check_implicit_conversions=True, ensure_visible=True): """ If HDA is accessible, return information about whether it could match this parameter and if so how. See valid_hda_match for more information. """ dataset = hda.dataset valid_state = dataset.state in self.dataset_matcher_factory.valid_input_states if valid_state and (not ensure_visible or hda.visible): # If we are sending data to an external application, then we need to make sure there are no roles # associated with the dataset that restrict its access from "public". require_public = self.tool and self.tool.tool_type == 'data_destination' if require_public and not self.trans.app.security_agent.dataset_is_public(dataset): return False return self.valid_hda_match(hda, check_implicit_conversions=check_implicit_conversions) def filter(self, hda): """ Filter out this value based on other values for job (if applicable). """ param = self.param return param.options and param.get_options_filter_attribute(hda) not in self.filter_values class HdaDirectMatch: """ Supplied HDA was a valid option directly (did not need to find implicit conversion). """ def __init__(self, hda): self.hda = hda @property def implicit_conversion(self): return False class HdaImplicitMatch: """ Supplied HDA was a valid option directly (did not need to find implicit conversion). """ def __init__(self, hda, target_ext, original_hda): self.original_hda = original_hda self.hda = hda self.target_ext = target_ext @property def implicit_conversion(self): return True class HdcaDirectMatch: implicit_conversion = False def __init__(self): pass class HdcaImplicitMatch: implicit_conversion = True def __init__(self): pass class SummaryDatasetCollectionMatcher: def __init__(self, dataset_matcher_factory, trans, dataset_matcher): self.dataset_matcher_factory = dataset_matcher_factory self._trans = trans self.dataset_matcher = dataset_matcher def hdca_match(self, history_dataset_collection_association): dataset_collection = history_dataset_collection_association.collection if not dataset_collection.populated_optimized: return False (states, extensions) = dataset_collection.dataset_states_and_extensions_summary for state in states: if state not in self.dataset_matcher_factory.valid_input_states: return False formats = self.dataset_matcher.param.formats uses_implicit_conversion = False for extension in extensions: datatypes_registry = self._trans.app.datatypes_registry direct_match, converted_ext, _ = datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension, formats) if direct_match: continue if not converted_ext: return False else: uses_implicit_conversion = True return HdcaImplicitMatch() if uses_implicit_conversion else HdcaDirectMatch() class DatasetCollectionMatcher: def __init__(self, trans, dataset_matcher): self.dataset_matcher = dataset_matcher self._trans = trans def __valid_element(self, element): # Simplify things for now and assume these are hdas and not implicit # converts. One could imagine handling both of those cases down the # road. if element.ldda: return False child_collection = element.child_collection if child_collection: return self.dataset_collection_match(child_collection) hda = element.hda if not hda: return False hda_match = self.dataset_matcher.hda_match(hda, ensure_visible=False) return hda_match def hdca_match(self, history_dataset_collection_association): dataset_collection = history_dataset_collection_association.collection return self.dataset_collection_match(dataset_collection) def dataset_collection_match(self, dataset_collection): # If dataset collection not yet populated, cannot determine if it # would be a valid match for this parameter. if not dataset_collection.populated: return False valid = True uses_implicit_conversion = False for element in dataset_collection.elements: match_element = self.__valid_element(element) if not match_element: valid = False break elif match_element.implicit_conversion: uses_implicit_conversion = True return valid and (HdcaImplicitMatch() if uses_implicit_conversion else HdcaDirectMatch()) __all__ = ('get_dataset_matcher_factory', 'set_dataset_matcher_factory', 'unset_dataset_matcher_factory')