Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tools.parameters.wrapped

from galaxy.tools.parameters.basic import (
    DataCollectionToolParameter,
    DataToolParameter,
    SelectToolParameter
)
from galaxy.tools.parameters.grouping import (
    Conditional,
    Repeat,
    Section
)
from galaxy.tools.wrappers import (
    DatasetCollectionWrapper,
    DatasetFilenameWrapper,
    DatasetListWrapper,
    ElementIdentifierMapper,
    InputValueWrapper,
    SelectToolParameterWrapper
)

PARAMS_UNWRAPPED = object()


def copy_identifiers(source, destination):
    if isinstance(source, dict):
        for k, v in source.items():
            if k.endswith('|__identifier__'):
                if isinstance(destination, dict):
                    destination[k] = v


[docs]class WrappedParameters(object):
[docs] def __init__(self, trans, tool, incoming, input_datasets=None): self.trans = trans self.tool = tool self.incoming = incoming self._params = PARAMS_UNWRAPPED self._input_datasets = input_datasets
@property def params(self): if self._params is PARAMS_UNWRAPPED: params = make_dict_copy(self.incoming) self.wrap_values(self.tool.inputs, params, skip_missing_values=not self.tool.check_values) self._params = params return self._params
[docs] def wrap_values(self, inputs, input_values, skip_missing_values=False): trans = self.trans tool = self.tool incoming = self.incoming element_identifier_mapper = ElementIdentifierMapper(self._input_datasets) # Wrap tool inputs as necessary for input in inputs.values(): if input.name not in input_values and skip_missing_values: continue value = input_values[input.name] copy_identifiers(destination=value, source=input_values) if isinstance(input, Repeat): for d in value: copy_identifiers(destination=d, source=value) self.wrap_values(input.inputs, d, skip_missing_values=skip_missing_values) elif isinstance(input, Conditional): values = value current = values["__current_case__"] self.wrap_values(input.cases[current].inputs, values, skip_missing_values=skip_missing_values) elif isinstance(input, Section): values = value self.wrap_values(input.inputs, values, skip_missing_values=skip_missing_values) elif isinstance(input, DataToolParameter) and input.multiple: dataset_instances = DatasetListWrapper.to_dataset_instances(value) input_values[input.name] = \ DatasetListWrapper(None, dataset_instances, datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name) elif isinstance(input, DataToolParameter): wrapper_kwds = dict( datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name ) element_identifier = element_identifier_mapper.identifier(value, input_values) if element_identifier: wrapper_kwds["identifier"] = element_identifier input_values[input.name] = DatasetFilenameWrapper(value, **wrapper_kwds) elif isinstance(input, SelectToolParameter): input_values[input.name] = SelectToolParameterWrapper(input, value, other_values=incoming) elif isinstance(input, DataCollectionToolParameter): input_values[input.name] = DatasetCollectionWrapper( None, value, datatypes_registry=trans.app.datatypes_registry, tool=tool, name=input.name, ) else: input_values[input.name] = InputValueWrapper(input, value, incoming)
[docs]def make_dict_copy(from_dict): """ Makes a copy of input dictionary from_dict such that all values that are dictionaries result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle other complex types ( e.g., lists, etc ), but not sure... Yes, we need to handle lists (and now are)... """ copy_from_dict = {} for key, value in from_dict.items(): if type(value).__name__ == 'dict': copy_from_dict[key] = make_dict_copy(value) elif isinstance(value, list): copy_from_dict[key] = make_list_copy(value) else: copy_from_dict[key] = value return copy_from_dict
def make_list_copy(from_list): new_list = [] for value in from_list: if isinstance(value, dict): new_list.append(make_dict_copy(value)) elif isinstance(value, list): new_list.append(make_list_copy(value)) else: new_list.append(value) return new_list __all__ = ('WrappedParameters', 'make_dict_copy')