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Source code for galaxy.tools.wrappers

import logging
import os
import tempfile

from six import string_types
from six.moves import shlex_quote

from galaxy import exceptions
from galaxy.util import odict
from galaxy.util.none_like import NoneDataset
from galaxy.util.object_wrapper import wrap_with_safe_string

log = logging.getLogger(__name__)

# Fields in .log files corresponding to paths, must have one of the following
# field names and all such fields are assumed to be paths. This is to allow
# remote ComputeEnvironments (such as one used by Pulsar) determine what values to
# rewrite or transfer...

# ... by default though - don't rewrite anything (if no ComputeEnviornment
# defined or ComputeEnvironment doesn't supply a rewriter).
[docs]def DEFAULT_PATH_REWRITER(x): return x
[docs]class ToolParameterValueWrapper(object): """ Base class for object that Wraps a Tool Parameter and Value. """ def __bool__(self): return bool(self.value) __nonzero__ = __bool__
[docs] def get_display_text(self, quote=True): """ Returns a string containing the value that would be displayed to the user in the tool interface. When quote is True (default), the string is escaped for e.g. command-line usage. """ rval = self.input.value_to_display_text(self.value) or '' if quote: return shlex_quote(rval) return rval
[docs]class RawObjectWrapper(ToolParameterValueWrapper): """ Wraps an object so that __str__ returns module_name:class_name. """
[docs] def __init__(self, obj): self.obj = obj
def __bool__(self): return bool(self.obj) # FIXME: would it be safe/backwards compatible to rename .obj to .value, so that we can just inherit this method? __nonzero__ = __bool__ def __str__(self): try: return "%s:%s" % (self.obj.__module__, self.obj.__class__.__name__) except: # Most likely None, which lacks __module__. return str(self.obj) def __getattr__(self, key): return getattr(self.obj, key)
[docs]class InputValueWrapper(ToolParameterValueWrapper): """ Wraps an input so that __str__ gives the "param_dict" representation. """
[docs] def __init__(self, input, value, other_values={}): self.input = input self.value = value self._other_values = other_values
def __eq__(self, other): if isinstance(other, string_types): return str(self) == other elif isinstance(other, int): return int(self) == other elif isinstance(other, float): return float(self) == other else: return super(InputValueWrapper, self) == other def __ne__(self, other): return not self == other def __str__(self): to_param_dict_string = self.input.to_param_dict_string(self.value, self._other_values) if isinstance(to_param_dict_string, list): return ','.join(to_param_dict_string) else: return to_param_dict_string def __iter__(self): to_param_dict_string = self.input.to_param_dict_string(self.value, self._other_values) if not isinstance(to_param_dict_string, list): return iter([to_param_dict_string]) else: return iter(to_param_dict_string) def __getattr__(self, key): return getattr(self.value, key) def __int__(self): return int(str(self)) def __float__(self): return float(str(self))
[docs]class SelectToolParameterWrapper(ToolParameterValueWrapper): """ Wraps a SelectTooParameter so that __str__ returns the selected value, but all other attributes are accessible. """
[docs] class SelectToolParameterFieldWrapper: """ Provide access to any field by name or index for this particular value. Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected). """
[docs] def __init__(self, input, value, other_values, path_rewriter): self._input = input self._value = value self._other_values = other_values self._fields = {} self._path_rewriter = path_rewriter
def __getattr__(self, name): if name not in self._fields: self._fields[name] = self._input.options.get_field_by_name_for_value(name, self._value, None, self._other_values) values = map(str, self._fields[name]) if name in PATH_ATTRIBUTES: # If we infer this is a path, rewrite it if needed. values = map(self._path_rewriter, values) return self._input.separator.join(values)
[docs] def __init__(self, input, value, other_values={}, path_rewriter=None): self.input = input self.value = value self.input.value_label = input.value_to_display_text(value) self._other_values = other_values self._path_rewriter = path_rewriter or DEFAULT_PATH_REWRITER self.fields = self.SelectToolParameterFieldWrapper(input, value, other_values, self._path_rewriter)
def __eq__(self, other): if isinstance(other, string_types): return str(self) == other else: return super(SelectToolParameterWrapper, self) == other def __ne__(self, other): return not self == other def __str__(self): # Assuming value is never a path - otherwise would need to pass # along following argument value_map=self._path_rewriter. return self.input.to_param_dict_string(self.value, other_values=self._other_values) def __add__(self, x): return '%s%s' % (self, x) def __getattr__(self, key): return getattr(self.input, key)
[docs]class DatasetFilenameWrapper(ToolParameterValueWrapper): """ Wraps a dataset so that __str__ returns the filename, but all other attributes are accessible. """
[docs] class MetadataWrapper: """ Wraps a Metadata Collection to return MetadataParameters wrapped according to the metadata spec. Methods implemented to match behavior of a Metadata Collection. """
[docs] def __init__(self, metadata): self.metadata = metadata
def __getattr__(self, name): rval = self.metadata.get(name, None) if name in self.metadata.spec: if rval is None: rval = self.metadata.spec[name].no_value rval = self.metadata.spec[name].param.to_safe_string(rval) # Store this value, so we don't need to recalculate if needed # again setattr(self, name, rval) else: # escape string value of non-defined metadata value rval = wrap_with_safe_string(rval) return rval def __bool__(self): return self.metadata.__nonzero__() __nonzero__ = __bool__ def __iter__(self): return self.metadata.__iter__()
[docs] def get(self, key, default=None): try: return getattr(self, key) except: return default
[docs] def items(self): return iter((k, self.get(k)) for k, v in self.metadata.items())
[docs] def __init__(self, dataset, datatypes_registry=None, tool=None, name=None, dataset_path=None, identifier=None): if not dataset: try: # TODO: allow this to work when working with grouping ext = tool.inputs[name].extensions[0] except: ext = 'data' self.dataset = wrap_with_safe_string(NoneDataset(datatypes_registry=datatypes_registry, ext=ext), no_wrap_classes=ToolParameterValueWrapper) else: # Tool wrappers should not normally be accessing .dataset directly, # so we will wrap it and keep the original around for file paths # Should we name this .value to maintain consistency with most other ToolParameterValueWrapper? self.unsanitized = dataset self.dataset = wrap_with_safe_string(dataset, no_wrap_classes=ToolParameterValueWrapper) self.metadata = self.MetadataWrapper(dataset.metadata) self.datatypes_registry = datatypes_registry self.false_path = getattr(dataset_path, "false_path", None) self.false_extra_files_path = getattr(dataset_path, "false_extra_files_path", None) self._element_identifier = identifier
@property def element_identifier(self): identifier = self._element_identifier if identifier is None: identifier = self.name return identifier @property def is_collection(self): return False
[docs] def is_of_type(self, *exts): datatypes = [] for e in exts: datatype = self.datatypes_registry.get_datatype_by_extension(e) if datatype is not None: datatypes.append(datatype) else: log.warning("Datatype class not found for extension '%s', which is used as parameter of 'is_of_type()' method" % (e)) return self.dataset.datatype.matches_any(datatypes)
def __str__(self): if self.false_path is not None: return self.false_path else: return self.unsanitized.file_name def __getattr__(self, key): if self.false_path is not None and key == 'file_name': # Path to dataset was rewritten for this job. return self.false_path elif self.false_extra_files_path is not None and key == 'extra_files_path': # Path to extra files was rewritten for this job. return self.false_extra_files_path elif key == 'extra_files_path': try: # Assume it is an output and that this wrapper # will be set with correct "files_path" for this # job. return self.files_path except AttributeError: # Otherwise, we have an input - delegate to model and # object store to find the static location of this # directory. try: return self.unsanitized.extra_files_path except exceptions.ObjectNotFound: # NestedObjectstore raises an error here # instead of just returning a non-existent # path like DiskObjectStore. raise else: return getattr(self.dataset, key) def __bool__(self): return bool(self.dataset) __nonzero__ = __bool__
[docs]class HasDatasets: def _dataset_wrapper(self, dataset, dataset_paths, **kwargs): wrapper_kwds = kwargs.copy() if dataset: real_path = dataset.file_name if real_path in dataset_paths: wrapper_kwds["dataset_path"] = dataset_paths[real_path] return DatasetFilenameWrapper(dataset, **wrapper_kwds)
[docs] def paths_as_file(self, sep="\n"): handle, filepath = tempfile.mkstemp(prefix="gx_file_list", dir=self.job_working_directory) contents = sep.join(map(str, self)) os.write(handle, contents) os.close(handle) return filepath
[docs]class DatasetListWrapper(list, ToolParameterValueWrapper, HasDatasets): """ """
[docs] def __init__(self, job_working_directory, datasets, dataset_paths=[], **kwargs): if not isinstance(datasets, list): datasets = [datasets] def to_wrapper(dataset): if hasattr(dataset, "dataset_instance"): element = dataset dataset = element.dataset_instance kwargs["identifier"] = element.element_identifier return self._dataset_wrapper(dataset, dataset_paths, **kwargs) list.__init__(self, map(to_wrapper, datasets)) self.job_working_directory = job_working_directory
[docs] @staticmethod def to_dataset_instances(dataset_instance_sources): dataset_instances = [] if not isinstance(dataset_instance_sources, list): dataset_instance_sources = [dataset_instance_sources] for dataset_instance_source in dataset_instance_sources: if dataset_instance_source is None: dataset_instances.append(dataset_instance_source) elif dataset_instance_source.history_content_type == "dataset": dataset_instances.append(dataset_instance_source) else: dataset_instances.extend(dataset_instance_source.collection.dataset_elements) return dataset_instances
def __str__(self): return ','.join(map(str, self))
[docs]class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
[docs] def __init__(self, job_working_directory, has_collection, dataset_paths=[], **kwargs): super(DatasetCollectionWrapper, self).__init__() self.job_working_directory = job_working_directory if has_collection is None: self.__input_supplied = False return else: self.__input_supplied = True if hasattr(has_collection, "name"): # It is a HistoryDatasetCollectionAssociation collection = has_collection.collection self.name = has_collection.name elif hasattr(has_collection, "child_collection"): # It is a DatasetCollectionElement instance referencing another collection collection = has_collection.child_collection self.name = has_collection.element_identifier else: collection = has_collection self.name = None elements = collection.elements element_instances = odict.odict() element_instance_list = [] for dataset_collection_element in elements: element_object = dataset_collection_element.element_object element_identifier = dataset_collection_element.element_identifier if dataset_collection_element.is_collection: element_wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection_element, dataset_paths, **kwargs) else: element_wrapper = self._dataset_wrapper(element_object, dataset_paths, identifier=element_identifier, **kwargs) element_instances[element_identifier] = element_wrapper element_instance_list.append(element_wrapper) self.__element_instances = element_instances self.__element_instance_list = element_instance_list
[docs] def keys(self): if not self.__input_supplied: return [] return self.__element_instances.keys()
@property def is_collection(self): return True @property def is_input_supplied(self): return self.__input_supplied def __getitem__(self, key): if not self.__input_supplied: return None if isinstance(key, int): return self.__element_instance_list[key] else: return self.__element_instances[key] def __getattr__(self, key): if not self.__input_supplied: return None return self.__element_instances[key] def __iter__(self): if not self.__input_supplied: return [].__iter__() return self.__element_instance_list.__iter__() def __bool__(self): # Fail `#if $param` checks in cheetah is optional input # not specified or if resulting collection is empty. return self.__input_supplied and bool(self.__element_instance_list) __nonzero__ = __bool__
[docs]class ElementIdentifierMapper(object): """Track mapping of dataset collection elements datasets to element identifiers."""
[docs] def __init__(self, input_datasets=None): if input_datasets is not None: self.identifier_key_dict = dict((v, "%s|__identifier__" % k) for k, v in input_datasets.items()) else: self.identifier_key_dict = {}
[docs] def identifier(self, dataset_value, input_values): identifier_key = self.identifier_key_dict.get(dataset_value, None) element_identifier = None if identifier_key: element_identifier = input_values.get(identifier_key, None) return element_identifier