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
def __init__(self,
dataset,
datatypes_registry=None,
tool=None,
name=None,
compute_environment=None,
identifier=None,
io_type="input",
formats=None):
if not dataset:
try:
# TODO: allow this to work when working with grouping
ext = tool.inputs[name].extensions[0]
except Exception:
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?
if formats:
target_ext, converted_dataset = dataset.find_conversion_destination(
formats)
if target_ext and converted_dataset:
dataset = converted_dataset
self.unsanitized = dataset
self.dataset = wrap_with_safe_string(
dataset, no_wrap_classes=ToolParameterValueWrapper)
self.metadata = self.MetadataWrapper(dataset, compute_environment)
if hasattr(dataset, 'tags'):
self.groups = {
tag.user_value.lower()
for tag in dataset.tags if tag.user_tname == 'group'
}
else:
# May be a 'FakeDatasetAssociation'
self.groups = set()
self.compute_environment = compute_environment
# TODO: lazy initialize this...
self.__io_type = io_type
if self.__io_type == "input":
path_rewrite = compute_environment and dataset and compute_environment.input_path_rewrite(
dataset)
if path_rewrite:
self.false_path = path_rewrite
else:
self.false_path = None
else:
path_rewrite = compute_environment and compute_environment.output_path_rewrite(
dataset)
if path_rewrite:
self.false_path = path_rewrite
else:
self.false_path = None
self.datatypes_registry = datatypes_registry
self._element_identifier = identifier
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 Exception:
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
def __sanitize_param_dict(self, param_dict):
"""
Sanitize all values that will be substituted on the command line, with the exception of ToolParameterValueWrappers,
which already have their own specific sanitization rules and also exclude special-cased named values.
We will only examine the first level for values to skip; the wrapping function will recurse as necessary.
Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place.
"""
# chromInfo is a filename, do not sanitize it.
skip = ['chromInfo'] + list(self.tool.template_macro_params.keys())
if not self.tool or not self.tool.options or self.tool.options.sanitize:
for key, value in list(param_dict.items()):
if key not in skip:
# Remove key so that new wrapped object will occupy key slot
del param_dict[key]
# And replace with new wrapped key
param_dict[wrap_with_safe_string(
key, no_wrap_classes=ToolParameterValueWrapper
)] = wrap_with_safe_string(
value, no_wrap_classes=ToolParameterValueWrapper)
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 __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 __sanitize_param_dict( self, param_dict ):
"""
Sanitize all values that will be substituted on the command line, with the exception of ToolParameterValueWrappers,
which already have their own specific sanitization rules and also exclude special-cased named values.
We will only examine the first level for values to skip; the wrapping function will recurse as necessary.
Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place.
"""
# chromInfo is a filename, do not sanitize it.
skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys()
if not self.tool or not self.tool.options or self.tool.options.sanitize:
for key, value in param_dict.items():
if key not in skip:
# Remove key so that new wrapped object will occupy key slot
del param_dict[key]
# And replace with new wrapped key
param_dict[ wrap_with_safe_string( key, no_wrap_classes=ToolParameterValueWrapper ) ] = wrap_with_safe_string( value, no_wrap_classes=ToolParameterValueWrapper )
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
metadata_param = self.metadata.spec[name].param
from galaxy.model.metadata import FileParameter
rval = metadata_param.to_safe_string(rval)
if isinstance(metadata_param, FileParameter) and self.compute_environment:
rewrite = self.compute_environment.input_metadata_rewrite(self.dataset, rval)
if rewrite is not None:
rval = rewrite
# 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
