def __init__(self, tool_requirements=None):
if tool_requirements:
if not isinstance(tool_requirements, list):
raise ToolRequirementsException('ToolRequirements Constructor expects a list')
self.tool_requirements = OrderedSet([r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements])
else:
self.tool_requirements = OrderedSet()
def __init__(self, tool_requirements=None):
if tool_requirements:
if not isinstance(tool_requirements, list):
raise ToolRequirementsException('ToolRequirements Constructor expects a list')
self.tool_requirements = OrderedSet([r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements])
else:
self.tool_requirements = OrderedSet()
class ToolRequirements(object):
"""
Represents all requirements (packages, env vars) needed to run a tool.
"""
def __init__(self, tool_requirements=None):
if tool_requirements:
if not isinstance(tool_requirements, list):
raise ToolRequirementsException(
'ToolRequirements Constructor expects a list')
self.tool_requirements = OrderedSet([
r if isinstance(r, ToolRequirement) else
ToolRequirement.from_dict(r) for r in tool_requirements
])
else:
self.tool_requirements = OrderedSet()
@staticmethod
def from_list(requirements):
return ToolRequirements(requirements)
@property
def resolvable(self):
return ToolRequirements([
r for r in self.tool_requirements
if r.type in {'package', 'set_environment'}
])
@property
def packages(self):
return ToolRequirements(
[r for r in self.tool_requirements if r.type == 'package'])
def to_list(self):
return [r.to_dict() for r in self.tool_requirements]
def append(self, requirement):
if not isinstance(requirement, ToolRequirement):
requirement = ToolRequirement.from_dict(requirement)
self.tool_requirements.add(requirement)
def __eq__(self, other):
return len(self.tool_requirements & other.tool_requirements) == len(
self.tool_requirements) == len(other.tool_requirements)
def __ne__(self, other):
return not self.__eq__(other)
def __iter__(self):
for r in self.tool_requirements:
yield r
def __getitem__(self, ii):
return list(self.tool_requirements)[ii]
def __len__(self):
return len(self.tool_requirements)
def __hash__(self):
return sum([r.__hash__() for r in self.tool_requirements])
class ToolRequirements(object):
"""
Represents all requirements (packages, env vars) needed to run a tool.
"""
def __init__(self, tool_requirements=None):
if tool_requirements:
if not isinstance(tool_requirements, list):
raise ToolRequirementsException('ToolRequirements Constructor expects a list')
self.tool_requirements = OrderedSet([r if isinstance(r, ToolRequirement) else ToolRequirement.from_dict(r) for r in tool_requirements])
else:
self.tool_requirements = OrderedSet()
@staticmethod
def from_list(requirements):
return ToolRequirements(requirements)
@property
def resolvable(self):
return ToolRequirements([r for r in self.tool_requirements if r.type in {'package', 'set_environment'}])
@property
def packages(self):
return ToolRequirements([r for r in self.tool_requirements if r.type == 'package'])
def to_list(self):
return [r.to_dict() for r in self.tool_requirements]
def append(self, requirement):
if not isinstance(requirement, ToolRequirement):
requirement = ToolRequirement.from_dict(requirement)
self.tool_requirements.add(requirement)
def __eq__(self, other):
return len(self.tool_requirements & other.tool_requirements) == len(self.tool_requirements) == len(other.tool_requirements)
def __ne__(self, other):
return not self.__eq__(other)
def __iter__(self):
for r in self.tool_requirements:
yield r
def __getitem__(self, ii):
return list(self.tool_requirements)[ii]
def __len__(self):
return len(self.tool_requirements)
def __hash__(self):
return sum([r.__hash__() for r in self.tool_requirements])
def dependency_shell_commands(self, requirements, **kwds):
requirements_to_dependencies = self.requirements_to_dependencies(
requirements, **kwds)
ordered_dependencies = OrderedSet(
requirements_to_dependencies.values())
return [
dependency.shell_commands() for dependency in ordered_dependencies
]
def dependency_shell_commands(self, requirements, **kwds):
requirements_to_dependencies = self.requirements_to_dependencies(
requirements, **kwds)
ordered_dependencies = OrderedSet(
requirements_to_dependencies.values())
return [
dependency.shell_commands() for dependency in ordered_dependencies
if not isinstance(dependency, ContainerDependency)
]
def set_collection_elements(dataset_collection, type, dataset_instances,
associated_identifiers):
new_element_keys = OrderedSet(
dataset_instances.keys()) - associated_identifiers
new_dataset_instances = {k: dataset_instances[k] for k in new_element_keys}
dataset_collection.element_count = dataset_collection.element_count or 0
element_index = dataset_collection.element_count
elements = []
for element in type.generate_elements(new_dataset_instances):
element.element_index = element_index
element.collection = dataset_collection
elements.append(element)
element_index += 1
associated_identifiers.add(element.element_identifier)
dataset_collection.element_count = element_index
return dataset_collection