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Source code for galaxy.tools.deps.dependencies
from galaxy.tools.deps.requirements import ToolRequirements
from galaxy.util import bunch
from .mulled.mulled_build import DEFAULT_CHANNELS
[docs]class AppInfo(object):
[docs] def __init__(
self,
galaxy_root_dir=None,
default_file_path=None,
outputs_to_working_directory=False,
container_image_cache_path=None,
library_import_dir=None,
enable_beta_mulled_containers=False,
containers_resolvers_config_file=None,
involucro_path=None,
involucro_auto_init=True,
mulled_channels=DEFAULT_CHANNELS,
):
self.galaxy_root_dir = galaxy_root_dir
self.default_file_path = default_file_path
# TODO: Vary default value for docker_volumes based on this...
self.outputs_to_working_directory = outputs_to_working_directory
self.container_image_cache_path = container_image_cache_path
self.library_import_dir = library_import_dir
self.enable_beta_mulled_containers = enable_beta_mulled_containers
self.containers_resolvers_config_file = containers_resolvers_config_file
self.involucro_path = involucro_path
self.involucro_auto_init = involucro_auto_init
self.mulled_channels = mulled_channels
[docs]class ToolInfo(object):
# TODO: Introduce tool XML syntax to annotate the optional environment
# variables they can consume (e.g. JVM options, license keys, etc..)
# and add these to env_path_through
[docs] def __init__(self, container_descriptions=[], requirements=[], requires_galaxy_python_environment=False, env_pass_through=["GALAXY_SLOTS"]):
self.container_descriptions = container_descriptions
self.requirements = requirements
self.requires_galaxy_python_environment = requires_galaxy_python_environment
self.env_pass_through = env_pass_through
[docs]class JobInfo(object):
[docs] def __init__(
self, working_directory, tool_directory, job_directory, tmp_directory, job_directory_type
):
self.working_directory = working_directory
self.job_directory = job_directory
# Tool files may be remote staged - so this is unintuitively a property
# of the job not of the tool.
self.tool_directory = tool_directory
self.tmp_directory = tmp_directory
self.job_directory_type = job_directory_type # "galaxy" or "pulsar"
[docs]class DependenciesDescription(object):
""" Capture (in a readily serializable way) context related a tool
dependencies - both the tool's listed requirements and the tool shed
related context required to resolve dependencies via the
ToolShedPackageDependencyResolver.
This is meant to enable remote resolution of dependencies, by the Pulsar or
other potential remote execution mechanisms.
"""
[docs] def __init__(self, requirements=[], installed_tool_dependencies=[]):
self.requirements = requirements
# tool shed installed tool dependencies...
self.installed_tool_dependencies = installed_tool_dependencies
[docs] def to_dict(self):
return dict(
requirements=[r.to_dict() for r in self.requirements],
installed_tool_dependencies=[DependenciesDescription._toolshed_install_dependency_to_dict(d) for d in self.installed_tool_dependencies]
)
[docs] @staticmethod
def from_dict(as_dict):
if as_dict is None:
return None
requirements_dicts = as_dict.get('requirements', [])
requirements = ToolRequirements.from_list(requirements_dicts)
installed_tool_dependencies_dicts = as_dict.get('installed_tool_dependencies', [])
installed_tool_dependencies = map(DependenciesDescription._toolshed_install_dependency_from_dict, installed_tool_dependencies_dicts)
return DependenciesDescription(
requirements=requirements,
installed_tool_dependencies=installed_tool_dependencies
)
@staticmethod
def _toolshed_install_dependency_from_dict(as_dict):
# Rather than requiring full models in Pulsar, just use simple objects
# containing only properties and associations used to resolve
# dependencies for tool execution.
repository_object = bunch.Bunch(
name=as_dict['repository_name'],
owner=as_dict['repository_owner'],
installed_changeset_revision=as_dict['repository_installed_changeset'],
)
dependency_object = bunch.Bunch(
name=as_dict['dependency_name'],
version=as_dict['dependency_version'],
type=as_dict['dependency_type'],
tool_shed_repository=repository_object,
)
return dependency_object
@staticmethod
def _toolshed_install_dependency_to_dict(tool_dependency):
tool_shed_repository = tool_dependency.tool_shed_repository
return dict(
dependency_name=tool_dependency.name,
dependency_version=tool_dependency.version,
dependency_type=tool_dependency.type,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_installed_changeset=tool_shed_repository.installed_changeset_revision,
)