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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=None, requirements=None, requires_galaxy_python_environment=False, env_pass_through=["GALAXY_SLOTS"]): if container_descriptions is None: container_descriptions = [] if requirements is None: requirements = [] 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, )