Source code for galaxy.tools.deps.resolvers.tool_shed_packages

from os.path import abspath, exists, join

from . import NullDependency
from .galaxy_packages import (
    BaseGalaxyPackageDependencyResolver,
    ToolShedDependency
)
from .resolver_mixins import UsesInstalledRepositoriesMixin


[docs]class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin): resolver_type = "tool_shed_packages" # Resolution of these dependencies depends on more than just the requirement # tag, it depends on the tool installation context - therefore these are # non-simple. dependency_type = ToolShedDependency resolves_simple_dependencies = False
[docs] def __init__(self, dependency_manager, **kwds): super(ToolShedPackageDependencyResolver, self).__init__(dependency_manager, **kwds)
def _find_dep_versioned(self, name, version, type='package', **kwds): installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds) if installed_tool_dependency: path = self._get_package_installed_dependency_path(installed_tool_dependency, name, version) return self._galaxy_package_dep(path, version, name, type, True) else: return NullDependency(version=version, name=name) def _find_dep_default(self, name, type='package', **kwds): if type == 'set_environment' and kwds.get('installed_tool_dependencies', None): installed_tool_dependency = self._get_installed_dependency(name, type, version=None, **kwds) if installed_tool_dependency: dependency = self._get_set_environment_installed_dependency_script_path(installed_tool_dependency, name) is_galaxy_dep = isinstance(dependency, ToolShedDependency) has_script_dep = is_galaxy_dep and dependency.script and dependency.path if has_script_dep: # Environment settings do not use versions. return ToolShedDependency(dependency.script, dependency.path, name, 'set_environment', None, True) return NullDependency(version=None, name=name) def _get_package_installed_dependency_path(self, installed_tool_dependency, name, version): tool_shed_repository = installed_tool_dependency.tool_shed_repository base_path = self.base_path return join( base_path, name, version, tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) def _get_set_environment_installed_dependency_script_path(self, installed_tool_dependency, name): tool_shed_repository = installed_tool_dependency.tool_shed_repository base_path = self.base_path path = abspath(join(base_path, 'environment_settings', name, tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision)) if exists(path): script = join(path, 'env.sh') return ToolShedDependency(script, path, name, 'set_environment', None, True) return NullDependency(version=None, name=name)
__all__ = ('ToolShedPackageDependencyResolver', )