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

from os.path import abspath, exists, join

from .galaxy_packages import BaseGalaxyPackageDependencyResolver, ToolShedDependency
from .resolver_mixins import UsesInstalledRepositoriesMixin
from ..resolvers import NullDependency


[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', )