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Source code for galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages
"""
This dependency resolver resolves tool shed dependencies (those defined
tool_dependencies.xml) installed using Platform Homebrew and converted
via shed2tap (e.g. https://github.com/jmchilton/homebrew-toolshed).
"""
import logging
import os
from xml.etree import ElementTree as ET
from . import (
DependencyResolver,
NullDependency
)
from .resolver_mixins import (
UsesHomebrewMixin,
UsesInstalledRepositoriesMixin,
UsesToolDependencyDirMixin,
)
log = logging.getLogger(__name__)
[docs]class HomebrewToolShedDependencyResolver(
DependencyResolver,
UsesHomebrewMixin,
UsesToolDependencyDirMixin,
UsesInstalledRepositoriesMixin,
):
resolver_type = "tool_shed_tap"
[docs] def __init__(self, dependency_manager, **kwds):
self._init_homebrew(**kwds)
self._init_base_path(dependency_manager, **kwds)
[docs] def resolve(self, requirement, **kwds):
name, version, type = requirement.name, requirement.version, requirement.type
if type != "package":
return NullDependency(version=version, name=name)
if version is None:
return NullDependency(version=version, name=name)
return self._find_tool_dependencies(name, version, type, **kwds)
def _find_tool_dependencies(self, name, version, type, **kwds):
installed_tool_dependency = self._get_installed_dependency(name, type, version=version, **kwds)
if installed_tool_dependency:
return self._resolve_from_installed_tool_dependency(name, version, installed_tool_dependency)
if "tool_dir" in kwds:
tool_directory = os.path.abspath(kwds["tool_dir"])
tool_depenedencies_path = os.path.join(tool_directory, "tool_dependencies.xml")
if os.path.exists(tool_depenedencies_path):
return self._resolve_from_tool_dependencies_path(name, version, tool_depenedencies_path)
return NullDependency(version=version, name=name)
def _resolve_from_installed_tool_dependency(self, name, version, installed_tool_dependency):
tool_shed_repository = installed_tool_dependency.tool_shed_repository
recipe_name = build_recipe_name(
package_name=name,
package_version=version,
repository_owner=tool_shed_repository.owner,
repository_name=tool_shed_repository.name,
)
return self._find_dep_default(recipe_name, None)
def _resolve_from_tool_dependencies_path(self, name, version, tool_dependencies_path):
try:
raw_dependencies = RawDependencies(tool_dependencies_path)
except Exception:
log.debug("Failed to parse dependencies in file %s" % tool_dependencies_path)
return NullDependency(version=version, name=name)
raw_dependency = raw_dependencies.find(name, version)
if not raw_dependency:
return NullDependency(version=version, name=name)
recipe_name = build_recipe_name(
package_name=name,
package_version=version,
repository_owner=raw_dependency.repository_owner,
repository_name=raw_dependency.repository_name
)
dep = self._find_dep_default(recipe_name, None)
return dep
class RawDependencies(object):
def __init__(self, dependencies_file):
self.root = ET.parse(dependencies_file).getroot()
dependencies = []
package_els = self.root.findall("package") or []
for package_el in package_els:
repository_el = package_el.find("repository")
if repository_el is None:
continue
dependency = RawDependency(self, package_el, repository_el)
dependencies.append(dependency)
self.dependencies = dependencies
def find(self, package_name, package_version):
target_dependency = None
for dependency in self.dependencies:
if dependency.package_name == package_name and dependency.package_version == package_version:
target_dependency = dependency
break
return target_dependency
class RawDependency(object):
def __init__(self, dependencies, package_el, repository_el):
self.dependencies = dependencies
self.package_el = package_el
self.repository_el = repository_el
def __repr__(self):
temp = "Dependency[package_name=%s,version=%s,dependent_package=%s]"
return temp % (
self.package_el.attrib["name"],
self.package_el.attrib["version"],
self.repository_el.attrib["name"]
)
@property
def repository_owner(self):
return self.repository_el.attrib["owner"]
@property
def repository_name(self):
return self.repository_el.attrib["name"]
@property
def package_name(self):
return self.package_el.attrib["name"]
@property
def package_version(self):
return self.package_el.attrib["version"]
def build_recipe_name(package_name, package_version, repository_owner, repository_name):
# TODO: Consider baking package_name and package_version into name? (would be more "correct")
owner = repository_owner.replace("-", "")
name = repository_name
name = name.replace("_", "").replace("-", "")
base = "%s_%s" % (owner, name)
return base
__all__ = ('HomebrewToolShedDependencyResolver', )