Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.tools.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', )