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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 galaxy.util import parse_xml
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(f"Failed to parse dependencies in file {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: def __init__(self, dependencies_file): self.root = parse_xml(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: 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 = f"{owner}_{name}" return base __all__ = ("HomebrewToolShedDependencyResolver",)