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Source code for galaxy.tool_util.deps

"""
Dependency management for tools.
"""

import json
import logging
import os.path
import shutil

from galaxy.util import (
    hash_util,
    plugin_config,
    string_as_bool,
)
from galaxy.util.oset import OrderedSet
from .container_resolvers import ContainerResolver
from .dependencies import ToolInfo
from .requirements import (
    ContainerDescription,
    ToolRequirement,
    ToolRequirements
)
from .resolvers import (
    ContainerDependency,
    NullDependency,
)
from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver

log = logging.getLogger(__name__)

CONFIG_VAL_NOT_FOUND = object()


[docs]def build_dependency_manager(app_config_dict=None, resolution_config_dict=None, conf_file=None, default_tool_dependency_dir=None): """Build a DependencyManager object from app and/or resolution config. If app_config_dict is specified, it should be application configuration information and configuration options are generally named to identify the context of dependency management (e.g. conda_prefix not prefix or use_cached_dependency_manager not cache). resolution_config_dict if specified is assumed to be the to_dict() version of a DependencyManager and should only contain dependency configuration options. """ if app_config_dict is None: app_config_dict = {} else: app_config_dict = app_config_dict.copy() tool_dependency_dir = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) if tool_dependency_dir and tool_dependency_dir.lower() == "none": app_config_dict["tool_dependency_dir"] = None if resolution_config_dict is None and "dependency_resolution" in app_config_dict: resolution_config_dict = app_config_dict["dependency_resolution"] if resolution_config_dict: # Convert local to_dict options into global ones. # to_dict() has "cache", "cache_dir", "use", "default_base_path", "resolvers", "precache" app_config_props_from_resolution_config = { "use_tool_dependencies": resolution_config_dict.get("use", None), "tool_dependency_dir": resolution_config_dict.get("default_base_path", None), "dependency_resolvers": resolution_config_dict.get("resolvers", None), "tool_dependency_cache_dir": resolution_config_dict.get("cache_dir", None), "precache_dependencies": resolution_config_dict.get("precache", None), "use_cached_dependency_manager": resolution_config_dict.get("cache", None), } for key, value in app_config_props_from_resolution_config.items(): if value is not None: app_config_dict[key] = value use_tool_dependencies = app_config_dict.get("use_tool_dependencies", None) # if we haven't set an explicit True or False, try to infer from config... if use_tool_dependencies is None: use_tool_dependencies = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) is not None or \ app_config_dict.get("dependency_resolvers") or \ (conf_file and os.path.exists(conf_file)) if use_tool_dependencies: dependency_manager_kwds = { "default_base_path": app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir), "conf_file": conf_file, "app_config": app_config_dict, } if string_as_bool(app_config_dict.get("use_cached_dependency_manager")): dependency_manager = CachedDependencyManager(**dependency_manager_kwds) else: dependency_manager = DependencyManager(**dependency_manager_kwds) else: dependency_manager = NullDependencyManager() return dependency_manager
[docs]class DependencyManager: """ A DependencyManager attempts to resolve named and versioned dependencies by searching for them under a list of directories. Directories should be of the form: $BASE/name/version/... and should each contain a file 'env.sh' which can be sourced to make the dependency available in the current shell environment. """ cached = False
[docs] def __init__(self, default_base_path, conf_file=None, app_config=None): """ Create a new dependency manager looking for packages under the paths listed in `base_paths`. The default base path is app.config.tool_dependency_dir. """ if app_config is None: app_config = {} if not os.path.exists(default_base_path): log.warning("Path '%s' does not exist, ignoring", default_base_path) if not os.path.isdir(default_base_path): log.warning("Path '%s' is not directory, ignoring", default_base_path) self.__app_config = app_config self.default_base_path = os.path.abspath(default_base_path) self.resolver_classes = self.__resolvers_dict() plugin_source = None dependency_resolver_dicts = app_config.get("dependency_resolvers") if dependency_resolver_dicts is not None: plugin_source = plugin_config.PluginConfigSource('dict', dependency_resolver_dicts) else: plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file) self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source) self._enabled_container_types = [] self._destination_for_container_type = {}
[docs] def set_enabled_container_types(self, container_types_to_destinations): """Set the union of all enabled container types.""" self._enabled_container_types = [container_type for container_type in container_types_to_destinations.keys()] # Just pick first enabled destination for a container type, probably covers the most common deployment scenarios self._destination_for_container_type = container_types_to_destinations
[docs] def get_destination_info_for_container_type(self, container_type, destination_id=None): if destination_id is None: return next(iter(self._destination_for_container_type[container_type])).params else: for destination in self._destination_for_container_type[container_type]: if destination.id == destination_id: return destination.params
@property def enabled_container_types(self): """Returns the union of enabled container types.""" return self._enabled_container_types
[docs] def get_resolver_option(self, resolver, key, explicit_resolver_options=None): """Look in resolver-specific settings for option and then fallback to global settings. """ if explicit_resolver_options is None: explicit_resolver_options = {} default = resolver.config_options.get(key) config_prefix = resolver.resolver_type global_key = f"{config_prefix}_{key}" value = explicit_resolver_options.get(key, CONFIG_VAL_NOT_FOUND) if value is CONFIG_VAL_NOT_FOUND: value = self.get_app_option(global_key, default) return value
[docs] def get_app_option(self, key, default=None): value = CONFIG_VAL_NOT_FOUND if isinstance(self.__app_config, dict): value = self.__app_config.get(key, CONFIG_VAL_NOT_FOUND) else: value = getattr(self.__app_config, key, CONFIG_VAL_NOT_FOUND) if value is CONFIG_VAL_NOT_FOUND and hasattr(self.__app_config, "config_dict"): value = self.__app_config.config_dict.get(key, CONFIG_VAL_NOT_FOUND) if value is CONFIG_VAL_NOT_FOUND: value = default return value
@property def precache(self): return string_as_bool(self.get_app_option("precache_dependencies", True))
[docs] def dependency_shell_commands(self, requirements, **kwds): requirements_to_dependencies = self.requirements_to_dependencies(requirements, **kwds) ordered_dependencies = OrderedSet(requirements_to_dependencies.values()) return [dependency.shell_commands() for dependency in ordered_dependencies if not isinstance(dependency, ContainerDependency)]
[docs] def requirements_to_dependencies(self, requirements, **kwds): """ Takes a list of requirements and returns a dictionary with requirements as key and dependencies as value caching these on the tool instance if supplied. """ requirement_to_dependency = self._requirements_to_dependencies_dict(requirements, **kwds) if 'tool_instance' in kwds: kwds['tool_instance'].dependencies = [dep.to_dict() for dep in requirement_to_dependency.values()] return requirement_to_dependency
def _requirements_to_dependencies_dict(self, requirements, search=False, **kwds): """Build simple requirements to dependencies dict for resolution.""" requirement_to_dependency = {} index = kwds.get('index') install = kwds.get('install', False) resolver_type = kwds.get('resolver_type') include_containers = kwds.get('include_containers', False) container_type = kwds.get('container_type') require_exact = kwds.get('exact', False) return_null_dependencies = kwds.get('return_null', False) resolvable_requirements = requirements.resolvable tool_info_kwds = dict(requirements=resolvable_requirements) if 'tool_instance' in kwds: tool = kwds['tool_instance'] tool_info_kwds['tool_id'] = tool.id tool_info_kwds['tool_version'] = tool.version tool_info_kwds['container_descriptions'] = tool.containers tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment tool_info = ToolInfo(**tool_info_kwds) for i, resolver in enumerate(self.dependency_resolvers): if index is not None and i != index: continue if resolver_type is not None and resolver.resolver_type != resolver_type: continue if container_type is not None and getattr(resolver, "container_type", None) != container_type: continue _requirement_to_dependency = {k: v for k, v in requirement_to_dependency.items() if not isinstance(v, NullDependency)} if len(_requirement_to_dependency) == len(resolvable_requirements): # Shortcut - resolution complete. break # Check requirements all at once all_unmet = len(_requirement_to_dependency) == 0 if hasattr(resolver, "resolve_all"): resolve = resolver.resolve_all elif isinstance(resolver, ContainerResolver): if not include_containers: continue if not install and resolver.builds_on_resolution: # don't want to build images here continue if not resolver.resolver_type.startswith(('cached', 'explicit', 'fallback')) and not (search or install): # These would look up available containers using the quay API, # we only want to do this if we search for containers continue resolve = resolver.resolve else: resolve = None if all_unmet and resolve is not None: # TODO: Handle specs. dependencies = resolve(requirements=resolvable_requirements, enabled_container_types=self.enabled_container_types, destination_for_container_type=self.get_destination_info_for_container_type, tool_info=tool_info, **kwds) if dependencies: if isinstance(dependencies, ContainerDescription): dependencies = [ContainerDependency(dependencies, name=r.name, version=r.version, container_resolver=resolver) for r in resolvable_requirements] assert len(dependencies) == len(resolvable_requirements) for requirement, dependency in zip(resolvable_requirements, dependencies): log.debug(dependency.resolver_msg) requirement_to_dependency[requirement] = dependency # Shortcut - resolution complete. break if not isinstance(resolver, ContainerResolver): # Check individual requirements for requirement in resolvable_requirements: if requirement in _requirement_to_dependency: continue dependency = resolver.resolve(requirement, **kwds) if require_exact and not dependency.exact: continue if not isinstance(dependency, NullDependency): log.debug(dependency.resolver_msg) requirement_to_dependency[requirement] = dependency elif return_null_dependencies: log.debug(dependency.resolver_msg) dependency.version = requirement.version requirement_to_dependency[requirement] = dependency return requirement_to_dependency
[docs] def uses_tool_shed_dependencies(self): return any(map(lambda r: isinstance(r, ToolShedPackageDependencyResolver), self.dependency_resolvers))
[docs] def find_dep(self, name, version=None, type='package', **kwds): log.debug(f'Find dependency {name} version {version}') requirements = ToolRequirements([ToolRequirement(name=name, version=version, type=type)]) dep_dict = self._requirements_to_dependencies_dict(requirements, **kwds) if len(dep_dict) > 0: return next(iter(dep_dict.values())) # get first dep else: return NullDependency(name=name, version=version)
def __build_dependency_resolvers_plugin_source(self, conf_file): if not conf_file: return self.__default_dependency_resolvers_source() if not os.path.exists(conf_file): log.debug("Unable to find config file '%s'", conf_file) return self.__default_dependency_resolvers_source() plugin_source = plugin_config.plugin_source_from_path(conf_file) return plugin_source def __default_dependency_resolvers_source(self): return plugin_config.PluginConfigSource('dict', [ {"type": "tool_shed_packages"}, {"type": "galaxy_packages"}, {"type": "conda"}, {"type": "galaxy_packages", "versionless": True}, {"type": "conda", "versionless": True}, ]) def __parse_resolver_conf_plugins(self, plugin_source): """ """ extra_kwds = dict(dependency_manager=self) # Use either 'type' from YAML definition or 'resolver_type' from to_dict definition. return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=['type', 'resolver_type']) def __resolvers_dict(self): import galaxy.tool_util.deps.resolvers return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers, 'resolver_type')
[docs] def to_dict(self): return { "use": True, "cache": self.cached, "precache": self.precache, "cache_dir": getattr(self, "tool_dependency_cache_dir", None), "default_base_path": self.default_base_path, "resolvers": [m.to_dict() for m in self.dependency_resolvers], }
[docs]class CachedDependencyManager(DependencyManager): cached = True
[docs] def __init__(self, default_base_path, **kwd): super().__init__(default_base_path=default_base_path, **kwd) self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") or os.path.join(default_base_path, "_cache")
[docs] def build_cache(self, requirements, **kwds): resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable] hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies) if os.path.exists(hashed_dependencies_dir): if kwds.get('force_rebuild', False): try: shutil.rmtree(hashed_dependencies_dir) except Exception: log.warning(f"Could not delete cached dependencies directory '{hashed_dependencies_dir}'") raise else: log.debug("Cached dependencies directory '%s' already exists, skipping build", hashed_dependencies_dir) return [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies]
[docs] def dependency_shell_commands(self, requirements, **kwds): """ Runs a set of requirements through the dependency resolvers and returns a list of commands required to activate the dependencies. If dependencies are cacheable and the cache does not exist, will try to create it. If cached environment exists or is successfully created, will generate commands to activate it. """ resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable] hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies) if not os.path.exists(hashed_dependencies_dir) and self.precache: # Cache not present, try to create it self.build_cache(requirements, **kwds) if os.path.exists(hashed_dependencies_dir): [dep.set_cache_path(hashed_dependencies_dir) for dep in cacheable_dependencies] commands = [dep.shell_commands() for dep in resolved_dependencies.values()] return commands
[docs] def hash_dependencies(self, resolved_dependencies): """Return hash for dependencies""" resolved_dependencies = [(dep.name, dep.version, dep.exact, dep.dependency_type) for dep in resolved_dependencies] hash_str = json.dumps(sorted(resolved_dependencies)) return hash_util.new_secure_hash(hash_str)[:8] # short hash
[docs] def get_hashed_dependencies_path(self, resolved_dependencies): """ Returns the path to the hashed dependencies directory (but does not evaluate whether the path exists). :param resolved_dependencies: list of resolved dependencies :type resolved_dependencies: list :return: path :rtype: str """ req_hashes = self.hash_dependencies(resolved_dependencies) return os.path.abspath(os.path.join(self.tool_dependency_cache_dir, req_hashes))
[docs]class NullDependencyManager(DependencyManager): cached = False
[docs] def __init__(self, default_base_path=None, conf_file=None, app_config=None): if app_config is None: app_config = {} self.__app_config = app_config self.resolver_classes = set() self.dependency_resolvers = [] self._enabled_container_types = [] self._destination_for_container_type = {} self.default_base_path = None
[docs] def uses_tool_shed_dependencies(self): return False
[docs] def dependency_shell_commands(self, requirements, **kwds): return []
[docs] def find_dep(self, name, version=None, type='package', **kwds): return NullDependency(version=version, name=name)
[docs] def to_dict(self): return {"use": False}