Source code for galaxy.tool_util.deps.views

from galaxy import exceptions
from galaxy.util import (
    asbool,
    listify,
)
from .dependencies import ToolInfo
from .resolvers import (
    ContainerDependency,
    NullDependency,
)


[docs]class DependencyResolversView: """Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver object. This can be adapted by the Galaxy web framework or other web apps. """
[docs] def __init__(self, app): self._app = app
[docs] def index(self): return [r.to_dict() for r in self._dependency_resolvers]
[docs] def show(self, index): return self._dependency_resolver(index).to_dict()
[docs] def reload(self): self.toolbox.reload_dependency_manager()
[docs] def manager_requirements(self): requirements = [] for index, resolver in enumerate(self._dependency_resolvers): if not hasattr(resolver, "list_dependencies"): continue for requirement in resolver.list_dependencies(): requirements.append({"index": index, "requirement": requirement.to_dict()}) return requirements
[docs] def resolver_requirements(self, index): requirements = [] resolver = self._dependency_resolver(index) if not hasattr(resolver, "list_dependencies"): raise exceptions.NotImplemented() for requirement in resolver.list_dependencies(): requirements.append(requirement.to_dict()) return requirements
[docs] def manager_dependency(self, **kwds): return self._dependency(**kwds)
[docs] def resolver_dependency(self, index, **kwds): return self._dependency(**kwds)
[docs] def show_dependencies(self, tool_requirements_d, installed_tool_dependencies=None, **kwd): """ Resolves dependencies to build a requirements status in the admin panel/API """ to_deps_kwds = { "install": False, "return_null": True, "installed_tool_dependencies": installed_tool_dependencies, } to_deps_kwds.update(kwd) dependencies_per_tool = { tool: self._dependency_manager.requirements_to_dependencies(requirements, **to_deps_kwds) for tool, requirements in tool_requirements_d.items() } return dependencies_per_tool
[docs] def uninstall_dependencies(self, index=None, resolver_type=None, container_type=None, **payload): """Attempt to uninstall requirements. Returns 0 if successfull, else None.""" requirements = payload.get("requirements") if not requirements: return None if index: resolver = self._dependency_resolvers[index] if resolver.can_uninstall_dependencies: return resolver.uninstall(requirements) elif resolver_type: for resolver in self._dependency_resolvers: if resolver.resolver_type == resolver_type and resolver.can_uninstall_dependencies: return resolver.uninstall(requirements) elif container_type: for resolver in self._dependency_resolvers: if getattr(resolver, "container_type", None) == container_type and resolver.can_uninstall_dependencies: return resolver.uninstall(requirements) else: for index in self.uninstallable_resolvers: return_code = self._dependency_resolvers[index].uninstall(requirements) if return_code == 0: return return_code return None
@property def unused_dependency_paths(self): """List dependencies that are not currently installed.""" unused_dependencies = [] toolbox_requirements_status = self.toolbox_requirements_status for resolver in self._dependency_resolvers: if hasattr(resolver, "unused_dependency_paths"): unused_dependencies.extend(resolver.unused_dependency_paths(toolbox_requirements_status)) return set(unused_dependencies)
[docs] def remove_unused_dependency_paths(self, envs): """ Remove dependencies that are not currently used. Returns a list of all environments that have been successfully removed. """ envs_to_remove = set(envs) toolbox_requirements_status = self.toolbox_requirements_status removed_environments = set() for resolver in self._dependency_resolvers: if hasattr(resolver, "unused_dependency_paths") and hasattr(resolver, "uninstall_environments"): unused_dependencies = resolver.unused_dependency_paths(toolbox_requirements_status) can_remove = envs_to_remove & set(unused_dependencies) exit_code = resolver.uninstall_environments(can_remove) if exit_code == 0: removed_environments = removed_environments.union(can_remove) envs_to_remove = envs_to_remove.difference(can_remove) return list(removed_environments)
[docs] def install_dependencies(self, requirements, **kwds): kwds["install"] = True return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds)
[docs] def install_dependency(self, index=None, **payload): """ Installs dependency using highest priority resolver that supports dependency installation (Currently only the conda resolver supports this). If index is given, attempt installation directly using the corresponding resolver. Returns True on success, False on failure. payload is dictionary that must container name, version and type, e.g. {'name': 'numpy', version='1.9.1', type='package'} """ if index: return self._install_dependency(index, **payload) else: for index in self.installable_resolvers: success = self._install_dependency(index, **payload) if success: return success return False
def _install_dependency(self, index, **payload): """ Resolver install dependency should return True when installation succeeds, False if not successful """ resolver = self._dependency_resolver(index) if resolver.read_only: raise exceptions.RequestParameterInvalidException( "Attempted to install on a read_only dependency resolver." ) if resolver.disabled: raise exceptions.RequestParameterInvalidException("Attempted to install on a disabled dependency resolver.") name, version, type, extra_kwds = self._parse_dependency_info(payload) return resolver.install_dependency(name=name, version=version, type=type, **extra_kwds) def _dependency(self, index=None, **kwds): if index is not None: index = int(index) name, version, type, extra_kwds = self._parse_dependency_info(kwds) resolve_kwds = dict(job_directory=None, index=index, **extra_kwds) dependency = self._dependency_manager.find_dep(name, version=version, type=type, **resolve_kwds) return dependency.to_dict() def _parse_dependency_info(self, kwds): extra_kwds = kwds.copy() name = extra_kwds.pop("name", None) if name is None: raise exceptions.RequestParameterMissingException("Missing 'name' parameter required for resolution.") version = extra_kwds.pop("version", None) type = extra_kwds.pop("type", "package") return name, version, type, extra_kwds def _dependency_resolver(self, index): index = int(index) return self._dependency_resolvers[index] @property def _dependency_manager(self): return self._app.toolbox.dependency_manager @property def _dependency_resolvers(self): dependency_manager = self._dependency_manager dependency_resolvers = dependency_manager.dependency_resolvers return dependency_resolvers @property def installable_resolvers(self): """ List index for all active resolvers that have the 'install_dependency' attribute. """ return [ index for index, resolver in enumerate(self._dependency_resolvers) if not resolver.read_only and not resolver.disabled ] @property def uninstallable_resolvers(self): """ List index for all active resolvers that can uninstall dependencies that have been installed through this resolver. """ return [ index for index, resolver in enumerate(self._dependency_resolvers) if resolver.can_uninstall_dependencies and not resolver.disabled ] @property def tool_ids_by_requirements(self): """Dictionary with requirements as keys, and tool_ids as values.""" tool_ids_by_requirements = {} if not self._app.toolbox.tools_by_id: return {} for tid, tool in self._app.toolbox.tools_by_id.items(): if tool.tool_requirements not in tool_ids_by_requirements: tool_ids_by_requirements[tool.tool_requirements] = [tid] else: tool_ids_by_requirements[tool.tool_requirements].append(tid) return tool_ids_by_requirements @property def toolbox_requirements_status(self): return self.summarize_requirements()
[docs] def summarize_requirements(self, **kwds): summary_kwds = {} if "index" in kwds: summary_kwds["index"] = int(kwds["index"]) if "include_containers" in kwds: summary_kwds["include_containers"] = asbool(kwds["include_containers"]) if "container_type" in kwds: summary_kwds["container_type"] = kwds["container_type"] if "resolver_type" in kwds: summary_kwds["resolver_type"] = kwds["resolver_type"] if "search" in kwds: summary_kwds["search"] = asbool(kwds["search"]) if "install" in kwds: summary_kwds["install"] = asbool(kwds["install"]) tool_ids_by_requirements = self.tool_ids_by_requirements statuses = { r: self.get_requirements_status( tool_requirements_d={tids[0]: r}, installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies, **summary_kwds, ) for r, tids in tool_ids_by_requirements.items() } if kwds.get("for_json", False): # All public attributes of this class should be returning JSON - this is meant to mimic a restful API. rval = [] for requirements, status in statuses.items(): item = {} item["requirements"] = requirements.to_dict() item["status"] = status item["tool_ids"] = tool_ids_by_requirements[requirements] rval.append(item) statuses = rval return statuses
[docs] def summarize_tools(self, **kwds): summary_kwds = {} if "index" in kwds: summary_kwds["index"] = int(kwds["index"]) if "include_containers" in kwds: summary_kwds["include_containers"] = asbool(kwds["include_containers"]) if "container_type" in kwds: summary_kwds["container_type"] = kwds["container_type"] if "resolver_type" in kwds: summary_kwds["resolver_type"] = kwds["resolver_type"] if "search" in kwds: summary_kwds["search"] = asbool(kwds["search"]) if "install" in kwds: summary_kwds["install"] = asbool(kwds["install"]) tool_ids = pop_tool_ids(kwds) rval = [] for tid, tool in self._app.toolbox.tools_by_id.items(): if tool_ids and tid not in tool_ids: continue requirements = tool.tool_requirements status = self.get_requirements_status( tool_requirements_d={tid: requirements}, installed_tool_dependencies=tool.installed_tool_dependencies, tool_instance=tool, **summary_kwds, ) item = {} item["requirements"] = requirements.to_dict() item["status"] = status item["tool_ids"] = [tid] rval.append(item) return rval
[docs] def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies=None, **kwd): dependencies = self.show_dependencies(tool_requirements_d, installed_tool_dependencies, **kwd) # dependencies is a dict keyed on tool_ids, value is a ToolRequirements object for that tool. # We use the union of resolvable ToolRequirements to get resolved dependencies without duplicates. requirements = [r.resolvable for r in tool_requirements_d.values()] flat_tool_requirements = set().union(*requirements) flat_dependencies = [] for requirements_odict in dependencies.values(): for requirement in requirements_odict: if requirement in flat_tool_requirements: flat_dependencies.append(requirements_odict[requirement]) flat_tool_requirements.remove(requirement) return [d.to_dict() for d in flat_dependencies]
[docs] def clean(self, index=None, **kwds): if index: resolver = self._dependency_resolver(index) if not hasattr(resolver, "clean"): raise exceptions.NotImplemented() else: resolver.clean() return "OK" else: [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, "clean")] return "OK"
[docs]class ContainerResolutionView: """ """
[docs] def __init__(self, app): self._app = app
[docs] def index(self): return [r.to_dict() for r in self._container_resolvers]
[docs] def show(self, index): return self._container_resolver(index).to_dict()
[docs] def resolve(self, index=None, **kwds): find_best_kwds = { "install": False, "enabled_container_types": ["docker", "singularity"], "resolution_cache": kwds.get("resolution_cache"), "session": kwds.get("session"), } if index is not None: find_best_kwds["index"] = int(index) if "container_type" in kwds: find_best_kwds["enabled_container_types"] = [kwds["container_type"]] if "resolver_type" in kwds: find_best_kwds["resolver_type"] = kwds["resolver_type"] if "install" in kwds: find_best_kwds["install"] = asbool(kwds["install"]) tool_info_kwds = {} tool_id = kwds["tool_id"] tool = self._app.toolbox.tools_by_id[tool_id] requirements = tool.tool_requirements tool_info_kwds = dict(requirements=requirements) requirements_only = asbool(kwds.get("requirements_only", False)) # If requirements_only, simply use the tool to load a requirement set from, # mimics the default behavior of searching for containers through the dependency resolution # component. Not useful for tool execution but perhaps when summarizing mulled containers for requirements. if not requirements_only: tool_info_kwds["container_descriptions"] = tool.containers tool_info_kwds["requires_galaxy_python_environment"] = tool.requires_galaxy_python_environment tool_info_kwds["tool_id"] = tool.id tool_info_kwds["tool_version"] = tool.version find_best_kwds["tool_info"] = ToolInfo(**tool_info_kwds) # Consider implementing 'search' to match dependency resolution API. resolved_container_description = self._app.container_finder.resolve(**find_best_kwds) if resolved_container_description: status = ContainerDependency( resolved_container_description.container_description, container_resolver=resolved_container_description.container_resolver, ).to_dict() else: status = NullDependency().to_dict() return {"tool_id": kwds["tool_id"], "status": status, "requirements": requirements.to_dict()}
[docs] def resolve_toolbox(self, **kwds): rval = [] resolve_kwds = kwds.copy() tool_ids = pop_tool_ids(resolve_kwds) resolve_kwds["resolution_cache"] = self._app.container_finder.resolution_cache() if tool_ids is not None: tool_ids = listify(tool_ids) for tool_id, tool in self._app.toolbox.tools_by_id.items(): if tool_ids is not None and tool_id not in tool_ids: continue if tool.tool_action.produces_real_jobs: rval.append(self.resolve(tool_id=tool_id, **resolve_kwds)) return rval
@property def _container_resolvers(self): return self._app.container_finder.default_container_registry.container_resolvers def _container_resolver(self, index): index = int(index) return self._container_resolvers[index]
[docs]def pop_tool_ids(kwds): tool_ids = None if "tool_ids" in kwds: tool_ids = listify(kwds.pop("tool_ids")) if "tool_ids[]" in kwds: tool_ids = listify(kwds.pop("tool_ids[]")) if "tool_id" in kwds: tool_ids = [kwds.pop("tool_id")] return tool_ids