"""Shared context objects that replace use of kwargs."""
import copy
import os
import shutil
import tempfile
import threading
from typing import (
IO,
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterable,
List,
Literal,
Optional,
TextIO,
Tuple,
Union,
)
from ruamel.yaml.comments import CommentedMap
from schema_salad.avro.schema import Names
from schema_salad.ref_resolver import Loader
from schema_salad.utils import FetcherCallableType
from .mpi import MpiConfig
from .pathmapper import PathMapper
from .stdfsaccess import StdFsAccess
from .utils import DEFAULT_TMP_PREFIX, CWLObjectType, HasReqsHints, ResolverType
if TYPE_CHECKING:
from _typeshed import SupportsWrite
from cwl_utils.parser.cwl_v1_2 import LoadingOptions
from .builder import Builder
from .cwlprov.provenance_profile import ProvenanceProfile
from .cwlprov.ro import ResearchObject
from .mutation import MutationManager
from .process import Process
from .secrets import SecretStore
from .software_requirements import DependenciesConfiguration
class ContextBase:
"""Shared kwargs based initializer for :py:class:`RuntimeContext` and :py:class:`LoadingContext`."""
def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
"""Initialize."""
if kwargs:
for k, v in kwargs.items():
if hasattr(self, k):
setattr(self, k, v)
def make_tool_notimpl(toolpath_object: CommentedMap, loadingContext: "LoadingContext") -> "Process":
"""Fake implementation of the make tool function."""
raise NotImplementedError()
default_make_tool = make_tool_notimpl
def log_handler(
outdir: str,
base_path_logs: str,
stdout_path: Optional[str],
stderr_path: Optional[str],
) -> None:
"""Move logs from log location to final output."""
if outdir != base_path_logs:
if stdout_path:
new_stdout_path = stdout_path.replace(base_path_logs, outdir)
shutil.copy2(stdout_path, new_stdout_path)
if stderr_path:
new_stderr_path = stderr_path.replace(base_path_logs, outdir)
shutil.copy2(stderr_path, new_stderr_path)
def set_log_dir(outdir: str, log_dir: str, subdir_name: str) -> str:
"""Set the log directory."""
if log_dir == "":
return outdir
else:
return log_dir + "/" + subdir_name
[docs]class LoadingContext(ContextBase):
[docs] def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
"""Initialize the LoadingContext from the kwargs."""
self.debug: bool = False
self.metadata: CWLObjectType = {}
self.requirements: Optional[List[CWLObjectType]] = None
self.hints: Optional[List[CWLObjectType]] = None
self.overrides_list: List[CWLObjectType] = []
self.loader: Optional[Loader] = None
self.avsc_names: Optional[Names] = None
self.disable_js_validation: bool = False
self.js_hint_options_file: Optional[str] = None
self.do_validate: bool = True
self.enable_dev: bool = False
self.strict: bool = True
self.resolver: Optional[ResolverType] = None
self.fetcher_constructor: Optional[FetcherCallableType] = None
self.construct_tool_object = default_make_tool
self.research_obj: Optional[ResearchObject] = None
self.orcid: str = ""
self.cwl_full_name: str = ""
self.host_provenance: bool = False
self.user_provenance: bool = False
self.prov_obj: Optional["ProvenanceProfile"] = None
self.do_update: Optional[bool] = None
self.jobdefaults: Optional[CommentedMap] = None
self.doc_cache: bool = True
self.relax_path_checks: bool = False
self.singularity: bool = False
self.podman: bool = False
self.eval_timeout: float = 60
self.codegen_idx: Dict[str, Tuple[Any, "LoadingOptions"]] = {}
self.fast_parser = False
self.skip_resolve_all = False
self.skip_schemas = False
super().__init__(kwargs)
[docs] def copy(self) -> "LoadingContext":
"""Return a copy of this :py:class:`LoadingContext`."""
return copy.copy(self)
[docs]class RuntimeContext(ContextBase):
outdir: Optional[str] = None
tmpdir: str = ""
tmpdir_prefix: str = DEFAULT_TMP_PREFIX
tmp_outdir_prefix: str = ""
stagedir: str = ""
[docs] def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
"""Initialize the RuntimeContext from the kwargs."""
select_resources_callable = Callable[
[Dict[str, Union[int, float]], RuntimeContext],
Dict[str, Union[int, float]],
]
self.user_space_docker_cmd: Optional[str] = None
self.secret_store: Optional["SecretStore"] = None
self.no_read_only: bool = False
self.custom_net: Optional[str] = None
self.no_match_user: bool = False
self.preserve_environment: Optional[Iterable[str]] = None
self.preserve_entire_environment: bool = False
self.use_container: bool = True
self.force_docker_pull: bool = False
self.rm_tmpdir: bool = True
self.pull_image: bool = True
self.rm_container: bool = True
self.move_outputs: Union[Literal["move"], Literal["leave"], Literal["copy"]] = "move"
self.log_dir: str = ""
self.set_log_dir = set_log_dir
self.log_dir_handler = log_handler
self.streaming_allowed: bool = False
self.singularity: bool = False
self.podman: bool = False
self.debug: bool = False
self.compute_checksum: bool = True
self.name: str = ""
self.default_container: Optional[str] = ""
self.find_default_container: Optional[Callable[[HasReqsHints], Optional[str]]] = None
self.cachedir: Optional[str] = None
self.part_of: str = ""
self.basedir: str = ""
self.toplevel: bool = False
self.mutation_manager: Optional["MutationManager"] = None
self.make_fs_access = StdFsAccess
self.path_mapper = PathMapper
self.builder: Optional["Builder"] = None
self.docker_outdir: str = ""
self.docker_tmpdir: str = ""
self.docker_stagedir: str = ""
self.js_console: bool = False
self.job_script_provider: Optional[DependenciesConfiguration] = None
self.select_resources: Optional[select_resources_callable] = None
self.eval_timeout: float = 60
self.postScatterEval: Optional[Callable[[CWLObjectType], Optional[CWLObjectType]]] = None
self.on_error: Union[Literal["stop"], Literal["continue"]] = "stop"
self.strict_memory_limit: bool = False
self.strict_cpu_limit: bool = False
self.cidfile_dir: Optional[str] = None
self.cidfile_prefix: Optional[str] = None
self.workflow_eval_lock: Optional[threading.Condition] = None
self.research_obj: Optional[ResearchObject] = None
self.orcid: str = ""
self.cwl_full_name: str = ""
self.process_run_id: Optional[str] = None
self.prov_obj: Optional[ProvenanceProfile] = None
self.mpi_config: MpiConfig = MpiConfig()
self.default_stdout: Optional[Union[IO[bytes], TextIO]] = None
self.default_stderr: Optional[Union[IO[bytes], TextIO]] = None
self.validate_only: bool = False
self.validate_stdout: Optional["SupportsWrite[str]"] = None
super().__init__(kwargs)
if self.tmp_outdir_prefix == "":
self.tmp_outdir_prefix = self.tmpdir_prefix
[docs] def get_outdir(self) -> str:
"""Return :py:attr:`outdir` or create one with :py:attr:`tmp_outdir_prefix`."""
if self.outdir:
return self.outdir
return self.create_outdir()
[docs] def get_tmpdir(self) -> str:
"""Return :py:attr:`tmpdir` or create one with :py:attr:`tmpdir_prefix`."""
if self.tmpdir:
return self.tmpdir
return self.create_tmpdir()
[docs] def get_stagedir(self) -> str:
"""Return :py:attr:`stagedir` or create one with :py:attr:`tmpdir_prefix`."""
if self.stagedir:
return self.stagedir
tmp_dir, tmp_prefix = os.path.split(self.tmpdir_prefix)
return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
[docs] def create_tmpdir(self) -> str:
"""Create a temporary directory that respects :py:attr:`tmpdir_prefix`."""
tmp_dir, tmp_prefix = os.path.split(self.tmpdir_prefix)
return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)
[docs] def create_outdir(self) -> str:
"""Create a temporary directory that respects :py:attr:`tmp_outdir_prefix`."""
out_dir, out_prefix = os.path.split(self.tmp_outdir_prefix)
return tempfile.mkdtemp(prefix=out_prefix, dir=out_dir)
[docs] def copy(self) -> "RuntimeContext":
"""Return a copy of this :py:class:`RuntimeContext`."""
return copy.copy(self)
[docs]def getdefault(val: Any, default: Any) -> Any:
"""Return the ``val`` using the ``default`` as backup in case the val is ``None``."""
if val is None:
return default
else:
return val