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Source code for cwltool.context
"""Shared context objects that replace use of kwargs."""
import copy
import threading
from typing import IO, Any, Callable, Dict, Iterable, List, Optional, TextIO, Union
# move to a regular typing import when Python 3.3-3.6 is no longer supported
from ruamel.yaml.comments import CommentedMap
from schema_salad.avro.schema import Names
from schema_salad.ref_resolver import FetcherCallableType, Loader
from typing_extensions import TYPE_CHECKING
from .builder import Builder, HasReqsHints
from .mpi import MpiConfig
from .mutation import MutationManager
from .pathmapper import PathMapper
from .secrets import SecretStore
from .software_requirements import DependenciesConfiguration
from .stdfsaccess import StdFsAccess
from .utils import DEFAULT_TMP_PREFIX, CWLObjectType, ResolverType
if TYPE_CHECKING:
from .process import Process
from .provenance import ResearchObject # pylint: disable=unused-import
from .provenance_profile import ProvenanceProfile
class ContextBase(object):
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":
raise NotImplementedError()
default_make_tool = make_tool_notimpl
[docs]class LoadingContext(ContextBase):
[docs] def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
"""Initialize the LoadingContext from the kwargs."""
self.debug = False # type: bool
self.metadata = {} # type: CWLObjectType
self.requirements = None # type: Optional[List[CWLObjectType]]
self.hints = None # type: Optional[List[CWLObjectType]]
self.overrides_list = [] # type: List[CWLObjectType]
self.loader = None # type: Optional[Loader]
self.avsc_names = None # type: Optional[Names]
self.disable_js_validation = False # type: bool
self.js_hint_options_file = None
self.do_validate = True # type: bool
self.enable_dev = False # type: bool
self.strict = True # type: bool
self.resolver = None # type: Optional[ResolverType]
self.fetcher_constructor = None # type: Optional[FetcherCallableType]
self.construct_tool_object = default_make_tool
self.research_obj = None # type: Optional[ResearchObject]
self.orcid = "" # type: str
self.cwl_full_name = "" # type: str
self.host_provenance = False # type: bool
self.user_provenance = False # type: bool
self.prov_obj = None # type: Optional[ProvenanceProfile]
self.do_update = None # type: Optional[bool]
self.jobdefaults = None # type: Optional[CommentedMap]
self.doc_cache = True # type: bool
super(LoadingContext, self).__init__(kwargs)
[docs]class RuntimeContext(ContextBase):
[docs] def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
"""Initialize the RuntimeContext from the kwargs."""
select_resources_callable = Callable[ # pylint: disable=unused-variable
[Dict[str, Union[int, float, str]], RuntimeContext],
Dict[str, Union[int, float, str]],
]
self.user_space_docker_cmd = "" # type: Optional[str]
self.secret_store = None # type: Optional[SecretStore]
self.no_read_only = False # type: bool
self.custom_net = "" # type: Optional[str]
self.no_match_user = False # type: bool
self.preserve_environment = "" # type: Optional[Iterable[str]]
self.preserve_entire_environment = False # type: bool
self.use_container = True # type: bool
self.force_docker_pull = False # type: bool
self.tmp_outdir_prefix = DEFAULT_TMP_PREFIX # type: str
self.tmpdir_prefix = DEFAULT_TMP_PREFIX # type: str
self.tmpdir = "" # type: str
self.rm_tmpdir = True # type: bool
self.pull_image = True # type: bool
self.rm_container = True # type: bool
self.move_outputs = "move" # type: str
self.singularity = False # type: bool
self.disable_net = False # type: bool
self.debug = False # type: bool
self.compute_checksum = True # type: bool
self.name = "" # type: str
self.default_container = "" # type: Optional[str]
self.find_default_container = (
None
) # type: Optional[Callable[[HasReqsHints], Optional[str]]]
self.cachedir = None # type: Optional[str]
self.outdir = None # type: Optional[str]
self.stagedir = "" # type: str
self.part_of = "" # type: str
self.basedir = "" # type: str
self.toplevel = False # type: bool
self.mutation_manager = None # type: Optional[MutationManager]
self.make_fs_access = StdFsAccess # type: Callable[[str], StdFsAccess]
self.path_mapper = PathMapper
self.builder = None # type: Optional[Builder]
self.docker_outdir = "" # type: str
self.docker_tmpdir = "" # type: str
self.docker_stagedir = "" # type: str
self.js_console = False # type: bool
self.job_script_provider = None # type: Optional[DependenciesConfiguration]
self.select_resources = None # type: Optional[select_resources_callable]
self.eval_timeout = 20 # type: float
self.postScatterEval = (
None
) # type: Optional[Callable[[CWLObjectType], Optional[CWLObjectType]]]
self.on_error = "stop" # type: str
self.strict_memory_limit = False # type: bool
self.cidfile_dir = None # type: Optional[str]
self.cidfile_prefix = None # type: Optional[str]
self.workflow_eval_lock = None # type: Optional[threading.Condition]
self.research_obj = None # type: Optional[ResearchObject]
self.orcid = "" # type: str
self.cwl_full_name = "" # type: str
self.process_run_id = None # type: Optional[str]
self.prov_obj = None # type: Optional[ProvenanceProfile]
self.mpi_config = MpiConfig() # type: MpiConfig
self.default_stdout = None # type: Optional[Union[IO[bytes], TextIO]]
self.default_stderr = None # type: Optional[Union[IO[bytes], TextIO]]
super(RuntimeContext, self).__init__(kwargs)
[docs]def getdefault(val, default):
# type: (Any, Any) -> Any
if val is None:
return default
else:
return val