view env/lib/python3.9/site-packages/cwltool/context.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""Shared context objects that replace use of kwargs."""
import copy
import os
import tempfile
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 Loader
from schema_salad.utils import FetcherCallableType
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:
    """Shared kwargs based initilizer for {Runtime,Loading}Context."""

    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


class LoadingContext(ContextBase):
    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
        self.relax_path_checks = False  # type: bool

        super().__init__(kwargs)

    def copy(self):
        # type: () -> LoadingContext
        return copy.copy(self)


class RuntimeContext(ContextBase):
    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 = ""  # 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().__init__(kwargs)
        if self.tmp_outdir_prefix == "":
            self.tmp_outdir_prefix = self.tmpdir_prefix

    def get_outdir(self) -> str:
        """Return self.outdir or create one with self.tmp_outdir_prefix."""
        if self.outdir:
            return self.outdir
        return self.create_outdir()

    def get_tmpdir(self) -> str:
        """Return self.tmpdir or create one with self.tmpdir_prefix."""
        if self.tmpdir:
            return self.tmpdir
        return self.create_tmpdir()

    def get_stagedir(self) -> str:
        """Return self.stagedir or create one with self.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)

    def create_tmpdir(self) -> str:
        """Create a temporary directory that respects self.tmpdir_prefix."""
        tmp_dir, tmp_prefix = os.path.split(self.tmpdir_prefix)
        return tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir)

    def create_outdir(self) -> str:
        """Create a temporary directory that respects self.tmp_outdir_prefix."""
        out_dir, out_prefix = os.path.split(self.tmp_outdir_prefix)
        return tempfile.mkdtemp(prefix=out_prefix, dir=out_dir)

    def copy(self):
        # type: () -> RuntimeContext
        return copy.copy(self)


def getdefault(val, default):
    # type: (Any, Any) -> Any
    if val is None:
        return default
    else:
        return val