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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

from collections import namedtuple
from typing import Dict, cast

from .errors import WorkflowException
from .utils import CWLObjectType

MutationState = namedtuple("MutationState", ["generation", "readers", "stepname"])

_generation = "http://commonwl.org/cwltool#generation"


class MutationManager:
    """Lock manager for checking correctness of in-place update of files.

    Used to validate that in-place file updates happen sequentially, and that a
    file which is registered for in-place update cannot be read or updated by
    any other steps.

    """

    def __init__(self) -> None:
        """Initialize."""
        self.generations = {}  # type: Dict[str, MutationState]

    def register_reader(self, stepname: str, obj: CWLObjectType) -> None:
        loc = cast(str, obj["location"])
        current = self.generations.get(loc, MutationState(0, [], ""))
        obj_generation = obj.get(_generation, 0)

        if obj_generation != current.generation:
            raise WorkflowException(
                "[job {}] wants to read {} from generation {} but current "
                "generation is {}(last updated by {})".format(
                    stepname, loc, obj_generation, current.generation, current.stepname
                )
            )

        current.readers.append(stepname)
        self.generations[loc] = current

    def release_reader(self, stepname: str, obj: CWLObjectType) -> None:
        loc = cast(str, obj["location"])
        current = self.generations.get(loc, MutationState(0, [], ""))
        obj_generation = obj.get(_generation, 0)

        if obj_generation != current.generation:
            raise WorkflowException(
                "[job {}] wants to release reader on {} from generation {}"
                " but current generation is {} (last updated by {})".format(
                    stepname, loc, obj_generation, current.generation, current.stepname
                )
            )

        self.generations[loc].readers.remove(stepname)

    def register_mutation(self, stepname: str, obj: CWLObjectType) -> None:
        loc = cast(str, obj["location"])
        current = self.generations.get(loc, MutationState(0, [], ""))
        obj_generation = obj.get(_generation, 0)

        if len(current.readers) > 0:
            raise WorkflowException(
                "[job {}] wants to modify {} but has readers: {}".format(
                    stepname, loc, current.readers
                )
            )

        if obj_generation != current.generation:
            raise WorkflowException(
                "[job {}] wants to modify {} from generation {} but current "
                "generation is {} (last updated by {})".format(
                    stepname, loc, obj_generation, current.generation, current.stepname
                )
            )

        self.generations[loc] = MutationState(
            current.generation + 1, current.readers, stepname
        )

    def set_generation(self, obj: CWLObjectType) -> None:
        loc = cast(str, obj["location"])
        current = self.generations.get(loc, MutationState(0, [], ""))
        obj[_generation] = current.generation

    def unset_generation(self, obj: CWLObjectType) -> None:
        obj.pop(_generation, None)