Source code for galaxy.job_execution.datasets

"""
Utility classes allowing Job interface to reason about datasets.
"""
import os.path
from abc import (
    ABCMeta,
    abstractmethod
)


[docs]def dataset_path_rewrites(dataset_paths):
    dataset_paths_with_rewrites = [path for path in dataset_paths if getattr(path, "false_path", None)]
    return {dp.real_path: dp for dp in dataset_paths_with_rewrites}


[docs]class DatasetPath:

[docs]    def __init__(
        self,
        dataset_id,
        real_path,
        false_path=None,
        false_extra_files_path=None,
        false_metadata_path=None,
        mutable=True,
        dataset_uuid=None,
        object_store_id=None,
    ):
        self.dataset_id = dataset_id
        self.dataset_uuid = dataset_uuid
        self.object_store_id = object_store_id
        self.real_path = real_path
        self.false_path = false_path
        self.false_extra_files_path = false_extra_files_path
        self.false_metadata_path = false_metadata_path
        self.mutable = mutable

    def __str__(self):
        if self.false_path is None:
            return self.real_path
        else:
            return self.false_path

[docs]    def with_path_for_job(self, false_path, false_extra_files_path=None, false_metadata_path=None):
        """
        Clone the dataset path but with a new false_path.
        """
        dataset_path = self
        if false_path is not None:
            dataset_path = DatasetPath(
                dataset_id=self.dataset_id,
                real_path=self.real_path,
                false_path=false_path,
                false_extra_files_path=false_extra_files_path,
                false_metadata_path=false_metadata_path,
                mutable=self.mutable,
            )
        return dataset_path


[docs]class DatasetPathRewriter(metaclass=ABCMeta):
    """ Used by runner to rewrite paths. """

[docs]    @abstractmethod
    def rewrite_dataset_path(self, dataset, dataset_type):
        """
        Dataset type is 'input' or 'output'.
        Return None to indicate not to rewrite this path.
        """


[docs]class NullDatasetPathRewriter:
    """ Used by default for jobwrapper, do not rewrite anything.
    """

[docs]    def rewrite_dataset_path(self, dataset, dataset_type):
        """ Keep path the same.
        """
        return None


[docs]class OutputsToWorkingDirectoryPathRewriter:
    """ Rewrites all paths to place them in the specified working
    directory for normal jobs when Galaxy is configured with
    app.config.outputs_to_working_directory. Job runner base class
    is responsible for copying these out after job is complete.
    """

[docs]    def __init__(self, working_directory, outputs_directory_name):
        self.working_directory = working_directory
        self.outputs_directory_name = outputs_directory_name

[docs]    def rewrite_dataset_path(self, dataset, dataset_type):
        """ Keep path the same.
        """
        if dataset_type == 'output':
            base_output_directory = os.path.abspath(self.working_directory)
            if self.outputs_directory_name is not None:
                base_output_directory = os.path.join(base_output_directory, self.outputs_directory_name)
            # set false_path to uuid, no harm even if object store uses id
            false_path = os.path.join(base_output_directory, "galaxy_dataset_%s.dat" % dataset.dataset.uuid)
            return false_path
        else:
            return None


[docs]class TaskPathRewriter:
    """ Rewrites all paths to place them in the specified working
    directory for TaskWrapper. TaskWrapper is responsible for putting
    them there and pulling them out.
    """

[docs]    def __init__(self, working_directory, job_dataset_path_rewriter):
        self.working_directory = working_directory
        self.job_dataset_path_rewriter = job_dataset_path_rewriter

[docs]    def rewrite_dataset_path(self, dataset, dataset_type):
        """
        """
        dataset_file_name = dataset.file_name
        job_file_name = self.job_dataset_path_rewriter.rewrite_dataset_path(dataset, dataset_type) or dataset_file_name
        return os.path.join(self.working_directory, os.path.basename(job_file_name))