Unverified Commit e8aeedaf authored by mvdbeek's avatar mvdbeek
Browse files

Defer to compute_environment.input_extra_files_rewrite for path_rewrite

parent 61f8123b

lib/galaxy/job_execution/compute_environment.py

+6 −2
Original line number Diff line number Diff line
@@ -121,7 +121,8 @@ class SharedComputeEnvironment(SimpleComputeEnvironment, ComputeEnvironment): 
        return self.job_io.get_output_fnames()



    def input_path_rewrite(self, dataset):

        return self.job_io.get_input_path(dataset).false_path

        dataset_path = self.job_io.get_input_path(dataset)

        return dataset_path.false_path or dataset_path.real_path



    def output_path_rewrite(self, dataset):

        dataset_path = self.job_io.get_output_path(dataset)
@@ -131,7 +132,10 @@ class SharedComputeEnvironment(SimpleComputeEnvironment, ComputeEnvironment): 
            return dataset_path.real_path



    def input_extra_files_rewrite(self, dataset):

        return None

        input_path_rewrite = self.input_path_rewrite(dataset)

        base_input_path = input_path_rewrite[0 : -len(".dat")]

        remote_extra_files_path_rewrite = f"{base_input_path}_files"

        return remote_extra_files_path_rewrite



    def output_extra_files_rewrite(self, dataset):

        output_path_rewrite = self.output_path_rewrite(dataset)

lib/galaxy/tools/wrappers.py

+5 −26
Original line number Diff line number Diff line
@@ -19,7 +19,6 @@ from typing import ( 
    Union,

)



from galaxy import exceptions

from galaxy.model import (

    DatasetCollection,

    DatasetCollectionElement,
@@ -476,33 +475,13 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper): 
            # Path to dataset was rewritten for this job.

            return self.false_path

        elif key in ("extra_files_path", "files_path"):

            if not self.compute_environment:

                # Only happens in WrappedParameters context, refactor!

                return self.unsanitized.extra_files_path

            if self.__io_type == "input":

                path_rewrite = self.compute_environment and self.compute_environment.input_extra_files_rewrite(

                    self.unsanitized

                )

            else:

                path_rewrite = self.compute_environment and self.compute_environment.output_extra_files_rewrite(

                    self.unsanitized

                )

            if path_rewrite:

                return path_rewrite

                return self.compute_environment.input_extra_files_rewrite(self.unsanitized)

            else:

                try:

                    # Assume it is an output and that this wrapper

                    # will be set with correct "files_path" for this

                    # job.

                    return self.files_path

                except AttributeError:

                    # Otherwise, we have an input - delegate to model and

                    # object store to find the static location of this

                    # directory.

                    try:

                        return self.unsanitized.extra_files_path

                    except exceptions.ObjectNotFound:

                        # NestedObjectstore raises an error here

                        # instead of just returning a non-existent

                        # path like DiskObjectStore.

                        raise

                return self.compute_environment.output_extra_files_rewrite(self.unsanitized)

        elif key == "serialize":

            return self.serialize

        else: