Unverified Commit ba0a6490 authored by mvdbeek's avatar mvdbeek
Browse files

Pick up extra files from outputs directory

parent 90d04a01

lib/galaxy/job_execution/datasets.py

+1 −1
Original line number Diff line number Diff line
@@ -94,7 +94,7 @@ class OutputsToWorkingDirectoryPathRewriter(DatasetPathRewriter): 
            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, f"galaxy_dataset_{dataset.dataset.uuid}.dat")

            false_path = os.path.join(base_output_directory, f"dataset_{dataset.dataset.uuid}.dat")

            return false_path

        else:

            return None

lib/galaxy/job_execution/output_collect.py

+8 −2
Original line number Diff line number Diff line
@@ -719,8 +719,14 @@ def default_exit_code_file(files_dir, id_tag): 




def collect_extra_files(object_store, dataset, job_working_directory):

    # TODO: should this use compute_environment to determine the extra files path ?

    file_name = dataset.dataset.extra_files_path_name_from(object_store)

    temp_file_path = os.path.join(job_working_directory, "working", file_name)

    output_location = "outputs"

    temp_file_path = os.path.join(job_working_directory, output_location, file_name)

    if not os.path.exists(temp_file_path):

        # Fall back to working dir, remove in 23.2

        output_location = "working"

        temp_file_path = os.path.join(job_working_directory, output_location, file_name)

    extra_dir = None

    try:

        # This skips creation of directories - object store
@@ -728,7 +734,7 @@ def collect_extra_files(object_store, dataset, job_working_directory): 
        # not be created in the object store at all, which might be a

        # problem.

        for root, _dirs, files in os.walk(temp_file_path):

            extra_dir = root.replace(os.path.join(job_working_directory, "working"), "", 1).lstrip(os.path.sep)

            extra_dir = root.replace(os.path.join(job_working_directory, output_location), "", 1).lstrip(os.path.sep)

            for f in files:

                object_store.update_from_file(

                    dataset.dataset,