Unverified Commit 472ebfe8 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #17067 from mvdbeek/fix_store_by_id_outputs_to_working_directory_extra_files 

[23.0] Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory`
parents 1b0c0bb3 7fe19a7c

lib/galaxy/job_execution/output_collect.py

+7 −3
Original line number Diff line number Diff line
@@ -718,9 +718,13 @@ def default_exit_code_file(files_dir, id_tag): 
    return os.path.join(files_dir, f"galaxy_{id_tag}.ec")





def collect_extra_files(object_store, dataset, job_working_directory):

def collect_extra_files(object_store, dataset, job_working_directory, outputs_to_working_directory=False):

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

    file_name = dataset.dataset.extra_files_path_name_from(object_store)

    real_file_name = file_name = dataset.dataset.extra_files_path_name_from(object_store)

    if outputs_to_working_directory:

        # OutputsToWorkingDirectoryPathRewriter always rewrites extra files to uuid path,

        # so we have to collect from that path even if the real extra files path is dataset_N_files

        file_name = f"dataset_{dataset.dataset.uuid}_files"

    output_location = "outputs"

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

    if not os.path.exists(temp_file_path):
@@ -739,7 +743,7 @@ def collect_extra_files(object_store, dataset, job_working_directory): 
            for f in files:

                object_store.update_from_file(

                    dataset.dataset,

                    extra_dir=os.path.normpath(os.path.join(file_name, os.path.relpath(root, temp_file_path))),

                    extra_dir=os.path.normpath(os.path.join(real_file_name, os.path.relpath(root, temp_file_path))),

                    alt_name=f,

                    file_name=os.path.join(root, f),

                    create=True,

lib/galaxy/jobs/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -1652,7 +1652,7 @@ class MinimalJobWrapper(HasResourceParameters): 
            dataset.dataset.uuid = context["uuid"]

        self.__update_output(job, dataset)

        if not purged:

            collect_extra_files(self.object_store, dataset, self.working_directory)

            collect_extra_files(self.object_store, dataset, self.working_directory, self.outputs_to_working_directory)

        if job.states.ERROR == final_job_state:

            dataset.blurb = "error"

            if not implicit_collection_jobs:

test/integration/test_change_datatype_with_store_by_id.py→test/integration/test_legacy_store_by.py

+18 −0
Original line number Diff line number Diff line
@@ -21,3 +21,21 @@ class TestChangeDatatypeStoreByIdIntegration(integration_util.IntegrationTestCas 
        super().setUp()

        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)

        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)





class StoreByIdTestCase(integration_util.IntegrationInstance):

    framework_tool_and_types = True



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

        config["object_store_store_by"] = "id"

        config["outputs_to_working_directory"] = True





instance = integration_util.integration_module_instance(StoreByIdTestCase)



test_tools = integration_util.integration_tool_runner(

    [

        "composite_output_tests",

    ]

)