Unverified Commit f0e09cc8 authored by mvdbeek's avatar mvdbeek
Browse files

Fix up tests

parent 3c7730c1

test/integration/objectstore/_purged_handling.py

+25 −9
Original line number Diff line number Diff line
@@ -4,7 +4,7 @@ import time 
from galaxy_test.base.populators import DatasetPopulator





def purge_while_job_running(dataset_populator: DatasetPopulator, sleep_before_purge=4):

def purge_while_job_running(dataset_populator: DatasetPopulator, extra_sleep=0):

    with dataset_populator.test_history() as history_id:

        response = dataset_populator.run_tool(

            "all_output_types",
@@ -14,15 +14,20 @@ def purge_while_job_running(dataset_populator: DatasetPopulator, sleep_before_pu 
            history_id=history_id,

        )

        job = dataset_populator.get_job_details(response["jobs"][0]["id"], full=True).json()

        # Sleep a second to make sure we template command before purging output

        time.sleep(sleep_before_purge)

        # Make sure job runs (and thus command is templated before purging output)

        dataset_populator.wait_for_job(job["id"], ok_states=["running"])

        time.sleep(extra_sleep)

        hda_ids = []

        hda_filenames = []

        for output_name, output in job["outputs"].items():

            if output_name == "static_output_2":

                # We need to keep one output so the job doesn't get cancelled

                continue

            details = dataset_populator.get_history_dataset_details(history_id=history_id, dataset_id=output["id"])

            details = dataset_populator.get_history_dataset_details(

                history_id=history_id, content_id=output["id"], wait=False

            )

            if not output_name.startswith("discovered_output"):

                # We're not precreating discovered outputs on disk

                hda_filenames.append(details["file_name"])

            dataset_populator.delete_dataset(

                history_id=history_id, content_id=output["id"], purge=True, wait_for_purge=True
@@ -33,23 +38,34 @@ def purge_while_job_running(dataset_populator: DatasetPopulator, sleep_before_pu 
                history_id=history_id, content_id=output_collection["id"]

            )

            for element in hdca["elements"]:

                # Technically the static pair elements are already included in job["outputs"],

                # but no harm purging them again here, in case we ever change that logic.

                hda_id = element["object"]["id"]

                dataset_populator.delete_dataset(

                    history_id=history_id, content_id=hda_id, purge=True, wait_for_purge=True

                )

                hda_ids.append(hda_id)

        dataset_populator.wait_for_job(job["id"], assert_ok=True)

        # Now make sure we can't find the datasets

        # Now make sure we can't find the datasets on disk

        # We're not covering discovered datasets here, those can't be purged while the job is running.

        for hda_id in hda_ids:

            exception = None

            try:

                dataset_populator.get_history_dataset_content(history_id=history_id, dataset_id=hda_id)

            except AssertionError as e:

                exception = e

            assert exception and "The dataset you are attempting to view has been purged" in str(exception)

            output_details = dataset_populator.get_history_dataset_details(history_id=history_id, dataset_id=hda_id)

            assert exception and "The dataset you are attempting to view has been purged" in str(exception), str(

                exception

            )

            output_details = dataset_populator.get_history_dataset_details(

                history_id=history_id, content_id=hda_id, wait=False

            )

            # Make sure that we don't revert state while finishing job

            assert output_details["purged"]

            assert output_details["purged"], f"expected output '{output_name}' to be purged, but it is not purged."

            assert not output_details.get("file_name")

            assert (

                output_details["file_size"] == 0

            ), f"expected file_size for '{output_name}' to be 0, but it is {output_details['file_size']}."

        for file_name in hda_filenames:

            # Make sure job didn't push to object store

            assert not os.path.exists(file_name), f"Expected {file_name} to be purged."

test/integration/test_extended_metadata.py

+3 −1
Original line number Diff line number Diff line
@@ -98,7 +98,9 @@ class TestExtendedMetadataIntegration(integration_util.IntegrationTestCase): 
        assert dataset["created_from_basename"] == "4.bed"



    def test_purge_while_job_running(self):

        purge_while_job_running(self.dataset_populator)

        # pass extra_sleep, since templating the command line will fail if the output

        # is deleted before remote_tool_eval runs.

        purge_while_job_running(self.dataset_populator, extra_sleep=4)





class TestExtendedMetadataDeferredIntegration(integration_util.IntegrationTestCase):

test/integration/test_pulsar_embedded_mq.py

+13 −0
Original line number Diff line number Diff line
@@ -82,6 +82,19 @@ class TestEmbeddedMessageQueuePulsarPurge(integration_util.IntegrationTestCase): 
        purge_while_job_running(self.dataset_populator)





class TestEmbeddedMessageQueuePulsarExtendedMetadataPurge(TestEmbeddedMessageQueuePulsarPurge):

    """Describe a Galaxy test instance with embedded pulsar and extended metadata configured.



    $ Setup RabbitMQ (e.g. https://www.rabbitmq.com/install-homebrew.html)

    $ GALAXY_TEST_AMQP_URL='amqp://guest:guest@localhost:5672//' pytest -s test/integration/test_pulsar_embedded_mq.py

    """



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

        config["metadata_strategy"] = "extended"

        _handle_galaxy_config_kwds(cls, config)





class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.IntegrationInstance):

    """Describe a Galaxy test instance with embedded pulsar configured.