Unverified Commit 435a8cd3 authored by mvdbeek's avatar mvdbeek
Browse files

Fix up test cases 

Add a sleep so we can delay output purging until command line is
templated. If we don't sleep we generate a command line where the
output path is just `''`. That needs another fix!
parent 65e9605f

test/functional/tools/all_output_types.xml

+8 −2
Original line number Diff line number Diff line 
<tool id="all_output_types" name="all_output_types" version="1.0.0" profile="24.0">

    <command><![CDATA[

        sleep $sleep_param &&

        echo hi > output.txt &&

        cp output.txt '$static_output' &&

        echo hi > '$static_output' &&

        echo hi > '$static_output_2' &&

        cp '$c1' galaxy.json

        ]]>

    </command>
@@ -13,8 +15,12 @@ 
  }}

        </configfile>

    </configfiles>

    <inputs>

        <param name="sleep_param" type="integer" value="0" />

    </inputs>

    <outputs>

        <data name="static_output" format="txt" />

        <data name="static_output_2" format="txt" />

        <data name="output_workdir" from_work_dir="output.txt" format="txt" />

        <data name="output_tool_supplied_metadata" from_work_dir="output.txt" format="auto" />

        <data format="txt" name="discovered_output">

test/integration/objectstore/_purged_handling.py

0 → 100644
+45 −0
Original line number Diff line number Diff line 
import time



from galaxy_test.base.populators import DatasetPopulator





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

    with dataset_populator.test_history() as history_id:

        response = dataset_populator.run_tool(

            "all_output_types",

            inputs={

                "sleep_param": 5,

            },

            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)

        hda_ids = []

        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

            dataset_populator.delete_dataset(

                history_id=history_id, content_id=output["id"], purge=True, wait_for_purge=True

            )

            hda_ids.append(output["id"])

        for output_collection in job["output_collections"].values():

            hdca = dataset_populator.get_history_collection_details(

                history_id=history_id, content_id=output_collection["id"]

            )

            for element in hdca["elements"]:

                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

        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)

test/integration/test_extended_metadata.py

+5 −0
Original line number Diff line number Diff line
@@ -5,6 +5,7 @@ from galaxy_test.base.populators import ( 
    LibraryPopulator,

)

from galaxy_test.driver import integration_util

from .objectstore._purged_handling import purge_while_job_running



TEST_TOOL_IDS = [

    "from_work_dir_glob",
@@ -47,6 +48,7 @@ TEST_TOOL_IDS = [ 


class TestExtendedMetadataIntegration(integration_util.IntegrationTestCase):

    dataset_populator: DatasetPopulator

    framework_tool_and_types = True



    def setUp(self):

        super().setUp()
@@ -95,6 +97,9 @@ class TestExtendedMetadataIntegration(integration_util.IntegrationTestCase): 
        assert dataset["file_ext"] == "bed", dataset

        assert dataset["created_from_basename"] == "4.bed"



    def test_purge_while_job_running(self):

        purge_while_job_running(self.dataset_populator)





class TestExtendedMetadataDeferredIntegration(integration_util.IntegrationTestCase):

    dataset_populator: DatasetPopulator

test/integration/test_pulsar_embedded_mq.py

+44 −16
Original line number Diff line number Diff line
@@ -7,7 +7,9 @@ import tempfile 
import pytest



from galaxy.util import safe_makedirs

from galaxy_test.base.populators import DatasetPopulator

from galaxy_test.driver import integration_util

from .objectstore._purged_handling import purge_while_job_running



SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))

EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_mq_job_conf.yml")
@@ -46,17 +48,7 @@ tools: 
"""





class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.IntegrationInstance):

    """Describe a Galaxy test instance with embedded pulsar 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

    """



    framework_tool_and_types = True



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

def _handle_galaxy_config_kwds(cls, config):

    amqp_url = os.environ.get("GALAXY_TEST_AMQP_URL", None)

    if amqp_url is None:

        pytest.skip("External AMQP URL not configured for test")
@@ -74,6 +66,42 @@ class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.Integration 
    config["galaxy_infrastructure_url"] = infrastructure_url





class TestEmbeddedMessageQueuePulsarPurge(integration_util.IntegrationTestCase):

    dataset_populator: DatasetPopulator

    framework_tool_and_types = True



    def setUp(self) -> None:

        super().setUp()

        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

        _handle_galaxy_config_kwds(cls, config)



    def test_purge_while_job_running(self):

        purge_while_job_running(self.dataset_populator)





class EmbeddedMessageQueuePulsarIntegrationInstance(integration_util.IntegrationInstance):

    """Describe a Galaxy test instance with embedded pulsar 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

    """



    dataset_populator: DatasetPopulator

    framework_tool_and_types = True



    @classmethod

    def handle_galaxy_config_kwds(cls, config):

        _handle_galaxy_config_kwds(cls, config)



    def test_purge_while_job_running(self):

        purge_while_job_running(self.dataset_populator)





instance = integration_util.integration_module_instance(EmbeddedMessageQueuePulsarIntegrationInstance)



test_tools = integration_util.integration_tool_runner(["simple_constructs", "composite_output_tests"])
 
test_tools = integration_util.integration_tool_runner(

    ["simple_constructs", "composite_output_tests", "all_output_types"]

)