Commit 5f5c43a3 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Clean up some of the test examples

parent 83bac803

src/nova/galaxy/job.py

+2 −1
Original line number Diff line number Diff line
@@ -9,6 +9,7 @@ from .tool import AbstractWork 


class Job:

    def __init__(self, work: AbstractWork):

        self.id = ""

        pass



    def submit_job(self, datastore: Datastore, params: Parameters) -> None:
@@ -17,7 +18,7 @@ class Job: 
    def cancel_job(self) -> None:

        pass



    def wait_for_job(self) -> None:

    def wait_for_results(self) -> None:

        pass



    def get_state(self) -> None:

src/nova/galaxy/tool.py

+26 −2
Original line number Diff line number Diff line
@@ -17,6 +17,7 @@ class WorkState(Enum): 


    NOT_STARTED = 1

    QUEUED = 2

    UPLOADING_DATA = 6

    RUNNING = 3

    FINISHED = 4

    ERROR = 5
@@ -43,9 +44,16 @@ class Tool(AbstractWork): 


    def __init__(self, id: str):

        super().__init__(id)

        self._job = None



    def run(self, data_store: Datastore, params: Parameters) -> Outputs:

    def run_async(self, data_store: Datastore, params: Parameters, async_execution: bool):

        # self.thread  = threading.new_thread(run)



        pass



    def run(self, data_store: Datastore, params: Parameters, async_execution: bool) -> Outputs:

        """Runs this tool in a blocking manner and returns a map of the output datasets and collections."""

        # TODO Most of this logic will be moved to job class

        outputs = Outputs()

        galaxy_instance = data_store.nova_connection.galaxy_instance

        datasets_to_upload = {}
@@ -57,7 +65,8 @@ class Tool(AbstractWork): 
                datasets_to_upload[param] = val

            else:

                tool_inputs.set_param(param, val)



        self.state = get_state()

        self._job.submit()

        ids = upload_datasets(store=data_store, datasets=datasets_to_upload)

        for param, val in ids.items():

            tool_inputs.set_dataset_param(param, val)
@@ -131,6 +140,21 @@ class Tool(AbstractWork): 
        else:

            raise Exception("Interactive tool was stopped unexpectedly.")



    def get_status(self):

        return self._job.get_status()



    def get_results(self):

        pass



    def stop(self):

        pass



    def cancel(self):

        pass



    def get_stdout(self):

        pass





def stop_all_tools_in_store(data_store: Datastore) -> None:

    galaxy_instance = data_store.nova_connection.galaxy_instance

tests/test_job.py

+10 −16
Original line number Diff line number Diff line 
from nova.galaxy.tool import Tool, WorkState

from nova.galaxy.parameters import Parameters

from nova.galaxy.tool import Tool, WorkState



TEST_INT_TOOL_ID = "interactive_tool_generic_output"





def test_status(nova_instance, galaxy_instance):

    with nova_instance.connect() as connection:

        store = connection.create_data_store(name="nova_galaxy_testing")

        test_tool = Tool(TEST_INT_TOOL_ID)

        params = Parameters()

        state = test_tool.status()

        state = test_tool.get_status()

        assert state == WorkState.NOT_STARTED

        link = test_tool.run_interactive(data_store=store, params=params, check_url=False)

        state = test_tool.status()

        # state = connection.get_status(test_tool)

        state = test_tool.get_status()

        test_tool.get_results()

        assert state == WorkState.RUNNING

        # TODO: Implement job canceling/stopping, then replace this with that stuff

        test_tool.stop()

        # galaxy_instance.make_get_request(f"{store.nova_connection.galaxy_url}/api/jobs/{test_tool.job_id}/finish")

        # galaxy_instance.wait_for_job(test_tool.job_id)

        state = connection.get_status(test_tool)

        state = test_tool.get_status()

        assert state == WorkState.FINISHED
@@ -27,10 +26,8 @@ def test_cancel_tool(nova_instance, galaxy_instance): 
        test_tool = Tool(TEST_INT_TOOL_ID)

        params = Parameters()

        link = test_tool.run_interactive(data_store=store, params=params, check_url=False)

        # TODO: Implement job canceling/stopping, then replace this with that stuff

        test_tool.cancel()

        # state = connection.get_status(test_tool)

        state = test_tool.status()

        state = test_tool.get_status()

        assert state == WorkState.ERROR
@@ -40,10 +37,7 @@ def test_get_tool_stdout(nova_instance): 
        test_tool = Tool(TEST_INT_TOOL_ID)

        params = Parameters()

        link = test_tool.run_interactive(data_store=store, params=params, check_url=False)

        # TODO: Implement job canceling/stopping, then replace this with that stuff

        state = test_tool.status()

        # state = connection.get_status(test_tool)

        state = test_tool.get_status()

        assert state == WorkState.RUNNING

        stdout = test_tool.get_stdout()

        assert stdout is not None  # TODO maybe check specific stdout here