Commit 83bac803 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Stub out tests and classes for job backend

parent 098203ce

src/nova/galaxy/job.py

0 → 100644
+36 −0
Original line number Diff line number Diff line 
"""

Job

"""



from .data_store import Datastore

from .parameters import Parameters

from .tool import AbstractWork





class Job:

    def __init__(self, work: AbstractWork):

        pass



    def submit_job(self, datastore: Datastore, params: Parameters) -> None:

        pass



    def cancel_job(self) -> None:

        pass



    def wait_for_job(self) -> None:

        pass



    def get_state(self) -> None:

        pass



    def get_outputs(self) -> None:

        pass



    def get_stdout(self) -> str:

        pass



    def get_stderr(self) -> str:

        pass



    def get_results(self) -> None:

        pass

src/nova/galaxy/nova.py

+3 −0
Original line number Diff line number Diff line
@@ -51,6 +51,9 @@ class NovaConnection: 
        history = self.galaxy_instance.histories.get_histories(name=store.name)[0]["id"]

        self.galaxy_instance.histories.delete_history(history_id=history, purge=True)



    def get_status(self, tool):

        pass





class Nova:

    """

src/nova/galaxy/tool.py

+11 −0
Original line number Diff line number Diff line 
"""Contains classes to run tools in Galaxy via Nova."""



import time

from enum import Enum

from typing import List, Optional, Union



from bioblend import galaxy
@@ -11,6 +12,16 @@ from .outputs import Outputs 
from .parameters import Parameters





class WorkState(Enum):

    """The state of a dataset in Galaxy."""



    NOT_STARTED = 1

    QUEUED = 2

    RUNNING = 3

    FINISHED = 4

    ERROR = 5





class AbstractWork:

    """Abstraction for a runnable object in Galaxy such as a tool or workflow."""

tests/test_job.py

0 → 100644
+49 −0
Original line number Diff line number Diff line 
from nova.galaxy.tool import Tool, WorkState

from nova.galaxy.parameters import Parameters

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()

        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)

        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)

        assert state == WorkState.FINISHED





def test_cancel_tool(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()

        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()

        assert state == WorkState.ERROR





def test_get_tool_stdout(nova_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()

        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)

        assert state == WorkState.RUNNING

        stdout = test_tool.get_stdout()

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