Commit f1c522c2 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

refactor stop/cancel functions

parent a422158d

src/nova/galaxy/job.py

+16 −14
Original line number Diff line number Diff line
@@ -161,11 +161,9 @@ class Job: 
        for dataset_id in datasets.values():

            galaxy_instance.histories.delete_dataset(history_id=history_id, dataset_id=dataset_id, purge=True)



    def cancel(self, stop: bool = False) -> bool:

        """Cancels or stops a job in Galaxy."""

    def stop(self) -> bool:

        """Stops a job in Galaxy."""

        self.url = None

        self.status.state = WorkState.CANCELING

        if stop:

        self.status.state = WorkState.STOPPING

        response = self.galaxy_instance.make_put_request(

            f"{self.store.nova_connection.galaxy_url}/api/jobs/{self.id}/finish"
@@ -175,9 +173,13 @@ class Job: 
        else:

            self.status.error_msg = "could not stop job"

            return False



    def cancel(self) -> bool:

        """Cancel a job in Galaxy."""

        self.url = None

        self.status.state = WorkState.CANCELING

        try:

            success = self.galaxy_instance.jobs.cancel_job(self.id)

            return success

            return self.galaxy_instance.jobs.cancel_job(self.id)

        except Exception:

            return False

src/nova/galaxy/tool.py

+2 −2
Original line number Diff line number Diff line
@@ -139,12 +139,12 @@ class Tool(AbstractWork): 
    def stop(self) -> None:

        """Stop the tool, but keep any existing results."""

        if self._job:

            self._job.cancel(stop=True)

            self._job.stop()



    def cancel(self) -> None:

        """Cancels the tool execution and gets rid of any results collected."""

        if self._job:

            self._job.cancel(stop=False)

            self._job.cancel()



    def get_stdout(self, position: Optional[int] = None, length: Optional[int] = None) -> Optional[str]:

        """Get the current STDOUT for a tool.