Commit 64f5e409 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

add stopping job status

parent 3055735b

src/nova/galaxy/job.py

+8 −7
Original line number Diff line number Diff line
@@ -55,7 +55,7 @@ class Job: 
            self.wait_for_results()

        except Exception as e:

            self.url = None

            if self.status.state == WorkState.STOPPING or self.status.state == WorkState.CANCELED:

            if self.status.state in [WorkState.STOPPING, WorkState.CANCELING, WorkState.CANCELED]:

                self.status.state = WorkState.CANCELED

                return

            self.status.state = WorkState.ERROR
@@ -116,7 +116,7 @@ class Job: 
                for param, val in ids.items():

                    tool_inputs.set_dataset_param(param, val)



        if self.status.state == WorkState.STOPPING:

        if self.status.state in [WorkState.STOPPING, WorkState.CANCELING]:

            self.status.state = WorkState.CANCELED

            return

        # Run tool and wait for job to finish
@@ -135,7 +135,7 @@ class Job: 
        history_id = galaxy_instance.histories.get_histories(name=self.store.name)[0]["id"]

        dataset_ids: Dict[str, str] = {}

        for name, dataset in datasets.items():

            if self.status.state == WorkState.STOPPING:

            if self.status.state in [WorkState.STOPPING, WorkState.CANCELING]:

                self.cleanup_datasets(dataset_ids)

                return None

            if len(dataset.path) < 1 and dataset.get_content():
@@ -148,7 +148,7 @@ class Job: 
            dataset.id = dataset_info["outputs"][0]["id"]

            dataset.store = self.store

        for dataset_output in dataset_ids.values():

            if self.status.state == WorkState.STOPPING:

            if self.status.state in [WorkState.STOPPING, WorkState.CANCELING]:

                self.cleanup_datasets(dataset_ids)

                return None

            dataset_client.wait_for_dataset(dataset_output)
@@ -160,11 +160,12 @@ 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, check_results: bool = False) -> bool:

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

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

        self.url = None

        self.status.state = WorkState.CANCELING

        if stop:

            self.status.state = WorkState.STOPPING

        if check_results:

            response = self.galaxy_instance.make_put_request(

                f"{self.store.nova_connection.galaxy_url}/api/jobs/{self.id}/finish"

            )

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(check_results=True)

            self._job.cancel(stop=True)



    def cancel(self) -> None:

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

        if self._job:

            self._job.cancel(check_results=False)

            self._job.cancel(stop=False)



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

        """Get the current STDOUT for a tool.

src/nova/galaxy/util.py

+1 −0
Original line number Diff line number Diff line
@@ -15,3 +15,4 @@ class WorkState(Enum): 
    DELETED = "deleted"

    CANCELED = "canceled"

    STOPPING = "stopping"

    CANCELING = "canceling"

tests/test_run_tool.py

+2 −2
Original line number Diff line number Diff line
@@ -90,7 +90,7 @@ def test_cancel_tool(nova_instance: Connection) -> None: 
        test_tool.run_interactive(data_store=store, params=params, check_url=False)

        test_tool.cancel()

        state = test_tool.get_status()

        assert state == WorkState.STOPPING

        assert state == WorkState.CANCELING





def test_cancel_tool_while_uploading(nova_instance: Connection, galaxy_instance: GalaxyInstance) -> None:
@@ -112,7 +112,7 @@ def test_cancel_tool_while_uploading(nova_instance: Connection, galaxy_instance: 
        assert state == WorkState.UPLOADING_DATA

        test_tool.cancel()

        state = test_tool.get_status()

        assert state == WorkState.STOPPING

        assert state == WorkState.CANCELING

        test_tool.wait_for_results()

        state = test_tool.get_status()

        assert state == WorkState.CANCELED