Commit df2b4682 authored by Cage, Gregory's avatar Cage, Gregory
Browse files

Add option to not check interactive tool url

parent 55c58631

src/nova/galaxy/tool.py

+5 −3
Original line number Diff line number Diff line 
"""Contains classes to run tools in Galaxy via Nova."""



import time

from typing import List, Union

from typing import List, Optional, Union



from bioblend import galaxy
@@ -77,7 +77,9 @@ class Tool(AbstractWork): 


        return outputs



    def run_interactive(self, data_store: Datastore, params: Parameters, max_tries: int = 100) -> str:

    def run_interactive(

        self, data_store: Datastore, params: Parameters, max_tries: int = 100, check_url: bool = True

    ) -> Optional[str]:

        galaxy_instance = data_store.nova_connection.galaxy_instance

        datasets_to_upload = {}

        # Set Tool Inputs
@@ -107,7 +109,7 @@ class Tool(AbstractWork): 
                if ep["job_id"] == job_id and ep.get("target", None):

                    url = f"{data_store.nova_connection.galaxy_url}{ep['target']}"

                    response = galaxy_instance.make_get_request(url)

                    if response.status_code == 200:

                    if response.status_code == 200 or not check_url:

                        return url

            timer -= 1

            time.sleep(1)