{"action":"created","issue":{"url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/33","repository_url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes","labels_url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/33/comments","events_url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/33/events","html_url":"https://github.com/ohsu-comp-bio/cwl-tes/pull/33","id":523024356,"node_id":"MDExOlB1bGxSZXF1ZXN0MzQxMTEwMzk2","number":33,"title":"Added importable function to use in external python modules","user":{"login":"medcelerate","id":32549017,"node_id":"MDQ6VXNlcjMyNTQ5MDE3","avatar_url":"https://avatars3.githubusercontent.com/u/32549017?v=4","gravatar_id":"","url":"https://api.github.com/users/medcelerate","html_url":"https://github.com/medcelerate","followers_url":"https://api.github.com/users/medcelerate/followers","following_url":"https://api.github.com/users/medcelerate/following{/other_user}","gists_url":"https://api.github.com/users/medcelerate/gists{/gist_id}","starred_url":"https://api.github.com/users/medcelerate/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/medcelerate/subscriptions","organizations_url":"https://api.github.com/users/medcelerate/orgs","repos_url":"https://api.github.com/users/medcelerate/repos","events_url":"https://api.github.com/users/medcelerate/events{/privacy}","received_events_url":"https://api.github.com/users/medcelerate/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2019-11-14T18:16:26Z","updated_at":"2019-11-25T22:09:37Z","closed_at":null,"author_association":"NONE","pull_request":{"url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/pulls/33","html_url":"https://github.com/ohsu-comp-bio/cwl-tes/pull/33","diff_url":"https://github.com/ohsu-comp-bio/cwl-tes/pull/33.diff","patch_url":"https://github.com/ohsu-comp-bio/cwl-tes/pull/33.patch"},"body":"Added a helper function to support loading in as a library for async execution."},"comment":{"url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/comments/558362390","html_url":"https://github.com/ohsu-comp-bio/cwl-tes/pull/33#issuecomment-558362390","issue_url":"https://api.github.com/repos/ohsu-comp-bio/cwl-tes/issues/33","id":558362390,"node_id":"MDEyOklzc3VlQ29tbWVudDU1ODM2MjM5MA==","user":{"login":"medcelerate","id":32549017,"node_id":"MDQ6VXNlcjMyNTQ5MDE3","avatar_url":"https://avatars3.githubusercontent.com/u/32549017?v=4","gravatar_id":"","url":"https://api.github.com/users/medcelerate","html_url":"https://github.com/medcelerate","followers_url":"https://api.github.com/users/medcelerate/followers","following_url":"https://api.github.com/users/medcelerate/following{/other_user}","gists_url":"https://api.github.com/users/medcelerate/gists{/gist_id}","starred_url":"https://api.github.com/users/medcelerate/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/medcelerate/subscriptions","organizations_url":"https://api.github.com/users/medcelerate/orgs","repos_url":"https://api.github.com/users/medcelerate/repos","events_url":"https://api.github.com/users/medcelerate/events{/privacy}","received_events_url":"https://api.github.com/users/medcelerate/received_events","type":"User","site_admin":false},"created_at":"2019-11-25T22:09:37Z","updated_at":"2019-11-25T22:09:37Z","author_association":"NONE","body":"We are using Cromwell but are looking to switch to another executor as we are having some issues that may or may not get resolved.\nOn Nov 18, 2019, 7:27 PM -0500, Evan Clark <evan.clark.professional@gmail.com>, wrote:\n> I can definitely move to another file. And make the other change. And you are right about the asynchronously execution issue. My thought is to have a helper function that returns a group of for running a workflow then when all the steps complete that is is marked as complete. Otherwise it is marked as failure if the entire set of tasks has the issue. Something closer akin to Cromwell but with functionality on a TES server.\n>\n> > On Mon, Nov 18, 2019 at 1:54 PM Adam Struck <notifications@github.com> wrote:\n> > > @adamstruck requested changes on this pull request.\n> > > In cwl_tes/tes.py:\n> > > > @@ -389,13 +405,31 @@ def run(self,\n> > >         )\n> > >         log.info(pformat(task))\n> > >\n> > > +        if self.lib:\n> > > Why not add this conditional check after the logging lines in the original code block rather than duplicate this whole code block?\n> > > In cwl_tes/main.py:\n> > > > +    job_executor = SingleJobExecutor()\n> > > +    job_executor.max_ram = job_executor.max_cores = float(\"inf\")\n> > > +    executor = functools.partial(\n> > > +        tes_execute, job_executor=job_executor,\n> > > +        loading_context=loading_context,\n> > > +        remote_storage_url=parsed_args.remote_storage_url,\n> > > +        ftp_access=ftp_fs_access)\n> > > +    cwltool.main.main(\n> > > +        args=parsed_args,\n> > > +        executor=executor,\n> > > +        loadingContext=loading_context,\n> > > +        runtimeContext=runtime_context,\n> > > +        versionfunc=versionstring,\n> > > +        logger_handler=console\n> > > +    )\n> > > +    return lib_helper.task_id\n> > > Since the steps are executing asynchronously, this method would break if you were to provide a multi-step workflow right?\n> > > Could you describe your envisioned use case in a bit more detail?\n> > > In cwl_tes/main.py:\n> > > > @@ -711,5 +713,72 @@ def arg_parser():  # type: () -> argparse.ArgumentParser\n> > >     return parser\n> > >\n> > >\n> > > +def non_interactive_executor(workflow_buffer,\n> > > I'd rather have this live in another file and not in main.py\n> > > —\n> > > You are receiving this because you authored the thread.\n> > > Reply to this email directly, view it on GitHub, or unsubscribe.\n"}}
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