Use existing Globus login to request new consents; Add balsam job mod…

…ify command

balsam/cmdline/job.py

@@ -313,6 +313,30 @@ def ls(
         list_table(job_qs, client)
 
 
+@job.command()
+@click.option("-i", "--id", "job_ids", multiple=True, type=int)
+@click.option("-s", "--state", "state", type=str)
+def modify(job_ids: List[int], state: List[str]) -> None:
+    """
+    Modify Jobs
+
+    1) Modify Job State
+
+        balsam job modify --id 41 --id 42 --id 43 -s RESTART_READY
+    """
+    client: RESTClient = load_client()
+    jobs = client.Job.objects.all()
+    if job_ids:
+        jobs = jobs.filter(id=job_ids)
+    else:
+        raise click.BadParameter("Provide either list of Job ids or tags to delete")
+    count = jobs.count()
+    assert count is not None
+    for job in jobs:
+        job.state = state
+        job.save()
+
+
 @job.command()
 @click.option("-i", "--id", "job_ids", multiple=True, type=int)
 @click.option("-t", "--tag", "tags", multiple=True, type=str, callback=validate_tags)

balsam/cmdline/site.py

@@ -216,15 +216,20 @@ def globus_login(endpoint_id: str) -> None:
     """
     Get credentials for the Globus CLI
 
-    Necessary before any Globus CLI commands which require authentication will work
+    Necessary before any Globus CLI commands which require authentication will work.
     This command directs you to the page necessary to permit the Globus CLI to make API
     calls for you, and gets the OAuth2 tokens needed to use those permissions.
     """
     # if not forcing, stop if user already logged in
     if globus_auth.check_logged_in():
         click.echo("You are already logged in!")
+        # user is logged in already, but let's ensure consents are in place for the 
+        # requested endpoints
+        # FIXME: Since the globus API doesn't allow query of consents, we should
+        # should store the list of successful consents so we know if this is needed
+        globus_auth.do_link_auth_flow(force_new_client=False, endpoint_ids=endpoint_id)
         return
 
     globus_auth.do_link_auth_flow(force_new_client=True, endpoint_ids=endpoint_id)
 
-    click.echo("You have successfully logged in to the Globus CLI!")
+    click.echo("You have successfully logged in to Globus")

balsam/platform/app_run/app_run.py

@@ -158,6 +158,11 @@ def start(self) -> None:
         self._set_envs()
         cmdline = self._build_preamble() + self._build_cmdline()
         logger.info(f"{self.__class__.__name__} Popen: {cmdline}")
+
+        import inspect
+
+        logger.info(f"current stack top: {inspect.stack()[0][1]}")
+
         self._outfile = self._open_outfile()
         self._pre_popen()
 

balsam/platform/scheduler/pbs_sched.py

@@ -187,6 +187,7 @@ def _parse_status_output(raw_output: str) -> Dict[int, SchedulerJobStatus]:
                 for jobidstr, job in j["Jobs"].items():
                     status = {}
                     try:
+                        jobidstr = jobidstr.replace("[]", "")
                         jobid = int(jobidstr.split(".")[0])
                         status["scheduler_id"] = jobid
                     except ValueError:

balsam/platform/transfer/globus_transfer.py

@@ -45,6 +45,8 @@ def submit_sdk(src_endpoint: UUID, dest_endpoint: UUID, batch: Sequence[SrcDestR
     try:
         res = client.submit_transfer(transfer_data)
     except GlobusAPIError as exc:
+        import traceback
+        traceback.print_exc()
         raise TransferSubmitError(str(exc))
     task_id = res.get("task_id", None)
     if task_id is None:

balsam/util/globus_auth.py

@@ -194,11 +194,11 @@ def internal_auth_client(requires_instance: bool = False, force_new_client: bool
         write_option(CLIENT_ID_OPTNAME, client_id)
         write_option(CLIENT_SECRET_OPTNAME, client_secret)
 
-        return ConfidentialAppAuthClient(client_id, client_secret, app_name="Globus CLI")
+        return ConfidentialAppAuthClient(client_id, client_secret, app_name="Balsam")
 
     # if we already have a client, just return it
     elif existing:
-        return ConfidentialAppAuthClient(client_id, client_secret, app_name="Globus CLI")
+        return ConfidentialAppAuthClient(client_id, client_secret, app_name="Balsam")
 
     # fall-back to a native client to not break old logins
     # TOOD: eventually remove this behavior
@@ -220,7 +220,7 @@ def get_client() -> RetryingTransferClient:
             on_refresh=_update_tokens,
         )
 
-    return RetryingTransferClient(authorizer=authorizer, app_name="Globus CLI v2.1.0")
+    return RetryingTransferClient(authorizer=authorizer, app_name="Balsam")
 
 
 def exchange_code_and_store_config(auth_client: EitherAuthClient, auth_code: str) -> None: