From d4431511d5312db1c426ccd0b71dd99b30ba0b4a Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Tue, 2 Mar 2021 09:03:22 -0500 Subject: [PATCH 1/4] Version 20.9.1 of data (tag galaxy-data-20.9.1). --- packages/data/HISTORY.rst | 2 +- packages/data/galaxy/project_galaxy_data.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 243f3eeb0c4..f0c1aca7328 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -6,7 +6,7 @@ History .. to_doc --------------------- -20.9.1.dev0 +20.9.1 (2021-03-02) --------------------- diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py index 35bc7ed8335..4e77c33f12a 100644 --- a/packages/data/galaxy/project_galaxy_data.py +++ b/packages/data/galaxy/project_galaxy_data.py @@ -1,6 +1,6 @@ # -*- coding: utf-8 -*- -__version__ = '20.9.1.dev0' +__version__ = '20.9.1' PROJECT_NAME = "galaxy-data" PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" From 55f4d5fdc105731e4296e38ae4976e1e2c22a4c0 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 21 Apr 2021 10:50:17 -0400 Subject: [PATCH 2/4] Fix user total walltime calculation when jobs are missing states in job state history. --- lib/galaxy/jobs/handler.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py index f27af3cfa8f..beccd62ed5b 100644 --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -611,7 +611,11 @@ class JobHandlerQueue(Monitors): elif history.state == "ok": finished = history.create_time - time_spent += finished - started + if started is not None and finished is not None: + time_spent += finished - started + else: + log.warning( + f"Unable to calculate time spent for job {job.id}; started: {started}, finished: {finished}") if time_spent > self.app.job_config.limits.total_walltime["delta"]: return JOB_USER_OVER_TOTAL_WALLTIME, job_destination From e015db024420bb777bae6ab7681c19150e3598b1 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 21 Apr 2021 11:07:48 -0400 Subject: [PATCH 3/4] No f-strings in 3.5. --- lib/galaxy/jobs/handler.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py index beccd62ed5b..acaaa1c10e3 100644 --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -614,8 +614,8 @@ class JobHandlerQueue(Monitors): if started is not None and finished is not None: time_spent += finished - started else: - log.warning( - f"Unable to calculate time spent for job {job.id}; started: {started}, finished: {finished}") + log.warning("Unable to calculate time spent for job %s; started: %s, finished: %s", + job.id, started, finished) if time_spent > self.app.job_config.limits.total_walltime["delta"]: return JOB_USER_OVER_TOTAL_WALLTIME, job_destination From 75e93a5d4387a9fd9413e830528d9f98126014d4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 26 Apr 2021 18:12:50 -0400 Subject: [PATCH 4/4] Fix package CI. --- lib/galaxy/config/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py index ee4c72db4eb..79d9338d59d 100644 --- a/lib/galaxy/config/script.py +++ b/lib/galaxy/config/script.py @@ -8,7 +8,7 @@ from argparse import ArgumentParser try: import pip except ImportError: - pip = None + pip = None # type: ignore CONFIGURE_URL = "https://docs.galaxyproject.org/en/master/admin/"