From dec32e5128730707429c063d1940c173e2074ff9 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Wed, 20 May 2020 16:53:45 +0200
Subject: [PATCH 1/2] fix: task logs are serialized
---
cwl_wes/tasks/celery_task_monitor.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/cwl_wes/tasks/celery_task_monitor.py b/cwl_wes/tasks/celery_task_monitor.py
index 6fac8ba..f7f147d 100644
--- a/cwl_wes/tasks/celery_task_monitor.py
+++ b/cwl_wes/tasks/celery_task_monitor.py
@@ -530,7 +530,7 @@ def __get_tes_task_log(
task_log = tes_client.get_task(
task_id=tes_id,
view=self.tes_config['query_params'],
- )
+ ).as_dict()
except Exception as e:
# TODO: handle more robustly: only 400/Bad Request is okay;
# TODO: other errors (e.g. 500) should be dealt with
From a595157925482343cb01867a09f1874ea487f6a4 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Wed, 20 May 2020 16:58:45 +0200
Subject: [PATCH 2/2] build: pass config vars to containers
---
docker-compose.yaml | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/docker-compose.yaml b/docker-compose.yaml
index b7c3141..d1243ae 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -12,8 +12,13 @@ services:
command: bash -c "cd /app/cwl_wes; gunicorn -c config.py wsgi:app"
volumes:
- ../data/cwl_wes:/data
+ - ${WES_CONFIG}:${WES_CONFIG}
+ - ${WES_CONFIG_LOG}:${WES_CONFIG_LOG}
ports:
- "7777:8080"
+ environment:
+ - WES_CONFIG
+ - WES_CONFIG_LOG
wes-worker:
image: elixircloud/cwl-wes:latest
@@ -26,6 +31,11 @@ services:
command: bash -c "cd /app/cwl_wes; celery worker -A celery_worker -E --loglevel=info"
volumes:
- ../data/cwl_wes:/data
+ - ${WES_CONFIG}:${WES_CONFIG}
+ - ${WES_CONFIG_LOG}:${WES_CONFIG_LOG}
+ environment:
+ - WES_CONFIG
+ - WES_CONFIG_LOG
rabbitmq:
image: "rabbitmq:3-management"