From 5d2ac56653d4e63f125e0d86f6682d392e2f9f7c Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 8 Jun 2021 09:21:32 +0200
Subject: [PATCH] Add docker tools
---
docker_tools/README.md | 2 +
docker_tools/toggl_galaxy_state.py | 62 ++++++++++++++++++++++++++++++
docker_tools/update_service.py | 39 +++++++++++++++++++
docker_tools/utilities.py | 18 +++++++++
4 files changed, 121 insertions(+)
create mode 100644 docker_tools/README.md
create mode 100644 docker_tools/toggl_galaxy_state.py
create mode 100644 docker_tools/update_service.py
create mode 100644 docker_tools/utilities.py
diff --git a/docker_tools/README.md b/docker_tools/README.md
new file mode 100644
index 0000000..0ee14b4
--- /dev/null
+++ b/docker_tools/README.md
@@ -0,0 +1,2 @@
+Useful tools to run docker commands for all running stacks
+=================
diff --git a/docker_tools/toggl_galaxy_state.py b/docker_tools/toggl_galaxy_state.py
new file mode 100644
index 0000000..9d5364b
--- /dev/null
+++ b/docker_tools/toggl_galaxy_state.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import argparse
+import logging
+import utilities
+import time
+
+def run_docker_service_scale(stack, service, state):
+ utilities.run_command(["docker", "service", "scale", stack + "_" + service + "=" + state])
+
+def run_docker_stack_services(stack, service):
+ stdout = utilities.run_command_and_get_stdout(["docker", "stack", "services",
+ "--format", "'{{.Replicas}}'",
+ "--filter", "name=" + stack + "_" + service,
+ stack])
+ return stdout
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Start or stop the Galaxy container for all the stacks")
+
+ parser.add_argument("-s", "--state",
+ type=int,
+ choices=[0,1],
+ help="State to set the Galaxy container in")
+
+ parser.add_argument("-v", "--verbose",
+ help="Increase output verbosity",
+ action="store_true")
+
+ args = parser.parse_args()
+ state = args.state
+
+ if args.verbose:
+ logging.basicConfig(level=logging.DEBUG)
+ logging.debug("Debug mode")
+ else:
+ logging.basicConfig(level=logging.INFO)
+
+ stacks = utilities.run_docker_stack_ls()
+
+ # Stop the Galaxy services
+ for stack in stacks:
+ if stack not in ["traefik", "portainer"]:
+ run_docker_service_scale(
+ stack=stack,
+ service="galaxy",
+ state=state
+ )
+
+ time.sleep(60)
+
+ # Check that the Galaxy services are down
+ for stack in stacks:
+ if stack not in ["traefik", "portainer"]:
+ stdout = run_docker_stack_services(
+ stack=stack,
+ service="galaxy"
+ )
+ if stdout != "0/1":
+ logging.error("The Galaxy service is not stopped for %s" % stack)
+
diff --git a/docker_tools/update_service.py b/docker_tools/update_service.py
new file mode 100644
index 0000000..9c7b57f
--- /dev/null
+++ b/docker_tools/update_service.py
@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import argparse
+import logging
+import utilities
+
+def run_docker_service_update(stack, service):
+ utilities.run_command(["docker", "service", "update", "--force", stack + "_" + service])
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Update a service for all the stacks")
+
+ parser.add_argument("-s", "--service",
+ choices=["tripal", "galaxy", "jbrowse", "tripal-db", "elasticsearch", "proxy"],
+ help="Service to update")
+
+ parser.add_argument("-v", "--verbose",
+ help="Increase output verbosity",
+ action="store_true")
+
+ args = parser.parse_args()
+ service = args.service
+
+ if args.verbose:
+ logging.basicConfig(level=logging.DEBUG)
+ logging.debug("Debug mode")
+ else:
+ logging.basicConfig(level=logging.INFO)
+
+ stacks = utilities.run_docker_stack_ls()
+
+ # Stop the Galaxy services
+ for stack in stacks:
+ if stack not in ["traefik", "portainer"]:
+ run_docker_service_update(
+ stack=stack,
+ service=service
+ )
diff --git a/docker_tools/utilities.py b/docker_tools/utilities.py
new file mode 100644
index 0000000..da8764e
--- /dev/null
+++ b/docker_tools/utilities.py
@@ -0,0 +1,18 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import subprocess
+import logging
+
+def run_command(command):
+ subprocess.run(command)
+
+def run_command_and_get_stdout(command):
+ completed_process = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
+ return completed_process.stdout
+
+def run_docker_stack_ls():
+ stdout = run_command_and_get_stdout(["docker", "stack", "ls", "--format", "{{.Name}}"])
+ stacks = stdout.splitlines()
+ logging.info("{0} stacks running: {1}".format(len(stacks), ", ".join(stacks)))
+ return stacks
--
GitLab