Add docker tools

docker_tools/README.md

+Useful tools to run docker commands for all running stacks
+=================

docker_tools/toggl_galaxy_state.py

+#!/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)
+

docker_tools/update_service.py

+#!/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
+            )

docker_tools/utilities.py

+#!/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