Merge branch 'feature/uWSGI' into develop (349785e6) · Commits · ExaCT / Rosetta

README.md

+3 −2

Original line number	Diff line number	Diff line
		@@ -45,7 +45,9 @@ Clean
		Example Webapp configuraion

		- SAFEMODE=False
		- DJANGO_LOG_LEVEL=CRITICAL
		- DJANGO_DEV_SERVER=True
		- DJANGO_DEBUG=True
		- DJANGO_LOG_LEVEL=ERROR
		- ROSETTA_LOG_LEVEL=ERROR
		- ROSETTA_TUNNEL_HOST=localhost # Not http or https
		- ROSETTA_WEBAPP_HOST=
		@@ -58,7 +60,6 @@ Example Webapp configuraion
		- DJANGO_PUBLIC_HTTP_HOST=http://localhost # Public facing, with http or https



		### Extras

		List all running services

docker-compose-dev.yml

+1 −0

Original line number	Diff line number	Diff line
		@@ -46,6 +46,7 @@ services:
		hostname: webapp
		environment:
		- SAFEMODE=False
		- DJANGO_DEV_SERVER=True
		- DJANGO_DEBUG=True
		- DJANGO_LOG_LEVEL=CRITICAL
		- ROSETTA_LOG_LEVEL=DEBUG

services/webapp/code/rosetta/core_app/api.py

+54 −74

Original line number	Diff line number	Diff line
		@@ -209,7 +209,6 @@ class UserViewSet(viewsets.ModelViewSet):
		class agent_api(PublicGETAPI):

		def _get(self, request):
		try:

		task_uuid = request.GET.get('task_uuid', None)
		if not task_uuid:
		@@ -326,23 +325,4 @@ print(port)
		return HttpResponse('Unknown action "{}"'.format(action))


		except Exception as e:
		logger.error(e)

services/webapp/code/rosetta/core_app/computing_managers.py

+9 −9

Original line number	Diff line number	Diff line
		@@ -205,7 +205,7 @@ class RemoteComputingManager(ComputingManager):
		else:
		binds += ',{}'.format(task.extra_binds)

		run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		run_command += '/bin/bash -c \'"rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp && mkdir -p /tmp/{}_data/home && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid)
		run_command += 'wget {}/api/v1/base/agent/?task_uuid={} -O /tmp/{}_data/agent.py &> /dev/null && export BASE_PORT=\$(python /tmp/{}_data/agent.py 2> /tmp/{}_data/task.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)
		run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
		@@ -262,7 +262,7 @@ class RemoteComputingManager(ComputingManager):
		user = task.computing.get_conf_param('user')

		# Stop the task remotely
		stop_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.pid)
		stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.pid)
		out = os_shell(stop_command, capture=True)
		if out.exit_code != 0:
		if not 'No such process' in out.stderr:
		@@ -286,7 +286,7 @@ class RemoteComputingManager(ComputingManager):
		user = task.computing.get_conf_param('user')

		# View log remotely
		view_log_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat /tmp/{}_data/task.log"\''.format(user_keys.private_key_file, user, host, task.uuid)
		view_log_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat /tmp/{}_data/task.log"\''.format(user_keys.private_key_file, user, host, task.uuid)

		out = os_shell(view_log_command, capture=True)
		if out.exit_code != 0:
		@@ -364,7 +364,7 @@ class SlurmComputingManager(ComputingManager):
		else:
		binds += ',{}'.format(task.extra_binds)

		run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		run_command += '\'bash -c "echo \\"#!/bin/bash\nwget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> \$HOME/{}.log && export BASE_PORT=\\\\\\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)
		run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\\\\\\$BASE_PORT && {} '.format(authstring)
		run_command += 'rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp &>> \$HOME/{}.log && mkdir -p /tmp/{}_data/home &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)
		@@ -431,7 +431,7 @@ class SlurmComputingManager(ComputingManager):
		user = task.computing.get_conf_param('user')

		# Stop the task remotely
		stop_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "scancel {}"\''.format(user_keys.private_key_file, user, host, task.pid)
		stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "scancel {}"\''.format(user_keys.private_key_file, user, host, task.pid)
		out = os_shell(stop_command, capture=True)
		if out.exit_code != 0:
		raise Exception(out.stderr)
		@@ -454,7 +454,7 @@ class SlurmComputingManager(ComputingManager):
		user = task.computing.get_conf_param('user')

		# View log remotely
		view_log_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat \$HOME/{}.log"\''.format(user_keys.private_key_file, user, host, task.uuid)
		view_log_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat \$HOME/{}.log"\''.format(user_keys.private_key_file, user, host, task.uuid)

		out = os_shell(view_log_command, capture=True)
		if out.exit_code != 0:
		@@ -518,7 +518,7 @@ class RemotehopComputingManager(ComputingManager):
		else:
		binds += ',{}'.format(task.extra_binds)

		run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		run_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} /bin/bash -c \''.format(second_user, second_host)

		if use_agent:
		@@ -592,7 +592,7 @@ class RemotehopComputingManager(ComputingManager):
		second_user = task.computing.get_conf_param('second_user')

		# Stop the task remotely
		stop_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		stop_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} '.format(second_user, second_host)
		stop_command += 'kill -9 {}"'.format(task.pid)

		@@ -621,7 +621,7 @@ class RemotehopComputingManager(ComputingManager):
		second_user = task.computing.get_conf_param('second_user')

		# View log remotely
		view_log_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		view_log_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
		view_log_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} '.format(second_user, second_host)
		view_log_command += 'cat \\\\\\$HOME/{}.log"'.format(task.uuid)

services/webapp/code/rosetta/core_app/decorators.py

+13 −17

Original line number	Diff line number	Diff line
		@@ -51,18 +51,16 @@ def public_view(wrapped_view):
		error_text = str(e)
		else:

		# Raise te exception if we are in debug mode
		# Log the exception
		logger.error(format_exception(e))

		# Raise the exception if we are in debug mode
		if settings.DEBUG:
		raise

		# Otherwise,
		# Otherwise, mask it
		else:

		# first log the exception
		logger.error(format_exception(e))

		# and then mask it.
		error_text = 'something went wrong'
		error_text = 'something went wrong ({})'.format(e)

		data = {'user': request.user,
		'title': 'Error',
		@@ -111,18 +109,16 @@ def private_view(wrapped_view):
		error_text = str(e)
		else:

		# Raise te exception if we are in debug mode
		# Log the exception
		logger.error(format_exception(e))

		# Raise the exception if we are in debug mode
		if settings.DEBUG:
		raise

		# Otherwise,
		# Otherwise, mask it
		else:

		# first log the exception
		logger.error(format_exception(e))

		# and then mask it.
		error_text = 'something went wrong'
		error_text = 'something went wrong ({})'.format(e)

		data = {'user': request.user,
		'title': 'Error',