diff --git a/services/webapp/code/rosetta/core_app/api.py b/services/webapp/code/rosetta/core_app/api.py
index abeca9696b7a5868d646fc5948b822e934fa1a7a..9fba588a8a99fb928b3a97c4e4cf9a7d61290dec 100644
--- a/services/webapp/code/rosetta/core_app/api.py
+++ b/services/webapp/code/rosetta/core_app/api.py
@@ -405,13 +405,13 @@ class FileManagerAPI(PrivateGETAPI, PrivatePOSTAPI):
dest = dest.replace('\ ', '\\\\\\ ')
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(computing, user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(computing, user)
# Command
if mode=='get':
- command = 'scp -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{}:{} {}'.format(computing_keys.private_key_file, computing_user, computing_host, source, dest)
+ command = 'scp -P {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{}:{} {}'.format(computing_port, computing_keys.private_key_file, computing_user, computing_host, source, dest)
elif mode == 'put':
- command = 'scp -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {} {}@{}:{}'.format(computing_keys.private_key_file, source, computing_user, computing_host, dest)
+ command = 'scp -P -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {} {}@{}:{}'.format(computing_port, computing_keys.private_key_file, source, computing_user, computing_host, dest)
else:
raise ValueError('Unknown mode "{}"'.format(mode))
@@ -423,10 +423,10 @@ class FileManagerAPI(PrivateGETAPI, PrivatePOSTAPI):
if storage.access_mode == 'ssh+cli':
if storage.access_through_computing:
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(storage.computing, user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(storage.computing, user)
# Command
- command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} "{}"'.format(computing_keys.private_key_file, computing_user, computing_host, command)
+ command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} "{}"'.format(computing_port, computing_keys.private_key_file, computing_user, computing_host, command)
else:
raise NotImplementedError('Not accessing through computing is not implemented for storage type "{}"'.format(storage.type))
elif storage.access_mode == 'cli':
diff --git a/services/webapp/code/rosetta/core_app/computing_managers.py b/services/webapp/code/rosetta/core_app/computing_managers.py
index 27e62005dbc4c338c30b7a6a68db318de1be801a..974f0af33737e5a9d8747c0702d3d0e82f71f374 100644
--- a/services/webapp/code/rosetta/core_app/computing_managers.py
+++ b/services/webapp/code/rosetta/core_app/computing_managers.py
@@ -203,7 +203,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
logger.debug('Starting a remote task "{}"'.format(self.computing))
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# Get webapp conn string
from.utils import get_webapp_conn_string
@@ -270,7 +270,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
else:
binds += ',{}:{}'.format(expanded_base_path, expanded_bind_path)
- run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_keys.private_key_file, computing_user, computing_host)
+ run_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_port, computing_keys.private_key_file, computing_user, computing_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(CHECK_WGET_CERT_STR, 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, varsstring)
@@ -333,7 +333,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
# TODO: remove this hardcoding
prefix = 'sudo' if (computing_host == 'slurmclusterworker' and container_engine=='docker') else ''
- run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_keys.private_key_file, computing_user, computing_host)
+ run_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_port, computing_keys.private_key_file, computing_user, computing_host)
run_command += '/bin/bash -c \'"rm -rf /tmp/{}_data && mkdir /tmp/{}_data && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid)
run_command += 'wget {} {}/api/v1/base/agent/?task_uuid={} -O /tmp/{}_data/agent.py &> /dev/null && export TASK_PORT=\$(python /tmp/{}_data/agent.py 2> /tmp/{}_data/task.log) && '.format(CHECK_WGET_CERT_STR, webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)
run_command += 'exec nohup {} {} run -p \$TASK_PORT:{} {} {} {} '.format(prefix, container_engine, task.container.interface_port, authstring, varsstring, binds)
@@ -367,7 +367,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
def _stop_task(self, task, **kwargs):
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# Handle container engine
container_engine = None
@@ -385,7 +385,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
else:
raise NotImplementedError('Container engine {} not supported'.format(container_engine))
- stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "{}"\''.format(computing_keys.private_key_file, computing_user, computing_host, internal_stop_command)
+ stop_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "{}"\''.format(computing_port, computing_keys.private_key_file, computing_user, computing_host, internal_stop_command)
out = os_shell(stop_command, capture=True)
if out.exit_code != 0:
if ('No such process' in out.stderr) or ('No such container' in out.stderr) or ('no container' in out.stderr) or ('missing' in out.stderr):
@@ -401,7 +401,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
def _get_task_log(self, task, **kwargs):
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# Handle container engine
container_engine = None
@@ -421,7 +421,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
raise NotImplementedError('Container engine {} not supported'.format(container_engine))
# Prepare full comand
- view_log_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "{}"\''.format(computing_keys.private_key_file, computing_user, computing_host, internal_view_log_command)
+ view_log_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "{}"\''.format(computing_port, computing_keys.private_key_file, computing_user, computing_host, internal_view_log_command)
# Execute
out = os_shell(view_log_command, capture=True)
@@ -437,7 +437,7 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag
logger.debug('Starting a remote task "{}"'.format(self.computing))
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# Get webapp conn string
from.utils import get_webapp_conn_string
@@ -524,7 +524,7 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag
else:
binds += ',{}:{}'.format(expanded_base_path, expanded_bind_path)
- run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_keys.private_key_file, computing_user, computing_host)
+ run_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(computing_port, computing_keys.private_key_file, computing_user, computing_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(CHECK_WGET_CERT_STR, 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, varsstring)
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)
@@ -568,7 +568,7 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag
def _stop_task(self, task, **kwargs):
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# Stop the task remotely
stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "scancel {}"\''.format(computing_keys.private_key_file, computing_user, computing_host, task.id)
@@ -584,10 +584,10 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag
def _get_task_log(self, task, **kwargs):
# Get credentials
- computing_user, computing_host, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
+ computing_user, computing_host, computing_port, computing_keys = get_ssh_access_mode_credentials(self.computing, task.user)
# View log remotely
- view_log_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat \$HOME/{}.log"\''.format(computing_keys.private_key_file, computing_user, computing_host, task.uuid)
+ view_log_command = 'ssh -p {} -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "cat \$HOME/{}.log"\''.format(computing_port, computing_keys.private_key_file, computing_user, computing_host, task.uuid)
out = os_shell(view_log_command, capture=True)
if out.exit_code != 0:
diff --git a/services/webapp/code/rosetta/core_app/utils.py b/services/webapp/code/rosetta/core_app/utils.py
index bef643ec17417f16c758ad55c89c5f27390c06fb..74c8897bf201b1241b465dfc4ac683e9ef490046 100644
--- a/services/webapp/code/rosetta/core_app/utils.py
+++ b/services/webapp/code/rosetta/core_app/utils.py
@@ -716,7 +716,9 @@ Listen '''+str(task.tcp_tunnel_port)+'''
def get_ssh_access_mode_credentials(computing, user):
+
from .models import KeyPair
+
# Get computing host
try:
computing_host = computing.conf.get('host')
@@ -724,7 +726,15 @@ def get_ssh_access_mode_credentials(computing, user):
computing_host = None
if not computing_host:
raise ValueError('No computing host?!')
-
+
+ # Get computing (SSH) port
+ try:
+ computing_port = computing.conf.get('port')
+ except AttributeError:
+ computing_port = 22
+ if not computing_host:
+ computing_port = 22
+
# Get computing user and keys
if computing.auth_mode == 'user_keys':
computing_user = user.profile.get_extra_conf('computing_user', computing)
@@ -739,7 +749,7 @@ def get_ssh_access_mode_credentials(computing, user):
raise NotImplementedError('Auth modes other than user_keys and platform_keys not supported.')
if not computing_user:
raise ValueError('No \'user\' parameter found for computing resource \'{}\' in its configuration'.format(computing.name))
- return (computing_user, computing_host, computing_keys)
+ return (computing_user, computing_host, computing_port, computing_keys)