Added supprt for setting environment variables for containers. (fc8f3bc7) · Commits · ExaCT / Rosetta

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

+48 −6

Original line number	Diff line number	Diff line
		from .models import TaskStatuses, KeyPair, Task, Storage
		from .utils import os_shell, get_ssh_access_mode_credentials
		from .utils import os_shell, get_ssh_access_mode_credentials, sanitize_container_env_vars
		from .exceptions import ErrorMessage, ConsistencyException
		from django.conf import settings

		@@ -107,6 +107,15 @@ class InternalStandaloneComputingManager(StandaloneComputingManager):
		if not task.requires_proxy and task.password:
		run_command += ' -eAUTH_PASS={} '.format(task.password)

		# Env vars if any
		if task.container.env_vars:

		# Sanitize again just in case the DB got somehow compromised:
		env_vars = sanitize_container_env_vars(task.container.env_vars)

		for env_var in env_vars:
		run_command += ' -e{}={} '.format(env_var, env_vars[env_var])

		# User data volume
		#run_command += ' -v {}/user-{}:/data'.format(settings.LOCAL_USER_DATA_DIR, task.user.id)

		@@ -204,7 +213,18 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
		# Set pass if any
		authstring = ''
		if not task.requires_proxy_auth and task.password:
		authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.password)
		authstring = ' && export SINGULARITYENV_AUTH_PASS={} '.format(task.password)

		# Env vars if any
		if task.container.env_vars:
		varsstring = ''
		# Sanitize again just in case the DB got somehow compromised:
		env_vars = sanitize_container_env_vars(task.container.env_vars)

		for env_var in env_vars:
		varsstring += ' && export SINGULARITYENV_{}={} '.format(env_var, env_vars[env_var])
		else:
		varsstring = ''

		# Handle storages (binds)
		binds = ''
		@@ -241,7 +261,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(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(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)
		run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT {} {} &&'.format(authstring, varsstring)
		run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home --containall --cleanenv '.format(binds, task.uuid, task.uuid)

		# Container part
		@@ -255,6 +275,17 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
		if not task.requires_proxy_auth and task.password:
		authstring = ' -e AUTH_PASS={} '.format(task.password)

		# Env vars if any
		if task.container.env_vars:
		varsstring = ''
		# Sanitize again just in case the DB got somehow compromised:
		env_vars = sanitize_container_env_vars(task.container.env_vars)

		for env_var in env_vars:
		varsstring += ' -e {}={} '.format(env_var, env_vars[env_var])
		else:
		varsstring = ''

		# Handle storages (binds)
		binds = ''
		storages = Storage.objects.filter(computing=self.computing)
		@@ -293,7 +324,7 @@ class SSHStandaloneComputingManager(StandaloneComputingManager, SSHComputingMana
		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(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(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)
		run_command += '{} {} run -p \$TASK_PORT:{} {} {} '.format(prefix, container_engine, task.container.interface_port, authstring, binds)
		run_command += '{} {} run -p \$TASK_PORT:{} {} {} {} '.format(prefix, container_engine, task.container.interface_port, authstring, varsstring, binds)
		if container_engine == 'podman':
		run_command += '--network=private --uts=private '
		#run_command += '-d -t {}/{}:{}'.format(task.container.registry, task.container.image_name, task.container.image_tag)
		@@ -435,7 +466,18 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag
		# Set pass if any
		authstring = ''
		if not task.requires_proxy_auth and task.password:
		authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.password)
		authstring = ' && export SINGULARITYENV_AUTH_PASS={} '.format(task.password)

		# Env vars if any
		if task.container.env_vars:
		varsstring = ''
		# Sanitize again just in case the DB got somehow compromised:
		env_vars = sanitize_container_env_vars(task.container.env_vars)

		for env_var in env_vars:
		varsstring += ' && export SINGULARITYENV_{}={} '.format(env_var, env_vars[env_var])
		else:
		varsstring = ''

		# Handle storages (binds)
		binds = ''
		@@ -471,7 +513,7 @@ class SlurmSSHClusterComputingManager(ClusterComputingManager, SSHComputingManag

		run_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(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(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 += '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)
		run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home --containall --cleanenv '.format(binds, task.uuid, task.uuid)

services/webapp/code/rosetta/core_app/migrations/0031_container_env_vars.py

0 → 100644

+25 −0

Original line number	Diff line number	Diff line
		# Generated by Django 2.2.1 on 2022-01-16 18:40

		from django.conf import settings
		from django.db import migrations

		# Load database-dependent JSON field
		if 'sqlite' in settings.DATABASES['default']['ENGINE']:
		from rosetta.core_app.fields import JSONField
		else:
		from django.contrib.postgres.fields import JSONField


		class Migration(migrations.Migration):

		dependencies = [
		('core_app', '0030_auto_20211218_2355'),
		]

		operations = [
		migrations.AddField(
		model_name='container',
		name='env_vars',
		field=JSONField(blank=True, null=True, verbose_name='Container env vars'),
		),
		]

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

+3 −0

Original line number	Diff line number	Diff line
		@@ -141,6 +141,9 @@ class Container(models.Model):
		supports_interface_auth = models.BooleanField('Supports interface auth', default=False) # AUTH_USER / AUTH_PASS
		interface_auth_user = models.CharField('Interface auth fixed user if any', max_length=36, blank=True, null=True)

		# Env vars for some container control
		env_vars = JSONField('Container env vars', blank=True, null=True)

		class Meta:
		ordering = ['name']

services/webapp/code/rosetta/core_app/templates/add_software.html

+7 −0

Original line number	Diff line number	Diff line
		@@ -135,6 +135,13 @@
		</td>
		</tr>

		<tr>
		<td><b>Environment variables</b></td>
		<td>
		<textarea name="container_env_vars" rows="2" cols="22" placeholder='JSON format: {"VAR"="VALUE"}'></textarea>
		</td>
		</tr>

		</table>
		</div>

services/webapp/code/rosetta/core_app/templates/components/container.html

+6 −0

Original line number	Diff line number	Diff line
		@@ -104,6 +104,12 @@
		{% endif %} </td>
		</tr>

		{% if container.env_vars %}
		<tr>
		<td><b>Env vars</b></td>
		<td><pre>{{container.env_vars}}</pre></td>
		</tr>
		{% endif %}

		{% if container.user %}
		<tr>