def run_cwltool(ctx, path, job_path, **kwds):
"""Translate planemo kwds to cwltool kwds and run cwltool main function."""
ensure_cwltool_available()
args = []
if ctx.verbose:
args.append("--verbose")
output_directory = kwds.get("output_directory", None)
if output_directory:
args.append("--outdir")
args.append(output_directory)
if kwds.get("no_container", False):
args.append("--no-container")
ensure_dependency_resolvers_conf_configured(ctx, kwds)
args.append("--beta-dependency-resolvers-configuration")
args.append(kwds["dependency_resolvers_config_file"])
if kwds.get("mulled_containers"):
args.append("--beta-use-biocontainers")
if kwds.get("non_strict_cwl", False):
args.append("--non-strict")
args.extend([path, job_path])
ctx.vlog("Calling cwltool with arguments %s" % args)
with tempfile.NamedTemporaryFile("w") as tmp_stdout, \
tempfile.NamedTemporaryFile("w") as tmp_stderr:
# cwltool passes sys.stderr to subprocess.Popen - ensure it has
# and actual fileno.
with real_io():
ret_code = main.main(
args,
stdout=tmp_stdout,
stderr=tmp_stderr,
)
tmp_stdout.flush()
tmp_stderr.flush()
with open(tmp_stderr.name, "r") as stderr_f:
log = stderr_f.read()
ctx.vlog("cwltool log output [%s]" % log)
with open(tmp_stdout.name, "r") as stdout_f:
try:
result = json.load(stdout_f)
except ValueError:
message = JSON_PARSE_ERROR_MESSAGE % (
open(tmp_stdout.name, "r").read(),
tmp_stdout.name,
log
)
error(message)
raise Exception(message)
if ret_code != 0:
return ErrorRunResponse("Error running cwltool", log=log)
outputs = result
return CwlToolRunResponse(
log,
outputs=outputs,
)
def run_cwltool(ctx, path, job_path, **kwds):
"""Translate planemo kwds to cwltool kwds and run cwltool main function."""
ensure_cwltool_available()
args = []
if ctx.verbose:
args.append("--verbose")
output_directory = kwds.get("output_directory", None)
if output_directory:
args.append("--outdir")
args.append(output_directory)
if kwds.get("no_container", False):
args.append("--no-container")
ensure_dependency_resolvers_conf_configured(ctx, kwds)
args.append("--beta-dependency-resolvers-configuration")
args.append(kwds["dependency_resolvers_config_file"])
if kwds.get("mulled_containers"):
args.append("--beta-use-biocontainers")
if kwds.get("non_strict_cwl", False):
args.append("--non-strict")
args.extend([path, job_path])
ctx.vlog("Calling cwltool with arguments %s" % args)
with tempfile.NamedTemporaryFile("w") as tmp_stdout, \
tempfile.NamedTemporaryFile("w") as tmp_stderr:
# cwltool passes sys.stderr to subprocess.Popen - ensure it has
# and actual fileno.
with real_io():
ret_code = main.main(
args,
stdout=tmp_stdout,
stderr=tmp_stderr,
)
tmp_stdout.flush()
tmp_stderr.flush()
with open(tmp_stderr.name, "r") as stderr_f:
log = stderr_f.read()
ctx.vlog("cwltool log output [%s]" % log)
with open(tmp_stdout.name, "r") as stdout_f:
try:
result = json.load(stdout_f)
except ValueError:
message = JSON_PARSE_ERROR_MESSAGE % (
open(tmp_stdout.name, "r").read(),
tmp_stdout.name,
log
)
error(message)
raise Exception(message)
if ret_code != 0:
return ErrorRunResponse("Error running cwltool", log=log)
outputs = result
return CwlToolRunResponse(
log,
outputs=outputs,
)
def local_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` in an auto-cleaned context."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
tool_data_table = _find_tool_data_table(tool_paths,
test_data_dir=test_data_dir,
**kwds)
galaxy_root = _find_galaxy_root(ctx, **kwds)
install_galaxy = kwds.get("install_galaxy", False)
if galaxy_root is not None:
if os.path.isdir(galaxy_root) and not os.listdir(galaxy_root):
os.rmdir(galaxy_root)
if os.path.isdir(galaxy_root) and install_galaxy:
raise Exception(
"%s is an existing non-empty directory, cannot install Galaxy again"
% galaxy_root)
# Duplicate block in docker variant above.
if kwds.get("mulled_containers", False) and not kwds.get("docker", False):
if ctx.get_option_source("docker") != OptionSource.cli:
kwds["docker"] = True
else:
raise Exception(
"Specified no docker and mulled containers together.")
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
install_env = {}
if kwds.get('galaxy_skip_client_build', True):
install_env['GALAXY_SKIP_CLIENT_BUILD'] = '1'
if galaxy_root is None:
galaxy_root = config_join("galaxy-dev")
if not os.path.isdir(galaxy_root):
_build_eggs_cache(ctx, install_env, kwds)
_install_galaxy(ctx, galaxy_root, install_env, kwds)
if parse_version(
kwds.get('galaxy_python_version')
or DEFAULT_PYTHON_VERSION) >= parse_version('3'):
# on python 3 we use gunicorn,
# which requires 'main' as server name
server_name = 'main'
else:
server_name = "planemo%d" % random.randint(0, 100000)
# Once we don't have to support earlier than 18.01 - try putting these files
# somewhere better than with Galaxy.
log_file = "%s.log" % server_name
pid_file = "%s.pid" % server_name
ensure_dependency_resolvers_conf_configured(
ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_config_file(config_directory, server_name, kwds)
_handle_job_metrics(config_directory, kwds)
file_path = kwds.get("file_path") or config_join("files")
_ensure_directory(file_path)
tool_dependency_dir = kwds.get("tool_dependency_dir") or config_join(
"deps")
_ensure_directory(tool_dependency_dir)
shed_tool_conf = kwds.get("shed_tool_conf") or config_join(
"shed_tools_conf.xml")
all_tool_paths = _all_tool_paths(runnables, **kwds)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_data_manager_config_file = config_join(
"shed_data_manager_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join(
"shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds)
database_location = config_join("galaxy.sqlite")
master_api_key = _get_master_api_key(kwds)
dependency_dir = os.path.join(config_directory, "deps")
preseeded_database = attempt_database_preseed(ctx, galaxy_root,
database_location,
**kwds)
_ensure_directory(shed_tool_path)
port = _get_port(kwds)
template_args = dict(
port=port,
host=kwds.get("host", "127.0.0.1"),
server_name=server_name,
temp_directory=config_directory,
shed_tool_path=shed_tool_path,
database_location=database_location,
tool_conf=tool_conf,
debug=kwds.get("debug", "true"),
id_secret=kwds.get("id_secret", "test_secret"),
log_level="DEBUG" if ctx.verbose else "INFO",
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
# Setup both galaxy_email and older test user [email protected]
# as admins for command_line, etc...
properties = _shared_galaxy_properties(config_directory,
kwds,
for_tests=for_tests)
properties.update(
dict(
server_name="main",
ftp_upload_dir_template="${ftp_upload_dir}",
ftp_upload_purge="False",
ftp_upload_dir=test_data_dir or os.path.abspath('.'),
ftp_upload_site="Test Data",
check_upload_content="False",
tool_dependency_dir=dependency_dir,
file_path=file_path,
new_file_path="${temp_directory}/tmp",
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
manage_dependency_relationships="False",
job_working_directory="${temp_directory}/job_working_directory",
template_cache_path="${temp_directory}/compiled_templates",
citation_cache_type="file",
citation_cache_data_dir="${temp_directory}/citations/data",
citation_cache_lock_dir="${temp_directory}/citations/lock",
database_auto_migrate="True",
enable_beta_tool_formats="True",
id_secret="${id_secret}",
log_level="${log_level}",
debug="${debug}",
watch_tools="auto",
default_job_shell="/bin/bash", # For conda dependency resolution
tool_data_table_config_path=tool_data_table,
integrated_tool_panel_config=(
"${temp_directory}/"
"integrated_tool_panel_conf.xml"),
migrated_tools_config=empty_tool_conf,
test_data_dir=test_data_dir, # TODO: make gx respect this
shed_data_manager_config_file=shed_data_manager_config_file,
))
_handle_container_resolution(ctx, kwds, properties)
write_file(config_join("logging.ini"),
_sub(LOGGING_TEMPLATE, template_args))
if not for_tests:
properties["database_connection"] = _database_connection(
database_location, **kwds)
_handle_kwd_overrides(properties, kwds)
# TODO: consider following property
# watch_tool = False
# datatypes_config_file = config/datatypes_conf.xml
# welcome_url = /static/welcome.html
# logo_url = /
# sanitize_all_html = True
# serve_xss_vulnerable_mimetypes = False
# track_jobs_in_database = None
# outputs_to_working_directory = False
# retry_job_output_collection = 0
env = _build_env_for_galaxy(properties, template_args)
env.update(install_env)
_build_test_env(properties, env)
env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf
# No need to download twice - would GALAXY_TEST_DATABASE_CONNECTION
# work?
if preseeded_database:
env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini")
env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
# Following are needed in 18.01 to prevent Galaxy from changing log and pid.
# https://github.com/galaxyproject/planemo/issues/788
env["GALAXY_LOG"] = log_file
env["GALAXY_PID"] = pid_file
web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
write_file(config_join("galaxy.ini"), web_config)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args)
# Write a new shed_tool_conf.xml if needed.
write_file(shed_tool_conf, shed_tool_conf_contents, force=False)
write_file(shed_data_manager_config_file,
SHED_DATA_MANAGER_CONF_TEMPLATE)
yield LocalGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
galaxy_root,
kwds,
)
def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` for Docker container."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
ensure_dependency_resolvers_conf_configured(
ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_metrics(config_directory, kwds)
shed_tool_conf = "config/shed_tool_conf.xml"
all_tool_paths = _all_tool_paths(runnables, **kwds)
tool_directories = set([]) # Things to mount...
for tool_path in all_tool_paths:
directory = os.path.dirname(os.path.normpath(tool_path))
if os.path.exists(directory):
tool_directories.add(directory)
# TODO: remap these.
tool_volumes = []
for tool_directory in tool_directories:
volume = simple_docker_volume(tool_directory)
tool_volumes.append(volume)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join(
"shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds)
port = _get_port(kwds)
properties = _shared_galaxy_properties(config_directory,
kwds,
for_tests=for_tests)
_handle_container_resolution(ctx, kwds, properties)
master_api_key = _get_master_api_key(kwds)
template_args = dict(
shed_tool_path=shed_tool_path,
tool_conf=tool_conf,
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
properties.update(
dict(
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
migrated_tools_config=empty_tool_conf,
))
server_name = "planemo%d" % random.randint(0, 100000)
# Value substitutions in Galaxy properties - for consistency with
# non-Dockerized version.
template_args = dict()
env = _build_env_for_galaxy(properties, template_args)
env["NONUSE"] = "nodejs,proftp,reports"
if ctx.verbose:
env["GALAXY_LOGGING"] = "full"
# TODO: setup FTP upload dir and disable FTP server in container.
_build_test_env(properties, env)
docker_target_kwds = docker_host_args(**kwds)
volumes = tool_volumes + [simple_docker_volume(config_directory)]
export_directory = kwds.get("export_directory", None)
if export_directory is not None:
volumes.append(DockerVolume("%s:/export:rw" % export_directory))
# TODO: Allow this to real Docker volumes and allow multiple.
extra_volume = kwds.get("docker_extra_volume")
if extra_volume:
volumes.append(simple_docker_volume(extra_volume))
yield DockerGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
docker_target_kwds=docker_target_kwds,
volumes=volumes,
export_directory=export_directory,
kwds=kwds,
)
def local_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` in an auto-cleaned context."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
tool_data_table = _find_tool_data_table(
tool_paths,
test_data_dir=test_data_dir,
**kwds
)
galaxy_root = _find_galaxy_root(ctx, **kwds)
install_galaxy = kwds.get("install_galaxy", False)
if galaxy_root is not None:
if os.path.isdir(galaxy_root) and not os.listdir(galaxy_root):
os.rmdir(galaxy_root)
if os.path.isdir(galaxy_root) and install_galaxy:
raise Exception("%s is an existing non-empty directory, cannot install Galaxy again" % galaxy_root)
# Duplicate block in docker variant above.
if kwds.get("mulled_containers", False) and not kwds.get("docker", False):
if ctx.get_option_source("docker") != OptionSource.cli:
kwds["docker"] = True
else:
raise Exception("Specified no docker and mulled containers together.")
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
install_env = {}
if kwds.get('galaxy_skip_client_build', True):
install_env['GALAXY_SKIP_CLIENT_BUILD'] = '1'
if galaxy_root is None:
galaxy_root = config_join("galaxy-dev")
if not os.path.isdir(galaxy_root):
_build_eggs_cache(ctx, install_env, kwds)
_install_galaxy(ctx, galaxy_root, install_env, kwds)
if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'):
# on python 3 we use gunicorn,
# which requires 'main' as server name
server_name = 'main'
else:
server_name = "planemo%d" % random.randint(0, 100000)
# Once we don't have to support earlier than 18.01 - try putting these files
# somewhere better than with Galaxy.
log_file = "%s.log" % server_name
pid_file = "%s.pid" % server_name
ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_config_file(config_directory, server_name, kwds)
_handle_job_metrics(config_directory, kwds)
file_path = kwds.get("file_path") or config_join("files")
_ensure_directory(file_path)
tool_dependency_dir = kwds.get("tool_dependency_dir") or config_join("deps")
_ensure_directory(tool_dependency_dir)
shed_tool_conf = kwds.get("shed_tool_conf") or config_join("shed_tools_conf.xml")
all_tool_paths = _all_tool_paths(runnables, **kwds)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_data_manager_config_file = config_join("shed_data_manager_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds
)
database_location = config_join("galaxy.sqlite")
master_api_key = _get_master_api_key(kwds)
dependency_dir = os.path.join(config_directory, "deps")
preseeded_database = attempt_database_preseed(
ctx,
galaxy_root,
database_location,
**kwds
)
_ensure_directory(shed_tool_path)
port = _get_port(kwds)
template_args = dict(
port=port,
host=kwds.get("host", "127.0.0.1"),
server_name=server_name,
temp_directory=config_directory,
shed_tool_path=shed_tool_path,
database_location=database_location,
tool_conf=tool_conf,
debug=kwds.get("debug", "true"),
id_secret=kwds.get("id_secret", "test_secret"),
log_level="DEBUG" if ctx.verbose else "INFO",
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
# Setup both galaxy_email and older test user [email protected]
# as admins for command_line, etc...
properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
properties.update(dict(
server_name="main",
ftp_upload_dir_template="${ftp_upload_dir}",
ftp_upload_purge="False",
ftp_upload_dir=test_data_dir or os.path.abspath('.'),
ftp_upload_site="Test Data",
check_upload_content="False",
tool_dependency_dir=dependency_dir,
file_path=file_path,
new_file_path="${temp_directory}/tmp",
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
manage_dependency_relationships="False",
job_working_directory="${temp_directory}/job_working_directory",
template_cache_path="${temp_directory}/compiled_templates",
citation_cache_type="file",
citation_cache_data_dir="${temp_directory}/citations/data",
citation_cache_lock_dir="${temp_directory}/citations/lock",
database_auto_migrate="True",
enable_beta_tool_formats="True",
id_secret="${id_secret}",
log_level="${log_level}",
debug="${debug}",
watch_tools="auto",
default_job_shell="/bin/bash", # For conda dependency resolution
tool_data_table_config_path=tool_data_table,
integrated_tool_panel_config=("${temp_directory}/"
"integrated_tool_panel_conf.xml"),
# Use in-memory database for kombu to avoid database contention
# during tests.
amqp_internal_connection="sqlalchemy+sqlite://",
migrated_tools_config=empty_tool_conf,
test_data_dir=test_data_dir, # TODO: make gx respect this
shed_data_manager_config_file=shed_data_manager_config_file,
))
_handle_container_resolution(ctx, kwds, properties)
write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))
if not for_tests:
properties["database_connection"] = _database_connection(database_location, **kwds)
_handle_kwd_overrides(properties, kwds)
# TODO: consider following property
# watch_tool = False
# datatypes_config_file = config/datatypes_conf.xml
# welcome_url = /static/welcome.html
# logo_url = /
# sanitize_all_html = True
# serve_xss_vulnerable_mimetypes = False
# track_jobs_in_database = None
# outputs_to_working_directory = False
# retry_job_output_collection = 0
env = _build_env_for_galaxy(properties, template_args)
env.update(install_env)
_build_test_env(properties, env)
env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf
# No need to download twice - would GALAXY_TEST_DATABASE_CONNECTION
# work?
if preseeded_database:
env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini")
env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
# Following are needed in 18.01 to prevent Galaxy from changing log and pid.
# https://github.com/galaxyproject/planemo/issues/788
env["GALAXY_LOG"] = log_file
env["GALAXY_PID"] = pid_file
web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
write_file(config_join("galaxy.ini"), web_config)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args)
# Write a new shed_tool_conf.xml if needed.
write_file(shed_tool_conf, shed_tool_conf_contents, force=False)
write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE)
yield LocalGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
galaxy_root,
kwds,
)
def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
"""Set up a ``GalaxyConfig`` for Docker container."""
tool_paths = [r.path for r in runnables if r.has_tools]
test_data_dir = _find_test_data(tool_paths, **kwds)
with _config_directory(ctx, **kwds) as config_directory:
def config_join(*args):
return os.path.join(config_directory, *args)
ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
_handle_job_metrics(config_directory, kwds)
shed_tool_conf = "config/shed_tool_conf.xml"
all_tool_paths = _all_tool_paths(runnables, **kwds)
tool_directories = set([]) # Things to mount...
for tool_path in all_tool_paths:
directory = os.path.dirname(os.path.normpath(tool_path))
if os.path.exists(directory):
tool_directories.add(directory)
# TODO: remap these.
tool_volumes = []
for tool_directory in tool_directories:
volume = simple_docker_volume(tool_directory)
tool_volumes.append(volume)
empty_tool_conf = config_join("empty_tool_conf.xml")
tool_conf = config_join("tool_conf.xml")
shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
_ensure_directory(shed_tool_path)
sheds_config_path = _configure_sheds_config_file(
ctx, config_directory, **kwds
)
port = _get_port(kwds)
properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
_handle_container_resolution(ctx, kwds, properties)
master_api_key = _get_master_api_key(kwds)
template_args = dict(
shed_tool_path=shed_tool_path,
tool_conf=tool_conf,
)
tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
_write_tool_conf(ctx, all_tool_paths, tool_conf)
write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
properties.update(dict(
tool_config_file=tool_config_file,
tool_sheds_config_file=sheds_config_path,
migrated_tools_config=empty_tool_conf,
))
server_name = "planemo%d" % random.randint(0, 100000)
# Value substitutions in Galaxy properties - for consistency with
# non-Dockerized version.
template_args = dict(
)
env = _build_env_for_galaxy(properties, template_args)
env["NONUSE"] = "nodejs,proftp,reports"
if ctx.verbose:
env["GALAXY_LOGGING"] = "full"
# TODO: setup FTP upload dir and disable FTP server in container.
_build_test_env(properties, env)
docker_target_kwds = docker_host_args(**kwds)
volumes = tool_volumes + [simple_docker_volume(config_directory)]
export_directory = kwds.get("export_directory", None)
if export_directory is not None:
volumes.append(DockerVolume("%s:/export:rw" % export_directory))
# TODO: Allow this to real Docker volumes and allow multiple.
extra_volume = kwds.get("docker_extra_volume")
if extra_volume:
volumes.append(simple_docker_volume(extra_volume))
yield DockerGalaxyConfig(
ctx,
config_directory,
env,
test_data_dir,
port,
server_name,
master_api_key,
runnables,
docker_target_kwds=docker_target_kwds,
volumes=volumes,
export_directory=export_directory,
kwds=kwds,
)
