logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
+def cleanup_name_for_collection(name):
+ return name.replace("/", " ")
+
class ArvadosContainer(JobBase):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
if runtimeContext.submit_runner_cluster:
extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
- container_request["output_name"] = "Output from step %s" % (self.name)
+ container_request["output_name"] = cleanup_name_for_collection("Output from step %s" % (self.name))
container_request["output_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["secret_mounts"] = secret_mounts
from arvados.errors import ApiError
import arvados_cwl.util
-from .arvcontainer import RunnerContainer
+from .arvcontainer import RunnerContainer, cleanup_name_for_collection
from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
if not self.output_name:
self.output_name = "Output from workflow %s" % runtimeContext.name
+ self.output_name = cleanup_name_for_collection(self.output_name)
+
if self.work_api == "containers":
if self.ignore_docker_for_reuse:
raise Exception("--ignore-docker-for-reuse not supported with containers API.")
{%- set passenger_mod = '/usr/lib64/nginx/modules/ngx_http_passenger_module.so'
if grains.osfinger in ('CentOS Linux-7',) else
'/usr/lib/nginx/modules/ngx_http_passenger_module.so' %}
-{%- set passenger_ruby = '/usr/local/rvm/rubies/ruby-2.7.2/bin/ruby'
+{%- set passenger_ruby = '/usr/local/rvm/wrappers/default/ruby'
if grains.osfinger in ('CentOS Linux-7', 'Ubuntu-18.04', 'Debian-10') else
'/usr/bin/ruby' %}
{%- set passenger_mod = '/usr/lib64/nginx/modules/ngx_http_passenger_module.so'
if grains.osfinger in ('CentOS Linux-7',) else
'/usr/lib/nginx/modules/ngx_http_passenger_module.so' %}
-{%- set passenger_ruby = '/usr/local/rvm/rubies/ruby-2.7.2/bin/ruby'
+{%- set passenger_ruby = '/usr/local/rvm/wrappers/default/ruby'
if grains.osfinger in ('CentOS Linux-7', 'Ubuntu-18.04', 'Debian-10') else
'/usr/bin/ruby' %}
{%- set passenger_mod = '/usr/lib64/nginx/modules/ngx_http_passenger_module.so'
if grains.osfinger in ('CentOS Linux-7',) else
'/usr/lib/nginx/modules/ngx_http_passenger_module.so' %}
-{%- set passenger_ruby = '/usr/local/rvm/rubies/ruby-2.7.2/bin/ruby'
+{%- set passenger_ruby = '/usr/local/rvm/wrappers/default/ruby'
if grains.osfinger in ('CentOS Linux-7', 'Ubuntu-18.04', 'Debian-10') else
'/usr/bin/ruby' %}