From: Ward Vandewege <ward@curii.com>
Date: Thu, 26 May 2022 16:05:00 +0000 (-0400)
Subject: Merge branch '19164-add-flags'
X-Git-Tag: 2.5.0~152
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/f3cb43d4be379703a965a1cb14cae5f5c855728f?hp=bed6d537db2e73cde17283d4f30117649ecce37f

Merge branch '19164-add-flags'

closes #19164

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>
---

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index f3e122e603..5094ea3bf1 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -37,6 +37,9 @@ from ._version import __version__
 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."""
 
@@ -320,7 +323,7 @@ class ArvadosContainer(JobBase):
         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
diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index fe078e3227..778af58ac3 100644
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -31,7 +31,7 @@ from arvados.keep import KeepClient
 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
@@ -630,6 +630,8 @@ The 'jobs' API is no longer supported.
         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.")
diff --git a/tools/salt-install/config_examples/multi_host/aws/pillars/nginx_passenger.sls b/tools/salt-install/config_examples/multi_host/aws/pillars/nginx_passenger.sls
index 2b6b96c3a4..c14fbd1f59 100644
--- a/tools/salt-install/config_examples/multi_host/aws/pillars/nginx_passenger.sls
+++ b/tools/salt-install/config_examples/multi_host/aws/pillars/nginx_passenger.sls
@@ -9,7 +9,7 @@
 {%- 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' %}
 
diff --git a/tools/salt-install/config_examples/single_host/multiple_hostnames/pillars/nginx_passenger.sls b/tools/salt-install/config_examples/single_host/multiple_hostnames/pillars/nginx_passenger.sls
index e51ec21eb9..dfddf3b623 100644
--- a/tools/salt-install/config_examples/single_host/multiple_hostnames/pillars/nginx_passenger.sls
+++ b/tools/salt-install/config_examples/single_host/multiple_hostnames/pillars/nginx_passenger.sls
@@ -9,7 +9,7 @@
 {%- 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' %}
 
diff --git a/tools/salt-install/config_examples/single_host/single_hostname/pillars/nginx_passenger.sls b/tools/salt-install/config_examples/single_host/single_hostname/pillars/nginx_passenger.sls
index 2b764eb2c2..21c1510de8 100644
--- a/tools/salt-install/config_examples/single_host/single_hostname/pillars/nginx_passenger.sls
+++ b/tools/salt-install/config_examples/single_host/single_hostname/pillars/nginx_passenger.sls
@@ -9,7 +9,7 @@
 {%- 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' %}