12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index b667dac1ca5cec6f272c390be8fcd17e1628764c..52f7d8a235977f9fd7562d26caf4bcb61b887531 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -36,8 +36,13 @@ class ArvadosCommandTool(CommandLineTool):
 
     def job(self, joborder, output_callback, **kwargs):
         if self.work_api == "containers":
-            kwargs["outdir"] = "/var/spool/cwl"
-            kwargs["docker_outdir"] = "/var/spool/cwl"
+            dockerReq, is_req = self.get_requirement("DockerRequirement")
+            if dockerReq.get("dockerOutputDirectory") and dockerReq.get("dockerOutputDirectory").startswith('/'):
+                kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
+                kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
+            else:
+                kwargs["outdir"] = "/var/spool/cwl"
+                kwargs["docker_outdir"] = "/var/spool/cwl"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
             kwargs["docker_outdir"] = "$(task.outdir)"

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 2ca63cfe5048a62f0a1853e2aca06be865ea1fd4..fb5d036e941969df71b6a3062d09bb87d4328739 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -161,7 +161,7 @@ def upload_docker(arvrunner, tool):
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
-            if docker_req.get("dockerOutputDirectory"):
+            if docker_req.get("dockerOutputDirectory") and arvrunner.work_api != "containers":
                 # TODO: can be supported by containers API, but not jobs API.
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")