[ARVADOS] updated: 1.1.2-56-g275aad6

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvtool.py | 9 +++++++--
 sdk/cwl/arvados_cwl/runner.py  | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

       via  275aad6e39b134bc11af3d6ef9d00e4abdddf2c8 (commit)
      from  e761c211063177d544c43e79abc8d184709ff79f (commit)

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commit 275aad6e39b134bc11af3d6ef9d00e4abdddf2c8
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Fri Jan 12 15:31:09 2018 -0500

    12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index b667dac..52f7d8a 100644
--- 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 28de7f3..dded8ad 100644
--- 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.")

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