[ARVADOS] updated: 05f0eefbaa31ef430a6ac71e4b8eb066f195d9df

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py     |  4 ++++
 sdk/cwl/arvados_cwl/arvcontainer.py | 10 +++++++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

       via  05f0eefbaa31ef430a6ac71e4b8eb066f195d9df (commit)
      from  0d62edcb9d25bf4dcdb20d8872ea7b438e12fc59 (commit)

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commit 05f0eefbaa31ef430a6ac71e4b8eb066f195d9df
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Dec 9 15:55:35 2016 -0500

    10576: Set name default to name of workflow when running single command line
    tools from workflow records.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index dfcde34..25bddc0 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -344,6 +344,9 @@ class ArvCwlRunner(object):
         kwargs["on_error"] = "continue"
         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
 
+        if not kwargs["name"]:
+            del kwargs["name"]
+
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"
             kwargs["docker_outdir"] = "/var/spool/cwl"
@@ -360,6 +363,7 @@ class ArvCwlRunner(object):
         if kwargs.get("submit"):
             if self.work_api == "containers":
                 if tool.tool["class"] == "CommandLineTool":
+                    kwargs["runnerjob"] = tool.tool["id"]
                     runnerjob = tool.job(job_order,
                                          self.output_callback,
                                          **kwargs).next()
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 2c2aa7f..30e7017 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -37,7 +37,8 @@ class ArvadosContainer(object):
             "output_path": self.outdir,
             "cwd": self.outdir,
             "priority": 1,
-            "state": "Committed"
+            "state": "Committed",
+            "properties": {}
         }
         runtime_constraints = {}
         mounts = {
@@ -113,6 +114,13 @@ class ArvadosContainer(object):
         container_request["use_existing"] = kwargs.get("enable_reuse", True)
         container_request["scheduling_parameters"] = scheduling_parameters
 
+        if kwargs.get("runnerjob", "").startswith("arvwf:"):
+            wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
+            wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute()
+            if container_request["name"] == "main":
+                container_request["name"] = wfrecord["name"]
+            container_request["properties"]["template_uuid"] = wfuuid
+
         try:
             response = self.arvrunner.api.container_requests().create(
                 body=container_request

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