[ARVADOS] updated: 7a194de4a1ea6638c2500fe89979d3610f37e1f2

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py |  4 ++--
 sdk/cwl/arvados_cwl/runner.py      | 13 +++++++++++--
 2 files changed, 13 insertions(+), 4 deletions(-)

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commit 7a194de4a1ea6638c2500fe89979d3610f37e1f2
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Sep 27 16:30:27 2016 -0400

    10129: Rename del_listing to trim_listing and add docstring about what it is
    for.

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 3bb0a34..f4ce446 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -11,7 +11,7 @@ from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
 
 import ruamel.yaml as yaml
 
-from .runner import upload_docker, upload_dependencies, del_listing
+from .runner import upload_docker, upload_dependencies, trim_listing
 from .arvtool import ArvadosCommandTool
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -23,7 +23,7 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
 
     packed = pack(document_loader, workflowobj, uri, tool.metadata)
 
-    adjustDirObjs(job_order, del_listing)
+    adjustDirObjs(job_order, trim_listing)
 
     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
     for inp in main["inputs"]:
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index aafe7c3..07f85bb 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -23,7 +23,16 @@ logger = logging.getLogger('arvados.cwl-runner')
 
 cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 
-def del_listing(obj):
+def trim_listing(obj):
+    """Remove 'listing' field from Directory objects that are keep references.
+
+    When Directory objects represent Keep references, it redundant and
+    potentially very expensive to pass fully enumerated Directory objects
+    between instances of cwl-runner (e.g. a submitting a job, or using the
+    RunInSingleContainer feature), so delete the 'listing' field when it is
+    safe to do so.
+    """
+
     if obj.get("location", "").startswith("keep:") and "listing" in obj:
         del obj["listing"]
     if obj.get("location", "").startswith("_:"):
@@ -135,7 +144,7 @@ class Runner(object):
                                         self.job_order.get("id", "#"),
                                         False)
 
-        adjustDirObjs(self.job_order, del_listing)
+        adjustDirObjs(self.job_order, trim_listing)
 
         if "id" in self.job_order:
             del self.job_order["id"]

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