From 511e36db2a5ed0380752d15e9c60364483d0e9f0 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curoverse.com>
Date: Mon, 19 Sep 2016 11:35:17 -0400
Subject: [PATCH] 10088: Bump cwltool dependency for another bugfix to
 scandeps.

---
 sdk/cwl/arvados_cwl/runner.py | 14 +++++++++++++-
 sdk/cwl/setup.py              |  2 +-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 570675bc4e..155c6a0503 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -25,6 +25,18 @@ cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 
 def upload_dependencies(arvrunner, name, document_loader,
                         workflowobj, uri, loadref_run):
+    """Upload the dependencies of the workflowobj document to Keep.
+
+    Returns a pathmapper object mapping local paths to keep references.  Also
+    does an in-place update of references in "workflowobj".
+
+    Use scandeps to find $import, $include, $schemas, run, File and Directory
+    fields that represent external references.
+
+    If workflowobj has an "id" field, this will reload the document to ensure
+    it is scanning the raw document prior to preprocessing.
+    """
+
     loaded = set()
     def loadref(b, u):
         joined = urlparse.urljoin(b, u)
@@ -54,7 +66,7 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     sc = scandeps(uri, scanobj,
                   loadref_fields,
-                  set(("$include", "$schemas")),
+                  set(("$include", "$schemas", "location")),
                   loadref)
 
     files = []
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 6922b90e17..fef9deca96 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
       # Make sure to update arvados/build/run-build-packages.sh as well
       # when updating the cwltool version pin.
       install_requires=[
-          'cwltool==1.0.20160918012352',
+          'cwltool==1.0.20160919152321',
           'arvados-python-client>=0.1.20160826210445'
       ],
       data_files=[
-- 
2.30.2