Update cwltool refs #14510

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

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 4f8c0338b3f04fb9a51afaf21a6d1ebbc47bf992..6a91d6ff3c5076a28e06a685ed8c73bf45a84218 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -133,7 +133,7 @@ class ArvadosContainer(JobBase):
                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
-                generatemapper = NoFollowPathMapper([self.generatefiles], "", "",
+                generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
                                                     separateDirs=False)
 
                 sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 2e4ef55015157c4196c649797029b1e9912e00bb..87d6d1049a08d349d8d45b41b47a5fccb99f237c 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -67,7 +67,7 @@ class ArvadosJob(JobBase):
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
                 script_parameters["task.vwd"] = {}
-                generatemapper = VwdPathMapper([self.generatefiles], "", "",
+                generatemapper = VwdPathMapper(self.generatefiles["listing"], "", "",
                                                separateDirs=False)
 
                 with Perf(metrics, "createfiles %s" % self.name):

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index f731db9555e4f1c0e73b0f300fdf3349ddb89f42..3bd62532a8b80b3d3513107470b827ba6ca4d02c 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,7 +33,7 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20181201184214',
+          'cwltool==1.0.20181217162649',
           'schema-salad==3.0.20181129082112',
           'typing >= 3.6.4',
           'ruamel.yaml >=0.15.54, <=0.15.77',