14198: Update cwltool and schema-salad

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

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 72ef8fd4f4b5beb3521be5e729964d8464968906..e80c06f00d283ef503eb9e1d171636a697ff99cd 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -132,7 +132,8 @@ class ArvadosWorkflow(Workflow):
 
     def job(self, joborder, output_callback, runtimeContext):
 
 
     def job(self, joborder, output_callback, runtimeContext):
 

-        check_cluster_target(self, self._init_job(joborder, runtimeContext), runtimeContext)
+        builder = self._init_job(joborder, runtimeContext)
+        check_cluster_target(self, builder, runtimeContext)

 
         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
         if not req:
 
         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
         if not req:


@@ -161,11 +162,6 @@ class ArvadosWorkflow(Workflow):
 
                 packed = pack(document_loader, workflowobj, uri, self.metadata)
 
 
                 packed = pack(document_loader, workflowobj, uri, self.metadata)
 

-                builder = Builder(joborder,
-                                  requirements=workflowobj["requirements"],
-                                  hints=workflowobj["hints"],
-                                  resources={})
-

                 def visit(item):
                     for t in ("hints", "requirements"):
                         if t not in item:
                 def visit(item):
                     for t in ("hints", "requirements"):
                         if t not in item:


@@ -205,11 +201,6 @@ class ArvadosWorkflow(Workflow):
 
 
         if self.dynamic_resource_req:
 
 
         if self.dynamic_resource_req:

-            builder = Builder(joborder,
-                              requirements=self.requirements,
-                              hints=self.hints,
-                              resources={})
-

             # Evaluate dynamic resource requirements using current builder
             rs = copy.copy(self.static_resource_req)
             for dyn_rs in self.dynamic_resource_req:
             # Evaluate dynamic resource requirements using current builder
             rs = copy.copy(self.static_resource_req)
             for dyn_rs in self.dynamic_resource_req:

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 2b7b31b9f3f4b4070cbd14d986ffe87259989200..91a03ed86559e184c4a8dfc927dde28db39c21f4 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -33,8 +33,8 @@ 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=[
       # 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==1.0.20180806194258',
-          'schema-salad==2.7.20180719125426',
+          'cwltool==1.0.20181114114354',
+          'schema-salad==2.7.20181017120439',

           'typing >= 3.6.4',
           # Need to limit ruamel.yaml version to 0.15.26 because of bug
           # https://bitbucket.org/ruamel/yaml/issues/227/regression-parsing-flow-mapping
           'typing >= 3.6.4',
           # Need to limit ruamel.yaml version to 0.15.26 because of bug
           # https://bitbucket.org/ruamel/yaml/issues/227/regression-parsing-flow-mapping