8442: raise UnsupportedRequirement for unsupported features in the conformance

tests.  Bump cwltool dependency.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 171d92db74fedce90cc3d11f71d4b38959b3f1b3..af74808e1dcc60689d5ee48c8d0752d1cdd76bb4 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -31,7 +31,7 @@ from .arvcontainer import ArvadosContainer
 from .arvjob import ArvadosJob
 from .arvdocker import arv_docker_get_image
 
-from cwltool.process import shortname, get_feature, adjustFiles, adjustFileObjs, scandeps
+from cwltool.process import shortname, get_feature, adjustFiles, adjustFileObjs, scandeps, UnsupportedRequirement
 from arvados.api import OrderedJsonModel
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -477,7 +477,7 @@ class ArvCwlRunner(object):
         if kwargs.get("submit"):
             runnerjob = RunnerJob(self, tool, job_order, kwargs.get("enable_reuse"))
 
-        if not kwargs.get("submit") and "cwl_runner_job" not in kwargs:
+        if not kwargs.get("submit") and "cwl_runner_job" not in kwargs and not self.crunch2:
             # Create pipeline for local run
             self.pipeline = self.api.pipeline_instances().create(
                 body={
@@ -543,11 +543,13 @@ class ArvCwlRunner(object):
                     self.cond.wait(1)
 
                 events.close()
+            except UnsupportedRequirement:
+                raise
             except:
                 if sys.exc_info()[0] is KeyboardInterrupt:
                     logger.error("Interrupted, marking pipeline as failed")
                 else:
-                    logger.error("Caught unhandled exception, marking pipeline as failed.  Error was: %s", sys.exc_info()[0], exc_info=(sys.exc_info()[1] if self.debug else False))
+                    logger.error("Caught unhandled exception, marking pipeline as failed.  Error was: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
                 if self.pipeline:
                     self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
                                                          body={"state": "Failed"}).execute(num_retries=self.num_retries)

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 0cb885f59b4588759bb5490f9d739650b77941a0..17fe8cb5c46fccad7ab161d479219c90b5958586 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -4,6 +4,7 @@ from cwltool.process import get_feature, adjustFiles
 from .arvdocker import arv_docker_get_image
 from . import done
 from cwltool.errors import WorkflowException
+from cwltool.process import UnsupportedRequirement
 
 logger = logging.getLogger('arvados.cwl-runner')
 
@@ -42,6 +43,8 @@ class ArvadosContainer(object):
             }
 
         if self.generatefiles:
+            raise UnsupportedRequirement("Stdin redirection currently not suppported")
+
             vwd = arvados.collection.Collection()
             container_request["task.vwd"] = {}
             for t in self.generatefiles:
@@ -60,13 +63,12 @@ class ArvadosContainer(object):
         if self.environment:
             container_request["environment"].update(self.environment)
 
-        # TODO, not supported by crunchv2 yet
-        #if self.stdin:
-        #    container_request["task.stdin"] = self.pathmapper.mapper(self.stdin)[1]
+        if self.stdin:
+            raise UnsupportedRequirement("Stdin redirection currently not suppported")
 
         if self.stdout:
             mounts["stdout"] = {"kind": "file",
-                                "path": self.stdout}
+                                "path": "/var/spool/cwl/%s" % (self.stdout)}
 
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
         if not docker_req:

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 591bddefeef822b47319c79ddac195530725315d..b1ff7f34b82100126efe56a62cf1cefc690b19bc 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -30,7 +30,7 @@ setup(name='arvados-cwl-runner',
           'bin/arvados-cwl-runner'
       ],
       install_requires=[
-          'cwltool==1.0.20160519182434',
+          'cwltool==1.0.20160609160402',
           'arvados-python-client>=0.1.20160322001610'
       ],
       data_files=[