15028: Bump cwltool to accept v1.1

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index f8069a3cb38e96dc0e416f86cea7e2558152c8e4..1f8edb70dbe6d0a85df7e090f645efbe8417e3af 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -219,12 +219,15 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 def add_arv_hints():
     cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
-    res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml')
-    res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml')
-    customschema = res.read()
-    use_custom_schema("v1.0", "http://arvados.org/cwl", customschema)
-    use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema)
-    res.close()
+    res10 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.0.yml')
+    res11 = pkg_resources.resource_stream(__name__, 'arv-cwl-schema-v1.1.yml')
+    customschema10 = res10.read()
+    customschema11 = res11.read()
+    use_custom_schema("v1.0", "http://arvados.org/cwl", customschema10)
+    use_custom_schema("v1.1.0-dev1", "http://arvados.org/cwl", customschema11)
+    use_custom_schema("v1.1", "http://arvados.org/cwl", customschema11)
+    res10.close()
+    res11.close()
     cwltool.process.supportedProcessRequirements.extend([
         "http://arvados.org/cwl#RunInSingleContainer",
         "http://arvados.org/cwl#OutputDirType",

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 9ff06fa4aa23b3f9f661566f24ffa56db6b0d47d..d2fd0088cadc0bba00009a76b98136908c3158b1 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -534,7 +534,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                 raise WorkflowException(
                     "`cwl:requirements` in the input object is not part of CWL "
                     "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
-                    "can set the cwlVersion to v1.1.0-dev1 or greater and re-run with "
+                    "can set the cwlVersion to v1.1 or greater and re-run with "
                     "--enable-dev.")
             job_reqs = job_order_object["https://w3id.org/cwl/cwl#requirements"]
             for req in job_reqs:

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index def79ece40b95c2dc3b0c4429ee9ae74eeb11f2f..31195fd372874bcfc2dce1b1846d8e5cec552362 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==1.0.20190503175737',
+          'cwltool==1.0.20190525125941',
           'schema-salad==4.1.20190305210046',
           'typing >= 3.6.4',
           'ruamel.yaml >=0.15.54, <=0.15.77',