16482: Merge branch 'master' into 16482-bump-cwltool-version

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 3dd04040ab5d728b5eac21bab601225135ce810e..adbce90d8d4215329d46eebbe06be66d1f71de43 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -23,7 +23,7 @@ import cwltool.workflow
 import cwltool.process
 import cwltool.argparser
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing
+from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
 
 import arvados
 import arvados.config
@@ -220,8 +220,8 @@ def add_arv_hints():
     cwltool.command_line_tool.ACCEPTLIST_RE = cwltool.command_line_tool.ACCEPTLIST_EN_RELAXED_RE
     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()
+    customschema10 = res10.read().decode('utf-8')
+    customschema11 = res11.read().decode('utf-8')
     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)

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 99d4c4e9a10a883abc54ce0fe1cbc476af7c7692..ec91eea6aa807eaea1f37012b0fa1f04d21a1f1f 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -42,7 +42,7 @@ from .context import ArvLoadingContext, ArvRuntimeContext
 from ._version import __version__
 
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing, visit_class
+from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing, visit_class
 from cwltool.command_line_tool import compute_checksums
 from cwltool.load_tool import load_tool
 

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 72969de94c767dd901654f4d569047df347b458e..40ee679857f4429b0e32cf491339e144695489de 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -39,8 +39,8 @@ setup(name='arvados-cwl-runner',
       # file to determine what version of cwltool and schema-salad to
       # build.
       install_requires=[
-          'cwltool==3.0.20200324120055',
-          'schema-salad==5.0.20200302192450',
+          'cwltool==3.0.20200530110633',
+          'schema-salad==6.0.20200601095207',
           'arvados-python-client{}'.format(pysdk_dep),
           'setuptools',
           'ciso8601 >= 2.0.0'