Merge branch 'patch-1' of https://github.com/mr-c/arvados into mr-c-patch-1

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 4c983858020ba52a8610c3b37e274e2d3643e487..6f2255b3f8b18f104a00fc2d4982171c51dbb0da 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
@@ -36,7 +36,7 @@ from .perf import Perf
 from ._version import __version__
 from .executor import ArvCwlExecutor
 
-# These arn't used directly in this file but
+# These aren't used directly in this file but
 # other code expects to import them from here
 from .arvcontainer import ArvadosContainer
 from .arvtool import ArvadosCommandTool
@@ -176,7 +176,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     parser.add_argument("--enable-dev", action="store_true",
                         help="Enable loading and running development versions "
-                             "of CWL spec.", default=False)
+                             "of the CWL standards.", default=False)
     parser.add_argument('--storage-classes', default="default",
                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 
@@ -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)
@@ -336,4 +336,5 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
                              logger_handler=arvados.log_handler,
                              custom_schema_callback=add_arv_hints,
                              loadingContext=executor.loadingContext,
-                             runtimeContext=executor.runtimeContext)
+                             runtimeContext=executor.runtimeContext,
+                             input_required=not (arvargs.create_workflow or arvargs.update_workflow))