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 088609fd79163259bc8fc4389c43d93a5bb0d777..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
@@ -96,10 +96,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-reuse", action="store_true",
                         default=True, dest="enable_reuse",
-                        help="Enable job or container reuse (default)")
+                        help="Enable container reuse (default)")
     exgroup.add_argument("--disable-reuse", action="store_false",
                         default=True, dest="enable_reuse",
-                        help="Disable job or container reuse")
+                        help="Disable container reuse")
 
     parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow containers, if not provided, will go to home project.")
     parser.add_argument("--output-name", help="Name to use for collection that stores the final output.", default=None)
@@ -154,10 +154,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--submit-request-uuid",
                          default=None,
-                         help="Update and commit to supplied container request instead of creating a new one (containers API only).",
+                         help="Update and commit to supplied container request instead of creating a new one.",
                          metavar="UUID")
     exgroup.add_argument("--submit-runner-cluster",
-                         help="Submit workflow runner to a remote cluster (containers API only)",
+                         help="Submit workflow runner to a remote cluster",
                          default=None,
                          metavar="CLUSTER_ID")
 
@@ -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.")
 
@@ -185,7 +185,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=0)
 
     parser.add_argument("--priority", type=int,
-                        help="Workflow priority (range 1..1000, higher has precedence over lower, containers api only)",
+                        help="Workflow priority (range 1..1000, higher has precedence over lower)",
                         default=DEFAULT_PRIORITY)
 
     parser.add_argument("--disable-validate", dest="do_validate",
@@ -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)
@@ -297,7 +297,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
         return 1
 
     # Note that unless in debug mode, some stack traces related to user
-    # workflow errors may be suppressed. See ArvadosJob.done().
+    # workflow errors may be suppressed.
     if arvargs.debug:
         logger.setLevel(logging.DEBUG)
         logging.getLogger('arvados').setLevel(logging.DEBUG)
@@ -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))