17417: Merge branch 'main' into 17417-add-arm64

[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 f3629b68972650e90f06e772404b8c5b29a46f94..71ef742e314633bab08b0f493f766227b19b7849 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: Apache-2.0
@@ -22,6 +22,7 @@ import cwltool.main
 import cwltool.workflow
 import cwltool.process
 import cwltool.argparser
+from cwltool.errors import WorkflowException
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
 from cwltool.utils import adjustFileObjs, adjustDirObjs, get_listing
 
@@ -178,7 +179,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Enable loading and running development versions "
                              "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.")
+                        help="Specify comma separated list of storage classes to be used when saving final workflow output to Keep.")
+    parser.add_argument('--intermediate-storage-classes', default="default",
+                        help="Specify comma separated list of storage classes to be used when saving intermediate workflow output to Keep.")
 
     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
                         help="If N > 0, intermediate output collections will be trashed N seconds after creation.  Default is 0 (don't trash).",
@@ -192,12 +195,16 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         action="store_false", default=True,
                         help=argparse.SUPPRESS)
 
+    parser.add_argument("--disable-color", dest="enable_color",
+                        action="store_false", default=True,
+                        help=argparse.SUPPRESS)
+
     parser.add_argument("--disable-js-validation",
                         action="store_true", default=False,
                         help=argparse.SUPPRESS)
 
     parser.add_argument("--thread-count", type=int,
-                        default=1, help="Number of threads to use for job submit and output collection.")
+                        default=0, help="Number of threads to use for job submit and output collection.")
 
     parser.add_argument("--http-timeout", type=int,
                         default=5*60, dest="http_timeout", help="API request timeout in seconds. Default is 300 seconds (5 minutes).")
@@ -241,7 +248,9 @@ def add_arv_hints():
         "http://commonwl.org/cwltool#LoadListingRequirement",
         "http://arvados.org/cwl#IntermediateOutput",
         "http://arvados.org/cwl#ReuseRequirement",
-        "http://arvados.org/cwl#ClusterTarget"
+        "http://arvados.org/cwl#ClusterTarget",
+        "http://arvados.org/cwl#OutputStorageClass",
+        "http://arvados.org/cwl#ProcessProperties"
     ])
 
 def exit_signal_handler(sigcode, frame):
@@ -255,10 +264,6 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
     job_order_object = None
     arvargs = parser.parse_args(args)
 
-    if len(arvargs.storage_classes.strip().split(',')) > 1:
-        logger.error(str(u"Multiple storage classes are not supported currently."))
-        return 1
-
     arvargs.use_container = True
     arvargs.relax_path_checks = True
     arvargs.print_supported_versions = False
@@ -296,7 +301,10 @@ def main(args, stdout, stderr, api_client=None, keep_client=None,
             api_client.users().current().execute()
         if keep_client is None:
             keep_client = arvados.keep.KeepClient(api_client=api_client, num_retries=4)
-        executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4)
+        executor = ArvCwlExecutor(api_client, arvargs, keep_client=keep_client, num_retries=4, stdout=stdout)
+    except WorkflowException as e:
+        logger.error(e, exc_info=(sys.exc_info()[1] if arvargs.debug else False))
+        return 1
     except Exception:
         logger.exception("Error creating the Arvados CWL Executor")
         return 1