10111: Merge branch 'master' into 10111-collection-labels

[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 1d2fa291ec1eee8953337f4ca1b97343ed7bcae2..46436b54dc730163faa7c431960cd9d76ebbda0f 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -247,10 +247,13 @@ class ArvCwlRunner(object):
                 raise Exception("Output source is not in keep or a literal")
             sp = k.split("/")
             srccollection = sp[0][5:]
-            reader = self.collection_cache.get(srccollection)
             try:
+                reader = self.collection_cache.get(srccollection)
                 srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
                 final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
+            except arvados.errors.ArgumentError as e:
+                logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
+                raise
             except IOError as e:
                 logger.warn("While preparing output collection: %s", e)
 
@@ -536,7 +539,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
                         type=float,
                         default=20)
-    parser.add_argument("--version", action="store_true", help="Print version and exit")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--print-dot", action="store_true",
+                         help="Print workflow visualization in graphviz format and exit")
+    exgroup.add_argument("--version", action="store_true", help="Print version and exit")
+    exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
@@ -608,6 +616,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
                         "Default is 'continue'.", default="continue", choices=("stop", "continue"))
 
+    parser.add_argument("--enable-dev", action="store_true",
+                        help="Enable loading and running development versions "
+                             "of CWL spec.", default=False)
+
     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 
@@ -615,6 +627,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 def add_arv_hints():
     cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
+    cwltool.draft2tool.ACCEPTLIST_RE = cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     use_custom_schema("v1.0", "http://arvados.org/cwl", res.read())
     res.close()