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)
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")
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.")
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()