import os
import json
import argparse
+import re
from arvados.api import OrderedJsonModel
-from cwltool.process import adjustFileObjs
+from cwltool.process import adjustFileObjs, adjustDirObjs
from cwltool.load_tool import load_tool
# Print package versions
try:
job_order_object = arvados.current_job()['script_parameters']
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
def keeppath(v):
- if arvados.util.keep_locator_pattern.match(v):
+ if pdh_path.match(v):
return "keep:%s" % v
else:
return v
}
adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))