logger = logging.getLogger('arvados.cwl-runner')
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
+cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
def trim_listing(obj):
"""Remove 'listing' field from Directory objects that are keep references.
class Runner(object):
- def __init__(self, runner, tool, job_order, enable_reuse):
+ def __init__(self, runner, tool, job_order, enable_reuse, output_name):
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.running = False
self.enable_reuse = enable_reuse
self.uuid = None
+ self.final_output = None
+ self.output_name = output_name
def update_pipeline_component(self, record):
pass
outputs = None
try:
try:
- outc = arvados.collection.Collection(record["output"])
+ self.final_output = record["output"]
+ outc = arvados.collection.CollectionReader(self.final_output,
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
with outc.open("cwl.output.json") as f:
outputs = json.load(f)
def keepify(fileobj):