from functools import partial
import logging
import json
-import subprocess
+import subprocess32 as subprocess
from collections import namedtuple
from StringIO import StringIO
sc = []
def only_real(obj):
+ # Only interested in local files than need to be uploaded,
+ # don't include file literals, keep references, etc.
if obj.get("location", "").startswith("file:"):
sc.append(obj)
visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
- for d in discovered:
- sc.extend(discovered[d])
+ for d in list(discovered.keys()):
+ # Only interested in discovered secondaryFiles which are local
+ # files that need to be uploaded.
+ if d.startswith("file:"):
+ sc.extend(discovered[d])
+ else:
+ del discovered[d]
mapper = ArvPathMapper(arvrunner, sc, "",
"keep:%s",
def __init__(self, runner, tool, job_order, enable_reuse,
output_name, output_tags, submit_runner_ram=0,
name=None, on_error=None, submit_runner_image=None,
- intermediate_output_ttl=0, merged_map=None, default_storage_classes="default",
+ intermediate_output_ttl=0, merged_map=None,
priority=None, secret_store=None):
self.arvrunner = runner
self.tool = tool
self.intermediate_output_ttl = intermediate_output_ttl
self.priority = priority
self.secret_store = secret_store
- self.default_storage_classes = default_storage_classes
+
+ self.submit_runner_cores = 1
+ self.submit_runner_ram = 1024 # defaut 1 GiB
+
+ runner_resource_req, _ = self.tool.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources")
+ if runner_resource_req:
+ if runner_resource_req.get("coresMin"):
+ self.submit_runner_cores = runner_resource_req["coresMin"]
+ if runner_resource_req.get("ramMin"):
+ self.submit_runner_ram = runner_resource_req["ramMin"]
if submit_runner_ram:
+ # Command line / initializer overrides default and/or spec from workflow
self.submit_runner_ram = submit_runner_ram
- else:
- self.submit_runner_ram = 3000
if self.submit_runner_ram <= 0:
- raise Exception("Value of --submit-runner-ram must be greater than zero")
+ raise Exception("Value of submit-runner-ram must be greater than zero")
+
+ if self.submit_runner_cores <= 0:
+ raise Exception("Value of submit-runner-cores must be greater than zero")
self.merged_map = merged_map or {}
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
- done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self), maxlen=40)
+ done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
self.final_output = record["output"]
outc = arvados.collection.CollectionReader(self.final_output,