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9308: Add test for KeepTmpOutput flag.
[arvados.git]
/
crunch_scripts
/
cwl-runner
diff --git
a/crunch_scripts/cwl-runner
b/crunch_scripts/cwl-runner
index fe4e8009aca1af0b04fb483983a09fd59de25390..89699f5eaf765aa997a223b2704934c4d5b38da7 100755
(executable)
--- a/
crunch_scripts/cwl-runner
+++ b/
crunch_scripts/cwl-runner
@@
-12,15
+12,16
@@
import arvados
import arvados_cwl
import arvados.collection
import arvados.util
import arvados_cwl
import arvados.collection
import arvados.util
-from cwltool.process import shortname
import cwltool.main
import logging
import os
import json
import argparse
import re
import cwltool.main
import logging
import os
import json
import argparse
import re
+import functools
+
from arvados.api import OrderedJsonModel
from arvados.api import OrderedJsonModel
-from cwltool.process import
adjustFileObjs, adjustDirObj
s
+from cwltool.process import
shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDir
s
from cwltool.load_tool import load_tool
# Print package versions
from cwltool.load_tool import load_tool
# Print package versions
@@
-53,10
+54,12
@@
try:
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
+ normalizeFilesDirs(job_order_object)
+ adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
- t = load_tool(job_order_object, runner.arv
MakeT
ool)
+ t = load_tool(job_order_object, runner.arv
_make_t
ool)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
@@
-67,7
+70,7
@@
try:
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
- outputObj = runner.arv
E
xecutor(t, job_order_object, **vars(args))
+ outputObj = runner.arv
_e
xecutor(t, job_order_object, **vars(args))
files = {}
def capture(fileobj):
files = {}
def capture(fileobj):