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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 eec5aad8b267b8cdd80f81a6a341d162e0f7eec1..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
@@
-53,6
+54,8
@@
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()))