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10081: Upload dependencies. Fix keep paths. Ensure correct quoting.
[arvados.git]
/
crunch_scripts
/
cwl-runner
diff --git
a/crunch_scripts/cwl-runner
b/crunch_scripts/cwl-runner
index 2a1873a84e6925f9c1edf6057dc2b01a392d25ff..fe4e8009aca1af0b04fb483983a09fd59de25390 100755
(executable)
--- a/
crunch_scripts/cwl-runner
+++ b/
crunch_scripts/cwl-runner
@@
-18,8
+18,9
@@
import logging
import os
import json
import argparse
import os
import json
import argparse
+import re
from arvados.api import OrderedJsonModel
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
from cwltool.load_tool import load_tool
# Print package versions
@@
-30,8
+31,10
@@
api = arvados.api("v1")
try:
job_order_object = arvados.current_job()['script_parameters']
try:
job_order_object = arvados.current_job()['script_parameters']
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
def keeppath(v):
def keeppath(v):
- if
arvados.util.keep_locator_pattern
.match(v):
+ if
pdh_path
.match(v):
return "keep:%s" % v
else:
return v
return "keep:%s" % v
else:
return v
@@
-49,6
+52,7
@@
try:
}
adjustFileObjs(job_order_object, keeppathObj)
}
adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))