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closes #3821
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
__init__.py
diff --git
a/sdk/cwl/arvados_cwl/__init__.py
b/sdk/cwl/arvados_cwl/__init__.py
index 024e9d0861743d2c84327b69cd3b23c4b38ae342..3b14701a9b9480cf6119e6d0e81e478e6da81214 100644
(file)
--- a/
sdk/cwl/arvados_cwl/__init__.py
+++ b/
sdk/cwl/arvados_cwl/__init__.py
@@
-11,6
+11,7
@@
import threading
import hashlib
import copy
import json
import hashlib
import copy
import json
+import re
from functools import partial
import pkg_resources # part of setuptools
from functools import partial
import pkg_resources # part of setuptools
@@
-314,6
+315,10
@@
class ArvCwlRunner(object):
body={
'output': self.final_output_collection.portable_data_hash(),
}).execute(num_retries=self.num_retries)
body={
'output': self.final_output_collection.portable_data_hash(),
}).execute(num_retries=self.num_retries)
+ self.api.collections().update(uuid=self.final_output_collection.manifest_locator(),
+ body={
+ 'is_trashed': True
+ }).execute(num_retries=self.num_retries)
except Exception as e:
logger.info("Setting container output: %s", e)
elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
except Exception as e:
logger.info("Setting container output: %s", e)
elif self.work_api == "jobs" and "TASK_UUID" in os.environ:
@@
-625,6
+630,7
@@
def arg_parser(): # type: () -> argparse.ArgumentParser
def add_arv_hints():
cache = {}
def add_arv_hints():
cache = {}
+ cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
cache["http://arvados.org/cwl"] = res.read()
res.close()
res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
cache["http://arvados.org/cwl"] = res.read()
res.close()