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Add the option to copy tree in addition to making a symlink tree from elsewhere.
[htsworkflow.git]
/
htsworkflow
/
submission
/
results.py
diff --git
a/htsworkflow/submission/results.py
b/htsworkflow/submission/results.py
index 50077523aca3970a517973adbd69f119f4f17e3d..5633745687c70cc9954685fa582b66c6d62a730f 100644
(file)
--- a/
htsworkflow/submission/results.py
+++ b/
htsworkflow/submission/results.py
@@
-2,6
+2,7
@@
"""
from collections import MutableMapping
import os
"""
from collections import MutableMapping
import os
+import shutil
import logging
from collections import namedtuple
import logging
from collections import namedtuple
@@
-75,11
+76,11
@@
class ResultMap(MutableMapping):
if not os.path.exists(source_pathname):
raise IOError(
"{0} does not exist".format(source_pathname))
if not os.path.exists(source_pathname):
raise IOError(
"{0} does not exist".format(source_pathname))
- if not
os.path.exists(target_pathname
):
+ if not
(os.path.exists(target_pathname) or os.path.isdir(source_pathname)
):
if link:
os.symlink(source_pathname, target_pathname)
else:
if link:
os.symlink(source_pathname, target_pathname)
else:
-
os
.copy(source_pathname, target_pathname)
+
shutil
.copy(source_pathname, target_pathname)
LOGGER.info(
'LINK {0} to {1}'.format(source_pathname,
target_pathname))
LOGGER.info(
'LINK {0} to {1}'.format(source_pathname,
target_pathname))