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Merge branch 'master' into 9307-cwl-use-tmp-output
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
fsaccess.py
diff --git
a/sdk/cwl/arvados_cwl/fsaccess.py
b/sdk/cwl/arvados_cwl/fsaccess.py
index e44e7a928218c04e377b04373d7ec44ea59b04a0..89a4308bf14ef2d5f9f3275ddcc4201e749205d8 100644
(file)
--- a/
sdk/cwl/arvados_cwl/fsaccess.py
+++ b/
sdk/cwl/arvados_cwl/fsaccess.py
@@
-12,9
+12,10
@@
import arvados.arvfile
class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
- def __init__(self, basedir, api_client=None):
+ def __init__(self, basedir, api_client=None
, keep_client=None
):
super(CollectionFsAccess, self).__init__(basedir)
self.api_client = api_client
super(CollectionFsAccess, self).__init__(basedir)
self.api_client = api_client
+ self.keep_client = keep_client
self.collections = {}
def get_collection(self, path):
self.collections = {}
def get_collection(self, path):
@@
-22,7
+23,8
@@
class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
pdh = p[0][5:]
if pdh not in self.collections:
if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]):
pdh = p[0][5:]
if pdh not in self.collections:
- self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client)
+ self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
+ keep_client=self.keep_client)
return (self.collections[pdh], "/".join(p[1:]))
else:
return (None, path)
return (self.collections[pdh], "/".join(p[1:]))
else:
return (None, path)