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9615: Add check_writable to check for "writable" field and raise UnsupportedRequirement.
[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 d2d38b00c35a89f2a1a1f179a0468b821e48670a..0970e72d71d0ce2cef056e05f94bd02ea1324549 100644
(file)
--- a/
sdk/cwl/arvados_cwl/fsaccess.py
+++ b/
sdk/cwl/arvados_cwl/fsaccess.py
@@
-1,14
+1,14
@@
import fnmatch
import os
import fnmatch
import os
-import cwltool.
pro
cess
+import cwltool.
stdfsac
cess
from cwltool.pathmapper import abspath
import arvados.util
import arvados.collection
import arvados.arvfile
from cwltool.pathmapper import abspath
import arvados.util
import arvados.collection
import arvados.arvfile
-class CollectionFsAccess(cwltool.
pro
cess.StdFsAccess):
+class CollectionFsAccess(cwltool.
stdfsac
cess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
def __init__(self, basedir, api_client=None):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
def __init__(self, basedir, api_client=None):
@@
-91,11
+91,11
@@
class CollectionFsAccess(cwltool.process.StdFsAccess):
def listdir(self, fn): # type: (unicode) -> List[unicode]
collection, rest = self.get_collection(fn)
def listdir(self, fn): # type: (unicode) -> List[unicode]
collection, rest = self.get_collection(fn)
- if rest:
- dir = collection.find(rest)
- else:
- dir = collection
if collection:
if collection:
+ if rest:
+ dir = collection.find(rest)
+ else:
+ dir = collection
return [abspath(l, fn) for l in dir.keys()]
else:
return super(CollectionFsAccess, self).listdir(fn)
return [abspath(l, fn) for l in dir.keys()]
else:
return super(CollectionFsAccess, self).listdir(fn)
@@
-104,3
+104,12
@@
class CollectionFsAccess(cwltool.process.StdFsAccess):
if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
return paths[-1]
return os.path.join(path, *paths)
if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
return paths[-1]
return os.path.join(path, *paths)
+
+ def realpath(self, path):
+ if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+ return path
+ collection, rest = self.get_collection(path)
+ if collection:
+ return path
+ else:
+ return os.path.realpath(path)