+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import functools
import mock
import sys
from arvados_cwl.pathmapper import ArvPathMapper
-def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
+def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None, collection=None):
pdh = "99999999999999999999999999999991+99"
for c in files:
c.keepref = "%s/%s" % (pdh, os.path.basename(c.fn))
arvrunner = arvados_cwl.ArvCwlRunner(self.api)
- def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
+ def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
st = arvados.commands.run.UploadFile("", "tests/hw.py")
return st
"""Test pathmapper handling previously uploaded files."""
arvrunner = arvados_cwl.ArvCwlRunner(self.api)
- arvrunner.add_uploaded('file:tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='', type='File', staged=True))
+ arvrunner.add_uploaded('file:tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999992+99/hw.py', target='', type='File', staged=True))
upl.side_effect = upload_mock
"location": "file:tests/hw.py"
}], "", "/test/%s", "/test/%s/%s")
- self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
+ self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999992+99/hw.py', target='/test/99999999999999999999999999999992+99/hw.py', type='File', staged=True)},
p._pathmap)
@mock.patch("arvados.commands.run.uploadfiles")
# An ArvFile object returned from arvados.commands.run.statfile means the file is located on a
# keep mount, so we can construct a direct reference directly without upload.
- def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
+ def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
st = arvados.commands.run.ArvFile("", fnPattern % ("99999999999999999999999999999991+99", "hw.py"))
return st
self.assertEqual({'file:tests/hw.py': MapperEnt(resolved='keep:99999999999999999999999999999991+99/hw.py', target='/test/99999999999999999999999999999991+99/hw.py', type='File', staged=True)},
p._pathmap)
+
+ @mock.patch("os.stat")
+ def test_missing_file(self, stat):
+ """Test pathmapper handling missing references."""
+ arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+
+ stat.side_effect = OSError(2, "No such file or directory")
+
+ with self.assertRaises(OSError):
+ p = ArvPathMapper(arvrunner, [{
+ "class": "File",
+ "location": "file:tests/hw.py"
+ }], "", "/test/%s", "/test/%s/%s")