import arvados.keep
import arvados.collection
import arvados_cwl
+import arvados_cwl.executor
from cwltool.pathmapper import MapperEnt
from .mock_discovery import get_rootDesc
from arvados_cwl.pathmapper import ArvPathMapper
-def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None, collection=None):
+def upload_mock(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None, collection=None, packed=None):
pdh = "99999999999999999999999999999991+99"
for c in files:
c.keepref = "%s/%s" % (pdh, os.path.basename(c.fn))
def test_keepref(self):
"""Test direct keep references."""
- arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+ arvrunner = arvados_cwl.executor.ArvCwlExecutor(self.api)
p = ArvPathMapper(arvrunner, [{
"class": "File",
def test_upload(self, statfile, upl):
"""Test pathmapper uploading files."""
- arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+ arvrunner = arvados_cwl.executor.ArvCwlExecutor(self.api)
def statfile_mock(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)", raiseOSError=False):
st = arvados.commands.run.UploadFile("", "tests/hw.py")
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("arvados.commands.run.uploadfiles")
- def test_prev_uploaded(self, upl):
- """Test pathmapper handling previously uploaded files."""
-
- arvrunner = arvados_cwl.ArvCwlRunner(self.api)
- arvrunner.add_uploaded('file:tests/hw.py', MapperEnt(resolved='keep:99999999999999999999999999999992+99/hw.py', target='', type='File', staged=True))
-
- upl.side_effect = upload_mock
-
- p = ArvPathMapper(arvrunner, [{
- "class": "File",
- "location": "file:tests/hw.py"
- }], "", "/test/%s", "/test/%s/%s")
-
- 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")
@mock.patch("arvados.commands.run.statfile")
def test_statfile(self, statfile, upl):
"""Test pathmapper handling ArvFile references."""
- arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+ arvrunner = arvados_cwl.executor.ArvCwlExecutor(self.api)
# 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.
@mock.patch("os.stat")
def test_missing_file(self, stat):
"""Test pathmapper handling missing references."""
- arvrunner = arvados_cwl.ArvCwlRunner(self.api)
+ arvrunner = arvados_cwl.executor.ArvCwlExecutor(self.api)
stat.side_effect = OSError(2, "No such file or directory")