def test_truncate_fails(research_object: ResearchObject) -> None:
with research_object.write_bag_file("file.txt") as fh:
fh.write("Hello there")
fh.truncate() # OK as we're always at end
# Will fail because the checksum can't rewind
with pytest.raises(OSError):
fh.truncate(0)
def test_writable_string(research_object: ResearchObject) -> None:
with research_object.write_bag_file("file.txt") as fh:
assert fh.writable()
fh.write("Hello\n")
sha1 = os.path.join(research_object.folder, "tagmanifest-sha1.txt")
assert os.path.isfile(sha1)
with open(sha1, encoding="UTF-8") as sha_file:
stripped_sha = sha_file.readline().strip()
assert stripped_sha.endswith("file.txt")
# stain@biggie:~/src/cwltool$ echo Hello | sha1sum
# 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 -
assert stripped_sha.startswith("1d229271928d3f9e2bb0375bd6ce5db6c6d348d9")
sha256 = os.path.join(research_object.folder, "tagmanifest-sha256.txt")
assert os.path.isfile(sha256)
with open(sha256, encoding="UTF-8") as sha_file:
stripped_sha = sha_file.readline().strip()
assert stripped_sha.endswith("file.txt")
# stain@biggie:~/src/cwltool$ echo Hello | sha256sum
# 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 -
assert stripped_sha.startswith(
"66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18")
sha512 = os.path.join(research_object.folder, "tagmanifest-sha512.txt")
assert os.path.isfile(sha512)
def test_data(research_object: ResearchObject) -> None:
with research_object.write_bag_file("data/file.txt") as fh:
assert fh.writable()
fh.write("Hello\n")
# Because this is under data/ it should add to manifest
# rather than tagmanifest
sha1 = os.path.join(research_object.folder, "manifest-sha1.txt")
assert os.path.isfile(sha1)
with open(sha1, encoding="UTF-8") as fh2:
stripped_sha = fh2.readline().strip()
assert stripped_sha.endswith("data/file.txt")
def __init__(self,
workflow_uri_path: str,
root_directory: str,
stove_provenance_directory: str,
executor: Optional[JobExecutor] = None,
loading_context: Optional[LoadingContext] = None,
runtime_context: Optional[RuntimeContext] = None) -> None:
"""Easy way to load a CWL document for execution."""
super().__init__(root_directory=root_directory,
executor=executor,
loading_context=loading_context,
runtime_context=runtime_context)
self.store_provenance_directory = stove_provenance_directory
self.loading_context, self.workflow_object, self.uri = fetch_document(
workflow_uri_path, self.loading_context)
make_fs_access = self.runtime_context.make_fs_access \
if self.runtime_context.make_fs_access is not None else StdFsAccess
ro = ResearchObject(make_fs_access(""), )
self.runtime_context.research_obj = ro
log_file_io = ro.open_log_file_for_activity(ro.engine_uuid)
prov_log_handler = logging.StreamHandler(cast(IO[str], log_file_io))
prov_log_handler.setFormatter(ProvLogFormatter())
_logger.addHandler(prov_log_handler)
_logger.debug("[provenance] Logging to %s", log_file_io)
def test_not_readable(research_object: ResearchObject) -> None:
with research_object.write_bag_file("file.txt") as fh:
assert not fh.readable()
with pytest.raises(OSError):
fh.read()
def test_writable_bytes(research_object: ResearchObject) -> None:
string = "Here is a snowman: \u2603 \n".encode()
with research_object.write_bag_file("file.txt", encoding=None) as fh:
fh.write(string) # type: ignore
def test_writable_unicode_string(research_object: ResearchObject) -> None:
with research_object.write_bag_file("file.txt") as fh:
assert fh.writable()
fh.write("Here is a snowman: \u2603 \n")
def test_climboutfails(research_object: ResearchObject) -> None:
with pytest.raises(ValueError):
research_object.write_bag_file("../../outside-ro")
def test_absolute_path_fails(research_object: ResearchObject) -> None:
with pytest.raises(ValueError):
research_object.write_bag_file("/absolute/path/fails")
def research_object() -> Generator[ResearchObject, None, None]:
re_ob = ResearchObject(StdFsAccess(""))
yield re_ob
re_ob.close()
def test_not_seekable(research_object: ResearchObject) -> None:
with research_object.write_bag_file("file.txt") as fh:
assert not fh.seekable()
with pytest.raises(IOError):
fh.seek(0)