def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
self.args = ["db"]
dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dir = dir.abspath()
cfg = dir / "etc" / "omero.properties"
cfg = cfg.abspath()
self.cli.dir = dir
self.data = {}
for line in cfg.text().split("\n"):
line = line.strip()
for x in ("version", "patch"):
key = "omero.db." + x
if line.startswith(key):
self.data[x] = line[len(key) + 1:]
self.file = create_path()
self.script_file = "%(version)s__%(patch)s.sql" % self.data
if os.path.isfile(self.script_file):
os.rename(self.script_file, self.script_file + '.bak')
assert not os.path.isfile(self.script_file)
self.mox = Mox()
self.mox.StubOutWithMock(getpass, 'getpass')
self.mox.StubOutWithMock(__builtin__, "raw_input")
class TestHdfList(TestCase):
def setup_method(self, method):
TestCase.setup_method(self, method)
self.mox = Mox()
def hdfpath(self):
tmpdir = self.tmpdir()
return path(tmpdir) / "test.h5"
def testLocking(self, monkeypatch):
lock1 = threading.RLock()
hdflist2 = HdfList()
lock2 = threading.RLock()
tmp = str(self.hdfpath())
# Using HDFLIST
hdf1 = HdfStorage(tmp, lock1)
# There are multiple guards against opening the same HDF5 file
# PyTables includes a check
monkeypatch.setattr(storage_module, 'HDFLIST', hdflist2)
with pytest.raises(ValueError) as exc_info:
HdfStorage(tmp, lock2)
assert exc_info.value.message.startswith(
"The file '%s' is already opened. " % tmp)
monkeypatch.undo()
# HdfList uses portalocker, test by mocking tables.open_file
if hasattr(tables, "open_file"):
self.mox.StubOutWithMock(tables, 'open_file')
tables.file._FILE_OPEN_POLICY = 'default'
tables.open_file(tmp,
mode='w',
title='OMERO HDF Measurement Storage',
rootUEP='/').AndReturn(open(tmp))
self.mox.ReplayAll()
else:
self.mox.StubOutWithMock(tables, 'openFile')
tables.openFile(tmp,
mode='w',
title='OMERO HDF Measurement Storage',
rootUEP='/').AndReturn(open(tmp))
monkeypatch.setattr(storage_module, 'HDFLIST', hdflist2)
with pytest.raises(omero.LockTimeout) as exc_info:
HdfStorage(tmp, lock2)
print exc_info.value
assert (
exc_info.value.message == 'Cannot acquire exclusive lock on: %s' %
tmp)
monkeypatch.undo()
hdf1.cleanup()
self.mox.UnsetStubs()
self.mox.VerifyAll()
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
self.args = ["db"]
self.data = {}
# FIXME: Use a different approach to get omero.db.version etc
# No-longer stored in "omero.properties"
if OMERODIR:
dir = path(OMERODIR).abspath()
cfg = dir / "etc" / "omero.properties"
cfg = cfg.abspath()
self.cli.dir = dir
for line in cfg.text().split("\n"):
line = line.strip()
for x in ("version", "patch"):
key = "omero.db." + x
if line.startswith(key):
self.data[x] = line[len(key) + 1:]
self.file = create_path()
self.script_file = ""
if "version" in self.data and "patch" in self.data:
self.script_file = "%(version)s__%(patch)s.sql" % self.data
if os.path.isfile(self.script_file):
os.rename(self.script_file, self.script_file + '.bak')
assert not os.path.isfile(self.script_file)
self.mox = Mox()
self.mox.StubOutWithMock(getpass, 'getpass')
self.mox.StubOutWithMock(__builtin__, "raw_input")
def setup_method(self, method):
self.mox = Mox()
self.client = self.mox.CreateMock(BaseClient)
self.sf = self.mox.CreateMock(ServiceFactoryPrx)
self.query = self.mox.CreateMock(IQueryPrx)
self.update = self.mox.CreateMock(IUpdatePrx)
self.client.sf = self.sf
self.cli = MockCLI()
self.cli._client = self.client
self.cli.set("tx.state", TxState(self.cli))
class AbstractCLITest(ITest):
def setup_method(self, method):
super(AbstractCLITest, self).setup_method(method)
self.cli = CLI()
self.cli.register("sessions", SessionsControl, "TEST")
def setup_mock(self):
self.mox = Mox()
def teardown_mock(self):
self.mox.UnsetStubs()
self.mox.VerifyAll()
class AbstractCLITest(ITest):
@classmethod
def setup_class(cls):
super(AbstractCLITest, cls).setup_class()
cls.cli = CLI()
cls.cli.register("sessions", SessionsControl, "TEST")
def setup_mock(self):
self.mox = Mox()
def teardown_mock(self):
self.mox.UnsetStubs()
self.mox.VerifyAll()
class AbstractCLITest(ITest):
warnings.warn("Deprecated in 5.4.2."
"Use omero.testlib.cli", DeprecationWarning)
@classmethod
def setup_class(cls):
super(AbstractCLITest, cls).setup_class()
cls.cli = CLI()
cls.cli.register("sessions", SessionsControl, "TEST")
def setup_mock(self):
self.mox = Mox()
def teardown_mock(self):
self.mox.UnsetStubs()
self.mox.VerifyAll()
class TxBase(object):
def setup_method(self, method):
self.mox = Mox()
self.client = self.mox.CreateMock(BaseClient)
self.sf = self.mox.CreateMock(ServiceFactoryPrx)
self.query = self.mox.CreateMock(IQueryPrx)
self.update = self.mox.CreateMock(IUpdatePrx)
self.client.sf = self.sf
self.cli = MockCLI()
self.cli._client = self.client
self.cli.set("tx.state", TxState(self.cli))
def teardown_method(self, method):
self.mox.UnsetStubs()
self.mox.VerifyAll()
def queries(self, obj):
self.sf.getQueryService().AndReturn(self.query)
self.query.get(IgnoreArg(), IgnoreArg(), IgnoreArg()).AndReturn(obj)
def saves(self, obj):
self.sf.getUpdateService().AndReturn(self.update)
self.update.saveAndReturnObject(IgnoreArg()).AndReturn(obj)
class TestDatabase(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
self.args = ["db"]
dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dir = dir.abspath()
cfg = dir / "etc" / "omero.properties"
cfg = cfg.abspath()
self.cli.dir = dir
self.data = {}
for line in cfg.text().split("\n"):
line = line.strip()
for x in ("version", "patch"):
key = "omero.db." + x
if line.startswith(key):
self.data[x] = line[len(key) + 1:]
self.file = create_path()
self.script_file = "%(version)s__%(patch)s.sql" % self.data
if os.path.isfile(self.script_file):
os.rename(self.script_file, self.script_file + '.bak')
assert not os.path.isfile(self.script_file)
self.mox = Mox()
self.mox.StubOutWithMock(getpass, 'getpass')
self.mox.StubOutWithMock(__builtin__, "raw_input")
def teardown_method(self, method):
self.file.remove()
if os.path.isfile(self.script_file):
os.remove(self.script_file)
if os.path.isfile(self.script_file + '.bak'):
os.rename(self.script_file + '.bak', self.script_file)
self.mox.UnsetStubs()
self.mox.VerifyAll()
def password(self, string, strict=True):
self.cli.invoke("db password " + string % self.data, strict=strict)
def testHelp(self):
self.args += ["-h"]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('subcommand', DatabaseControl().get_subcommands())
def testSubcommandHelp(self, subcommand):
self.args += [subcommand, "-h"]
self.cli.invoke(self.args, strict=True)
def testBadVersionDies(self):
with pytest.raises(NonZeroReturnCode):
self.cli.invoke("db script NONE NONE pw", strict=True)
def testPasswordIsAskedForAgainIfDiffer(self):
self.expectPassword("ome")
self.expectConfirmation("bad")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
def testPasswordIsAskedForAgainIfEmpty(self):
self.expectPassword("")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('user_id', ['', '0', '1'])
@pytest.mark.parametrize('password', ['', 'ome'])
def testPassword(self, user_id, password, no_salt, capsys):
args = ""
if user_id:
args += "--user-id=%s " % user_id
if no_salt:
args += "%s " % no_salt
if password:
args += "%s" % password
else:
self.expectPassword("ome", id=user_id)
self.expectConfirmation("ome", id=user_id)
self.mox.ReplayAll()
self.password(args)
out, err = capsys.readouterr()
assert out.strip() == self.password_output(user_id, no_salt)
@pytest.mark.parametrize('file_arg', ['', '-f', '--file'])
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('password', ['', '--password ome'])
def testScript(self, no_salt, file_arg, password, capsys):
"""
Recommended usage of db script
"""
args = "db script " + password
if no_salt:
args += " %s" % no_salt
if file_arg:
args += " %s %s" % (file_arg, str(self.file))
output = self.file
else:
output = self.script_file
if not password:
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.cli.invoke(args, strict=True)
out, err = capsys.readouterr()
assert 'Using %s for version' % self.data['version'] in err
assert 'Using %s for patch' % self.data['patch'] in err
if password:
assert 'Using password from commandline' in err
with open(output) as f:
lines = f.readlines()
for line in lines:
if line.startswith('insert into password values (0'):
assert line.strip() == self.script_output(no_salt)
@pytest.mark.parametrize('file_arg', ['', '-f', '--file'])
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize(
'pos_args', ['%s %s %s', '--version %s --patch %s --password %s'])
def testScriptDeveloperArgs(self, pos_args, no_salt, file_arg, capsys):
"""
Deprecated and developer usage of db script
"""
arg_values = ('VERSION', 'PATCH', 'PASSWORD')
args = "db script " + pos_args % arg_values
if no_salt:
args += " %s" % no_salt
if file_arg:
args += " %s %s" % (file_arg, str(self.file))
self.file
else:
self.script_file
self.mox.ReplayAll()
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(args, strict=True)
out, err = capsys.readouterr()
assert 'Using %s for version' % (arg_values[0]) in err
assert 'Using %s for patch' % (arg_values[1]) in err
assert 'Using password from commandline' in err
assert 'Invalid Database version/patch' in err
def password_ending(self, user, id):
if id and id != '0':
rv = "user %s: " % id
else:
rv = "%s user: "******"password for OMERO " + rv
def expectPassword(self, pw, user="******", id=None):
getpass.getpass("Please enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def expectConfirmation(self, pw, user="******", id=None):
getpass.getpass("Please re-enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def password_output(self, user_id, no_salt):
update_msg = "UPDATE password SET hash = \'%s\'" \
" WHERE experimenter_id = %s;"
if not user_id:
user_id = "0"
return update_msg % (hash_map[(user_id, no_salt)], user_id)
def script_output(self, no_salt):
root_password_msg = "insert into password values (0,\'%s\');"
return root_password_msg % (hash_map[("0", no_salt)])
def setup_mock(self):
self.mox = Mox()
def setup_method(self, method):
TestCase.setup_method(self, method)
self.mox = Mox()
class TestDatabase(object):
def setup_method(self, method):
self.cli = CLI()
self.cli.register("db", DatabaseControl, "TEST")
dir = path(__file__) / ".." / ".." / ".." / ".." / ".." / ".." /\
".." / "dist" # FIXME: should not be hard-coded
dir = dir.abspath()
cfg = dir / "etc" / "omero.properties"
cfg = cfg.abspath()
self.cli.dir = dir
self.data = {}
for line in cfg.text().split("\n"):
line = line.strip()
for x in ("version", "patch"):
key = "omero.db." + x
if line.startswith(key):
self.data[x] = line[len(key) + 1:]
self.file = create_path()
self.script_file = "%(version)s__%(patch)s.sql" % self.data
if os.path.isfile(self.script_file):
os.rename(self.script_file, self.script_file + '.bak')
assert not os.path.isfile(self.script_file)
self.mox = Mox()
self.mox.StubOutWithMock(getpass, 'getpass')
self.mox.StubOutWithMock(__builtin__, "raw_input")
def teardown_method(self, method):
self.file.remove()
if os.path.isfile(self.script_file):
os.remove(self.script_file)
if os.path.isfile(self.script_file + '.bak'):
os.rename(self.script_file + '.bak', self.script_file)
self.mox.UnsetStubs()
self.mox.VerifyAll()
def password(self, string, strict=True):
self.cli.invoke("db password " + string % self.data, strict=strict)
def testBadVersionDies(self):
with pytest.raises(NonZeroReturnCode):
self.cli.invoke("db script NONE NONE pw", strict=True)
def testPasswordIsAskedForAgainIfDiffer(self):
self.expectPassword("ome")
self.expectConfirmation("bad")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
def testPasswordIsAskedForAgainIfEmpty(self):
self.expectPassword("")
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.password("")
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('user_id', ['', '0', '1'])
@pytest.mark.parametrize('password', ['', 'ome'])
def testPassword(self, user_id, password, no_salt, capsys):
args = ""
if user_id:
args += "--user-id=%s " % user_id
if no_salt:
args += "%s " % no_salt
if password:
args += "%s" % password
else:
self.expectPassword("ome", id=user_id)
self.expectConfirmation("ome", id=user_id)
self.mox.ReplayAll()
self.password(args)
out, err = capsys.readouterr()
assert out.strip() == self.password_output(user_id, no_salt)
@pytest.mark.parametrize('file_arg', ['', '-f', '--file'])
@pytest.mark.parametrize('no_salt', ['', '--no-salt'])
@pytest.mark.parametrize('pos_input', [
"", "%(version)s", "%(version)s %(patch)s", "%(version)s %(patch)s ome"
])
def testScript(self, pos_input, no_salt, file_arg):
args = "db script "
args += pos_input
if no_salt:
args += " %s" % no_salt
if file_arg:
args += " %s %s" % (file_arg, str(self.file))
output = self.file
else:
output = self.script_file
if "version" not in pos_input or "patch" not in pos_input:
self.expectVersion(self.data["version"])
self.expectPatch(self.data["patch"])
if "ome" not in pos_input:
self.expectPassword("ome")
self.expectConfirmation("ome")
self.mox.ReplayAll()
self.cli.invoke(args % self.data, strict=True)
with open(output) as f:
lines = f.readlines()
for line in lines:
if line.startswith('insert into password values (0'):
assert line.strip() == self.script_output(no_salt)
def password_ending(self, user, id):
if id and id != '0':
rv = "user %s: " % id
else:
rv = "%s user: "******"password for OMERO " + rv
def expectPassword(self, pw, user="******", id=None):
getpass.getpass("Please enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def expectConfirmation(self, pw, user="******", id=None):
getpass.getpass("Please re-enter %s" %
self.password_ending(user, id)).AndReturn(pw)
def expectVersion(self, version):
raw_input("Please enter omero.db.version [%s]: " %
self.data["version"]).AndReturn(version)
def expectPatch(self, patch):
raw_input("Please enter omero.db.patch [%s]: " %
self.data["patch"]).AndReturn(patch)
def password_output(self, user_id, no_salt):
update_msg = "UPDATE password SET hash = \'%s\'" \
" WHERE experimenter_id = %s;"
if not user_id:
user_id = "0"
return update_msg % (hash_map[(user_id, no_salt)], user_id)
def script_output(self, no_salt):
root_password_msg = "insert into password values (0,\'%s\');"
return root_password_msg % (hash_map[("0", no_salt)])