def test_list_tables_ann(self, name, ann_space, parent):
r1, r2, iid = self.setup_tables_for_list()
r1noann = tuple(r1[:-1] + (None,))
r2noann = tuple(r2[:-1] + (None,))
if parent is None:
parentim = None
elif parent:
parentim = "Image:%s" % iid
else:
# Non-existent
parentim = "Image:%s" % (iid + 1)
expected1 = (
(not name or name == "name-1")
and (not ann_space or ann_space == "ann_space-1")
and (parent is None or parent)
)
expected2 = (not name or name == "name-2") and (not ann_space) and (parent is None)
if name is None and ann_space is None and parent is None:
with pytest.raises(OmeroTablesFeatureStore.OmeroTableException):
tables = OmeroTablesFeatureStore.list_tables(self.sess, name=name, ann_space=ann_space, parent=parentim)
else:
tables = OmeroTablesFeatureStore.list_tables(self.sess, name=name, ann_space=ann_space, parent=parentim)
assert len(tables) in (0, 1, 2)
if ann_space is None and parent is None:
assert (r1noann in tables) == expected1
assert (r2noann in tables) == expected2
else:
assert (r1 in tables) == expected1
assert (r2 in tables) == expected2
def test_new_table(self, parent):
tcols, meta, ftnames = TableStoreHelper.get_columns([2], "multi", False)
if parent:
iid = unwrap(TableStoreHelper.create_image(self.sess).getId())
store = OmeroTablesFeatureStore.new_table(
self.sess, self.name, self.ft_space, self.ann_space, meta, ftnames, "Image:%d" % iid
)
else:
store = OmeroTablesFeatureStore.new_table(
self.sess, self.name, self.ft_space, self.ann_space, meta, ftnames
)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
if parent:
tid = unwrap(store.get_table().getOriginalFile().getId())
q = "SELECT link.child FROM ImageAnnotationLink link " "WHERE link.parent.id=:id"
p = omero.sys.ParametersI()
p.addId(iid)
r = self.sess.getQueryService().findAllByQuery(q, p)
assert len(r) == 1
assert isinstance(r[0], omero.model.FileAnnotation)
assert unwrap(r[0].getFile().getId()) == tid
store.close()
def test_list_tables_noann(self, name, ft_space, owner):
uid = unwrap(self.user.getId())
r1, r2, iid = self.setup_tables_for_list()
# Ignore ann_space
r1noann = tuple(r1[:-1] + (None,))
r2noann = tuple(r2[:-1] + (None,))
if owner == "uid":
ownerid = uid
else:
ownerid = owner
expected1 = (
(not name or name == "name-1")
and (not ft_space or ft_space == "ft_space-12")
and (ownerid is None or ownerid == -1 or ownerid == uid)
)
expected2 = (
(not name or name == "name-2")
and (not ft_space or ft_space == "ft_space-12")
and (ownerid is None or ownerid == -1 or ownerid == uid)
)
if name is None and ft_space is None and (owner in (None, -1)):
with pytest.raises(OmeroTablesFeatureStore.OmeroTableException):
tables = OmeroTablesFeatureStore.list_tables(self.sess, name=name, ft_space=ft_space, ownerid=ownerid)
else:
tables = OmeroTablesFeatureStore.list_tables(self.sess, name=name, ft_space=ft_space, ownerid=ownerid)
assert len(tables) in (0, 1, 2)
assert (r1noann in tables) == expected1
assert (r2noann in tables) == expected2
def test_create(self):
ownerid = 123
session = MockSession(None, None, ownerid)
fs = MockFeatureTable(None)
self.mox.StubOutWithMock(OmeroTablesFeatureStore, 'list_tables')
self.mox.StubOutWithMock(OmeroTablesFeatureStore, 'new_table')
fsname = 'fsname'
meta = [('Float', 'f')]
colnames = ['x1', 'x2']
OmeroTablesFeatureStore.list_tables(
session, fsname, 'x/features', ownerid=ownerid).AndReturn([])
OmeroTablesFeatureStore.new_table(
session, fsname, 'x/features', 'x/source', meta, colnames
).AndReturn(fs)
self.mox.ReplayAll()
fts = OmeroTablesFeatureStore.FeatureTableManager(
session, namespace='x')
assert fts.create(fsname, meta, colnames) == fs
assert len(fts.fss) == 1
assert fts.fss.get((fsname, ownerid)) == fs
self.mox.VerifyAll()
def test_list_tables_noann(self, name, ft_space, ownerid):
session = MockSession(None, None, 1)
perms = self.mox.CreateMock(MockPermissionsHandler)
store = MockFeatureTable(None)
store.perms = perms
self.mox.StubOutWithMock(session.qs, 'projection')
self.mox.StubOutWithMock(session.qs, 'findAllByQuery')
params = omero.sys.ParametersI()
# Need to reconstruct the dict to get the conditions in the
# same order
kvs = {}
if name:
kvs['name'] = name
params.addString('name', name)
if ft_space:
kvs['path'] = ft_space
params.addString('path', ft_space)
if ownerid > -1:
kvs['details.owner.id'] = ownerid
params.addLong('details_owner_id', ownerid)
q = ('FROM OriginalFile')
gotwhere = False
for k in kvs:
if not gotwhere:
q += ' WHERE '
gotwhere = True
else:
q += ' AND '
if k == 'details.owner.id':
q += 'details.owner.id = :details_owner_id'
else:
q += '%s = :%s' % (k, k)
if name or ft_space or ownerid > -1:
mf = MockOriginalFile(1L, name, ft_space)
session.qs.findAllByQuery(q, mox.Func(
lambda o: TestFeatureTable.parameters_equal(
params, o))).AndReturn([mf])
self.mox.ReplayAll()
if name or ft_space or ownerid > -1:
result = OmeroTablesFeatureStore.list_tables(
session, name, ft_space, None, ownerid, None)
assert len(result) == 1
assert result[0] == (1L, name, ft_space, None)
else:
with pytest.raises(OmeroTablesFeatureStore.OmeroTableException):
result = OmeroTablesFeatureStore.list_tables(
session, name, ft_space, None, ownerid, None)
self.mox.VerifyAll()
def setup_tables_for_list(self):
tcols, meta, ftnames = TableStoreHelper.get_columns([2], "multi", False)
iid = unwrap(TableStoreHelper.create_image(self.sess).getId())
store1 = OmeroTablesFeatureStore.new_table(
self.sess, "name-1", "ft_space-12", "ann_space-1", meta, ftnames, "Image:%s" % iid
)
store2 = OmeroTablesFeatureStore.new_table(self.sess, "name-2", "ft_space-12", "ann_space-2", meta, ftnames)
r1 = (self.get_table_id(store1), "name-1", "ft_space-12", "ann_space-1")
r2 = (self.get_table_id(store2), "name-2", "ft_space-12", "ann_space-2")
store1.close()
store2.close()
return r1, r2, iid
def test_open_table(self):
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [1], "multi", False
)
store = OmeroTablesFeatureStore.open_table(self.sess, tid, self.ann_space)
assert unwrap(store.get_table().getOriginalFile().getId()) == tid
assert store.ann_space == self.ann_space
store.close()
def test_list_tables_ann(self, name, ft_space, ann_space, ownerid, parent):
if not parent and not ann_space:
return
session = MockSession(None, None, 1)
self.mox.StubOutWithMock(session.qs, 'projection')
self.mox.StubOutWithMock(session.qs, 'findAllByQuery')
params = omero.sys.ParametersI()
if parent:
q = ('SELECT child.file.id, child.file.name, child.file.path, '
'child.ns '
'FROM DatasetAnnotationLink '
'WHERE child.class=FileAnnotation '
'AND parent.id=:id')
if ann_space:
q += ' AND child.ns=:ns'
if name:
q += ' AND child.file.name=:name'
if ft_space:
q += ' AND child.file.path=:ft_space'
if ownerid > -1:
q += ' AND child.file.details.owner.id=:ownerid'
if ann_space and not parent:
q = ('SELECT file.id, file.name, file.path, ns '
'FROM FileAnnotation WHERE ns=:ns')
if name:
q += ' AND file.name=:name'
if ft_space:
q += ' AND file.path=:ft_space'
if ownerid > -1:
q += ' AND file.details.owner.id=:ownerid'
if parent:
params.addId(2)
if ann_space:
params.addString('ns', ann_space)
if name:
params.addString('name', name)
if ft_space:
params.addString('ft_space', ft_space)
if ownerid > -1:
params.addLong('ownerid', ownerid)
r = [1L, 'table-name', '/test/features/ft_space',
'/test/features/ann_space']
session.qs.projection(q, mox.Func(
lambda o: TestFeatureTable.parameters_equal(
params, o))).AndReturn([r])
self.mox.ReplayAll()
result = OmeroTablesFeatureStore.list_tables(
session, name, ft_space, ann_space, ownerid, parent)
assert len(result) == 1
assert result[0] == tuple(r)
self.mox.VerifyAll()
def test_get(self, state):
ownerid = 123
session = MockSession(None, None, ownerid)
fs = MockFeatureTable(session)
fs.table = object()
self.mox.StubOutWithMock(OmeroTablesFeatureStore, 'list_tables')
self.mox.StubOutWithMock(OmeroTablesFeatureStore, 'open_table')
fsname = 'fsname'
fts = OmeroTablesFeatureStore.FeatureTableManager(
session, namespace='x')
self.mox.StubOutWithMock(fts.fss, 'get')
self.mox.StubOutWithMock(fts.fss, 'insert')
k = (fsname, ownerid)
if state == 'opened':
fts.fss.get(k).AndReturn(fs)
else:
if state == 'unopened':
fts.fss.get(k).AndReturn(None)
if state == 'closed':
fsold = MockFeatureTable(None)
fts.fss.get(k).AndReturn(fsold)
r = (1234, None, None, None)
OmeroTablesFeatureStore.list_tables(
session, fsname, 'x/features', ownerid=ownerid).AndReturn([r])
OmeroTablesFeatureStore.open_table(
session, r[0], 'x/source').AndReturn(fs)
fts.fss.insert(k, fs)
self.mox.ReplayAll()
assert fts.get(fsname, ownerid) == fs
self.mox.VerifyAll()
def test_list_tables_ann(self, name, ft_space, ann_space, ownerid, parent):
if not parent and not ann_space:
return
session = MockSession(None, None, 1)
self.mox.StubOutWithMock(session.qs, 'projection')
self.mox.StubOutWithMock(session.qs, 'findAllByQuery')
params = omero.sys.ParametersI()
if parent:
q = ('SELECT child.file.id, child.file.name, child.file.path, '
'child.ns '
'FROM DatasetAnnotationLink '
'WHERE child.class=FileAnnotation '
'AND parent.id=:id')
if ann_space:
q += ' AND child.ns=:ns'
if name:
q += ' AND child.file.name=:name'
if ft_space:
q += ' AND child.file.path=:ft_space'
if ownerid > -1:
q += ' AND child.file.details.owner.id=:ownerid'
if ann_space and not parent:
q = ('SELECT file.id, file.name, file.path, ns '
'FROM FileAnnotation WHERE ns=:ns')
if name:
q += ' AND file.name=:name'
if ft_space:
q += ' AND file.path=:ft_space'
if ownerid > -1:
q += ' AND file.details.owner.id=:ownerid'
if parent:
params.addId(2)
if ann_space:
params.addString('ns', ann_space)
if name:
params.addString('name', name)
if ft_space:
params.addString('ft_space', ft_space)
if ownerid > -1:
params.addLong('ownerid', ownerid)
r = [
1L, 'table-name', '/test/features/ft_space',
'/test/features/ann_space'
]
session.qs.projection(
q, mox.Func(lambda o: TestFeatureTable.parameters_equal(params, o))
).AndReturn([r])
self.mox.ReplayAll()
result = OmeroTablesFeatureStore.list_tables(session, name, ft_space,
ann_space, ownerid,
parent)
assert len(result) == 1
assert result[0] == tuple(r)
self.mox.VerifyAll()