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, 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_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_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 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 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, 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_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()