def test_get_objects(self):
ims = [
TableStoreHelper.create_image(self.sess, name="image-test"),
TableStoreHelper.create_image(self.sess, name="other-test"),
TableStoreHelper.create_image(self.sess, name="image-test"),
]
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
rs = store.get_objects("Image", {"name": "image-test"})
assert sorted(unwrap(r.getId()) for r in rs) == unwrap([ims[0].getId(), ims[2].getId()])
store.close()
def test_filter_raw(self, emptyquery):
tid = self.create_table_for_fetch(True, [1], 'multi', False)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
if emptyquery:
rvalues = store.filter_raw('')
assert len(rvalues) == 4
assert sorted(rvalues) == [
(-1, 34, 'bb', [90]),
(12, -1, 'aa', [10]),
(12, 56, 'cc', [20]),
(13, -1, 'dd', [30]),
]
else:
rvalues = store.filter_raw(
'(ImageID==13) | (RoiID==34) | (Name=="cc")')
assert len(rvalues) == 3
assert sorted(rvalues) == [
(-1, 34, 'bb', [90]),
(12, 56, 'cc', [20]),
(13, -1, 'dd', [30]),
]
store.close()
def test_get_objects(self):
ims = [
TableStoreHelper.create_image(self.sess, name='image-test'),
TableStoreHelper.create_image(self.sess, name='other-test'),
TableStoreHelper.create_image(self.sess, name='image-test')
]
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
rs = store.get_objects('Image', {'name': 'image-test'})
assert sorted(unwrap(r.getId()) for r in rs) == unwrap(
[ims[0].getId(), ims[2].getId()])
store.close()
def test_get_table(self):
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
with pytest.raises(OmeroTablesFeatureStore.TableUsageException):
store.get_table()
tcols, meta, ftnames = TableStoreHelper.get_columns(
[2], 'multi', False)
store.new_table(meta, ftnames)
assert store.get_table()
store.close()
def test_get_table(self):
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
with pytest.raises(OmeroTablesFeatureStore.TableUsageException):
store.get_table()
tcols, meta, ftnames = TableStoreHelper.get_columns([2], "multi", False)
store.new_table(meta, ftnames)
assert store.get_table()
store.close()
def test_create_file_annotation(self):
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [1], 'multi', False)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
ofile = self.sess.getQueryService().get(
'omero.model.OriginalFile', tid)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
assert store._file_annotation_exists(
'Image', imageid, self.ann_space, tid) == []
link = store.create_file_annotation(
'Image', imageid, self.ann_space, ofile)
p = link.getParent()
c = link.getChild()
assert isinstance(p, omero.model.Image)
assert isinstance(c, omero.model.FileAnnotation)
assert unwrap(p.getId()) == imageid
assert unwrap(c.getFile().getId()) == tid
links = store._file_annotation_exists(
'Image', imageid, self.ann_space, tid)
assert len(links) == 1
assert links[0].__class__ == link.__class__ and links[0].id == link.id
store.close()
def test_open_table(self):
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [1], 'multi', False)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.metadata_names() == tuple(m[1] for m in meta)
assert store.feature_names() == ftnames
store.close()
def test_open_table(self):
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [1], "multi", False
)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.metadata_names() == tuple(m[1] for m in meta)
assert store.feature_names() == ftnames
store.close()
def test_store_unowned(self):
width = 2
user2 = self.create_user_same_group()
tablesess = self.create_client_session(user2)
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
tablesess, self.ft_space, self.name, [width], 'multi', False)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
assert imageid
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
with pytest.raises(
OmeroTablesFeatureStore.FeaturePermissionException):
store.store([0, 0, ''], [10, 20])
store.close()
def test_fetch_by_metadata2(self, meta, coltype, interleave):
tid = self.create_table_for_fetch(True, [1], coltype, interleave)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
fr = store.fetch_by_metadata(meta)
assert len(fr) == 1
fr = fr[0]
assert fr.infonames == ('ImageID', 'RoiID', 'Name')
assert fr.infovalues == (12, 56, 'cc')
assert fr.names == ('x1',)
assert fr.values == (20,)
store.close()
def test_fetch_by_metadata_raw(self, meta, widths):
tid = self.create_table_for_fetch(True, widths, 'multi', False)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
rvalues = store.fetch_by_metadata_raw(meta)
assert len(rvalues) == 2
if widths == [1]:
assert rvalues[0] == (12, -1, 'aa', [10])
assert rvalues[1] == (12, 56, 'cc', [20])
else:
assert rvalues[0] == (12, -1, 'aa', [11, 12], [13, 14, 15])
assert rvalues[1] == (12, 56, 'cc', [31, 32], [33, 34, 35])
store.close()
def test_new_table(self):
tcols, meta, ftnames = TableStoreHelper.get_columns(
[2], 'multi', False)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.new_table(meta, ftnames)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.metadata_names() == tuple(m[1] for m in meta)
assert store.feature_names() == ftnames
# Need to reload
# ofile = store.table.getOriginalFile()
tid = unwrap(store.table.getOriginalFile().getId())
ofile = self.sess.getQueryService().get('OriginalFile', tid)
assert unwrap(ofile.getName()) == self.name
assert unwrap(ofile.getPath()) == self.ft_space
store.close()
def test_store_unowned(self):
width = 2
user2 = self.create_user_same_group()
tablesess = self.create_client_session(user2)
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
tablesess, self.ft_space, self.name, [width], "multi", False
)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
assert imageid
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
with pytest.raises(OmeroTablesFeatureStore.FeaturePermissionException):
store.store([0, 0, ""], [10, 20])
store.close()
def test_fetch_by_metadata2(self, meta, coltype, interleave):
tid = self.create_table_for_fetch(True, [1], coltype, interleave)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
fr = store.fetch_by_metadata(meta)
assert len(fr) == 1
fr = fr[0]
assert fr.infonames == ("ImageID", "RoiID", "Name")
assert fr.infovalues == (12, 56, "cc")
assert fr.names == ("x1",)
assert fr.values == (20,)
store.close()
def test_filter(self, coltype, interleave, widths):
tid = self.create_table_for_fetch(True, widths, coltype, interleave)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
fr = store.filter('(ImageID==12345) | (RoiID==34) | (Name=="abcde")')
assert len(fr) == 1
fr = fr[0]
assert fr.infonames == ('ImageID', 'RoiID', 'Name')
assert fr.infovalues == (-1, 34, 'bb')
if widths == [1]:
assert fr.names == ('x1',)
assert fr.values == (90,)
else:
assert fr.names == ('x1', 'x2', 'x3', 'x4', 'x5')
assert fr.values == (21, 22, 23, 24, 25)
store.close()
def test_new_table(self):
tcols, meta, ftnames = TableStoreHelper.get_columns([2], "multi", False)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.new_table(meta, ftnames)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.metadata_names() == tuple(m[1] for m in meta)
assert store.feature_names() == ftnames
# Need to reload
# ofile = store.table.getOriginalFile()
tid = unwrap(store.table.getOriginalFile().getId())
ofile = self.sess.getQueryService().get("OriginalFile", tid)
assert unwrap(ofile.getName()) == self.name
assert unwrap(ofile.getPath()) == self.ft_space
store.close()
def test_fetch_by_metadata_raw(self, meta, widths):
tid = self.create_table_for_fetch(True, widths, "multi", False)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
rvalues = store.fetch_by_metadata_raw(meta)
assert len(rvalues) == 2
if widths == [1]:
assert rvalues[0] == (12, -1, "aa", [10])
assert rvalues[1] == (12, 56, "cc", [20])
else:
assert rvalues[0] == (12, -1, "aa", [11, 12], [13, 14, 15])
assert rvalues[1] == (12, 56, "cc", [31, 32], [33, 34, 35])
store.close()
def test_fetch_by_metadata3(self, coltype, interleave):
tid = self.create_table_for_fetch(True, [2, 3], coltype, interleave)
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
meta = {'ImageID': 12}
fr = store.fetch_by_metadata(meta)
assert len(fr) == 2
fr0, fr1 = fr
assert fr0.infonames == ('ImageID', 'RoiID', 'Name')
assert fr1.infonames == ('ImageID', 'RoiID', 'Name')
assert fr0.infovalues == (12, -1, 'aa')
assert fr1.infovalues == (12, 56, 'cc')
assert fr0.names == ('x1', 'x2', 'x3', 'x4', 'x5')
assert fr1.names == ('x1', 'x2', 'x3', 'x4', 'x5')
assert fr0.values == (11, 12, 13, 14, 15)
assert fr1.values == (31, 32, 33, 34, 35)
store.close()
def test_filter_raw(self, emptyquery):
tid = self.create_table_for_fetch(True, [1], "multi", False)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
if emptyquery:
rvalues = store.filter_raw("")
assert len(rvalues) == 4
assert sorted(rvalues) == [
(-1, 34, "bb", [90]),
(12, -1, "aa", [10]),
(12, 56, "cc", [20]),
(13, -1, "dd", [30]),
]
else:
rvalues = store.filter_raw('(ImageID==13) | (RoiID==34) | (Name=="cc")')
assert len(rvalues) == 3
assert sorted(rvalues) == [(-1, 34, "bb", [90]), (12, 56, "cc", [20]), (13, -1, "dd", [30])]
store.close()
def test_filter(self, coltype, interleave, widths):
tid = self.create_table_for_fetch(True, widths, coltype, interleave)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
fr = store.filter('(ImageID==12345) | (RoiID==34) | (Name=="abcde")')
assert len(fr) == 1
fr = fr[0]
assert fr.infonames == ("ImageID", "RoiID", "Name")
assert fr.infovalues == (-1, 34, "bb")
if widths == [1]:
assert fr.names == ("x1",)
assert fr.values == (90,)
else:
assert fr.names == ("x1", "x2", "x3", "x4", "x5")
assert fr.values == (21, 22, 23, 24, 25)
store.close()
def test_fetch_by_metadata3(self, coltype, interleave):
tid = self.create_table_for_fetch(True, [2, 3], coltype, interleave)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
meta = {"ImageID": 12}
fr = store.fetch_by_metadata(meta)
assert len(fr) == 2
fr0, fr1 = fr
assert fr0.infonames == ("ImageID", "RoiID", "Name")
assert fr1.infonames == ("ImageID", "RoiID", "Name")
assert fr0.infovalues == (12, -1, "aa")
assert fr1.infovalues == (12, 56, "cc")
assert fr0.names == ("x1", "x2", "x3", "x4", "x5")
assert fr1.names == ("x1", "x2", "x3", "x4", "x5")
assert fr0.values == (11, 12, 13, 14, 15)
assert fr1.values == (31, 32, 33, 34, 35)
store.close()
def test_create_file_annotation(self):
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [1], "multi", False
)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
ofile = self.sess.getQueryService().get("omero.model.OriginalFile", tid)
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
assert store._file_annotation_exists("Image", imageid, self.ann_space, tid) == []
link = store.create_file_annotation("Image", imageid, self.ann_space, ofile)
p = link.getParent()
c = link.getChild()
assert isinstance(p, omero.model.Image)
assert isinstance(c, omero.model.FileAnnotation)
assert unwrap(p.getId()) == imageid
assert unwrap(c.getFile().getId()) == tid
links = store._file_annotation_exists("Image", imageid, self.ann_space, tid)
assert len(links) == 1
assert links[0].__class__ == link.__class__ and links[0].id == link.id
store.close()
def test_store(self, exists, replace):
width = 2
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [width], "multi", False
)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
if exists:
store.store([imageid, -1, "aa"], [10, 20])
assert store.table.getNumberOfRows() == 1
store.store([imageid, -1, "aa"], [10, 20], replace=replace)
if exists and not replace:
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, imageid]
assert d[1].values == [-1, -1]
assert d[2].values == ["aa", "aa"]
assert d[3].values == [[10, 20], [10, 20]]
else:
assert store.table.getNumberOfRows() == 1
d = store.table.readCoordinates(range(0, 1)).columns
assert len(d) == 4
assert d[0].values == [imageid]
assert d[1].values == [-1]
assert d[2].values == ["aa"]
assert d[3].values == [[10, 20]]
store.store([-1, roiid, "bb"], [90, 80], replace=replace)
if exists and not replace:
assert store.table.getNumberOfRows() == 3
d = store.table.readCoordinates(range(0, 3)).columns
assert len(d) == 4
assert d[0].values == [imageid, imageid, -1]
assert d[1].values == [-1, -1, roiid]
assert d[2].values == ["aa", "aa", "bb"]
assert d[3].values == [[10, 20], [10, 20], [90, 80]]
else:
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, -1]
assert d[1].values == [-1, roiid]
assert d[2].values == ["aa", "bb"]
assert d[3].values == [[10, 20], [90, 80]]
# qs = self.sess.getQueryService()
# q = 'SELECT l.child FROM %sAnnotationLink l WHERE l.parent.id=%d'
# anns = qs.findAllByQuery(q % ('Image', imageid), None)
# assert len(anns) == 1
# assert unwrap(anns[0].getFile().getId()) == tid
# anns = qs.findAllByQuery(q % ('Roi', roiid), None)
# assert len(anns) == 1
# assert unwrap(anns[0].getFile().getId()) == tid
store.close()
def test_delete(self, owned):
if owned:
tablesess = self.sess
else:
user2 = self.create_user_same_group()
tablesess = self.create_client_session(user2)
iid1 = unwrap(TableStoreHelper.create_image(self.sess).getId())
iid2 = unwrap(TableStoreHelper.create_image(self.sess).getId())
store = FeatureTable(tablesess, self.name, self.ft_space, self.ann_space)
store.new_table([("Long", "id")], ["x"])
ofile = store.get_table().getOriginalFile()
link1 = store.create_file_annotation("Image", iid1, self.ann_space, ofile)
link2 = store.create_file_annotation("Image", iid2, self.ann_space, ofile)
if not owned:
store.close()
# Reopen the store with a different session
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(unwrap(ofile.getId()))
def get(obj):
# Fetch the latest copy of an object
return self.sess.getQueryService().find("omero.model.%s" % obj.__class__.__name__, unwrap(obj.getId()))
assert get(link1) is not None
assert get(link1.getParent()) is not None
assert get(link1.getChild())
assert get(link1.getChild().getFile())
assert get(link2)
assert get(link2.getParent())
assert get(link2.getChild())
assert get(link2.getChild().getFile())
if owned:
store.delete()
assert get(link1) is None
assert get(link1.getParent())
assert get(link1.getChild()) is None
assert get(link1.getChild().getFile()) is None
assert get(link2) is None
assert get(link2.getParent())
assert get(link2.getChild()) is None
assert get(link2.getChild().getFile()) is None
else:
with pytest.raises(OmeroTablesFeatureStore.FeaturePermissionException):
store.delete()
store.close()
def test_store_multi(self, coltype, interleave):
widths = [2, 3]
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, widths, coltype, interleave)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
store.store([imageid, -1, 'aa'], [10, 20, 30, 40, 50])
assert store.table.getNumberOfRows() == 1
assert store.table.getNumberOfRows() == 1
d = store.table.readCoordinates(range(0, 1)).columns
if coltype == 'single':
assert len(d) == 8
if interleave:
assert [c.values for c in d] == [
[imageid], [10], [-1], [20], ['aa'], [30], [40], [50]]
else:
assert [c.values for c in d] == [
[imageid], [-1], ['aa'], [10], [20], [30], [40], [50]]
else:
assert len(d) == 5
if interleave:
assert [c.values for c in d] == [
[imageid], [[10, 20]], [-1], [[30, 40, 50]], ['aa']]
else:
assert [c.values for c in d] == [
[imageid], [-1], ['aa'], [[10, 20]], [[30, 40, 50]]]
store.store([-1, roiid, 'bb'], [90, 80, 70, 60, 50])
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
if coltype == 'single':
assert len(d) == 8
if interleave:
assert [c.values for c in d] == [
[imageid, -1],
[10, 90],
[-1, roiid],
[20, 80],
['aa', 'bb'],
[30, 70],
[40, 60],
[50, 50]]
else:
assert [c.values for c in d] == [
[imageid, -1],
[-1, roiid],
['aa', 'bb'],
[10, 90],
[20, 80],
[30, 70],
[40, 60],
[50, 50]]
else:
assert len(d) == 5
if interleave:
assert [c.values for c in d] == [
[imageid, -1],
[[10, 20], [90, 80]],
[-1, roiid],
[[30, 40, 50], [70, 60, 50]],
['aa', 'bb']]
else:
assert [c.values for c in d] == [
[imageid, -1],
[-1, roiid],
['aa', 'bb'],
[[10, 20], [90, 80]],
[[30, 40, 50], [70, 60, 50]]]
store.close()
def test_store(self, exists, replace):
width = 2
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [width], 'multi', False)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
if exists:
store.store([imageid, -1, 'aa'], [10, 20])
assert store.table.getNumberOfRows() == 1
store.store([imageid, -1, 'aa'], [10, 20], replace=replace)
if exists and not replace:
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, imageid]
assert d[1].values == [-1, -1]
assert d[2].values == ['aa', 'aa']
assert d[3].values == [[10, 20], [10, 20]]
else:
assert store.table.getNumberOfRows() == 1
d = store.table.readCoordinates(range(0, 1)).columns
assert len(d) == 4
assert d[0].values == [imageid]
assert d[1].values == [-1]
assert d[2].values == ['aa']
assert d[3].values == [[10, 20]]
store.store([-1, roiid, 'bb'], [90, 80], replace=replace)
if exists and not replace:
assert store.table.getNumberOfRows() == 3
d = store.table.readCoordinates(range(0, 3)).columns
assert len(d) == 4
assert d[0].values == [imageid, imageid, -1]
assert d[1].values == [-1, -1, roiid]
assert d[2].values == ['aa', 'aa', 'bb']
assert d[3].values == [[10, 20], [10, 20], [90, 80]]
else:
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, -1]
assert d[1].values == [-1, roiid]
assert d[2].values == ['aa', 'bb']
assert d[3].values == [[10, 20], [90, 80]]
# qs = self.sess.getQueryService()
# q = 'SELECT l.child FROM %sAnnotationLink l WHERE l.parent.id=%d'
# anns = qs.findAllByQuery(q % ('Image', imageid), None)
# assert len(anns) == 1
# assert unwrap(anns[0].getFile().getId()) == tid
# anns = qs.findAllByQuery(q % ('Roi', roiid), None)
# assert len(anns) == 1
# assert unwrap(anns[0].getFile().getId()) == tid
store.close()
def test_store_pending_flush(self):
width = 2
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [width], "multi", False
)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
store.store_pending([imageid, -1, "aa"], [10, 20])
assert store.table.getNumberOfRows() == 0
store.store_pending([-1, roiid, "bb"], [90, 80])
assert store.table.getNumberOfRows() == 0
store.store_flush()
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, -1]
assert d[1].values == [-1, roiid]
assert d[2].values == ["aa", "bb"]
assert d[3].values == [[10, 20], [90, 80]]
store.store_flush()
assert store.table.getNumberOfRows() == 2
store.close()
def test_store_multi(self, coltype, interleave):
widths = [2, 3]
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, widths, coltype, interleave
)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
store.store([imageid, -1, "aa"], [10, 20, 30, 40, 50])
assert store.table.getNumberOfRows() == 1
assert store.table.getNumberOfRows() == 1
d = store.table.readCoordinates(range(0, 1)).columns
if coltype == "single":
assert len(d) == 8
if interleave:
assert [c.values for c in d] == [[imageid], [10], [-1], [20], ["aa"], [30], [40], [50]]
else:
assert [c.values for c in d] == [[imageid], [-1], ["aa"], [10], [20], [30], [40], [50]]
else:
assert len(d) == 5
if interleave:
assert [c.values for c in d] == [[imageid], [[10, 20]], [-1], [[30, 40, 50]], ["aa"]]
else:
assert [c.values for c in d] == [[imageid], [-1], ["aa"], [[10, 20]], [[30, 40, 50]]]
store.store([-1, roiid, "bb"], [90, 80, 70, 60, 50])
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
if coltype == "single":
assert len(d) == 8
if interleave:
assert [c.values for c in d] == [
[imageid, -1],
[10, 90],
[-1, roiid],
[20, 80],
["aa", "bb"],
[30, 70],
[40, 60],
[50, 50],
]
else:
assert [c.values for c in d] == [
[imageid, -1],
[-1, roiid],
["aa", "bb"],
[10, 90],
[20, 80],
[30, 70],
[40, 60],
[50, 50],
]
else:
assert len(d) == 5
if interleave:
assert [c.values for c in d] == [
[imageid, -1],
[[10, 20], [90, 80]],
[-1, roiid],
[[30, 40, 50], [70, 60, 50]],
["aa", "bb"],
]
else:
assert [c.values for c in d] == [
[imageid, -1],
[-1, roiid],
["aa", "bb"],
[[10, 20], [90, 80]],
[[30, 40, 50], [70, 60, 50]],
]
store.close()
def test_delete(self, owned):
if owned:
tablesess = self.sess
else:
user2 = self.create_user_same_group()
tablesess = self.create_client_session(user2)
iid1 = unwrap(TableStoreHelper.create_image(self.sess).getId())
iid2 = unwrap(TableStoreHelper.create_image(self.sess).getId())
store = FeatureTable(
tablesess, self.name, self.ft_space, self.ann_space)
store.new_table([('Long', 'id')], ['x'])
ofile = store.get_table().getOriginalFile()
link1 = store.create_file_annotation(
'Image', iid1, self.ann_space, ofile)
link2 = store.create_file_annotation(
'Image', iid2, self.ann_space, ofile)
if not owned:
store.close()
# Reopen the store with a different session
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(unwrap(ofile.getId()))
def get(obj):
# Fetch the latest copy of an object
return self.sess.getQueryService().find(
'omero.model.%s' % obj.__class__.__name__, unwrap(obj.getId()))
assert get(link1) is not None
assert get(link1.getParent()) is not None
assert get(link1.getChild())
assert get(link1.getChild().getFile())
assert get(link2)
assert get(link2.getParent())
assert get(link2.getChild())
assert get(link2.getChild().getFile())
if owned:
store.delete()
assert get(link1) is None
assert get(link1.getParent())
assert get(link1.getChild()) is None
assert get(link1.getChild().getFile()) is None
assert get(link2) is None
assert get(link2.getParent())
assert get(link2.getChild()) is None
assert get(link2.getChild().getFile()) is None
else:
with pytest.raises(
OmeroTablesFeatureStore.FeaturePermissionException):
store.delete()
store.close()
def test_store_pending_flush(self):
width = 2
tid, tcols, meta, ftnames = TableStoreHelper.create_table(
self.sess, self.ft_space, self.name, [width], 'multi', False)
imageid = unwrap(TableStoreHelper.create_image(self.sess).getId())
roiid = unwrap(TableStoreHelper.create_roi(self.sess).getId())
store = FeatureTable(
self.sess, self.name, self.ft_space, self.ann_space)
store.open_table(tid)
store.store_pending([imageid, -1, 'aa'], [10, 20])
assert store.table.getNumberOfRows() == 0
store.store_pending([-1, roiid, 'bb'], [90, 80])
assert store.table.getNumberOfRows() == 0
store.store_flush()
assert store.table.getNumberOfRows() == 2
d = store.table.readCoordinates(range(0, 2)).columns
assert len(d) == 4
assert d[0].values == [imageid, -1]
assert d[1].values == [-1, roiid]
assert d[2].values == ['aa', 'bb']
assert d[3].values == [[10, 20], [90, 80]]
store.store_flush()
assert store.table.getNumberOfRows() == 2
store.close()