def testMetadataException(self):
"""
Check whether metadata set methods are blocked on a v1 (pre-5.1) table
"""
ofile = self.uploadHdf5("service-reference-dev_4_4_5.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
expected = 'Tables metadata is only supported for OMERO.tables >= 2'
with pytest.raises(omero.ApiUsageException) as exc:
table.setMetadata('a', rint(1))
with pytest.raises(omero.ApiUsageException) as exc:
table.setAllMetadata({'a': rint(1)})
assert exc.value.message == expected
def testAllColumns_4_4_5(self):
"""
Check whether a table created under 4.4.5 or older is still usable
with a newer server
"""
ofile = self.uploadHdf5("service-reference-dev_4_4_5.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
assert table
expectedTypes = [
omero.grid.FileColumn,
omero.grid.ImageColumn,
omero.grid.RoiColumn,
omero.grid.WellColumn,
omero.grid.PlateColumn,
omero.grid.BoolColumn,
omero.grid.DoubleColumn,
omero.grid.LongColumn,
omero.grid.StringColumn,
omero.grid.MaskColumn
]
# omero.grid.FloatArrayColumn,
# omero.grid.DoubleArrayColumn,
# omero.grid.LongArrayColumn,
expectedNames = [
'filecol',
'imagecol',
'roicol',
'wellcol',
'platecol',
'boolcol',
'doublecol',
'longcol',
'stringcol',
'mask'
]
# 'longarr'
# 'floatarr'
# 'doublearr'
headers = table.getHeaders()
assert [type(x) for x in headers] == expectedTypes
assert [x.name for x in headers] == expectedNames
assert table.getNumberOfRows() == 2
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
# testla = data.columns[10].values
# assert [-2, -1] == testla[0]
# assert [1, 2] == testla[1]
# testda = data.columns[11].values
# assert [-0.25, -0.5] == testda[0]
# assert [0.125, 0.0625] == testda[1]
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updateData = omero.grid.Data(rowNumbers=[1], columns=[updatel])
table.update(updateData)
assert table.getNumberOfRows() == 2
data2 = table.readCoordinates([0, 1])
for n in [0, 1, 2, 3, 4, 5, 6, 8]:
assert data.columns[n].values == data2.columns[n].values
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
assert -1 == testl2[0]
assert 12345 == testl2[1]
def testAllColumnsAndMetadata_5_3_4(self):
"""
Check whether a table created under 5.3.4-5.5.1 prior to the Python 3
work is still usable with a newer server
"""
ofile = self.uploadHdf5("service-reference-dev_5_3_4.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
assert table
metadata = table.getAllMetadata()
assert metadata['__version'] == rstring('2')
assert isinstance(metadata['double'], RFloatI)
assert abs(metadata['double'].val - 0.1) < 1e-8
# WARNING: On the OMERO-server 5.3.4 Docker image this returns an
# RLongI not an RIntI! Maybe pytables already made the decision to
# treat int and longs the same?
# assert isinstance(metadata['int'], RIntI)
assert isinstance(metadata['int'], RLongI)
assert metadata['int'].val == 1
assert isinstance(metadata['long'], RLongI)
assert metadata['long'].val == 1
assert isinstance(metadata['string'], RStringI)
assert metadata['string'].val == 'a'
expectedTypes = [
omero.grid.FileColumn,
omero.grid.ImageColumn,
omero.grid.RoiColumn,
omero.grid.WellColumn,
omero.grid.PlateColumn,
omero.grid.BoolColumn,
omero.grid.DoubleColumn,
omero.grid.LongColumn,
omero.grid.StringColumn,
omero.grid.MaskColumn,
omero.grid.LongArrayColumn,
omero.grid.FloatArrayColumn,
omero.grid.DoubleArrayColumn,
]
expectedNames = [
'filecol',
'imagecol',
'roicol',
'wellcol',
'platecol',
'boolcol',
'doublecol',
'longcol',
'stringcol',
'mask',
'longarr',
'floatarr',
'doublearr',
]
headers = table.getHeaders()
assert [type(x) for x in headers] == expectedTypes
assert [x.name for x in headers] == expectedNames
assert table.getNumberOfRows() == 2
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
testla = data.columns[10].values
assert [-2, -1] == testla[0]
assert [1, 2] == testla[1]
testfa = data.columns[11].values
assert [-0.25, -0.5] == testfa[0]
assert [0.125, 0.0625] == testfa[1]
testda = data.columns[12].values
assert [-0.25, -0.5] == testda[0]
assert [0.125, 0.0625] == testda[1]
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updateData = omero.grid.Data(rowNumbers=[1], columns=[updatel])
table.update(updateData)
assert table.getNumberOfRows() == 2
data2 = table.readCoordinates([0, 1])
for n in [0, 1, 2, 3, 4, 5, 6, 8, 10, 11, 12]:
assert data.columns[n].values == data2.columns[n].values
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
assert -1 == testl2[0]
assert 12345 == testl2[1]
table.close()
def testAllColumns_4_4_5(self):
"""
Check whether a table created under 4.4.5 or older is still usable
with a newer server
"""
ofile = self.uploadHdf5("service-reference-dev_4_4_5.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
assert table
expectedTypes = [
omero.grid.FileColumn,
omero.grid.ImageColumn,
omero.grid.RoiColumn,
omero.grid.WellColumn,
omero.grid.PlateColumn,
omero.grid.BoolColumn,
omero.grid.DoubleColumn,
omero.grid.LongColumn,
omero.grid.StringColumn,
omero.grid.MaskColumn
]
#omero.grid.FloatArrayColumn,
#omero.grid.DoubleArrayColumn,
#omero.grid.LongArrayColumn,
expectedNames = [
'filecol',
'imagecol',
'roicol',
'wellcol',
'platecol',
'boolcol',
'doublecol',
'longcol',
'stringcol',
'mask'
]
#'longarr'
#'floatarr'
#'doublearr'
headers = table.getHeaders()
assert [type(x) for x in headers] == expectedTypes
assert [x.name for x in headers] == expectedNames
assert table.getNumberOfRows() == 2
data = table.readCoordinates([0,1])
testf = data.columns[0].values
assert 10 == testf[0]
assert 20 == testf[1]
testi = data.columns[1].values
assert 30 == testi[0]
assert 40 == testi[1]
testr = data.columns[2].values
assert 50 == testr[0]
assert 60 == testr[1]
testw = data.columns[3].values
assert 70 == testw[0]
assert 80 == testw[1]
testp = data.columns[4].values
assert 90 == testp[0]
assert 100 == testp[1]
testb = data.columns[5].values
assert testb[0]
assert not testb[1]
testd = data.columns[6].values
assert 0.25 == testd[0]
assert 0.5 == testd[1]
testl = data.columns[7].values
assert -1 == testl[0]
assert -2 == testl[1]
tests = data.columns[8].values
assert "abc" == tests[0]
assert "de" == tests[1]
testm = data.columns[9]
self.checkMaskCol(testm)
#testla = data.columns[10].values
#assert [-2, -1] == testla[0]
#assert [1, 2] == testla[1]
#testda = data.columns[11].values
#assert [-0.25, -0.5] == testda[0]
#assert [0.125, 0.0625] == testda[1]
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updateData = omero.grid.Data(rowNumbers = [1], columns = [updatel])
table.update(updateData)
assert table.getNumberOfRows() == 2
data2 = table.readCoordinates([0,1])
for n in [0, 1, 2, 3, 4, 5, 6, 8]:
assert data.columns[n].values == data2.columns[n].values
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
assert -1 == testl2[0]
assert 12345 == testl2[1]
def testAllColumns_4_4_5(self):
"""
Check whether a table created under 4.4.5 or older is still usable
with a newer server
"""
ofile = self.uploadHdf5("service-reference-dev_4_4_5.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
self.assert_(table)
expectedTypes = [
omero.grid.FileColumn,
omero.grid.ImageColumn,
omero.grid.RoiColumn,
omero.grid.WellColumn,
omero.grid.PlateColumn,
omero.grid.BoolColumn,
omero.grid.DoubleColumn,
omero.grid.LongColumn,
omero.grid.StringColumn,
omero.grid.MaskColumn
]
#omero.grid.FloatArrayColumn,
#omero.grid.DoubleArrayColumn,
#omero.grid.LongArrayColumn,
expectedNames = [
'filecol',
'imagecol',
'roicol',
'wellcol',
'platecol',
'boolcol',
'doublecol',
'longcol',
'stringcol',
'mask'
]
#'longarr'
#'floatarr'
#'doublearr'
headers = table.getHeaders()
self.assertEquals([type(x) for x in headers], expectedTypes)
self.assertEquals([x.name for x in headers], expectedNames)
self.assertEquals(table.getNumberOfRows(), 2)
data = table.readCoordinates([0,1])
testf = data.columns[0].values
self.assertEquals(10, testf[0])
self.assertEquals(20, testf[1])
testi = data.columns[1].values
self.assertEquals(30, testi[0])
self.assertEquals(40, testi[1])
testr = data.columns[2].values
self.assertEquals(50, testr[0])
self.assertEquals(60, testr[1])
testw = data.columns[3].values
self.assertEquals(70, testw[0])
self.assertEquals(80, testw[1])
testp = data.columns[4].values
self.assertEquals(90, testp[0])
self.assertEquals(100, testp[1])
testb = data.columns[5].values
self.assertEquals(True, testb[0])
self.assertEquals(False, testb[1])
testd = data.columns[6].values
self.assertEquals(0.25, testd[0])
self.assertEquals(0.5, testd[1])
testl = data.columns[7].values
self.assertEquals(-1, testl[0])
self.assertEquals(-2, testl[1])
tests = data.columns[8].values
self.assertEquals("abc", tests[0])
self.assertEquals("de", tests[1])
testm = data.columns[9]
self.checkMaskCol(testm)
#testla = data.columns[10].values
#self.assertEquals([-2, -1], testla[0])
#self.assertEquals([1, 2], testla[1])
#testda = data.columns[11].values
#self.assertEquals([-0.25, -0.5], testda[0])
#self.assertEquals([0.125, 0.0625], testda[1])
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updateData = omero.grid.Data(rowNumbers = [1], columns = [updatel])
table.update(updateData)
self.assertEquals(table.getNumberOfRows(), 2)
data2 = table.readCoordinates([0,1])
for n in [0, 1, 2, 3, 4, 5, 6, 8]:
self.assertEquals(data.columns[n].values, data2.columns[n].values)
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
self.assertEquals(-1, testl2[0])
self.assertEquals(12345, testl2[1])
def testAllColumns_4_4_5(self):
"""
Check whether a table created under 4.4.5 or older is still usable
with a newer server
"""
ofile = self.uploadHdf5("service-reference-dev_4_4_5.h5.bz2")
grid = self.client.sf.sharedResources()
table = grid.openTable(ofile)
self.assert_(table)
expectedTypes = [
omero.grid.FileColumn, omero.grid.ImageColumn,
omero.grid.RoiColumn, omero.grid.WellColumn,
omero.grid.PlateColumn, omero.grid.BoolColumn,
omero.grid.DoubleColumn, omero.grid.LongColumn,
omero.grid.StringColumn, omero.grid.MaskColumn
]
#omero.grid.FloatArrayColumn,
#omero.grid.DoubleArrayColumn,
#omero.grid.LongArrayColumn,
expectedNames = [
'filecol', 'imagecol', 'roicol', 'wellcol', 'platecol', 'boolcol',
'doublecol', 'longcol', 'stringcol', 'mask'
]
#'longarr'
#'floatarr'
#'doublearr'
headers = table.getHeaders()
self.assertEquals([type(x) for x in headers], expectedTypes)
self.assertEquals([x.name for x in headers], expectedNames)
self.assertEquals(table.getNumberOfRows(), 2)
data = table.readCoordinates([0, 1])
testf = data.columns[0].values
self.assertEquals(10, testf[0])
self.assertEquals(20, testf[1])
testi = data.columns[1].values
self.assertEquals(30, testi[0])
self.assertEquals(40, testi[1])
testr = data.columns[2].values
self.assertEquals(50, testr[0])
self.assertEquals(60, testr[1])
testw = data.columns[3].values
self.assertEquals(70, testw[0])
self.assertEquals(80, testw[1])
testp = data.columns[4].values
self.assertEquals(90, testp[0])
self.assertEquals(100, testp[1])
testb = data.columns[5].values
self.assertEquals(True, testb[0])
self.assertEquals(False, testb[1])
testd = data.columns[6].values
self.assertEquals(0.25, testd[0])
self.assertEquals(0.5, testd[1])
testl = data.columns[7].values
self.assertEquals(-1, testl[0])
self.assertEquals(-2, testl[1])
tests = data.columns[8].values
self.assertEquals("abc", tests[0])
self.assertEquals("de", tests[1])
testm = data.columns[9]
self.checkMaskCol(testm)
#testla = data.columns[10].values
#self.assertEquals([-2, -1], testla[0])
#self.assertEquals([1, 2], testla[1])
#testda = data.columns[11].values
#self.assertEquals([-0.25, -0.5], testda[0])
#self.assertEquals([0.125, 0.0625], testda[1])
# Now try an update
updatel = omero.grid.LongColumn('longcol', '', [12345])
updateData = omero.grid.Data(rowNumbers=[1], columns=[updatel])
table.update(updateData)
self.assertEquals(table.getNumberOfRows(), 2)
data2 = table.readCoordinates([0, 1])
for n in [0, 1, 2, 3, 4, 5, 6, 8]:
self.assertEquals(data.columns[n].values, data2.columns[n].values)
self.checkMaskCol(data2.columns[9])
testl2 = data2.columns[7].values
self.assertEquals(-1, testl2[0])
self.assertEquals(12345, testl2[1])