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Regression
OmeroPy.test.integration.tablestest.test_service.TestTables.testAllColumnsSameTable (from pytest)
Error Message
omero.InternalException: exception ::omero::InternalException
{
serverStackTrace = Traceback (most recent call last):
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 71, in exc_handler
rv = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 31, in handler
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/tables.py", line 285, in addData
self.storage.append(cols)
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 96, in with_lock
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/hdfstorageV2.py", line 85, in flush_after
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/hdfstorageV2.py", line 514, in append
col.append(self.__mea) # Potential corruption !!!
^^^^^^^^^^^^^^^^^^^^^^
File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/columns.py", line 543, in append
masks.append(numpy.fromstring(x, count=len(x),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: The binary mode of fromstring is removed, use frombuffer instead
serverExceptionClass =
message = Internal exception
}Stacktrace
self = <test_service.TestTables object at 0x7fdff3b57a10>
def testAllColumnsSameTable(self):
"""
Check all column types can coexist in the same table
"""
grid = self.client.sf.sharedResources()
repoMap = grid.repositories()
repoObj = repoMap.descriptions[0]
table = grid.newTable(repoObj.id.val, "/test")
assert table
fcol = columns.FileColumnI('filecol', 'file col')
fcol.values = [10, 20]
icol = columns.ImageColumnI('imagecol', 'image col')
icol.values = [30, 40]
rcol = columns.RoiColumnI('roicol', 'roi col')
rcol.values = [50, 60]
wcol = columns.WellColumnI('wellcol', 'well col')
wcol.values = [70, 80]
pcol = columns.PlateColumnI('platecol', 'plate col')
pcol.values = [90, 100]
bcol = columns.BoolColumnI('boolcol', 'bool col')
bcol.values = [True, False]
dcol = columns.DoubleColumnI('doublecol', 'double col')
dcol.values = [0.25, 0.5]
lcol = columns.LongColumnI('longcol', 'long col')
lcol.values = [-1, -2]
scol = columns.StringColumnI('stringcol', 'string col', 46)
scol.values = ["მიკროსკოპის პონი", "de"]
mask = self.createMaskCol()
larr = columns.LongArrayColumnI('longarr', 'longarr col', 2)
larr.values = [[-2, -1], [1, 2]]
farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2)
farr.values = [[-8.0, -4.0], [16.0, 32.0]]
darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2)
darr.values = [[-0.25, -0.5], [0.125, 0.0625]]
cols = [fcol, icol, rcol, wcol, pcol,
bcol, dcol, lcol, scol, mask,
larr, farr, darr]
table.initialize(cols)
> table.addData(cols)
test/integration/tablestest/test_service.py:488:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = 3aa67d8f-2c17-47ea-9909-83f8171ca65c/Table-1ce28416-1aba-4d8b-bdba-9d9d9a885b90 -t -e 1.1:tcp -h 172.18.0.11 -p 36999 -t 60000
cols = [object #0 (::omero::grid::FileColumn)
{
name = filecol
description = file col
values =
{
[0]...
name = boolcol
description = bool col
values =
{
[0] = True
[1] = False
}
}, ...]
_ctx = None
def addData(self, cols, _ctx=None):
> return _M_omero.grid.Table._op_addData.invoke(self, ((cols, ), _ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E omero.InternalException: exception ::omero::InternalException
E {
E serverStackTrace = Traceback (most recent call last):
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 71, in exc_handler
E rv = func(*args, **kwargs)
E ^^^^^^^^^^^^^^^^^^^^^
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 31, in handler
E return func(*args, **kwargs)
E ^^^^^^^^^^^^^^^^^^^^^
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/tables.py", line 285, in addData
E self.storage.append(cols)
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/util/decorators.py", line 96, in with_lock
E return func(*args, **kwargs)
E ^^^^^^^^^^^^^^^^^^^^^
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/hdfstorageV2.py", line 85, in flush_after
E return func(*args, **kwargs)
E ^^^^^^^^^^^^^^^^^^^^^
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/hdfstorageV2.py", line 514, in append
E col.append(self.__mea) # Potential corruption !!!
E ^^^^^^^^^^^^^^^^^^^^^^
E File "/home/omero/workspace/OMERO-test-integration/.venv3/lib64/python3.11/site-packages/omero/columns.py", line 543, in append
E masks.append(numpy.fromstring(x, count=len(x),
E ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E ValueError: The binary mode of fromstring is removed, use frombuffer instead
E
E serverExceptionClass =
E message = Internal exception
E }
../../../../.venv3/lib64/python3.11/site-packages/omero_Tables_ice.py:1273: InternalException