[bpindelski@3141592 openmicroscopy (dev_4_4)]$ ./build.py -f components/tools/OmeroPy/build.xml test -DTEST=tablestest Buildfile: /usr/local/dev/openmicroscopy/components/tools/OmeroPy/build.xml Entering /usr/local/dev/openmicroscopy/components/tools/OmeroPy... python-test: Entering /usr/local/dev/openmicroscopy/components/tools/OmeroPy... python-test-single: WARNING: '' not a valid package name; please use only.-separated package names in setup.py running test running egg_info writing target/omero_client.egg-info/PKG-INFO writing top-level names to target/omero_client.egg-info/top_level.txt writing dependency_links to target/omero_client.egg-info/dependency_links.txt reading manifest file 'target/omero_client.egg-info/SOURCES.txt' writing manifest file 'target/omero_client.egg-info/SOURCES.txt' running build_ext testAllColumns_4_4_5 (tablestest.backwards_compatibility.BackwardsCompatibilityTest) ... ok testAddSingleRow (tablestest.hdfstorage.TestHdfStorage) ... ok testCreationWithMetadata (tablestest.hdfstorage.TestHdfStorage) ... ok testHandlesExistingDirectory (tablestest.hdfstorage.TestHdfStorage) ... ok testInitializationOnInitializedFileFails (tablestest.hdfstorage.TestHdfStorage) ... ok testInvalidFile (tablestest.hdfstorage.TestHdfStorage) ... ok testLocking (tablestest.hdfstorage.TestHdfStorage) ... ok testMaskColumn (tablestest.hdfstorage.TestHdfStorage) ... ok testModifyRow (tablestest.hdfstorage.TestHdfStorage) ... ok testReadTicket1951 (tablestest.hdfstorage.TestHdfStorage) ... ok testSimpleCreation (tablestest.hdfstorage.TestHdfStorage) ... ok testSorting (tablestest.hdfstorage.TestHdfStorage) ... ok testStringCol (tablestest.hdfstorage.TestHdfStorage) ... ok testValidFile (tablestest.hdfstorage.TestHdfStorage) ... ok testErrorInGet (tablestest.servants.TestTables) ... ERROR testErrorInStorage (tablestest.servants.TestTables) ... HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5F.c line 1522 in H5Fopen( unable to open file major: File accessability minor: Unable to open file #001: H5F.c line 1313 in H5F_open( unable to read superblock major: File accessability minor: Read failed #002: H5Fsuper.c line 334 in H5F_super_read( unable to find file signature major: File accessability minor: Not an HDF5 file #003: H5Fsuper.c line 155 in H5F_locate_signature( unable to find a valid file signature major: Low-level I/O minor: Unable to initialize object HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5F.c line 2589 in H5Fget_mdc_config( not a file ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5F.c line 2628 in H5Fset_mdc_config( not a file ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5Adeprec.c line 208 in H5Aopen_name( not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc( invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5Gdeprec.c line 296 in H5Gopen1( not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc( invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8. thread 0: #000: H5G.c line 766 in H5Gclose( not a group major: Invalid arguments to routine minor: Inappropriate type Exception tables.exceptions.HDF5ExtError: HDF5ExtError('Problems closing the Group /',) in ignored ok testTableAddData (tablestest.servants.TestTables) ... ERROR testTableIncrDecr (tablestest.servants.TestTables) ... ERROR testTableModifications (tablestest.servants.TestTables) ... ERROR testTablePreInitialized (tablestest.servants.TestTables) ... ERROR testTableSearch (tablestest.servants.TestTables) ... ERROR testTables (tablestest.servants.TestTables) ... ERROR testTablesIGetDirGetsRepoGetsSFCantFindRepoFile (tablestest.servants.TestTables) ... ok testTablesIGetDirGetsRepoGetsSFCantFindRepoObject (tablestest.servants.TestTables) ... ok testTablesIGetDirGetsRepoGetsSFGetsRepo (tablestest.servants.TestTables) ... ok testTablesIGetDirGetsRepoThenNoSF (tablestest.servants.TestTables) ... ok testTablesIGetDirNoRepoCreated (tablestest.servants.TestTables) ... ok testTablesIGetDirNoRepoSet (tablestest.servants.TestTables) ... ok test10049openTableUnreadable (tablestest.service.TestTables) ... ok test2098 (tablestest.service.TestTables) ... ERROR test2855MetadataMethods (tablestest.service.TestTables) ... ERROR test2910 (tablestest.service.TestTables) ... ERROR test3714GetWhereListVars (tablestest.service.TestTables) ... ERROR test4000TableRead (tablestest.service.TestTables) ... ERROR testAllColumnsSameTable (tablestest.service.TestTables) ... ERROR testArrayColumn (tablestest.service.TestTables) ... ok testArrayColumnSize1 (tablestest.service.TestTables) ... ok testBlankTable (tablestest.service.TestTables) ... ERROR testCallContext (tablestest.service.TestTables) ... ok testDelete (tablestest.service.TestTables) ... ok testMask (tablestest.service.TestTables) ... ERROR testTicket2175 (tablestest.service.TestTables) ... ok testUpdate (tablestest.service.TestTables) ... ERROR ====================================================================== ERROR: testErrorInGet (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 318, in testErrorInGet table = tables.getTable(f, self.sf, self.current).table # From mock File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: testTableAddData (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 275, in testTableAddData mocktable = self.testTables(newfile) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 232, in testTables table = tables.getTable(f, self.sf, self.current) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: testTableIncrDecr (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 240, in testTableIncrDecr table = omero.tables.TableI(self.ctx, omero.model.OriginalFileI(1,None), self.sf, storage) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) ====================================================================== ERROR: testTableModifications (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 265, in testTableModifications mocktable = self.testTables() File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 232, in testTables table = tables.getTable(f, self.sf, self.current) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: testTablePreInitialized (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 246, in testTablePreInitialized mocktable = self.testTables() File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 232, in testTables table = tables.getTable(f, self.sf, self.current) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: testTableSearch (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 290, in testTableSearch table = self.testTableAddData(True, False) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 275, in testTableAddData mocktable = self.testTables(newfile) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 232, in testTables table = tables.getTable(f, self.sf, self.current) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: testTables (tablestest.servants.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/servants.py", line 232, in testTables table = tables.getTable(f, self.sf, self.current) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 71, in exc_handler raise omero.InternalException(msg, None, "Internal exception") InternalException: exception ::omero::InternalException { serverStackTrace = Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 61, in exc_handler rv = func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/util/decorators.py", line 28, in handler return func(*args, **kwargs) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 858, in getTable call_context=current.ctx) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero/tables.py", line 505, in __init__ self.can_write = factory.getAdminService().canUpdate(file_obj, call_context) TypeError: canUpdate() takes exactly 2 arguments (3 given) serverExceptionClass = None message = Internal exception } ====================================================================== ERROR: test2098 (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 123, in test2098 table.initialize([lc]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: test2855MetadataMethods (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 159, in test2855MetadataMethods table.initialize([lc]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: test2910 (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 190, in test2910 table.initialize([lc]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: test3714GetWhereListVars (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 228, in test3714GetWhereListVars table.initialize([lc]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: test4000TableRead (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 242, in test4000TableRead table.initialize([lc]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: testAllColumnsSameTable (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 377, in testAllColumnsSameTable table.initialize(cols) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: testBlankTable (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 71, in testBlankTable table.initialize(cols) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: testMask (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 102, in testMask table.initialize([mask]) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ====================================================================== ERROR: testUpdate (tablestest.service.TestTables) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 78, in testUpdate ofile = self.testBlankTable() File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/test/tablestest/service.py", line 71, in testBlankTable table.initialize(cols) File "/usr/local/dev/openmicroscopy/components/tools/OmeroPy/target/omero_Tables_ice.py", line 844, in initialize return _M_omero.grid.Table._op_initialize.invoke(self, ((cols, ), _ctx)) ValidationException: exception ::omero::ValidationException { serverStackTrace = serverExceptionClass = message = Already initialized. } ---------------------------------------------------------------------- Ran 43 tests in 14.090s FAILED (errors=16) Uploaded OriginalFile: 19 22 Closing remaining open files: /Users/bpindelski/omero/tmp/omero_bpindelski/4908/omerovLJ2gN.tmp/mock.h5... Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/local/src/tables/tables/file.py", line 2331, in close_open_files fileh.close() File "/usr/local/src/tables/tables/file.py", line 2135, in close self.root._f_close() AttributeError: 'File' object has no attribute 'root' Error in sys.exitfunc: Traceback (most recent call last): File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/local/src/tables/tables/file.py", line 2331, in close_open_files fileh.close() File "/usr/local/src/tables/tables/file.py", line 2135, in close self.root._f_close() AttributeError: 'File' object has no attribute 'root' Result: 1 Entering /usr/local/dev/openmicroscopy/components/tools/OmeroPy... BUILD SUCCESSFUL Total time: 16 seconds