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@maedoc
Created July 25, 2014 10:02
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cff importer failure
(env)duke@fob:~/dev/tvb.svn/tvb/trunk$ python framework_tvb/tvb/tests/framework/adapters/uploaders/cff_importer_test.py
2014-07-25 12:00:46,434 - WARNING - tvb.core.entities.model_manager - Your Database tables will be deleted.
2014-07-25 12:00:48,078 - INFO - tvb.core.entities.model_manager - Database was cleanup!
2014-07-25 12:00:48,089 - INFO - tvb.core.entities.model_manager - Initializing Database
2014-07-25 12:00:48,986 - INFO - tvb.core.entities.model_manager - Database Default Tables created successfully!
2014-07-25 12:00:49,663 - ERROR - tvb.datatypes.surfaces_scientific - Failed to import geodesic distance package from externals...
2014-07-25 12:00:49,663 - ERROR - tvb.datatypes.surfaces_scientific - Check it's configured, externals/geodesic_distance/setup.py
2014-07-25 12:00:52,829 - INFO - tvb.core.adapters.introspector - tvb.adapters.creators.local_connectivity_creator will be stored new in DB
2014-07-25 12:00:53,075 - INFO - tvb.core.adapters.introspector - tvb.adapters.creators.stimulus_creator will be stored new in DB
2014-07-25 12:00:53,338 - INFO - tvb.core.adapters.introspector - tvb.adapters.creators.stimulus_creator will be stored new in DB
2014-07-25 12:00:53,730 - INFO - tvb.simulator.noise - Additive(ntau, random_stream, nsig): initing...
2014-07-25 12:00:53,757 - INFO - tvb.simulator.integrators - HeunDeterministic(dt): initing...
2014-07-25 12:00:55,721 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.cross_correlation_adapter will be stored new in DB
2014-07-25 12:00:56,001 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.cross_correlation_adapter will be stored new in DB
2014-07-25 12:00:56,262 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.fmri_balloon_adapter will be stored new in DB
2014-07-25 12:00:56,509 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.fourier_adapter will be stored new in DB
2014-07-25 12:00:56,748 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.ica_adapter will be stored new in DB
2014-07-25 12:00:56,987 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.metrics_group_timeseries will be stored new in DB
2014-07-25 12:00:57,227 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.node_coherence_adapter will be stored new in DB
2014-07-25 12:00:57,457 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.node_complex_coherence_adapter will be stored new in DB
2014-07-25 12:00:57,686 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.node_covariance_adapter will be stored new in DB
2014-07-25 12:00:57,905 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.pca_adapter will be stored new in DB
2014-07-25 12:00:58,141 - INFO - tvb.core.adapters.introspector - tvb.adapters.analyzers.wavelet_adapter will be stored new in DB
/usr/lib/python2.7/dist-packages/nose/util.py:14: DeprecationWarning: The compiler package is deprecated and removed in Python 3.x.
from compiler.consts import CO_GENERATOR
2014-07-25 12:00:58,770 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.cff_importer will be stored new in DB
2014-07-25 12:00:59,006 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.connectivity_measure_importer will be stored new in DB
2014-07-25 12:00:59,233 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.csv_connectivity_importer will be stored new in DB
2014-07-25 12:00:59,463 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.gifti_surface_importer will be stored new in DB
2014-07-25 12:00:59,683 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.gifti_timeseries_importer will be stored new in DB
2014-07-25 12:00:59,915 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.lookup_table_importer will be stored new in DB
2014-07-25 12:01:00,145 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.mat_timeseries_importer will be stored new in DB
2014-07-25 12:01:00,383 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.networkx_importer will be stored new in DB
2014-07-25 12:01:00,614 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.nifti_importer will be stored new in DB
2014-07-25 12:01:00,850 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.obj_importer will be stored new in DB
2014-07-25 12:01:01,081 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.projection_matrix_importer will be stored new in DB
2014-07-25 12:01:01,307 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.projection_matrix_importer will be stored new in DB
2014-07-25 12:01:01,538 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.region_mapping_importer will be stored new in DB
2014-07-25 12:01:01,854 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.sensors_importer will be stored new in DB
2014-07-25 12:01:02,090 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.tvb_importer will be stored new in DB
2014-07-25 12:01:02,329 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.zip_connectivity_importer will be stored new in DB
2014-07-25 12:01:02,579 - INFO - tvb.core.adapters.introspector - tvb.adapters.uploaders.zip_surface_importer will be stored new in DB
2014-07-25 12:01:03,284 - INFO - tvb.simulator.models - Generic2dOscillator(**kwargs): initing...
2014-07-25 12:01:03,310 - INFO - tvb.simulator.integrators - HeunDeterministic(dt): initing...
2014-07-25 12:01:03,311 - INFO - tvb.simulator.monitors - TemporalAverage(period, variables_of_interest): initing...
2014-07-25 12:01:03,439 - INFO - tvb.core.adapters.introspector - tvb.adapters.simulator.simulator_adapter will be stored new in DB
2014-07-25 12:01:05,467 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be stored new in DB
2014-07-25 12:01:05,701 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be stored new in DB
2014-07-25 12:01:05,937 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be stored new in DB
2014-07-25 12:01:06,169 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be stored new in DB
2014-07-25 12:01:06,398 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.eeg_monitor will be stored new in DB
2014-07-25 12:01:06,621 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.connectivity will be stored new in DB
2014-07-25 12:01:06,841 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.cross_coherence will be stored new in DB
2014-07-25 12:01:07,066 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.cross_correlation will be stored new in DB
2014-07-25 12:01:07,284 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.covariance will be stored new in DB
2014-07-25 12:01:07,512 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.matrix_viewer will be stored new in DB
2014-07-25 12:01:07,742 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.histogram will be stored new in DB
2014-07-25 12:01:07,958 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.ica will be stored new in DB
2014-07-25 12:01:08,196 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.eeg_monitor will be updated
2014-07-25 12:01:08,315 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.local_connectivity_view will be stored new in DB
2014-07-25 12:01:08,539 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.matrix_viewer will be updated
2014-07-25 12:01:08,672 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.mplh5_coherence_spectrum will be stored new in DB
2014-07-25 12:01:08,916 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.mplh5_cross_correlation will be stored new in DB
2014-07-25 12:01:09,235 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.mplh5_fourier_spectrum will be stored new in DB
2014-07-25 12:01:09,471 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.mplh5_topographic will be stored new in DB
2014-07-25 12:01:09,707 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.mplh5_wavelet_spectrogram will be stored new in DB
2014-07-25 12:01:09,942 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.pca will be stored new in DB
2014-07-25 12:01:10,185 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.pse_discrete will be stored new in DB
2014-07-25 12:01:10,452 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.pse_isocline will be stored new in DB
2014-07-25 12:01:10,688 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be updated
2014-07-25 12:01:10,821 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be updated
2014-07-25 12:01:10,943 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.sensors will be stored new in DB
2014-07-25 12:01:11,181 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.sensors will be stored new in DB
2014-07-25 12:01:11,405 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.sensors will be stored new in DB
2014-07-25 12:01:11,639 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.brain will be updated
2014-07-25 12:01:11,768 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.surface_view will be stored new in DB
2014-07-25 12:01:12,001 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.surface_view will be stored new in DB
2014-07-25 12:01:12,219 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.time_series will be stored new in DB
2014-07-25 12:01:12,435 - INFO - tvb.core.adapters.introspector - tvb.adapters.visualizers.time_series_volume will be stored new in DB
2014-07-25 12:01:13,273 - WARNING - tvb.core.adapters.introspector - No group having class=MatlabAdapter stored for portlet ISOS.
2014-07-25 12:01:13,279 - WARNING - tvb.core.adapters.introspector - No group having class=MatlabAdapter stored for portlet CCWD.
2014-07-25 12:01:13,284 - WARNING - tvb.core.adapters.introspector - No group having class=MatlabAdapter stored for portlet ISOSTOPO.
2014-07-25 12:01:13,289 - WARNING - tvb.core.adapters.introspector - No group having class=MatlabAdapter stored for portlet STW.
2014-07-25 12:01:13,295 - WARNING - tvb.core.adapters.introspector - No group having class=MatlabAdapter stored for portlet NBCB.
2014-07-25 12:01:15,375 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter1 will be stored new in DB
2014-07-25 12:01:15,695 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter1 will be stored new in DB
2014-07-25 12:01:15,926 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter2 will be stored new in DB
2014-07-25 12:01:16,163 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter2 will be stored new in DB
2014-07-25 12:01:16,402 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter3 will be stored new in DB
2014-07-25 12:01:16,644 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter3 will be stored new in DB
2014-07-25 12:01:16,883 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.testadapter3 will be stored new in DB
2014-07-25 12:01:17,118 - INFO - tvb.core.adapters.introspector - tvb.tests.framework.adapters.ndimensionarrayadapter will be stored new in DB
2014-07-25 12:01:17,435 - ERROR - tvb.core.portlets.xml_reader. - The XML file /home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/tests/framework/core/portlets/test_portlet.xml is not valid. Error message: http://www.thevirtualbrain.org/schema/tvb.xsd: ExpatError: syntax error: line 1, column 49
2014-07-25 12:01:17,437 - ERROR - tvb.core.adapters.introspector - The XML file /home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/tests/framework/core/portlets/test_portlet.xml is not valid. Error message: http://www.thevirtualbrain.org/schema/tvb.xsd: ExpatError: syntax error: line 1, column 49
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/adapters/introspector.py", line 179, in __get_portlets
portlet_reader = XMLPortletReader.get_instance(complete_file_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/adapters/xml_reader.py", line 138, in get_instance
new_reader = cls(xml_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/adapters/xml_reader.py", line 158, in __init__
raise XmlParserException(msg + "Error message: " + str(errstr))
XmlParserException: The XML file /home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/tests/framework/core/portlets/test_portlet.xml is not valid. Error message: http://www.thevirtualbrain.org/schema/tvb.xsd: ExpatError: syntax error: line 1, column 49
2014-07-25 12:01:17,438 - ERROR - tvb.core.adapters.introspector - Invalid Portlet description File test_portlet.xml will continue without it!!
2014-07-25 12:01:17,445 - WARNING - tvb.core.adapters.introspector - Could not import events folder.
'module' object has no attribute 'EVENTS_FOLDER'
2014-07-25 12:01:17,562 - INFO - tvb.core.services.user_service - Registering user admin !
2014-07-25 12:01:18,056 - INFO - tvb.core.services.flow_service - Starting operation CFF_Importer.launch
2014-07-25 12:01:18,107 - ERROR - tvb.adapters.uploaders.cff_importer - 'dn_position'
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 113, in launch
self._parse_connectome_network(network)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 150, in _parse_connectome_network
conn = networkx2connectivity(net.data, self.storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_connectivity.py", line 87, in networkx2connectivity
return networkx_cmt_2connectivity(network, storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_connectivity.py", line 167, in networkx_cmt_2connectivity
positions.append(list(node_data[KEY_CMT_COORDINATES]))
KeyError: 'dn_position'
2014-07-25 12:01:18,122 - ERROR - tvb.adapters.uploaders.cff_importer - 'h5py.h5f.FileID' object has no attribute 'valid'
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 120, in launch
self._parse_connectome_surfaces(surfaces, cdatas)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 181, in _parse_connectome_surfaces
triangles, self.storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_surface.py", line 176, in gifti2surface
surface.set_metadata(meta)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/traits/types_mapped.py", line 333, in set_metadata
store_manager.set_metadata(meta_dictionary, data_name, tvb_specific_metadata, where)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 314, in set_metadata
self.close_file()
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 514, in close_file
self.__close_file()
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 567, in __close_file
if hdf5_file is not None and hdf5_file.fid.valid:
AttributeError: 'h5py.h5f.FileID' object has no attribute 'valid'
2014-07-25 12:01:18,135 - INFO - tvb.adapters.uploaders.cff_importer - Output from cfflib2 library: Loading file. Created temporary file: /tmp/cff_74794894/CNetwork/tvb_connectivity_matrix.gpickle
Succeed.
Will not remove file /tmp/cff_74794894/CNetwork/tvb_connectivity_matrix.gpickle from file system
Remove .data attribute
Remove .tmpsrc attribute
2014-07-25 12:01:18,164 - INFO - tvb.core.services.flow_service - Finished operation:CFF_Importer.launch
F2014-07-25 12:01:18,242 - INFO - tvb.core.services.flow_service - Starting operation CFF_Importer.launch
2014-07-25 12:01:18,290 - ERROR - tvb.adapters.uploaders.cff_importer - 'dn_position'
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 113, in launch
self._parse_connectome_network(network)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 150, in _parse_connectome_network
conn = networkx2connectivity(net.data, self.storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_connectivity.py", line 87, in networkx2connectivity
return networkx_cmt_2connectivity(network, storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_connectivity.py", line 167, in networkx_cmt_2connectivity
positions.append(list(node_data[KEY_CMT_COORDINATES]))
KeyError: 'dn_position'
2014-07-25 12:01:18,305 - ERROR - tvb.adapters.uploaders.cff_importer - 'h5py.h5f.FileID' object has no attribute 'valid'
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 120, in launch
self._parse_connectome_surfaces(surfaces, cdatas)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/cff_importer.py", line 181, in _parse_connectome_surfaces
triangles, self.storage_path)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/adapters/uploaders/handler_surface.py", line 176, in gifti2surface
surface.set_metadata(meta)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/traits/types_mapped.py", line 333, in set_metadata
store_manager.set_metadata(meta_dictionary, data_name, tvb_specific_metadata, where)
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 314, in set_metadata
self.close_file()
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 514, in close_file
self.__close_file()
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/core/entities/file/hdf5_storage_manager.py", line 567, in __close_file
if hdf5_file is not None and hdf5_file.fid.valid:
AttributeError: 'h5py.h5f.FileID' object has no attribute 'valid'
2014-07-25 12:01:18,317 - INFO - tvb.adapters.uploaders.cff_importer - Output from cfflib2 library: Loading file. Created temporary file: /tmp/cff_74246875/CNetwork/tvb_connectivity_matrix.gpickle
Succeed.
Will not remove file /tmp/cff_74246875/CNetwork/tvb_connectivity_matrix.gpickle from file system
Remove .data attribute
Remove .tmpsrc attribute
2014-07-25 12:01:18,344 - INFO - tvb.core.services.flow_service - Finished operation:CFF_Importer.launch
F
======================================================================
FAIL: test_full_import (__main__.CFFUploadTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/tests/framework/core/base_testcase.py", line 229, in dec
result = func(*args, **kwargs)
File "framework_tvb/tvb/tests/framework/adapters/uploaders/cff_importer_test.py", line 80, in test_full_import
self.assertEquals(count, 1)
AssertionError: 0 != 1
======================================================================
FAIL: test_happy_flow_import (__main__.CFFUploadTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/duke/dev/tvb.svn/tvb/trunk/framework_tvb/tvb/tests/framework/core/base_testcase.py", line 229, in dec
result = func(*args, **kwargs)
File "framework_tvb/tvb/tests/framework/adapters/uploaders/cff_importer_test.py", line 67, in test_happy_flow_import
self.assertTrue(0 < len(all_dt))
AssertionError: False is not true
----------------------------------------------------------------------
Ran 2 tests in 0.337s
FAILED (failures=2)
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