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jakesylvestre / cing

Automatically exported from code.google.com/p/cing
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Bad read of CCPN Molecular system #212

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Read Helge's project file. Available from helge.meyer@ch.tum.de
This is a continuation of issue 210.
Wim has the project. Wim, can I ask you to look at the trace below. The project 
reads fine with Analysis so this is somewhat CING specific perhaps?

What is the expected output? What do you see instead?

==> Importing data from Ccpn project "Qua1"
Error loading file for:  None
Reading:  <open file 
'/Users/jd/tmp/cingTmp/Qua1/ccp/molecule/MolSystem/._Molecularsystem+Qua1_meyer_
2009-10-28-17-16-28-165_00001.xml', mode 'r' at 
0x590b728>
Last xml tag read:  None
Parser state was:  starting
Object stack was empty
E
======================================================================
ERROR: testInitCcpn (__main__.AllChecks)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/test/test_ccpn.py", line 78, in testInitCcpn
    self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=modelCount))
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 2262, in initCcpn
    if not ccpn.importFromCcpn(modelCount = modelCount):
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 331, in importFromCcpn
    if not self.importFromCcpnMolecule(modelCount = modelCount):
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 405, in importFromCcpnMolecule
    if not self._getCcpnMolSystemList():
  File "/Users/jd/workspace34/cing/python/cing/PluginCode/Ccpn.py", line 291, in _getCcpnMolSystemList
    ccpnMolSystemList = self.ccpnProject.sortedMolSystems()
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 21522, in sortedMolSystems
    root.refreshTopObjects('ccp.molecule.MolSystem')
  File "/Users/jd/workspace34/ccpn/python/memops/api/Implementation.py", line 16976, in refreshTopObjects
    topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 251, in loadFromFile
    partialLoad=partialLoad)
  File "/Users/jd/workspace34/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace34/ccpn/python/memops/xml/Implementation.py", line 4390, in loadFromStream
    for event, elem in ElementTree.iterparse(stream, events=("start", "end")):
  File "<string>", line 64, in __iter__
SyntaxError: not well-formed (invalid token): line 1, column 0

----------------------------------------------------------------------
Ran 1 test in 2.394s

FAILED (errors=1)

Original issue reported on code.google.com by jurge...@gmail.com on 30 Oct 2009 at 11:18

GoogleCodeExporter commented 9 years ago 
I need to keep the list fresh.

Original comment by jurge...@gmail.com on 5 Nov 2009 at 1:10