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Not accept invalid CCPN project anymore. #272

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Processing 1lcc produces an invalid CCPN project file. This issue is to 
validate these at NRG and not except invalid ones that would cause problems 
down stream.

Original issue reported on code.google.com by jurge...@gmail.com on 8 Apr 2011 at 2:26

GoogleCodeExporter commented 9 years ago 
Originally started at CING: http://code.google.com/p/cing/issues/detail?id=266

I now leave this to this NRG project.

Original comment by jurge...@gmail.com on 11 Apr 2011 at 12:19

GoogleCodeExporter commented 9 years ago 
Ok, I've setup a test in NRG from processDOCR_FRED.csh to read and validate the 
CCPN project.
If the validate fails this entry's CCPN file will not get into DOCR. 

The original and parsed data will still be maintained in NRG!

Chris could you please:

-1- update NRG to r178. You probably want to customize:
from nmrrestrntsgrid.settings.localConstants import nrg_tmp_dir
-2- check my code by running the unit check:
python  $dir_nrg_python/nmrrestrntsgrid/util/test/test_checkCcpnProject.py
This will check 1brv and 1lcc . 1brv should pass whereas 1lcc should fail.
-3- Reprocess these same 2 entries in production.
Then make sure 1lcc is no longer in DOCR and 1brv still is.

When this is done we can reprocess the other few bad entries.

Original comment by jurge...@gmail.com on 13 Apr 2011 at 9:41

GoogleCodeExporter commented 9 years ago 
It's just 5 entries now: 

1gnc
1lcc
1lcd
1qch
2neo

There might be more soon though when I reprocess the full NRG-CING.

Chris can you do all 5 above then?

Original comment by jurge...@gmail.com on 13 Apr 2011 at 9:52

GoogleCodeExporter commented 9 years ago 
Actually, it's only 1lcc/d. The others aren't in for other reasons perhaps. So 
only need to do 2.

Original comment by jurge...@gmail.com on 13 Apr 2011 at 10:05

GoogleCodeExporter commented 9 years ago 
I find another one that gives an inconsistent project 2l2z. And perhaps 2l2e 
2l2w 2l2x 2l2y.

Wim, could you fix this bug? I believe it's different from others. The log is 
below.
Chris, can you rerun 1lcc/d as per above? Then I will implement that we skip 
the CCPN output for these (we should keep the NMR-STAR of course) entries from 
NRG as we can not produce output that is no good.

Thanks guys!

jd:duvel/~/ analysis 2l2z
Model read finished. Duration 1.17767095566 
Model validity check skipped
CcpNmr Analysis Version 2.1. Release 5 (Copyright 2003-2010 CCPN)
Distribution created Wed Aug 11 17:37:18 2010

If you use CcpNmr Analysis, please quote the following reference:

Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne 
Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides
and Ernest D. Laue (2005). The CCPN Data Model for NMR Spectroscopy: 
Development of a Software Pipeline. Proteins 59, 687 - 696.

A copy of the in-program documentation is located at:
http://www.ccpn.ac.uk/documentation

For how-tos and FAQs visit the CCPN wiki site at:
http://www.ccpn.ac.uk/wiki

To report bugs use the bug tracker at:
http://www.ccpn.ac.uk/bugs

For help and support join the mailing list at:
http://www.ccpn.ac.uk/support

For Python API documentation, tutorials and CCPN web applications visit:
http://www.ccpn.ac.uk/

Error loading file for:  <ccp.molecule.ChemComp.NonStdChemComp ['protein', 
'Qua']>
Reading:  <open file 
'/Users/jd/2l2z/ccp/molecule/ChemComp/protein+Qua+2l2z_user_2011-01-31-12-30-21-
116_00001.xml', mode 'r' at 0x72311d8>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
Error loading file for:  <ccp.molecule.MolSystem.MolSystem ['2l2z']>
Reading:  <open file 
'/Users/jd/2l2z/ccp/molecule/MolSystem/2l2z+2l2z_user_2011-01-31-12-30-16-988_00
002.xml', mode 'r' at 0x39555a0>
Last xml tag read:  _StorageUnit
Parser state was:  checking validity
Object stack was empty
Traceback (most recent call last):
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 226, in <module>
    main(projectDir, max_size, glDirect)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisGui.py", line 111, in main
    top.initProject(project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/AnalysisPopup.py", line 1516, in initProject
    Analysis.initProject(self, project)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 303, in initProject
    self.initAtomSetMappings()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/Analysis.py", line 976, in initAtomSetMappings
    for chain in molSystem.chains:
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 13109, in getChains
    self.load()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/xml/Implementation.py", line 4940, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/MolSystem.py", line 20447, in checkValid
    ('chemCompVars', (self.linking,  self.descriptor))
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 3974, in getByNavigation
    result.load()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5030, in load
    self.loadFrom(repositories[0])
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/api/Implementation.py", line 5064, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
    partialLoad=partialLoad)
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/memops/xml/Implementation.py", line 4940, in loadFromStream
    obj.checkValid()
  File "/Users/jd/workspace35/ccpnmr/ccpnmr2.1/python/ccp/api/molecule/ChemComp.py", line 26753, in checkValid
    + ": %s" % (self,)
memops.general.Implementation.ApiError: 
ccp.molecule.ChemComp.NonStdChemComp.checkValid:
         constraint protein_DNA_RNA_are_linear_polymers violated: <ccp.molecule.ChemComp.NonStdChemComp ['protein', 'Qua']>
>>> jd:duvel/~/

Original comment by jurge...@gmail.com on 16 Jun 2011 at 1:22

GoogleCodeExporter commented 9 years ago 
I should have made a note of this before. When I updated this, everything 
crashed. I still have processDOCR_FRED.csh.update20110419 saved. I'll see if I 
can get it to work, later.

Original comment by schulte....@gmail.com on 16 Jun 2011 at 1:34

GoogleCodeExporter commented 9 years ago 
Can you take a look at this again?

Also, I have the entries: 2l2e 2l2w 2l2x 2l2y that are failing in the same way. 
I think reprocessing will correct this. All in all this issue according to my 
notes only apply to entries:

1lcc 1lcd 2l2z 2neo 2l2e 2l2w 2l2x 2l2y

so I'm taking off 1brv.

Original comment by jurge...@gmail.com on 16 Feb 2012 at 10:46

GoogleCodeExporter commented 9 years ago 
Yes I can reproduce this one... 

1lcd: there is a lot of confusion for the water sequence codes/ids, basically 
because the numbering is pretty random, and since we're treating water as 
single chains in CCPN since about 2 years problems occur (no sequential 
numbering, ...).

This is not one that I can solve quickly, and at the moment I cannot put in the 
effort to fix this (it'll be complicated), but I will try sometime over the 
next months.

Original comment by wfvran...@gmail.com on 16 Feb 2012 at 12:54

GoogleCodeExporter commented 9 years ago 
Chris, thanks for reprocessing. Now I rerun 2l2e 2l2w 2l2x 2l2y 2l2z fine.

The entries 1lcc 1lcd 2neo are presumably still a problem.

Original comment by jurge...@gmail.com on 24 Feb 2012 at 9:25

GoogleCodeExporter commented 9 years ago 
I reprocessed 1lcc 1lcd 2neo. 1lcc 1lcd only had restraints of type 'MR format' 
and did not convert. 2neo did not have any restraints at all. I could not find 
it in /dumpzone/pdb/data/status of 
/dumpzone/pdb/data/structures/divided/nmr_restraints. It is in 
/dumpzone/pdb/data/structures/divided/pdb, however.

Original comment by schulte....@gmail.com on 24 Feb 2012 at 3:29

GoogleCodeExporter commented 9 years ago 
Ok, I see in the rsync log that 1lcc and d didn't change so no need for me to 
rerun. It's a hard issue to solve so we'll have to change the status on this 
one.

The entry 2neo is indeed without restraints and therefore can be taken off 
here. I've included it in the CING issue list at: 
http://code.google.com/p/cing/issues/detail?id=266

Thanks for checking!

Original comment by jurge...@gmail.com on 27 Feb 2012 at 9:03