doExportsForGrid is hosed

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Every time I run processDOCR_FRED, I get errors like this:

ERROR 1j7p in /big/docr/workspace/recoord/python/recoord2/msd/exportCns.py
ERROR 1j7p found in doExportsForGrid

The errors in linkNmrStarData.summary and linkNmrStarData.log clean up, but the 
grid remains the 
same - errors and all. 

Original issue reported on code.google.com by schulte....@gmail.com on 2 Apr 2009 at 6:23

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I find in: $dir_export/1j7p/Cns/1j7p_fc_export_Cns.log 
Wim, do you recognize the cause?
Chris can't continue processing with this issue unless we disable the FC export.

Model read finished. Duration 2.3555328846
Model validity check skipped
No compatibility module found for version 2.0.b1
Error loading file for:  None
Reading:  <open file 
'/big/docr/ccpn_tmp/data/recoord/1j7p/linkNmrStarData/memops/Implementation/1j7p
.xml', mode 'r' at 0x36afc60>
Last xml tag read:  _StorageUnit
Parser state was:  starting
Object stack was empty
No compatibility module found for version 2.0.b1
Error loading file for:  <memops.Implementation.MemopsRoot id:72423888>
Reading:  <open file 
'/big/docr/ccpn_tmp/data/recoord/1j7p/linkNmrStarData/memops/Implementation/1j7p
.xml', mode 'r' at 0x36b8648>
Last xml tag read:  IMPL.MemopsRoot.packageLocators
Parser state was:  handling version compatibility
Current object was:  <memops.Implementation.MemopsRoot id:72423888>
Traceback (most recent call last):
  File "/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py", line 99, in ?
    project = loadProject(os.path.join(projectDir,pdbCode,ccpnProjectName))
  File "/big/docr/workspace/ccpn/python/memops/general/Io.py", line 531, in loadProject
    project = XmlIO.loadProject(path, projectName, partialLoad=True)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 205, in loadProject
    return loadProjectFile(filePath, partialLoad=partialLoad)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 217, in loadProjectFile
    partialLoad=partialLoad)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/big/docr/workspace/ccpn/python/memops/xml/Implementation.py", line 4831, in loadFromStream
    Converters1.minorPostProcess(fileVersion, result, delayDataDict, objectDict, mapping)
  File "/big/docr/workspace/ccpn/python/memops/format/compatibility/part1/Converters1.py", line 894, in minorPostProcess
    mod = getCompatibilityModule(fromVersionStr)
  File "/big/docr/workspace/ccpn/python/memops/format/compatibility/part1/Converters1.py", line 869, in getCompatibilityModule
    result = __import__(moduleDir, {}, {}, compModules)
ImportError: No module named v_2_0_b1

Original comment by jurge...@gmail.com on 3 Apr 2009 at 8:22

• Added labels: Component-FormatConverter, Usability

[GoogleCodeExporter]

I do recognise this - you need to regenerate the API:

1. go to python/memops/scripts_v2/
2. run 'python makePython.py'
3. go get a coffee

Should work when finished. If step 2. doesn't work, try remaking the symbolic 
links
with copyFromRep.py (depending on the installation).

Original comment by wfvran...@gmail.com on 3 Apr 2009 at 8:28

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thanks Wim, I just started the 'make'.
Chris can you retry?

Original comment by jurge...@gmail.com on 3 Apr 2009 at 8:31

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Also the case for entry 1bde today after many updates..

Reclassifying this issue as only essential for Milestone-wwPDB-remediation but 
so that we can continue with 
putting data in NRG.

Parser state was:  checking validity
Object stack was empty
Error loading file for:  <ccp.nmr.NmrConstraint.NmrConstraintStore [1]>
Reading:  <open file 
'/big/docr/ccpn_tmp/data/recoord/1bde/linkNmrStarData/ccp/nmr/NmrConstraint/1+1b
de_user_2009-03-
31-10-29-03-336_00001.xml', mode 'r' at 0x36b43f0>
Last xml tag read:  NMRC.FixedAtomSet.atoms
Parser state was:  reading
Current object was:  <ccp.nmr.NmrConstraint.FixedAtomSet [1, 1]>
Traceback (most recent call last):
  File "/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py", line 105, in ?
    exportCnsInputFiles(origStrucGen,outputDirectory,pdbCode)
  File "/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py", line 47, in exportCnsInputFiles
    constraintLists = strucGen.nmrConstraintStore.findAllConstraintLists(className = constraintListClassName)
  File "/big/docr/workspace/ccpn/python/ccp/api/nmr/Nmr.py", line 84269, in getNmrConstraintStore
    tobj.load()
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 5036, in load
    self.loadFrom(repositories[0])
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 5070, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 267, in loadFromStream
    partialLoad=partialLoad)
  File "/big/docr/workspace/ccpn/python/memops/xml/Implementation.py", line 4777, in loadFromStream
    val[ii] = clazz.getByKey(oo,vv[1:-1])
  File "/big/docr/workspace/ccpn/python/ccp/api/molecule/MolSystem.py", line 1278, in getByKey
    obj1.load()
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 5036, in load
    self.loadFrom(repositories[0])
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 5070, in loadFrom
    XmlIO.loadTopObject(repository.url.getDataLocation(), self)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 236, in loadTopObject
    return loadFromStream(open(filePath), topObjId=topObjId, topObject=topObject)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 273, in loadFromStream
    partialLoad=partialLoad)
  File "/big/docr/workspace/ccpn/python/memops/xml/Implementation.py", line 4853, in loadFromStream
    obj.checkValid()
  File "/big/docr/workspace/ccpn/python/ccp/api/molecule/MolSystem.py", line 3223, in checkValid
    raise ApiError("""%s.checkValid:
memops.general.Implementation.ApiError: ccp.molecule.MolSystem.Chain.checkValid:
       constraint seqCode_and_seqInsertCode_form_secondary_key_for_residues violated: 
<ccp.molecule.MolSystem.Chain ['1bde', 'A']>
                                                                                                                               46,5          Bot

Original comment by jurge...@gmail.com on 9 Apr 2009 at 2:25

• Added labels: Priority-Medium, Milestone-wwPDB-remediation
• Removed labels: Priority-Critical

[GoogleCodeExporter]

I ran exportCns 1bde

output:
/msd/ python -u exportCns.py 1bde
Model read finished. Duration 2.1482000351 
Model validity check skipped
Traceback (most recent call last):
  File "exportCns.py", line 89, in ?
    projectDir = sys.argv[2]
IndexError: list index out of range

Original comment by schulte....@gmail.com on 9 Apr 2009 at 2:27

[GoogleCodeExporter]

Issue 159 has been merged into this issue.

Original comment by jurge...@gmail.com on 9 Apr 2009 at 3:04

[GoogleCodeExporter]

OK not sure if this went through in issue 159. Anyway the problem with the 
invalid
CCPN project is now fixed, need to update, in CCPN SF rep:

python/ccp/format/nmrStar/sequenceIO.py

There is still a problem with the coordinate handling as far as I can tell, so 
will
look into that later (have to go home!).

Original comment by wfvran...@gmail.com on 21 Apr 2009 at 3:54

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Did you get a chance to look at this entry?

Original comment by jurge...@gmail.com on 26 Jun 2009 at 1:25

• Added labels: Entry-1bde

[GoogleCodeExporter]

This seems to be working for me now, the project is valid at least and the 
restraint
lists are exported OK (from a quick check). So note that you have to use this 
syntax:

python exportCns.py <pdbCode> <directory with CCPN projects> <output directory>

Original comment by wfvran...@gmail.com on 1 Jul 2009 at 11:57

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I need to check on this.

Original comment by jurge...@gmail.com on 24 Jul 2009 at 8:18

• Changed state: Started

[GoogleCodeExporter]

Works like a charm.
Checked only for this entry.

Original comment by jurge...@gmail.com on 5 Aug 2009 at 9:30

• Changed state: Fixed