linkNmrStarData.py setup with ccpn/recoord has compatibility problem on tang

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What steps will reproduce the problem?
1. Running: set x = 1brv ; $scripts_dir/processDOCR_FRED.csh $x
on tang. I was not able to get this problem on my development machine stella.
2. Updated ccpn, recoord, and the chem comps today as documented in wiki. 

What is the expected output? What do you see instead?
From: /big/docr/NRG/link/1brv/1brv_merge.log

Model read finished. Duration 2.20856714249
Model validity check skipped
Read msd.adatah.localConstants.py version 4.5.7
Read msd.adatah.localConstants.py version 1.2.3.4
Read msd.adatah.localConstants.py version 1.2.3.4
Doing 1brv...
  Using preset values...
Traceback (most recent call last):
  File "/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py", line 680, in ?
    LinkNmrStarData(sys.argv)
  File "/big/docr/workspace/ccpn/python/msd/adatah/Generic.py", line 87, in __init__
    self.catchError(raiseError,timeFlag)
  File "/big/docr/workspace/ccpn/python/msd/adatah/Generic.py", line 80, in __init__
    self.runSpecific()
  File "/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py", line 169, in runSpecific
    self.readNmrStarFile(inNmrStarFile, version = self.originalNmrStarVersion, maxNum = self.numModelsToRead)
  File "/big/docr/workspace/ccpn/python/msd/adatah/NmrStar.py", line 37, in readNmrStarFile
    self.formatObjectDict[formatKey].readProject(nmrStarFile, entry = self.entry, molSystem = self.molSystem, strucGen = self.strucGen, useOriginalChainCode = True, linkAtoms = False, version = 
version, chemCompPath = chemCompArchiveDataDir, minimalPrompts = 1, 
**localKeywds)
  File "/big/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 934, in readProject
    self.getFullProject(fileName,**keywds)
  File "/big/docr/workspace/ccpn/python/ccpnmr/format/converters/NmrStarFormat.py", line 555, in getFullProject
    chains = self.readSequence(molSystem = molSystem, minimalPrompts = self.minimalPrompts, version = self.version, **localKeywds)
  File "/big/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 1054, in readSequence
    (createMoleculeDict,molSystemBonds) = self.checkMolecules()
  File "/big/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 5871, in checkMolecules
    chemComp = self.getChemComp(residueType,code3Letter, download = False)
  File "/big/docr/workspace/ccpn/python/ccpnmr/format/converters/DataFormat.py", line 6617, in getChemComp
    ccpCode=ccpCode)
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 11554, in findFirstChemComp
    root.refreshTopObjects('ccp.molecule.ChemComp')
  File "/big/docr/workspace/ccpn/python/memops/api/Implementation.py", line 16534, in refreshTopObjects
    topObject = XmlIO.loadFromFile(self, filePath, partialLoad=True)
  File "/big/docr/workspace/ccpn/python/memops/format/xml/XmlIO.py", line 251, in loadFromFile
    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 4585, in loadFromStream
    lm = getLoadingMaps(packageGuid, fileVersion)
  File "/big/docr/workspace/ccpn/python/memops/xml/Implementation.py", line 4918, in getLoadingMaps
    globalMapping = getGlobalMap(fileVersion)
  File "/big/docr/workspace/ccpn/python/memops/xml/Implementation.py", line 235, in getGlobalMap
    modifyIoMap(oldVersionStr, versionMapping)
  File "/big/docr/workspace/ccpn/python/memops/format/compatibility/part1/Converters1.py", line 529, in modifyIoMap
    compatibilityModule = getCompatibilityModule(oldVersionStr)
  File "/big/docr/workspace/ccpn/python/memops/format/compatibility/part1/Converters1.py", line 872, in getCompatibilityModule
    raise ApiError("""Could not import %s
memops.general.Implementation.ApiError: Could not import 
memops.format.compatibility.upgrade.v_2_0_a3
Backwards compatibility from 2.0.a3 to 2.0.b3 missing.

I did note that there was a nonstandard file:
/big/docr/workspace/ccpn/python/msd/adatah/not_localConstants.py

Adding back a /big/docr/workspace/recoord/python/recoord2/msd/localConstants.py 
with content below didn't change the above report.
import os

# Contain dirs: data with dirs: allChemComps, archives, and recoord
localTopDir = "/big/docr/ccpn_tmp"
dataDir             = os.path.join(localTopDir,'data')
archivesDataDir     = os.path.join(dataDir,'archives')
#archivesCcpnDataDir = os.path.join(dataDir,'archivesCcpn')
pythonCommand       = "python"
numCpu              = 2
allChemCompDataPath = dataDir

print "Read msd.adatah.localConstants.py version 1.2.3.4"

Wim, are the chem comps out of phase with the stable ccpn api?

Original issue reported on code.google.com by jurge...@gmail.com on 16 Sep 2009 at 1:48

[GoogleCodeExporter]

No. Did you update the SourceForge repository very recently? I should've given a
warning that they're in the middle of a release... anyway what should fix this
problem is to remake the API:

python memops/scripts_v2/makePython.py

Original comment by wfvran...@gmail.com on 16 Sep 2009 at 2:09

[GoogleCodeExporter]

Wasn't fully updated, did that and remade API, try again!

Original comment by wfvran...@gmail.com on 16 Sep 2009 at 2:38

[GoogleCodeExporter]

Weird, before I did as per wiki:
cd $WS/ccpn
cvs -z3 -d:ext:jurgenfd@ccpn.cvs.sourceforge.net:/cvsroot/ccpn update -r stable
python -u $CCPNMR_TOP_DIR/python/memops/scripts_v2/makePython.py
and I saw no obvious mistakes.

Anyway, I must have missed one.

Thanks a lot Wim!

Original comment by jurge...@gmail.com on 16 Sep 2009 at 2:49

• Changed state: Verified