Hello,
Yes, the upgrade script fails for non-standard chemComps. What worked
before (I think) is the following recipe. Open the Save As dialog. Click
on the Storages tab to make that table visible (and possibly widen the
dialog so you can see more of the columns).
Find the row with the non-standard chemComp (look at the sixth, or Path,
column to find it). Look at the fourth (Url serial) column for that row.
It will be the same as all the other chemComps (so there will be a lot of
rows with that Url serial). In the example I have to hand it is serial
number 8.
Now find the row with Path ccpnmr/Analysis.xml (or ccp/nmr/Nmr.xml or
ccp/molecule/MolSystem.xml or similar) and determine that serial. In the
example I have it is serial 2 (and it probably is always that).
In the non-standard chemComp row change the 8 (or whatever it is) to a 2
(or whatever it is).
Then click the "Detailed Save" button. That should save the non-standard
chemComp in the project directory (in a sub-directory called protein or
..., depending on the chemComp type).
Then tar up the project as you have done and upload to the upgrade server.
Wayne
On Mon, 22 Sep 2008, Justin Douglas wrote:
> Hi Wayne,
>
> The upgrade server was not able to convert my project to v2.
>
> I've attached the error message. I think the problem might be that
> the Molecular System is really funky. It has two molecules including
> a highly modified RNA with 2'-fluoropyrimidines and
> 2'-O-methylpurines. If you recall we had a discussion about getting
> the molecule into analysis (see
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=CCPNMR&T=0&F=&S=&P=16219).
>
> Is there a clever way for me to get these monomers into V2 and convert
> my project?
>
> Justin
>
> Job failed: ApiError: [Errno 2] No such file or directory:
> '/data/ccpn/upgrade/cvsroot_branch4/ccpn/data/ccp/chemComp/other/CFL.xml'
> File "/prg/local/apache/cgi-bin/ccpn/upgrade/upgrade", line 572, in
> convertMajorProject
> doMajorConvert(dataStem)
> File "/prg/local/apache/cgi-bin/ccpn/upgrade/upgrade", line 546, in
> doMajorConvert
> p = Converters.doMajorUpgradeToCurrent(oldPath, oldTag, newDir=newDir)
> File "/data/ccpn/upgrade/cvsroot_branch_2_0_3/ccpn/python/memops/format/compatibility/Converters.py",
> line 65, in doMajorUpgradeToCurrent
> oldRoot, oldVersionStr, oldTags = getOldData(oldPath, oldTag,
> oldName=oldName)
> File "/data/ccpn/upgrade/cvsroot_branch_2_0_3/ccpn/python/memops/format/compatibility/part2/Converters2.py",
> line 146, in getOldData
> storage.load()
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 9066, in load
> ioModule.load(stream, self.project)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccpnmr/xml/Analysis.py",
> line 109, in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 414, in load
> name='auto%s' % time.time(), nmrProject=headObject.currentNmrProject
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 18782, in getCurrentNmrProject
> result = self.findFirstNmrProject()
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 13173, in findFirstNmrProject
> otherStorage.load()
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 9066, in load
> ioModule.load(stream, self.project)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/xml/nmr/Nmr.py",
> line 114, in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 429, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 614, in doLoad
> loadDelayedData(objectDict, delayedLoadData)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 1101, in loadDelayedData
> val = getByKey(clazz,fullKey)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/general/Implementation.py",
> line 331, in getByKey
> value = current.__dict__[downlinks[ii]] or getattr(current,downlinks[ii])
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 12456, in getMolSystems
> otherStorage.load()
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 9066, in load
> ioModule.load(stream, self.project)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/xml/molecule/MolSystem.py",
> line 101, in load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 429, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/format/xml/XmlIO.py",
> line 649, in doLoad
> headObject.checkAllValid(checkPackage=packageName)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 17094, in checkAllValid
> value.checkAllValid(complete)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/api/molecule/MolSystem.py",
> line 13448, in checkAllValid
> value.checkAllValid(complete)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/api/molecule/MolSystem.py",
> line 4994, in checkAllValid
> value.checkAllValid(complete)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/api/molecule/MolSystem.py",
> line 19795, in checkAllValid
> self.checkValid(complete)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/api/molecule/MolSystem.py",
> line 19208, in checkValid
> ('chemCompVars', ( ('linking', self.__dict__['linking']),
> ('descriptor', self.__dict__['descriptor']) ) )
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/general/Implementation.py",
> line 414, in getByNavigation
> current = current.__dict__.get(role) or getattr(current,role)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/ccp/api/molecule/Molecule.py",
> line 1225, in getChemComp
> contentStorage.load()
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/api/Implementation.py",
> line 7450, in load
> stream = self.url.getStream(self.package, path=self.path,
> headObject=self.headObject)
> File "/data/ccpn/upgrade/cvsroot_branch4/ccpn/python/memops/general/Implementation.py",
> line 525, in getStream
> raise ApiError(str(e))
>
>
> This job page: http://www.bio.cam.ac.uk/ccpn/upgrade/jobStatus/justindo_fbe8cbea/1222124598.html
>
> All jobs page: http://www.bio.cam.ac.uk/ccpn/upgrade/jobStatus/justindo_fbe8cbea/
>
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