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Dear Benjamin,

It is clear what is wrong, but not how it got there.

If you look into the details you will find that ContentStorages serial=42
and serial=43 both point to the same file (the 'path' is the same and the
'url' is the same). This is wrong. The NmrConstraints file knows that its
parent should have serial=2, which is correct for one of the cases but
wrong for the other, and quite correctly reports the error.

Now, when you made this test project, did you edit the XML files in order
to get there? If so, that may be where the error came from. If you just
used FormatConverter, there may be an error there (that Wim should
then look at).

Thanks for a short, clear, and very informative bug report.

Yours,

Rasmus

---------------------------------------------------------------------------
Dr. Rasmus H. Fogh                  Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK.     FAX (01223)766002

On Tue, 7 Mar 2006, Benjamin Bardiaux wrote:

> Hi all,
>
> I'm trying to create a ccpn test project with 2 StructureGeneration with
> a distanceConstraintList for each ones.
> No problems during the project creation with formatConverter. Bugs
> appear when I start to navigate into it.
>
> ex:
>  >>> from memops.general.Io import loadXmlProjectFile
>  >>> ccpn_project = loadXmlProjectFile(file = 'test2.xml')
>  >>> structure_generations = ccpn_project.structureGenerations
>  >>> print structure_generations
> (<ccp.Nmr.StructureGeneration [1]>, <ccp.Nmr.StructureGeneration [2]>)
>  >>> structure_generation = structure_generations[0]
>  >>> head = structure_generation.nmrConstraintHead
>  >>> head
> <ccp.Nmr.NmrConstraintHead [1]>
>  >>> constraint_list = head.findAllConstraintLists()
> last xml element read:
> </parent>
>
>
>
> parser state was:
> reading
>
> ERROR loading xml ccp.NmrConstraints constraintSet01/NmrConstraints.xml
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/home/Bis/bardiaux/ccpnmr/ccpnmr1.0/python/ccp/api/Nmr.py", line
> 57204, in findAllConstraintLists
>    contentStorage.load()
>  File
> "/home/Bis/bardiaux/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 7259, in load
>    ioModule.load(stream, self.headObject)
>  File
> "/home/Bis/bardiaux/ccpnmr/ccpnmr1.0/python/ccp/xml/NmrConstraints.py",
> line 107, in load
>    return GeneralXmlIO.load(stream, mapping, parentObject)
>  File
> "/home/Bis/bardiaux/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 370, in load
>    result = doLoad(stream, mapping, headObject)
>  File
> "/home/Bis/bardiaux/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 705, in doLoad
>    raise ApiError(loadError +
> memops.general.Implementation.ApiError: Error loading fileHeadObject
> ccp.Nmr.NmrConstraintHead:[1] differs from file parent
> ccp.Nmr.NmrConstraintHead:[2]
>  >>>
>
>
> Many thanks for your help.
> Here are some interesting parts of the test2 projects data.
>
> *part of test2.xml*
>
>  <ContentStorage _ID="_47" serial="42" isStored="true"
> isModifiable="true" package="ccp.NmrConstraints" format="xml" url="_4">
>    <path>constraintSet01/NmrConstraints.xml</path>
>  </ContentStorage>
>  <ContentStorage _ID="_48" serial="43" isStored="true"
> isModifiable="true" package="ccp.NmrConstraints" format="xml" url="_4">
>    <path>constraintSet01/NmrConstraints.xml</path>
>  </ContentStorage>
>
>
> *test2/ccp/Nmr.xml:*
>
> <?xml version="1.0" encoding="UTF-8"?>
> <_StorageUnit time="Tue Mar  7 09:31:23 2006" release="1.0.210"
> packageName="ccp.Nmr" root="test2" originator="CCPN Python XmlIO">
>
> <NmrConstraintHead _ID="_1" serial="1">
>  <structureGenerations _IDREF="_2"/>
>  <contentStorage>
>    <key1 serial="42"/>
>  </contentStorage>
> </NmrConstraintHead>
> <NmrConstraintHead _ID="_3" serial="2">
>  <structureGenerations _IDREF="_4"/>
>  <contentStorage>
>    <key1 serial="43"/>
>  </contentStorage>
> </NmrConstraintHead>
> <StructureGeneration _ID="_2" serial="1" generationType="denovo"
> nmrConstraintHead="_1">
>  <name>it0</name>
> </StructureGeneration>
> <StructureGeneration _ID="_4" serial="2" generationType="denovo"
> nmrConstraintHead="_3">
>  <name>it1</name>
> </StructureGeneration>
>
> </_StorageUnit>
> <!--End of Memops Data-->
>
> *head test2/constraintSet01/NmrConstraints.xml:*
>
> <?xml version="1.0" encoding="UTF-8"?>
> <_StorageUnit time="Tue Mar  7 09:31:24 2006" release="1.0.210"
> packageName="ccp.NmrConstraints" root="test2" originator="CCPN Python
> XmlIO">
>
> <parent>
>  <key1 serial="2"/>
> </parent>
>
> <DistanceConstraintList _ID="_1" serial="1" usedForCalculation="true">
>  <name>unambig_2</name>
>
>
> --
> -----------------------------------------------------
> Benjamin Bardiaux       | Bioinformatique Structurale
> [log in to unmask]     | Institut Pasteur
> 25,28 rue du Docteur Roux 75018 Paris, France
> -----------------------------------------------------
>