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On 11/30/2010 09:54 AM, Andreas Draeger wrote:
> Dear all,
>
> It seems that after the latest changes in the repository reading SBML
> files does not work properly anymore.
>
> First, what is not so important, the parser now writes these
> (unnecessary) messages when reading Level 2 Version 4 models:
>
> WARN (SBMLCoreParser.java:405) - No unitDefinition matches the
> areaUnitsID of Model.
> WARN (SBMLCoreParser.java:415) - No unitDefinition matches the
> lengthUnitsID of Model.
> WARN (SBMLCoreParser.java:419) - No unitDefinition matches the
> substanceUnitsID of Model.
> WARN (SBMLCoreParser.java:422) - No unitDefinition matches the
> timeUnitsID of Model.
> WARN (SBMLCoreParser.java:425) - No unitDefinition matches the
> volumeUnitsID of Model.
This messages where always there but were not printed. I put them on, so
that we can perfect the parser.
Of course for L2, we should not have this warnings and we should not
have them either for L3 if the attribute are not defined in the model.

> In L2V4 the model doesn't have all these attributes, hence, it is not
> necessary to write this.
>
> It seems that the parser does not set the Level/Version attribute
> correctly. When trying to call the method
>
> setHasOnlySubstanceUnits
>
> in Species, we receive an
>
> Exception in thread "AWT-EventQueue-0" Property hasOnlySubstanceUnits is
> not defined for Level -1 and Version -1
> at org.sbml.jsbml.Species.setHasOnlySubstanceUnits(Species.java:747)
>
>
> Furthermore, there is also the problem of log4j that it is impossible to
> find the log file. Is there a way to switch logging completely off?
>
> log4j:ERROR setFile(null,true) call failed.
> java.io.FileNotFoundException: ./log/jsbml.log (No such file or directory)
I just answered about that, just do an update and it will works.

To configure log4j, you need to edit the file src/log4j.properties
At the moment, log4j is setup to print at the DEBUG level on the console
and on the jsbml.log file.

You have also lines like that :

log4j.logger.org.sbml.jsbml.util=WARN
log4j.logger.org.sbml.jsbml.xml.parsers.StringParser=WARN

Which prevent to display the DEBUG output of the classes in the
org.sbml.jsbml.util package and of the class
org.sbml.jsbml.xml.parsers.StringParser.
You need to comment these line, they will then inherit the glogal level,
so DEBUG or you can set something else than WARN.

Cheers,
Nico




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