Conversion SBML -> Escher creates mistake in file

[MariaHei]

Apparently, something goes wrong in the conversion from SBML to Escher.
Converting from SBML to Escher works:
java -jar -Xms8G -Xmx8G -Duser.language=en EscherConverter-1.2.1.jar --input=GlycolysisLayout_small.sbml.xml --format=Escher --output=glycolysis.json --gui=false
But going back doesn't work, so presumably, the converted output of the first command is wrong:
java -jar -Xms8G -Xmx8G -Duser.language=en EscherConverter-1.2.1.jar --input=glycolysis.json --format=SBML --output=glycolysis.sbml --gui=false

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.lang.String.charAt(String.java:658)
        at de.zbit.sbml.util.SBMLtools.toSId(SBMLtools.java:255)
        at edu.ucsd.sbrg.escher.converter.Escher2SBML.createSpeciesReferenceGlyphs(Escher2SBML.java:681)
        at edu.ucsd.sbrg.escher.converter.Escher2SBML.convertReaction(Escher2SBML.java:278)
        at edu.ucsd.sbrg.escher.converter.Escher2SBML.convert(Escher2SBML.java:112)
        at edu.ucsd.sbrg.escher.EscherConverter.convert(EscherConverter.java:143)
        at edu.ucsd.sbrg.escher.EscherConverter.convert(EscherConverter.java:195)
        at edu.ucsd.sbrg.escher.EscherConverter.convert(EscherConverter.java:450)
        at edu.ucsd.sbrg.escher.EscherConverter.batchProcess(EscherConverter.java:327)
        at edu.ucsd.sbrg.escher.EscherConverter.commandLineMode(EscherConverter.java:384)
        at de.zbit.Launcher.launchCommandLineMode(Launcher.java:725)
        at de.zbit.Launcher.run(Launcher.java:862)
        at de.zbit.Launcher.<init>(Launcher.java:211)
        at edu.ucsd.sbrg.escher.EscherConverter.<init>(EscherConverter.java:263)
        at edu.ucsd.sbrg.escher.EscherConverter.main(EscherConverter.java:253)

The reason for this error is a mistake in a metabolite, which presumably is caused by the first conversion:
Metabolite [coefficient=NaN, id=, nodeRefId=null]

[MariaHei]

This might be due to a mistake in GlycolysisLayout_small.sbml.xml, since for many species in it, a warning is given, like for example:

ERROR (SBMLCoreParser.java:179) - "Glucose-6-phosphate" is not a valid identifier for this species.
 INFO (SBMLCoreParser.java:180) - Attribute = id, value 'Glucose-6-phosphate' , element name = species
 WARN (SBMLCoreParser.java:211) - Could not recognize the attribute 'id' on the element species. Please check the specification for SBML.

and

ERROR (SBMLCoreParser.java:179) - "Glucose-6-phosphate" is not a valid identifier for this speciesReference.
 INFO (SBMLCoreParser.java:180) - Attribute = species, value 'Glucose-6-phosphate' , element name = speciesReference
 WARN (SBMLCoreParser.java:211) - Could not recognize the attribute 'species' on the element speciesReference. Please check the specification for SBML.

[DEVetter]

For me, the SBML->Escher direction already does not work (java -jar EscherConverter-1.2.1.jar --input=data/GlycolysisLayout_small.sbml.xml --output=out/glycolysis.sbml --format=Escher --gui=false):

Exception in thread "main" java.lang.NullPointerException
        at edu.ucsd.sbrg.escher.converter.SBML2Escher.createMultiMarkers(SBML2Escher.java:372)
        at edu.ucsd.sbrg.escher.converter.SBML2Escher.lambda$convert$2(SBML2Escher.java:140)
        ...

In the file, roles are given as numbers (1,2,3,4) instead of strings like 'product', and the call sRG.getRole() thus yields null (leading to the above exception)

[draeger]

@DEVetter could you please add a link to the file GlycolysisLayout_small.sbml.xml so that it is easier to find?

If the roles are given as numbers, we might be able to circumvent this problem using the enum data structure that JSBML uses to parse the file. We should check if the error comes from JSBML already or if the file is corrupt. In the latter case, the file needs to be fixed first. If the file was erroneously generated by EscherConverter, the source of this problem needs to be fixed.

[DEVetter]

It's in the data folder, for example in line 53

[draeger]

This is indeed unusual. It seems when writing the model, the role attribute was incorrectly written to the file, which seems to be a JSBML problem. Could you please take a look at how JSBML writes this attribute? The file will need to be fixed before continuing with fixing this bug.

[DEVetter]

As far as i can tell, from JSBML's end, the role attribute has to be set to a legal SpeciesReferenceRole and is then handed through via SpeciesReferenceRole.writeXMLAttributes to the LayoutParser.

[draeger]

Maybe it would be best to just fix the errors in this example file directly.