Conversion to SBML and to image
When using neuron_cd.xml and trying to convert this CD file to SBML and then getting an image of that (no matter what format), I am getting
lcsb.mapviewer.converter.InvalidInputDataExecption: lcsb.mapviewer.common.exception.InvalidArgumentException: Line undefined for element csa1910 in reaction re5868__re5868_247 at lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser.mergeLayout(SbmlReactionParser.java:217) at lcsb.mapviewer.converter.model.sbml.SbmlParser.createModel(SbmlParser.java:96) ...
I created a failing test for that in conversion-rest-api-scaling -> rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java -> testCellDesigner2Sbml2Svg.
Ultimately, what I am going for is to go from CD to SBML or SBGN and back and at each step to generate images in all the supported format. I want to do this for the neuron compartment and whole pdmap. I am attaching the shell script for that, including pdmap in CD. Could you then try whether it is working so that we don't go there and back if something else is not working?