Consecutive conversions result in NullPointerException

[gokberkkaraca]

By using the compartment_closeup.xml file that is provided under samples folder, I tried converting the file from cd to sbgnml and from sbgnml to cd consecutively.

Cell Designer -> SBGNML conversion was successful.
SBGNML -> Cell Designer conversion was successful.
Cell Designer -> SBGNML conversion resulted in a NullPointerException with the following error message,

Exception in thread "main" java.lang.NullPointerException at fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper.addBasicLists(ModelWrapper.java:105) at fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper.create(ModelWrapper.java:62) at fr.curie.cd2sbgnml.CD2SBGNML.toSbgn(CD2SBGNML.java:53) at fr.curie.cd2sbgnml.CD2SBGNML.convert(CD2SBGNML.java:789) at fr.curie.cd2sbgnml.Cd2SbgnmlScript.convert(Cd2SbgnmlScript.java:48) at fr.curie.cd2sbgnml.Cd2SbgnmlScript.main(Cd2SbgnmlScript.java:33)

Because of this issue, I am not able to import the file that is exported by using cd2sbgnml library.

[royludo]

That is not surprising, chaining conversions back and forth has always lead to unpredictable behaviors. Some things cannot be converted properly, there is some degree of loss, due to the 2 formats being quite different. I thought I had put a warning about that in the wiki, but it appears I didn't. That will be added.

As for the issue itself, I'm afraid it would require some serious effort to fix it.