Overview of pathways doesn't link them

[egonw]

For example, if I compare http://www.wikipathways.org/index.php/Pathway:WP1849 with the original [0] then the arrows seem to be missing.

0.http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=556833

[pennatula]

This pathway converted in Version 50 but the one from Version 53 gives this error.

converting pathway #556833 Metabolism of lipids and lipoproteins...
Creating new GPML pathway 556835
Warning creating a new DataSource with systemCode Re and null fullName!
Exception in thread "main" java.lang.ExceptionInInitializerError
at org.pathvisio.core.biopax.BiopaxNode.(BiopaxNode.java:41)
at org.pathvisio.core.biopax.PublicationXref.(PublicationXref.java:32)
at org.gk.gpml.ReactometoGPML2013.addLitRef(ReactometoGPML2013.java:226)
at org.gk.gpml.ReactometoGPML2013.convertNode(ReactometoGPML2013.java:520)
at org.gk.gpml.ReactometoGPML2013.convertPathway(ReactometoGPML2013.java:794)
at org.gk.gpml.CLIConverter.convertReactomeToGPML(CLIConverter.java:170)
at org.gk.gpml.CLIConverter.convertReactomeToGPMLByID(CLIConverter.java:206)
at org.gk.gpml.CLIConverter.main(CLIConverter.java:63)
Caused by: java.lang.IllegalArgumentException: Full name does not match for DataSource Re was null so it can not be changed to Reactome
at org.bridgedb.DataSource.findOrRegister(DataSource.java:629)
at org.bridgedb.DataSource.register(DataSource.java:595)
at org.bridgedb.bio.DataSourceTxt.loadLine(DataSourceTxt.java:69)
at org.bridgedb.bio.DataSourceTxt.loadAnInputStream(DataSourceTxt.java:63)
at org.bridgedb.bio.DataSourceTxt.init(DataSourceTxt.java:42)
at org.pathvisio.core.model.GpmlFormat.(GpmlFormat.java:55)
... 8 more

[egonw]

Anwesha, can you please try the following:

1. Replace

   DataSource ds = DataSource.getBySystemCode("Re");
   

   with

     DataSource ds = DataSource.getExistingBySystemCode("Re");
   

2. initialize the DataSourceTxt yourself, at the very start of the convertPathway() method, with:

   DataSourceTxt.init();