Comments (2)
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
from reactome2gpml-converter.
Anwesha, can you please try the following:
-
Replace
DataSource ds = DataSource.getBySystemCode("Re");
with
DataSource ds = DataSource.getExistingBySystemCode("Re");
-
initialize the DataSourceTxt yourself, at the very start of the convertPathway() method, with:
DataSourceTxt.init();
from reactome2gpml-converter.
Related Issues (20)
- WP2785, WP3334, WP3574, WP3339, WP2790, WP2766 not present in version 66 HOT 4
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from reactome2gpml-converter.