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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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StackOverFlow error during index() #260

Closed IgorRodchenkov closed 7 years ago

IgorRodchenkov commented 7 years ago

Got this when running cpath2-cli.sh -index command from console (preparing for PC9 release): java.lang.StackOverflowError at antlr.BaseAST.toString(BaseAST.java:333) at antlr.BaseAST.toStringList(BaseAST.java:341) at antlr.BaseAST.toStringList(BaseAST.java:347) at antlr.BaseAST.toStringList(BaseAST.java:347) at antlr.BaseAST.toStringList(BaseAST.java:347) at antlr.BaseAST.toStringList(BaseAST.java:347) ... etc.. (- not detailed information on where exactly this happens)

After some research, it looks like this has to do with a Hibernate bug and too long list of IDs we're trying to map to UniProt or ChEBI IDs (using mappingsRepository.findByDestIgnoreCaseAndDestIdIn function).