Error and crash: Exception in thread "main" java.lang.IllegalArgumentException: Illegal group reference: group index is missing

[mluerig]

I am running CERMINE through 10000 or so pdfs, but some of them throw this error, and the program stops running. Can I somehow fix this, or tell CERMINE to skip errors an continue?

File processed: /home/moritz/Desktop/pdf_extraction/pdfs/Other/��ztun΍ et al. 1991 - A new haloether from Laurencia possessing a lauroxacyclododecane ring. Structure and conformational studies.pdf Exception in thread "main" java.lang.IllegalArgumentException: Illegal group reference: group index is missing at java.util.regex.Matcher.appendReplacement(Matcher.java:819) at pl.edu.icm.cermine.content.cleaning.ContentCleaner.cleanHyphenationAndBreaks(ContentCleaner.java:180) at pl.edu.icm.cermine.content.cleaning.ContentCleaner.cleanAllAndBreaks(ContentCleaner.java:236) at pl.edu.icm.cermine.metadata.model.DocumentMetadata.clean(DocumentMetadata.java:277) at pl.edu.icm.cermine.metadata.EnhancerMetadataExtractor.extractMetadata(EnhancerMetadataExtractor.java:106) at pl.edu.icm.cermine.metadata.EnhancerMetadataExtractor.extractMetadata(EnhancerMetadataExtractor.java:36) at pl.edu.icm.cermine.ExtractionUtils.cleanMetadata(ExtractionUtils.java:101) at pl.edu.icm.cermine.InternalContentExtractor.doWork(InternalContentExtractor.java:341) at pl.edu.icm.cermine.InternalContentExtractor.doWork(InternalContentExtractor.java:320) at pl.edu.icm.cermine.InternalContentExtractor.getContentAsNLM(InternalContentExtractor.java:286) at pl.edu.icm.cermine.ContentExtractor.getContentAsNLM(ContentExtractor.java:612) at pl.edu.icm.cermine.ContentExtractor.getContentAsNLM(ContentExtractor.java:628) at pl.edu.icm.cermine.ContentExtractor.main(ContentExtractor.java:724)

��ztun΍ et al. 1991 - A new haloether from Laurencia possessing a lauroxacyclododecane ring. Structure and conformational studies.pdf

[dtkaczyk]

Hi @mluerig
Thanks for reporting this. I just committed a bug fix, it should be included in the newest snapshot available here If you still experience any problems, please let us know.

[dtkaczyk]

I am closing this now assuming the bug is fixed, please reopen if you still experience any problems.