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SynBioDex / libSBOLj

Java Library for Synthetic Biology Open Language (SBOL)
Apache License 2.0
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Opaque failure while reading GenBank #623

Open jakebeal opened 2 years ago

jakebeal commented 2 years ago

Importing this genbank file produces an opaque error: Other_GenBank_imports.txt The GenBank file parses correctly with BioPython

Converting GenBank to SBOL Version 2 Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 
1 at org.sbolstandard.core2.GenBank.read(GenBank.java:1334) at 
org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:700) at 
org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:625) at 
org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:512) at 
org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:437) at 
org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:422) at 
org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:2726) at 
org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:3028)
jakebeal commented 2 years ago

The triggering issue, BTW, is apparently that line 9602 in the file had an extra newline. I think you're not really supposed to to this, but other GenBank parsers are tolerant of this and libSBOLj is not.