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NCBI-Hackathons / seqr

Creative Commons Zero v1.0 Universal
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Parser Error #12

Closed nabihlme closed 9 years ago

nabihlme commented 9 years ago

When I run Seqr -h, I get the help info twice and:

net.sourceforge.argparse4j.internal.HelpScreenException: Help Screen at net.sourceforge.argparse4j.impl.action.HelpArgumentAction.run(HelpArgumentAction.java:53) at net.sourceforge.argparse4j.internal.ArgumentImpl.run(ArgumentImpl.java:469) at net.sourceforge.argparse4j.internal.ArgumentParserImpl.processArg(ArgumentParserImpl.java:935) at net.sourceforge.argparse4j.internal.ArgumentParserImpl.parseArgs(ArgumentParserImpl.java:828) at net.sourceforge.argparse4j.internal.ArgumentParserImpl.parseArgs(ArgumentParserImpl.java:699) at net.sourceforge.argparse4j.internal.ArgumentParserImpl.parseArgs(ArgumentParserImpl.java:593) at net.sourceforge.argparse4j.internal.ArgumentParserImpl.parseArgs(ArgumentParserImpl.java:586) at gov.nih.nlm.ncbi.seqr.Seqr.main(Seqr.java:61) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at com.intellij.rt.execution.application.AppMain.main(AppMain.java:140)

(I changed line 65 to give the full stack trace for a second...)

averagehat commented 9 years ago

I haven't been able to recreate this.

nabihlme commented 9 years ago

As far as I can tell, argparse4j always throws a HelpScreenException when asked to display help.

https://github.com/tatsuhiro-t/argparse4j/blob/master/src/main/java/net/sourceforge/argparse4j/impl/action/HelpArgumentAction.java

I added another catch to exit gracefully when this happens. commit: eef2c40f1af76cae6acf8e17c96314d97f472e62 If it truly can't be recreated by you guys, just remove that additional catch block.

averagehat commented 9 years ago

Looks good, thanks Nathan.