#3 NullPointerException from TextProcessor.getEnglishWordTokens()

[Kuni Katsuya]

FYI, if a null string is passed to TextProcessor.getEnglishWordTokens() fails with a NullPointerException at https://sourceforge.net/p/gnat/code/HEAD/tree/GNAT/src/gnat/preprocessing/TextPreprocessor.java#l73

java.lang.NullPointerException
    at gnat.preprocessing.TextPreprocessor.getEnglishWordTokens(TextPreprocessor.java:73)
    at gnat.representation.GeneContextModel.addEntrezGeneSummary(GeneContextModel.java:56)
    at gnat.database.GeneRepositoryFromDatabase.getGeneRepositoryFAST(GeneRepositoryFromDatabase.java:371)
    at gnat.filter.nei.GeneRepositoryLoader.filter(GeneRepositoryLoader.java:192)
    at gnat.client.Run.runFilters(Run.java:189)

I was able to work around it by updating the GNAT.GR_Summary table as:

update GR_Summary set summary="" where summary is null;

Cheers

[Jörg Hakenberg]

Fixed in source code; still need to re-up new binaries.

[Jörg Hakenberg]

Thanks for pointing this out!
I committed a code fix to Sourceforge but still need to generate new
binaries for people to download if they are not working off the source code.
Thanks again,
Joerg

On Sat, Nov 18, 2017 at 6:35 PM, Kuni Katsuya kczi@users.sf.net wrote:

---

• [tickets:#3] https://sourceforge.net/p/gnat/tickets/3/
  NullPointerException from TextProcessor.getEnglishWordTokens()*

Status: open
Milestone: 1.0
Labels: bug
Created: Sun Nov 19, 2017 02:35 AM UTC by Kuni Katsuya
Last Updated: Sun Nov 19, 2017 02:35 AM UTC
Owner: nobody

FYI, if a null string is passed to TextProcessor.getEnglishWordTokens()
fails with a NullPointerException at https://sourceforge.net/p/
gnat/code/HEAD/tree/GNAT/src/gnat/preprocessing/TextPreprocessor.java#l73

java.lang.NullPointerException
at gnat.preprocessing.TextPreprocessor.getEnglishWordTokens(TextPreprocessor.java:73)
at gnat.representation.GeneContextModel.addEntrezGeneSummary(GeneContextModel.java:56)
at gnat.database.GeneRepositoryFromDatabase.getGeneRepositoryFAST(GeneRepositoryFromDatabase.java:371)
at gnat.filter.nei.GeneRepositoryLoader.filter(GeneRepositoryLoader.java:192)
at gnat.client.Run.runFilters(Run.java:189)

I was able to work around it by updating the GNAT.GR_Summary table as:

update GR_Summary set summary="" where summary is null;

Cheers

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