#4 GnatService.sh won't start

[Kuni Katsuya]

While attempting to get GnatService running, discovered an issue with scripts/startGnatService.sh.

For the binary release 1.31, the jaxen library version is incorrect and the linnaeus library is missing. It was:

nohup java -cp lib/gnat.jar:lib/jdom-1.0.jar:lib/jaxen-1.1-beta-9.jar gnat.server.GnatService start -p=8081 -log=0 &

but should be:

nohup java -cp lib/gnat.jar:lib/jdom-1.0.jar:lib/jaxen-1.1.3.jar:lib/linnaeus-2.0.jar gnat.server.GnatService start -p=8081 -log=0 &

Without the above fix, running scripts/startGnatService.sh will result in:

Exception in thread "main" java.lang.NoClassDefFoundError: martin/common/ArgParser
    at gnat.server.GnatService.main(GnatService.java:110)
Caused by: java.lang.ClassNotFoundException: martin.common.ArgParser
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 1 more

[Jörg Hakenberg]

Thanks for filing this issue. Let me take a look and update the binary downloads + example scripts.

[Kuni Katsuya]

Cool, thanks, Jörg!

[Kuni Katsuya]

On a related note...

When I got GnatService running with the above changes, I was able to successfully see the help page at http://localhost:8081.

However, when I try http://localhost:8081/?pmid=20832752&task=gner, I get the following error:

org.jdom.input.JDOMParseException: Error on line 1: White spaces are required between publicId and systemId.
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851)
    at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndTextFromXML(PubmedAccess.java:152)
    at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndText(PubmedAccess.java:95)
    at gnat.server.GnatServiceHandler.getTexts(GnatService.java:381)
    at gnat.server.GnatServiceHandler.handle(GnatService.java:296)
...

Haven't dug into it yet, but am I doing anything obviously wrong?

Cheers

[Kuni Katsuya]

Hi Jörg,

I'm trying to debug the above JDOMParseException, but I am unable to compile the GNAT source. Is there a build file or script (e.g. Maven pom.xml, Ant build.xml, etc.) that I can use?

Thanks

[Jörg Hakenberg]

I believe NHI's PubMed XML output might have changed, that's why we're getting the Exception.
We don't have a build script :( --- what errors are you getting?

[Kuni Katsuya]

On http://localhost:8081/?pmid=20832752&task=gner , the error:

org.jdom.input.JDOMParseException: Error on line 1: White spaces are required between publicId and systemId.
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468)
    at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851)
    at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndTextFromXML(PubmedAccess.java:152)
    at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndText(PubmedAccess.java:95)
    at gnat.server.GnatServiceHandler.getTexts(GnatService.java:381)
    at gnat.server.GnatServiceHandler.handle(GnatService.java:296)
...

But yeah, I suppose Pubmed DTD change could be the cause.

[Kuni Katsuya]

I took a quick look at the code and the XML for PMID 20832752 and the expected format still appears to be valid:

  PubmedArticle
    MedlineCitation
      Article
        ArticleTitle
        Abstract
          AbstractText

Hard to say what's causing the JDomParseException without throwing a debugger on it.

Is there any chance of resurrecting the build script? :)