psicquic solr ws 1.3.8 - xgmml format not working (file not found)

[Karin (innatedb.com)]

Hi there,

I finally got around to use the new reference implementation with InnateDB! So far so good, but for some reason the xgmml format doesn't work - I'm getting a "file not found" (eg. http://solr.innatedb.com/webservices/current/search/query/ENSG00000057657?format=xgmml). I suspect it has something to do with my apache/tomcat setup, but can't find anything in the logs.

Before I start diving into the source code I was wondering if someone could briefly explain how the converter utils work, and if and where they would write to the disc (and thus might encounter permission problems)?

Thanks!

Cheers,
Karin

[Bruno Aranda]

Hi Karin! (and everybody else! :)

I would recommend that you check the logs, as there seems to be some problem with the conversion and the class that is supposed to stream the results. Doing the request from the command line, I get this:

#] curl "http://solr.innatedb.com/webservices/current/search/query/ENSG00000057657?format=xgmml"

#] Error serializing the response, please check the server logs, response class : XgmmlStreamingOutput

So the logs may show more information about this.

I have checked some of the other formats: http://solr.innatedb.com/webservices/current/search/formats

And there seems to be a problem with biopax and the rdf related formats as well. In that case, the 500 http error is displayed, hinting to a NullPointerException.

I haven't seen much of the code for the last year, so I am not sure I can help :)

Cheers!

Bruno

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[Karin (innatedb.com)]

Thanks Bruno! Didn't think of trying it from the command line, ugh.
I did notice that there's a problem with the other XML-based formats, it seems to come from missing data (ExperimentDescription) in the underlying mitab-file. Not sure if that's why the xgmml fails though.
Will do some more digging, thanks again!

[Karin (innatedb.com)]

Quick follow-up: I figured out the NullPointerException (one intx had no year for it's pmid), and now all the formats are working - except the xgmml. Still getting a 404, and nothing in the logs.
I'll keep digging!

[Lukasz Salwinski]

Hello,
is there any way to get replace (actually, quite old version of) saxon
with xalan ? or just maybe use what's provided by default within java
runtime ?

I'm getting some sort of conflict between saxon and spring or struts 2:
>....
>Caused by: Unable to load
jar:file:/opt-local/apache-tomcat-7.0.37/webapps/psicquic-solr-server/WEB-INF/lib/struts2->core-2.3.12.jar!/struts-default.xml -
Class: net.sf.saxon.event.SerializerFactory
>File: SerializerFactory.java
>Method: getReceiver
>Line: 154 - net/sf/saxon/event/SerializerFactory.java:154:-1
> at
>com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadConfigurationFiles(XmlConfigurationProvider.java:1014)
> at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.loadDocuments(XmlConfigurationProvider.java:165)
> at com.opensymphony.xwork2.config.providers.XmlConfigurationProvider.init(XmlConfigurationProvider.java:132)
> at com.opensymphony.xwork2.config.impl.DefaultConfiguration.reloadContainer(DefaultConfiguration.java:225)
> at com.opensymphony.xwork2.config.ConfigurationManager.getConfiguration(ConfigurationManager.java:67)
> ... 21 more
>Caused by: Unknown type of result: class javax.xml.transform.dom.DOMResult - Class: net.sf.saxon.event.SerializerFactory
>File: SerializerFactory.java
>Method: getReceiver
>Line: 154 - net/sf/saxon/event/SerializerFactory.java:154:-1
> at com.opensymphony.xwork2.util.DomHelper.parse(DomHelper.java:119)
> at
> ....



Strangly enough the problem pops up only on tomcat 6 (or 7). Running
under jetty seems fine; yanking out saxon-related jars from the
WEB-INF/lib directory seems to fix the problem on tomcat...

lukasz

--
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Lukasz Salwinski PHONE: 310-825-1402
UCLA-DOE Institute for Genomics & Proteomics FAX: 310-206-3914
UCLA, Los Angeles EMAIL: luk...@mbi.ucla.edu
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[Lukasz Salwinski]

Conveniently enough I was able to check psi25-xml sources out of svn,
remove saxon dependency and build the jar after skipping (the failing)
tests. the resulting jar gets integrated into my war file which can be
then deployed on a tomcat server without any obvious problems. I'm
guessing XslTransformerUtils might be dysfunctional but, as I use
psi25-xml only to marshal EntrySet objects into XML, it shouldn't be
a problem...

[Karin (innatedb.com)]

Another follow-up for those interested:

I have nailed it down to the following error (which is 'only' a Throwable, not an Exception and thus didn't show up):

javax.xml.stream.XMLOutputFactory.newFactory()Ljavax/xml/stream/XMLOutputFactory;

java.lang.NoSuchMethodError: javax.xml.stream.XMLOutputFactory.newFactory()Ljavax/xml/stream/XMLOutputFactory;

        at org.hupo.psi.calimocho.xgmml.XgmmlStreamingGrapBuilder.open(XgmmlStreamingGrapBuilder.java:148)

        at org.hupo.psi.mi.psicquic.ws.utils.XgmmlStreamingOutput.write(XgmmlStreamingOutput.java:43)

        at org.apache.cxf.jaxrs.provider.BinaryDataProvider.writeTo(BinaryDataProvider.java:117)

Still digging ..

[Bruno Aranda]

Hi,

This problem rings the bell. It may be due to an incompatibility with one of the PSICQUIC libraries and the version of Java. What JDK are you using? Having you tried with JDK 7?

Cheers,

Bruno

[Karin (innatedb.com)]

Hi Bruno,

Thanks for you input!
Yes, turns out there was a conflict between my Tomcat libraries (I think) and the web service - it's solved in the new ws version (psicquic-solr-ws-1.3.9) which Marine promptly provided. Again, huge thanks to Marine for helping me out on this and fixing it so quickly!

Cheers,
Karin