[ome-users] omero integration

Johan Henriksson johen at student.chalmers.se
Mon Feb 25 09:59:06 GMT 2008 

if the example wasn't broken it had to mean it was the XML libraries. and
indeed I found the inclusion of my gnujaxp.jar to break everything; I have
to replace it.

thanks!



>
> Hi Johan. That's a pretty nasty XML exception, if I've ever seen
> one. Could you tell me what Java version you're using and how you
> executed this? For example,
>
> $ java -version
> java version "1.5.0_13"
> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_13-b05-241)
> Java HotSpot(TM) Client VM (build 1.5.0_13-121, mixed mode, sharing)
>
> $ java -cp .... evplugin.imagesetOME.Test
>
> The example itself, however, is still valid. I just tested it against
> the latest version.
>
> Best wishes,
> ~josh
>
> Johan Henriksson writes:
>  > I've started hacking but run into examples with the example:
>  > http://trac.openmicroscopy.org.uk/omero/wiki/examples/ExampleOne
>  >
>  >
>  > log4j:WARN No appenders could be found for logger
>  > (org.springframework.util.ClassUtils).
>  > log4j:WARN Please initialize the log4j system properly.
>  > Exception in thread "main"
>  > org.springframework.beans.factory.xml.XmlBeanDefinitionStoreException:
>  > Line 98 in XML document from class path resource
> [ome/client/spring.xml]
>  > is invalid; nested exception is org.xml.sax.SAXParseException:
> namespace
>  > nonconformant attribute value: <bean id='managed:ome.api.IAdmin' ...>
>  > Caused by: org.xml.sax.SAXParseException: namespace nonconformant
>  > attribute value: <bean id='managed:ome.api.IAdmin' ...>
>  > 	at
> gnu.xml.pipeline.DomConsumer$Handler.namespaceError(DomConsumer.java:937)
>  > 	at
>  > gnu.xml.pipeline.DomConsumer$Handler.populateAttributes(DomConsumer.java:641)
>  > 	at
> gnu.xml.pipeline.DomConsumer$Handler.startElement(DomConsumer.java:604)
>  > 	at gnu.xml.dom.Consumer$Backdoor.startElement(Consumer.java:203)
>  > 	at gnu.xml.pipeline.EventFilter.startElement(EventFilter.java:570)
>  > 	at
>  > gnu.xml.pipeline.ValidationConsumer.startElement(ValidationConsumer.java:1177)
>  > 	at gnu.xml.aelfred2.SAXDriver.startElement(SAXDriver.java:836)
>  > 	at gnu.xml.aelfred2.XmlParser.parseElement(XmlParser.java:1037)
>  > 	at gnu.xml.aelfred2.XmlParser.parseContent(XmlParser.java:1207)
>  > 	at gnu.xml.aelfred2.XmlParser.parseElement(XmlParser.java:1038)
>  > 	at gnu.xml.aelfred2.XmlParser.parseDocument(XmlParser.java:416)
>  > 	at gnu.xml.aelfred2.XmlParser.doParse(XmlParser.java:167)
>  > 	at gnu.xml.aelfred2.SAXDriver.parse(SAXDriver.java:320)
>  > 	at gnu.xml.aelfred2.XmlReader.parse(XmlReader.java:294)
>  > 	at gnu.xml.dom.JAXPFactory$JAXPBuilder.parse(JAXPFactory.java:186)
>  > 	at
>  > org.springframework.beans.factory.xml.DefaultDocumentLoader.loadDocument(DefaultDocumentLoader.java:76)
>  > 	at
>  > org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:351)
>  > 	at
>  > org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:303)
>  > 	at
>  > org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:280)
>  > 	at
>  > org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:131)
>  > 	at
>  > org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:147)
>  > 	at
>  > org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:173)
>  > 	at
>  > org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:112)
>  > 	at
>  > org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:79)
>  > 	at
>  > org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:101)
>  > 	at
>  > org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:389)
>  > 	at
>  > org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:324)
>  > 	at ome.system.OmeroContext.getContext(OmeroContext.java:159)
>  > 	at ome.system.OmeroContext.getClientContext(OmeroContext.java:125)
>  > 	at ome.system.ServiceFactory.<init>(ServiceFactory.java:115)
>  > 	at evplugin.imagesetOME.Test2.main(Test2.java:28)
>  >
>  >
>  > offending line is:
>  >
>  > ome.system.ServiceFactory sf = new
> ome.system.ServiceFactory(server,login);
>  >
>  > I copied (most) of the jars from insight, OMERO Beta 2.3. it doesn't
> look
>  > like a missing file, only a crash in the parser so I assume this is not
>  > the problem.
>  >
>  > to be precise, I have:
>  > _jboss_remoting.jar
>  > client-3.0-Beta2.3.jar
>  > common-3.0-Beta2.3.jar
>  > commons-codec-1.3.jar
>  > commons-httpclient-3.0.1.jar
>  > commons-logging-1.0.4.jar
>  > jboss-annotations-ejb3-4.2.1.GA.jar
>  > jboss-aop-jdk50-4.2.1.GA.jar
>  > jboss-aop-jdk50-client-4.2.1.GA.jar
>  > jboss-aspect-library-jdk50-4.2.1.GA.jar
>  > jboss-ejb3-4.2.1.GA.jar
>  > jboss-ejb3x-4.2.1.GA.jar
>  > jbossall-client-4.2.1.GA.jar
>  > jcommon-1.0.9.jar
>  > log4j-1.2.14.jar
>  > spring-2.0.6.jar
>  >
>  >
>  > is the example out of date?
>  >
>  > thanks,
>  > /Johan
>  >
>  >
>  >
>  >
>  > > Hi Johan-
>  > >
>  > > Thanks for your email.  We'd welcome and support  the development of
>  > > new clients for OMERO-- that's what this is all about!  We've tried
>  > > to document the system as much as possible.  All of the relevant
>  > > resources on the OMERO trac:
>  > >
>  > > http://trac.openmicroscopy.org.uk/omero.
>  > >
>  > > The best starting point will be
>  > >
>  > > http://trac.openmicroscopy.org.uk/omero/wiki/OmeroClientLibrary
>  > >
>  > > This cross-references much of what you will need.  Obviously, we're
>  > > glad to answer any questions might have.
>  > >
>  > > However, please note:  the OMERO API is changing, definitely for the
>  > > better.  A number of new features are coming in Beta3:
>  > >
>  > > http://trac.openmicroscopy.org.uk/omero/milestone/3.0-Beta3
>  > >
>  > > If you start working with the OMERO server in earnest, let us know,
>  > > and we will point you to docs on the trac that will tell you where
>  > > the new stuff is going.  We plan to announce these publicly in the
>  > > next 2-3 weeks, once the code has solidified and we've done more
>  > > testing.
>  > >
>  > > Thanks very much for your interest.
>  > >
>  > > Cheers,
>  > >
>  > > Jason
>  > >
>  > > On 18 Feb 2008, at 09:44, Johan Henriksson wrote:
>  > >
>  > >> ome-users at lists.openmicroscopy.org.uk
>  > >>
>  > >>
>  > >> Hello,
>  > >> I am thinking of adding a full Omero integration to my image
> analysis
>  > >> software (http://www.endrov.net) at some point. This would have to
>  > >> include
>  > >> something like a mini-insight client for the sake of selection,
>  > >> browsing
>  > >> etc. it would be nice if one could just get a handle for getting/
>  > >> putting
>  > >> data without worrying too much about the omero internals, and
>  > >> especially
>  > >> not reinvent Insight.
>  > >>
>  > >> I therefore wonder if something like this with the purpose of third-
>  > >> party
>  > >> program integration has been developed already and how stable the
>  > >> API is.
>  > >>
>  > >> /Johan
>


--
------------------------------------------------
Johan Henriksson aka Mahogny aka Stålis
mahogny at areta.org / johen at student.chalmers.se / johan.henriksson at biosci.ki.se

MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org

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