[ome-users] omero integration
josh.moore at gmx.de
josh.moore at gmx.de
Mon Feb 25 10:03:49 GMT 2008
Johan-
You're welcome, and thanks for letting us know. Happy coding.
~Josh.
Johan Henriksson writes:
> 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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