[ome-users] omero integration

Sun Feb 24 22:38:08 GMT 2008

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