[ome-users] omero integration

Sun Feb 24 13:24:12 GMT 2008

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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> **************************
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> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone:  44 1382 385819
> FAX   (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
>
>

--
------------------------------------------------
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