[ome-users] Big problems with OMERO.importer on Mac OSx

[» Ruben Alves]

Hi everyone,
Finally, i've come back with a big conclusion. In fact, my guess was 
right. The problem was with the Java Virtual Machine and Mac OS, and 
certainly not with OMERO.importer or my configuration file. The problem 
is one of big problems of Java: networking. In every platform, 
OMERO.importer try to open some ports on the client site when he logins 
(i don't understand why Importer opens those ports, because the main 
function of this application is to upload pictures). Anyway, and this 
port and network connection seems to be a big problem in Mac OSx, 
because he only establish to OMERO.server if he logged as a 
Administrator (the root one, not a simple Admin). So problem is truly 
the main engine of Mac OSx and Java. I'll try to sudothem'all, but is 
not a secure way to resolve this issue. If i found something more useful 
for the community i ll write /howto/ use OMERO.Importer with a standard 
Mac account.

My best regards,

// ruben

Paulo Almeida wrote:
> Hi Ruben,
>
> For what it's worth, I can connect to the server with Omero.importer (latest 
> versions of both), on OSX (Tiger). It might be a firewall issue on the client 
> side, but it seems weird that Insight would work and Importer not.
>
> - Paulo 
>
> On Monday 12 May 2008 11:12, » Ruben Alves wrote:
>   
>> Hi everyone,
>> I'm a fresh new user of OMERO (maybe one month), and i've build a fresh
>> new Linux Server with OMERO here at IMM.
>> Everything is working fine in every aspect. But, recently one of the
>> project manager whanted to try it, but he just can't connect to OMERO on
>> is MacOSx. But he only can't connect on the OMERO.importer, because the
>> OMERO.insight is currently working perfectly in Windows , Linux and of
>> course Mac.
>> I've exported the error log. It's important to know, at the connection
>> time, my firewall was off (iptables -F | iptables -X). And at the same
>> time (with 1 or 2 minutes difference), another connection was
>> established with a Windows client AND a Linux (ubuntu) client. The
>> windows client was on the network, and the ubuntu client was on a
>> Virtual Machine.
>>
>> I Really hope someone had this kind of bad experience. I've spent so
>> many hours on that, and now i can't get a neutral view of the problematic.
>>
>> Best regards,
>>
>> // Ruben
>> ps: actually, on the log "ruben" is the login and "10.20.20.52" is the
>> server ip address.
>>
>> 0          [  Thread-5] DEBUG            ome.formats.OMEROMetadataStore
>> - Initializing store: ruben/<3chars> 10.20.20.52:1099
>> 1013       [  Thread-5] INFO          ome.formats.importer.LoginHandler
>> - java.lang.Exception:
>> org.springframework.jndi.JndiLookupFailureException:
>> JndiObjectTargetSource failed to obtain new target object; nested
>> exception is javax.naming.CommunicationException [Root exception is
>> java.rmi.ConnectException: Connection refused to host: ubuntu.fm.ul.pt;
>> nested exception is:
>>    java.net.ConnectException: Connection refused]
>>    at ome.formats.OMEROMetadataStore.<init>(OMEROMetadataStore.java:152)
>>    at ome.formats.importer.LoginHandler.isValidLogin(LoginHandler.java:227)
>>    at ome.formats.importer.LoginHandler.access$10(LoginHandler.java:223)
>>    at ome.formats.importer.LoginHandler$1.run(LoginHandler.java:137)
>> Caused by: org.springframework.jndi.JndiLookupFailureException:
>> JndiObjectTargetSource failed to obtain new target object; nested
>> exception is javax.naming.CommunicationException [Root exception is
>> java.rmi.ConnectException: Connection refused to host: ubuntu.fm.ul.pt;
>> nested exception is:
>>    java.net.ConnectException: Connection refused]
>>    at
>> org.springframework.jndi.JndiObjectTargetSource.getTarget(JndiObjectTargetS
>> ource.java:138)
>>
>>    at ome.client.JBossTargetSource.getTarget(JBossTargetSource.java:73)
>>    at
>> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopPr
>> oxy.java:184)
>>
>>    at $Proxy6.findByString(Unknown Source)
>>    at ome.formats.OMEROMetadataStore.<init>(OMEROMetadataStore.java:149)
>>    ... 3 more
>> Caused by: javax.naming.CommunicationException [Root exception is
>> java.rmi.ConnectException: Connection refused to host: ubuntu.fm.ul.pt;
>> nested exception is:
>>    java.net.ConnectException: Connection refused]
>>    at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:724)
>>    at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:589)
>>    at javax.naming.InitialContext.lookup(InitialContext.java:351)
>>    at
>> org.springframework.jndi.JndiTemplate$1.doInContext(JndiTemplate.java:123)
>>    at org.springframework.jndi.JndiTemplate.execute(JndiTemplate.java:85)
>>    at org.springframework.jndi.JndiTemplate.lookup(JndiTemplate.java:121)
>>    at org.springframework.jndi.JndiTemplate.lookup(JndiTemplate.java:146)
>>    at
>> org.springframework.jndi.JndiLocatorSupport.lookup(JndiLocatorSupport.java:
>> 93)
>>
>>    at
>> org.springframework.jndi.JndiObjectLocator.lookup(JndiObjectLocator.java:10
>> 5)
>>
>>    at
>> org.springframework.jndi.JndiObjectTargetSource.getTarget(JndiObjectTargetS
>> ource.java:131)
>>
>>    ... 7 more
>> Caused by: java.rmi.ConnectException: Connection refused to host:
>> ubuntu.fm.ul.pt; nested exception is:
>>    java.net.ConnectException: Connection refused
>>    at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:574)
>>    at
>> sun.rmi.transport.tcp.TCPChannel.createConnection(TCPChannel.java:185)
>>    at sun.rmi.transport.tcp.TCPChannel.newConnection(TCPChannel.java:171)
>>    at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:94)
>>    at org.jnp.server.NamingServer_Stub.lookup(Unknown Source)
>>    at org.jnp.interfaces.NamingContext.lookup(NamingContext.java:627)
>>    ... 16 more
>> Caused by: java.net.ConnectException: Connection refused
>>    at java.net.PlainSocketImpl.socketConnect(Native Method)
>>    at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
>>    at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
>>    at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
>>    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:430)
>>    at java.net.Socket.connect(Socket.java:520)
>>    at java.net.Socket.connect(Socket.java:470)
>>    at java.net.Socket.<init>(Socket.java:367)
>>    at java.net.Socket.<init>(Socket.java:180)
>>    at
>> sun.rmi.transport.proxy.RMIDirectSocketFactory.createSocket(RMIDirectSocket
>> Factory.java:22)
>>
>>    at
>> sun.rmi.transport.proxy.RMIMasterSocketFactory.createSocket(RMIMasterSocket
>> Factory.java:128)
>>
>>    at sun.rmi.transport.tcp.TCPEndpoint.newSocket(TCPEndpoint.java:569)
>>    ... 21 more
>>     
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>   


-- 
Ruben Alves
USI @ Instituto de Medicina Molecular
Edifício Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999400 ext 47026