[ome-users] Big problems with OMERO.importer on Mac OSx
Brian Loranger
brian.loranger at lifesci.dundee.ac.uk
Tue May 13 10:13:22 BST 2008
I'm glad you got it working Ruben,
I was a bit surprised that you needed administrator access to use the
importer. It does open one port (1066) but this should be above the
range normally requiring administrator privledges. Do you have some
user setup there that restricts ALL ports from being opened (even
those above 1024)?
Cheers,
Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
On 13 May 2008, at 09:25, » Ruben Alves wrote:
> 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
>>>
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>>
>
>
> --
> Ruben Alves
> USI @ Instituto de Medicina Molecular
> Edifício Egas Moniz
> Av. Prof. Egas Moniz 1649-028 Lisboa Portugal
> tel: 217999400 ext 47026
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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