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

» Ruben Alves rubenalves at fm.ul.pt
Tue May 13 10:32:51 BST 2008 

Sorry Brian, it still not working for everyone :P
It only works for the Mac with one User (the root admin account). 
Because, for shared Mac with multiple users, I will have to configure 
and try something in order to put all this working like a charm.
In fact, this is very strange, if is the 1066 port, is actually above 
the 1024, but, like i say, Java for me is like glue, impossible to get 
off... and now is still better than in 1998.
There nothing to see with restrictions or firewall, because i've tried 
with/without firewall, all kinds of Mac users. The problem is really JVM 
and Mac...
Yesterday I made a screenshot of the Console Debugging window while i 
was trying to establish a connection with a regular user (with 
administration privileges):

/    /

The error msg is not very clear, but is understandable that the Client 
can't import some classes. all this because of the Java rights on Mac OSx.


// ruben


Brian Loranger wrote:
> 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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>>> ome-users at lists.openmicroscopy.org.uk 
>>> <mailto: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
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk 
>> <mailto: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

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