[ome-users] Big problems with OMERO.importer on Mac OSx
Chris Allan
callan at blackcat.ca
Thu May 15 08:51:39 BST 2008
Hello Ruben,
Along the lines of the permission issues you were mentioning earlier.
Can you also run:
ls -alR /path/to/OMERO.importer.app
Thanks for your patience.
Ciao.
-Chris
On 14 May 2008, at 12:25, Brian Loranger wrote:
> Hi Ruben,
>
> Just a follow up.. and news on getting it working?
>
> Oh and also, someone was nice enough to point out its port 1099 (not
> 1066)... old age must be creeping up on me *g*
>
> Let me know what you find, I have tested it here with no user
> privledges and was able to log in, but clearly something is up.
>
> Cheers,
>
> Brian Loranger
> Software Developer, Open Microscopy Environment
> Division of Gene Regulation and Expression
> University of Dundee
>
>
>
> On 13 May 2008, at 12:38, Brian Loranger wrote:
>
>> Hi Ruben,
>>
>> I just went to one of our mac workstations and logged in with the
>> importer using a user account that had no administration
>> privledges. No problems here.
>>
>> It does seem like your user account setup there is restricting port
>> 1066. This might be something locking up the port (I doubt that),
>> but my top suggestion is to check that some admin policy isn't
>> restricting upper port use.
>>
>> Hope that helps,
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>>
>>
>>
>> On 13 May 2008, at 12:24, » Ruben Alves wrote:
>>
>>> Hi Paulo!
>>> Thanks for you help. But this is very confusing. I have at the
>>> moment:
>>> 2 - Mac Book (the same)
>>> 1 - Mac Pro
>>> 2 - iMac
>>>
>>> The two Mac Book and the Mac pro are running Root account (just
>>> one person by computer), the two iMac are group computers, every
>>> person of the investigation team have is own login. With the Mac
>>> Book and Mac Pro, there is NO problem to connect to OMERO.server
>>> from OMERO.importer, although the two iMac have different
>>> configurations, one is 64 bits with Leopard, the other is 32 Bits
>>> with Tiger, but both of them can't connect to OMERO.server. with
>>> their scientist account (regular user with admin rights). But,
>>> when i logged in with THE administrator account (root), i was able
>>> to connect and upload images to OMERO.server....
>>>
>>> This time i've attached the picture. I Hope it work this time.
>>>
>>> In your e-mail you said:
>>>
>>> - to rule out any port restrictions from the network
>>> I try better than that, i just connect the RJ45 cable of the iMac
>>> to the Mac book, and it worked perfectly, so i can conclude that
>>> the problem is not from the network, or from the infrastructure.
>>>
>>> - I tested Importer in a regular user account
>>> And it worked? What OS are you running? Are you sure the "regular
>>> user" don't have any kind of administrative privilege?
>>> - installing the server on the Mac and see if you can connect to it
>>> I would like to, but i own a Linux box, i can't get a Mac just for
>>> testing :-(
>>>
>>>
>>> thanks for you Help Paulo!
>>>
>>>
>>> // Ruben
>>>
>>>
>>>
>>> Paulo Almeida wrote:
>>>> Hi Ruben,
>>>>
>>>> You mentioned you tried a direct connection to a switch; maybe
>>>> you could try connecting the Mac directly to the server, to rule
>>>> out any port restrictions from the network. I tested Importer in
>>>> a regular user account, on MacOSX, and I'm sure others have too,
>>>> so even if it is related to the JVM, it should not be a general
>>>> issue but rather something specific to your configuration. You
>>>> could also try installing the server on the Mac and see if you
>>>> can connect to it, from the Mac and from a Linux client, but I'm
>>>> not sure that would help.
>>>>
>>>> - Paulo
>>>>
>>>> On Tuesday 13 May 2008 10:32, » Ruben Alves wrote:
>>>>
>>>>> 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(JndiObjectTa
>>>>>>>>> rgetS ource.java:138)
>>>>>>>>>
>>>>>>>>> at
>>>>>>>>> ome
>>>>>>>>> .client.JBossTargetSource.getTarget(JBossTargetSource.java:
>>>>>>>>> 73) at
>>>>>>>>> org
>>>>>>>>> .springframework
>>>>>>>>> .aop.framework.JdkDynamicAopProxy.invoke(JdkDynamic
>>>>>>>>> AopPr 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.ja
>>>>>>>>> va:10 5)
>>>>>>>>>
>>>>>>>>> at
>>>>>>>>> org
>>>>>>>>> .springframework
>>>>>>>>> .jndi.JndiObjectTargetSource.getTarget(JndiObjectTa
>>>>>>>>> rgetS 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(RMIDirectS
>>>>>>>>> ocket Factory.java:22)
>>>>>>>>>
>>>>>>>>> at
>>>>>>>>> sun
>>>>>>>>> .rmi
>>>>>>>>> .transport
>>>>>>>>> .proxy.RMIMasterSocketFactory.createSocket(RMIMasterS
>>>>>>>>> ocket 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
>>>>>>>> <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
>>>>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> <Picture-3.jpg>_______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
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