[ome-users] Big problems with OMERO.importer on Mac OSx [RESOLVED]
Brian Loranger
brian.loranger at lifesci.dundee.ac.uk
Thu May 15 16:36:48 BST 2008
Hi Ruben,
I'm glad you found a solution!
There have been a string of problems with the base "apple installer"
and file permissions, which is the reason we are moving away from it
in the future in favor of a more generic install process. Currently,
the OMERO Beta 2.3 Downloads (Dec 07) client installer is set to use
fairly liberal user permissions (755 I believe). The reason for that
is because of earlier problems. We thought this level of file
permissions fixed the problem, but as you discovered, it seems to
still cause issues in some situations.
May I ask what version of the importer you have installed? The
versions above OMERO Beta 2.3 Downloads (Dec 07) are currently in a
zip folder, so the file permissions set when you unzip that file
should allow the user to access them. Did one user install the client
and then someone else try to access them?
Thanks again for being diligent and for your support!
Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
On 15 May 2008, at 16:06, » Ruben Alves wrote:
> Dear Brian, Chirs and Paulo,
>
> Finally I was able to establish the connection. This morning Chris
> Allan suggest me to check the files permission, and I discover that
> all the files installed by Omero Installer where owned by the sudo
> user (that's why i maybe suggest to take off this option in the
> installer), and for a unknown reason OMERO.insight works perfectly
> with this kind of permission, but OMERO.importer don't. To put all
> this working, my task was very simple, i've just change the
> owner:group and permission of all OMERO.importer.app
> There is the inputs:
>
> ON LEOPARD
>
> moscardo-2:OMERO.beta2.3 umo$ sudo chown -R nobody:everyone
> OMERO.importer.app/
> moscardo-2:OMERO.beta2.3 umo$ sudo chmod -R 775 OMERO.importer.app
>
>
> ON TIGER
>
> melga:/Applications/OMERO.beta2.3 marcoantunes$ sudo chmod -R 775
> OMERO.importer.app/
> melga:/Applications/OMERO.beta2.3 marcoantunes$ sudo chown -R
> nobody:nobody OMERO.importer.app/
>
>
> Note that "nobody" group seems not exist on Leopard I had to put
> "everyone" in order to work.
>
> I would like to suggest to include this note in the OMERO wiki,
> because I think this issue may affect other Mac Users. Anyway,
> this week I've receive Brian and Paulo feedbacks saying that
> they're able to connect to OMERO.server in a regular account with
> no kind of modifications of hacks. For that reason, my issue may be
> resolved but the problem continue to be unknown. The question is:
> why did this happen on differents Macs here at IMM, and why at IGC
> and Dundee not.
>
> My best regards to all.
> And congratulations for this project. If you guys need some help,
> you can count on me.
>
> // Ruben Alves
>
>
>
> Chris Allan wrote:
>> 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.invok
>>>>>>>>>>> e(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.createSock
>>>>>>>>>>> et(RMIDirectS
>>>>>>>>>>> ocket Factory.java:22)
>>>>>>>>>>>
>>>>>>>>>>> at
>>>>>>>>>>> sun .rmi .transport .proxy.RMIMasterSocketFactory.createSock
>>>>>>>>>>> et(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
>>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
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>>>>
>>> _______________________________________________
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>>
>> _______________________________________________
>> ome-users mailing list
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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
>
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