Open Microscopy Environment

Hi there,
I'm considering deploying an OMERO server and use JAVA APIs in a program that I already wrote to access it. To test if this solution will answer my needs and to get the basics I installed the OMERO 5.2.4/ICE 3.5 server on a virtual machine running Ubuntu 14.04 LTS.
I managed to install the server and deploy OMERO.web and everything is working perfectly: I can connect through OMERO.web from both the guest and the host (by the way, the walkthrough is very well done considering that I've never worked before with linux and this was the first server I installed ). Then to play a bit with the Java APIs I wrote a little project in ECLIPSE that would connect to the server and display the number of projects owned by the omero_user. When I run it in the virtual machine everything works fine problems arise when I try to run it from the host OS (Windows 10). I think that the problem is related to the server hostname as port, usermame and password would be the same. So far, what I tried was to get the IP of the virtual machine, assign it a name in the ../drivers/etc/hosts file and then use this name as the server hostname. This is obviously not working, any suggestion?

Hi Alex,

what do you use for running the virtual machine, is it VirtualBox? My first guess would be that there are some OMERO specific ports blocked for the virtual machine.
By the way, there's actually no need for assigning a name, you can use the IP directly as hostname. We should probably make that a bit clearer in the API documentation.

Regards,
Dominik

Hi Dominik,
I've actually already tried to feed the IP but the result is the same
To give you more info:
I'm running virtualbox with network set to NAT and in the advanced tab I assigned the rules for port forwarding as described for the OMERO virtual appliance (only difference is that the guest IP is 10.0.3.15). Doing some research on the net I've seen that you can check if something is listening to the ports with the command: netstat -ntlp | grep LISTEN
What I get for this ports is:

tcp6 0 0 :::80 :::* LISTEN 1644/apache2
tcp6 0 0 :::4063 :::* LISTEN 3080/glacier2router
tcp6 0 0 :::4064 :::* LISTEN 3080/glacier2router

but unfortunately given my limited knowledge this does not tell me anything
Any idea?

That's good, it means the OMERO.server is running and listening on these ports. I wonder if you can access these ports from your Windows machine. Can you enable the telnet client on you Windows machine?
Unfortunately I only found a description for Windows 7, but I guess for 10 it will be similar (it's an optional Windows Feature): https://social.technet.microsoft.com/wi ... lient.aspx

Then open a command line terminal and run 'telnet', this will give you a telnet prompt. Then try to connect to the OMERO.server port with 'open [IP address] 4064'. The connection should be established and you see "Press any key to continue", and after a few seconds the connection will be closed again. If the connection can't be established, you should get a "Connect failed" (or something similar) right away.

Regards,
Dominik

I just realized, if you set up the port forwarding according to the "OMERO virtual appliance" page, you have to use "localhost" (or "127.0.0.1") as hostname to connect to the server. Could you try that?

Regards,
Dominik

Hi Dominik,
I tried all you suggested and here are the results:
using "localhost" or "127.0.0.1" in the Eclipse project does not work, actually this does not work neither when I try to connect to OMERO.web through firefox on the host.
The telnet client is giving me a "failed connection" error.
To test whether the problem could arise from the ports on the host machine being closed I added some rules on my firewall to explicitly open them but did not work. I even tried to disable the firewall entirely but it did not work
To continue investigate this in the windows cmd I typed: "netstat -an" and got:

TCP 127.0.0.1:2222 0.0.0.0:0 LISTENING
TCP 127.0.0.1:4063 0.0.0.0:0 LISTENING
TCP 127.0.0.1:4064 0.0.0.0:0 LISTENING
TCP 127.0.0.1:8080 0.0.0.0:0 LISTENING

doesn't this mean that the host is listening on these ports?

Hi Alex,

everything looks fine, I'm running a bit out of ideas...

I think I mixed things up with respect to virtual machine IP and localhost. Could you test again, with using localhost/127.0.0.1 only. Your portforwarding looks fine, so you should be able to use localhost/127.0.0.1 as hostname throughout.

1) OMERO.web on localhost, that should be the address: "http://localhost:8080"
2) telnet localhost: "open 127.0.0.1 4064"

I tried that locally on my machine (only OSX instead of Windows) using the pre-build OMERO virtual appliance, no problems. As last resort, could you test that? Download, import and run the VM from http://downloads.openmicroscopy.org/ome ... nce/5.2.1/ and try to connect to that virtual machine. It's a bit outdated (5.2.1), because we stopped building the VM for newer versions. But it would be interesting if that works for you.

Regards,
Dominik

Hi Dominik,
as you suggested I downloaded the virtual appliance and did some test:
localhost:8080 in the host's web browser correctly redirects to OMERO.web
OMERO.insight with hostname:localhost works
Eclipse project with Java APIs works
This clearly indicates that I did something wrong when I deployed the server in my virtual machine
Thanks a lot for your help, keep up the good work
Alex

You're welcome. I still wonder why it doesn't work with your VM, what's the difference to the prebuilt 5.2.1 one. For some reason your VM seems to block the OMERO ports (4063, 4064), although netstat claims the server is listening on these ports. In case you find out, please let me know!
Regards,
Dominik