Open Microscopy Environment

Hi,

I am developing a software and I want to use OMERO APIs without having the server installed. I just want to access a remote server. For this purpose, I got an advise to install OMERO.py package. However, I could not find any instruction for its installation. I just know ZeroC Ice package is required. Since I am new in python, I appreciate it if you could provide me some detailed information.

Best regards
pz3977

The easiest way is to download and unzip OMERO.py, start a command-prompt/terminal in the directory you've just unzipped, and run

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bin/omero shell

or

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bin/omero shell --login

. Alternatively you can add lib/python to your PYTHONPATH, and import the omero module from your Python script.

Thanks manics for your reply. I appreciate it. Could you please tell me which settings is required.

I got an error represented:
ERROR:omero.util.UpgrageCheck:<urlopen error [Errno 113] No route to host>

Hi,

The error you are seeing is related to http://www.openmicroscopy.org/site/supp ... Check.html. I'm guessing that your network settings prohibit the OMERO upgrade check from reaching the destination URL. Please make sure you also have an active Internet connection.

Alternatively, you could try setting omero.upgrades.url to an empty string using bin/omero config set omero.upgrades.url.

Regards,
Blazej

Hi Blazej,

Thanks for your reply.
I tried a free line without proxy with

bin/omero shell --login

I got following error:

InternalException: Failed to connect: exception ::Ice::PluginInitializationException
{
reason = unable to load entry point `IceSSL:createIceSSL': libIceSSL.so.34: cannot open shared object file: No such file or directory
}

it seems there is a problem in installing zero-ice. Could you please help me to solve it?

Best regards,
pz3977

Could you give us some details about your setup, including your operating system and version, which Ice package you installed, your Python version:

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python --version

and the output of:

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python -c "import Ice; print Ice.stringVersion()"

Hi manics,

I am using:

Ubuntu 12.04 on VMware 6.0,
Python 2.7.3
I installed ice via sudo apt-get install zeroc-ice34,

output of
python -c "import Ice; print Ice.stringVersion()" :
3.4.2

I hope it helps to find the problem.

Best regards,
pz3977

Your earlier error message suggests one of the Ice libraries, libIceSSL.so.34, can't be found, though it should've been installed as part of zeroc-ice.

What does this show:

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ls -l /usr/lib/libIceSSL*

Assuming it's present can you also run:

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ldd /usr/lib/libIceSSL.so.34

Have you modified any of these environment variables: PATH, PYTHONPATH, LD_LIBRARY_PATH?

Thanks, Simon

Hi manics,

I think zeroc-ice was not insalled properlly due to some restirictions of proxy etc. I tried to install it again using a free line. I do not get the previous error any more.

Sorry if it is stupid question, when I run it, it ask for a server, user and password. I guess it assumes I have installed a server, while I did not and I do not have plan to do that. My plan is to connect to a test remote server and search on metadata using existing APIs. I tried "https://omero.ohsu.edu" as well but it failed. It is not clear to me which server I should connect?

Thanks for your help and your patience.

Regads,
pz3977


FYI:
output of : ls -l /usr/lib/libIceSSL* :

lrwxrwxrwx 1 root root 15 Oct 27 2011 /usr/lib/libIceSSL.so -> libIceSSL.so.34
lrwxrwxrwx 1 root root 18 Oct 27 2011 /usr/lib/libIceSSL.so.34 -> libIceSSL.so.3.4.2
-rw-r--r-- 1 root root 354712 Oct 27 2011 /usr/lib/libIceSSL.so.3.4.2

output of ldd /usr/lib/libIceSSL.so.34:

linux-vdso.so.1 => (0x00007fff9c8dd000)
libIce.so.34 => /usr/lib/libIce.so.34 (0x00007f0152d01000)
libIceUtil.so.34 => /usr/lib/libIceUtil.so.34 (0x00007f0152abf000)
libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007f0152860000)
libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007f0152485000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f0152268000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f0151f67000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f0151d51000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f0151991000)
libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f0151780000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f015157c000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0151374000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f015115c000)
/lib64/ld-linux-x86-64.so.2 (0x00007f0153454000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f0150e60000)

Hi

You should be able to connect to omero.ohsu.edu (without the https://). You'll need to ensure ports 4063 and 4064 are accessible.

Simon