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combining TIFF and CSV file with metadata

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Re: combining TIFF and CSV file with metadata

Postby jmoore » Fri Apr 20, 2012 3:33 pm

Sorry, it looks like your Python installation has become very confused. Do you have a history of all the recent steps you took?

~Josh
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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Mon Apr 23, 2012 8:40 am

good question:
actually python 2.4.3 is installed.
I just installed hdf5, numpy, numexpr and pytables
and I installed ice 3.4 noticed this won't work and reinstalled 3.3.1.

now I try to get it to work again. Great start into the new week, hopefully I get it to work today.

edit: another question, when I finally can upload csv files with omero.tables will this data be viewable with omero.client, by clicking on the plate/well and viewing the meta data.

edit2: should I probably just reinstall python?
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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Mon Apr 23, 2012 11:08 am

Code: Select all
********************************************************************************

        ERROR: Could not import omero.cli! (No module named Ice)

        This means that your installation is incomplete. Contact
        the OME mailing lists for more information:

        https://www.openmicroscopy.org/site/community

        If you are building from source, please supply the build log
        as well as which version you are building from. If you
        downloaded a distribution, please provide which link you
        used.
       
********************************************************************************

        Debugging Info:
        --------------
        CWD=/data/applications/OMERO.server-Beta-4.3.4/bin
        VERSION=2.6.5 (r265:79063, Feb 28 2011, 21:55:45)  [GCC 4.1.2 20080704 (Red Hat 4.1.2-50)]
        OMERO_HOME=/data/applications/OMERO.server-Beta-4.3.4
        PYTHONPATH=['/data/applications/OMERO.server-Beta-4.3.4/lib/python', '/data/applications/OMERO.server-Beta-4.3.4/var/lib', '/data/applications/OMERO.server-Beta-4.3.4/bin', '/data/applications/OMERO.server-Beta-4.3.4/lib/python', '/data/applications/OMERO.server-Beta-4.3.4/bin', '/usr/lib64/python26.zip', '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages', '/usr/lib/python2.6/site-packages', '/data/applications/OMERO.server-Beta-4.3.4/lib/fallback']



installed python2.6 now and I get this message. any ideas?

edit:
using ./omero admin startasync and /omero admin diagnosticsgives the same output as above.
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Re: combining TIFF and CSV file with metadata

Postby cxallan » Tue Apr 24, 2012 1:17 pm

You're going to get yourself in real trouble mixing and matching Python versions and Ice versions. What distribution are you trying to install on?
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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Wed Apr 25, 2012 6:42 am

well, I can easily switch between python2.4 or 2.6.
CentOS 5.5 x86_64 GNU/Linux
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Re: combining TIFF and CSV file with metadata

Postby cxallan » Wed Apr 25, 2012 7:50 am

If you're on Centos 5, unless you want to compile Ice and all the Python libraries yourself you should stick with the system Python 2.4 and ZeroC's Ice 3.3 RPMs from their Yum repository. You can then install HDF5 either from source or via RPM from any number of repositories and finally easy_install PyTables. If you can run the following, you should be set:

Code: Select all
$ python
Python 2.4.3 (#1, Nov 11 2010, 13:30:19)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.__version__
'2.2.1'
>>>
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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Wed Apr 25, 2012 7:53 am

I can already do:

Code: Select all
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.__version__
'2.3.1'
>>>


the problem is that "omero admin start" is not working anymore, for whatever reason, somehow cli.py is involved (see above posts).
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Re: combining TIFF and CSV file with metadata

Postby cxallan » Wed Apr 25, 2012 8:02 am

That error message above is telling you that Ice is not importable. What about:

Code: Select all
$ python
Python 2.4.3 (#1, Nov 11 2010, 13:30:19)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
>>>
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Re: combining TIFF and CSV file with metadata

Postby Thorondor » Wed Apr 25, 2012 8:08 am

Code: Select all
Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
>>>


also working. :-/
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Re: combining TIFF and CSV file with metadata

Postby cxallan » Thu Apr 26, 2012 12:52 pm

Okay, then what's happening when you run a bin/omero admin start now? Are you still getting something to the effect of ERROR: Could not import omero.cli! (No module named Ice)? The error in the brackets at the end is critical. If it's saying No module named Ice you should check import Ice with Python in the same terminal session.
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