OMERO.tables

OMERO.tables provide a way to efficiently store large, tabular results within OMERO. If you would like to find out more about the use of the OMERO.tables API, see OMERO.analysis

Requirements

If you would like to help test the Tables API, you will need the following installed:

Unix

PyTables is likely available from the package repository of your Unix-flavor. This includes Mac OS X (homebrew), Debian and Ubuntu (apt-get), CentOS (yum), and SuSE (yast). Here we’ve shown manual instructions using virtualenv.

Manually

$ virtualenv $HOME/virtualenv
$ uname -o -p
unknown GNU/Linux
$ gcc --version
gcc-4.8.real (Debian 4.8.1-9) 4.8.1
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ wget "https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.11.tar.gz"
$ tar xzf hdf5-1.8.11.tar.gz
$ cd hdf5-1.8.11
$ ./configure --prefix=$HOME/virtualenv
$ make
$ make install
$ export LD_LIBRARY_PATH=$HOME/virtualenv/lib
$ . $HOME/virtualenv/bin/activate
$ easy_install tables

Checking that it works

After that, the following should succeed:

% python
Python 2.7.5+ (default, Aug  4 2013, 10:07:17)
[GCC 4.8.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  2.4.0
HDF5 version:      1.8.11
NumPy version:     1.7.1
Numexpr version:   2.0.1 (not using Intel's VML/MKL)
Zlib version:      1.2.8 (in Python interpreter)
LZO version:       2.06 (Aug 12 2011)
BZIP2 version:     1.0.6 (6-Sept-2010)
Blosc version:     1.1.3 (2010-11-16)
Python version:    2.7.5+ (default, Aug  4 2013, 10:07:17)
[GCC 4.8.1]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    8
…

Note

If the above test fails with:

ImportError: No module named mock

then this is fixed by installing the corresponding Python module. Use your operating system’s package installer if possible or if you must instead use PyPI directly:

pip install mock

Once the required Python libraries are installed, starting OMERO will automatically start up the OMERO.tables service; there should be no need for further configuration or interaction.