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
:doc:`OMERO.analysis `
Requirements
------------
If you would like to help test the Tables API, you will need the following installed:
- `HDF5 `_
- `NumPy `_ points to downloads at
http://sourceforge.net/projects/numpy/
- `PyTables `_ (Some packages include HDF5)
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.