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stav text annotation visualiser (stav)

About

stav is a text visualisation tool, developed for the purpose of visualising data from the BioNLP'11 Shared Task. It aims to provide a clear and easily graspable representation of event structures and the associated textual spans.

Citing

If you make use of stav in your publications please cite the publication below which is provided in BibTeX format:

@InProceedings{stenetorp2011supporting,
  author    = {Stenetorp, Pontus and Topi\'{c}, Goran and Pyysalo, Sampo
      and Ohta, Tomoko and Kim, Jin-Dong and Tsujii, Jun'ichi},
  title     = {BioNLP Shared Task 2011: Supporting Resources},
  booktitle = {Proceedings of BioNLP Shared Task 2011 Workshop},
  month     = {June},
  year      = {2011},
  address   = {Portland, Oregon, USA},
  publisher = {Association for Computational Linguistics},
  pages     = {112--120},
  url       = {http://www.aclweb.org/anthology/W11-1816}
}

If you have enough space we would be very happy if you also link to the stav repository to make it easier for readers to get straight-to-the-software:

...the stav text annotation visualiser\footnote{
    \url{https://github.com/TsujiiLaboratory/stav}
}

License

stav is open source software, please see LICENSE.md for details.

Installation

This section describes how to install stav and its third-party dependencies. Do note that stav is a served through a web server and we currently develop against Apache 2.x, these instructions will assume that you use the same but we do have LigHTTPD configuration files in the repository if you feel like trying it out.

WARNING

Since stav (and this document) is very much under development the information on this document may not be up to date. If it isn't, bash the developers ASAP. You are also very welcome to file issues for bugs that you may find or features that you would like to see in stav, do so at our GitHub page or by mailing the authors. We appreciate if you supply the version you are working on and as much details on your system as possible (we have received tar-balls of whole installations at some points since the installation can be self-contained in a single directory).

stav

Check out stav using git.

git clone git@github.com:TsujiiLaboratory/stav.git

Enter the stav directory:

cd stav

When running stav it needs to read and write data to several directories, let's create them.

mkdir data work

We now need to set the permissions of the directories so that they can be read and written by the webserver. The command-line below is likely to give you the Apache 2 group if you have Apache currently running. If not, see the "Finding Your Apache 2 Group" section of this document:

groups `ps aux | grep apache | grep -v 'grep' \
        | cut -d ' ' -f 1 | grep -v 'root' | head -n 1` \
    | cut -d : -f 2 | sed 's|\ ||g'

Then simply change the group of the directories (change ${YOUR_APACHE_GROUP} into the output you got above) and set the correct permissions:

sudo chgrp -R ${YOUR_APACHE_GROUP} data work
chmod -R g+rwx data work

If you can't succeed with the above or you are not concerned with security (say that it is a single-user system), you can run the command below instead or refer to your operating system manual and look-up Apache 2 for their instructions on how to get the Apache group. This will make the directories write-able and read-able by every user on your system:

chmod 777 data work

Extract all the library dependencies.

( cd server/lib && tar xfz simplejson-2.1.5.tar.gz )

Put a configuration in place.

cp config_template.py config.py

Edit the configuration to suit your environment.

vim config.py

Your installation should now be ready, just place your data in the data directory and make sure it has the right permissions using chmod as you did above.

Third-party Stuff

This part largely focuses on Ubuntu, but use your *NIX-fu to turn it into what you need if you don't have the misfortune to have the "Brown Lunix Distribution".

Apache 2.x

stav supports FastCGI which can speed up your installation by roughly x10 since you won't have to invoke the Python interpreter for every request. If you want to use FastCGI as opposed to CGI keep an eye out for configuration comments regarding it. For FastCGI you need the flup Python library:

( cd server/lib/ && tar xfz flup-1.0.2.tar.gz )

Install Apache 2.x if you don't have it already:

sudo apt-get install apache2

Let's edit the httpd.conf.

sudo vim /etc/apache2/httpd.conf

If you are installing stav into your home directory, add the following lines.

<Directory /home/*/public_html>
    AllowOverride Options Indexes FileInfo
    AddType application/xhtml+xml .xhtml
    AddType font/ttf .ttf
    # For CGI support
    AddHandler cgi-script .cgi
    # Comment out the line above and uncomment the line below for FastCGI
    #AddHandler fastcgi-script fcgi
</Directory>

# For FastCGI, Single user installs should be fine with anything over 8
#FastCgiConfig -maxProcesses 16

If you are not installing into your home directory adjust the above lines accordingly. If you installed into your home directory make sure that you have the userdir module enabled.

sudo a2enmod userdir

For FastCGI you also want to install its module and then add it and the rewrite module that we use to redirect the CGI requests to FastCGI:

sudo apt-get install libapache2-mod-fastcgi
sudo a2enmod fastcgi
sudo a2enmod rewrite

The final FastCGI step is detailed in .htaccess in the stav installation directory, which involves uncommenting and configuring the rewrite module.

Finally tell Apache 2.x to load your new configuration.

sudo /etc/init.d/apache2 reload

Finding Four Apache 2 Group

Ideally you should set all permissions as needed for the Apache 2 group, but finding it can be painful.

Find out what the Apache group name is, it is usually apache or www-data; it can be found in apache2.conf or httpd.conf under /etc/apache2/ or /etc/httpd/. Let's assume it's www-data. Then:

sudo chgrp -R www-data data work
chmod -R g+rwx data work

Actually, due to the joy of Linux segmentation you can find the group elsewhere as well. Here is a small heuristic that works on at least two Linux distributions:

locate --regex '(apache2|httpd)\.conf$' | xargs cat | grep 'Group'

If what you get from this looks funky, say with a leading $, try this:

locate envvars | grep -E '(apache2|httpd)' | grep '/etc/' \
    | xargs cat | grep -i 'group'

If this doesn't work either dive into /etc/group and hope that you can find something that at least looks like apache or www-data:

cat /etc/group | cut -d : -f 1 | sort

On a Mac

On a Mac, Apache configuration is quite different, and Aptitude is not available.

Setting up Apache

Clone this repository into ~/Sites. Edit /private/etc/apache2/users/$USER.conf. Then invoke sudo apachectl reload. The default user and group name for Apache is _www (as found in /private/etc/apache2/httpd.conf), for use in chgrp.

Contact

For help and feedback please contact the authors below, preferably with all on them on CC since their responsibilities and availability may vary: