Description

The BioCASE UI is a search portal that can be used to query European ABCD and Darwincore providers. It has been developed within the Synthesys European project, as a new portal to access European data. The portal is based on the prior work done by the BioCASE interface project. You can also try this portal.

The new BioCASE portal provides two kinds of search for the units level:

  • a "simple search" allows you to perform a search based on scientific names
  • an "advanced search" allows you to perform a search based on scientific names, common names, collector names, or family names. It also enables you to restrict your search by choosing institutions, collections, countries, localities and multimedia contents.



Installation


Per default, the application's name is "europe". You can replace it by your own application's name.
  1. The BioCASE UI requires the following:
    • Python (version 2.4)
    • Cherrypy, a pythonic web application framework (version 2.2.1)
    • Kid templates are used (version >= 0.9.2)
    • Elementtree and setuptools are required too, and should be automatically installed with Kid
    • psycopg, a python module used to query Postgresql databases
    • MySQLdb, a python module used to query MySQL databases
    • pyexcelerator, a python module used to generate Excel files
    • libxml and libxslt
    • feedparser, to handle RSS feeds

    • You will also need local databases to query units level data (collection and observation). To get a sample, please contact us.

    Modify the file site.py (in your python path, ie /usr/lib/python2.4/site.py or C:\Python24\site.py): replace the line 364 with encoding = "utf-8" (instead of encoding="ascii")


  2. To run the portal behind Apache2:
    • Install the mod_python module (with libapache2 for Linux) for CherryPy

Configuration


  1. Be sure that the application will be allowed to write in the following folders and subfolders:
    • /appName/session
    • /appName/log
    • /appName/webapp/static/files

  2. If the application's name (appName) you choosed differs from "europe", replace the default name in the following files:
    • appName/config/config.ini
    • appName/config/logconf.ini
    • appName/webapp/static/js/gmap.js
    • appName/webapp/static/js/form.js
    • appName/webapp/static/rico/js/divers.js
    • appName/webapp/static/php/dojotree/teleport_xmlrpc.js
    • appName/webapp/static/css/tao.css
    • appName/webapp/static/css/print.css

  3. The databases properties have to be set in /lib/requestHandler/settings.txt


  4. For the thesaurus service, you can add Thesaurus with its concept in the appName/webapp/static/xml/thesaurusList.xml
    You must add the whole block for each new Thesaurus.
    5. <thesaurus type="the concept's name here (taxon, country, common, ...)">
    <url>the thesaurus url here</url>
    </thesaurus>
    You can set the default time out for the thesauri's connection in the file appName/config/config.ini

  5. Finally, adapt your Apache configuration file httpd.conf.

    It should look like the following lines:

    #######
    #portal
    #The values of PythonInterpreter don't really matter, as long as they're different between the two Location blocks.
    ######
    <Location /appName>
    SetHandler mod_python
    PythonPath "['yourPath/appName']+['yourPath/appName/webapp']+['yourPath/appName/lib']+['yourPath/appName/log']+sys.path" PythonInterpreter appName
    PythonHandler mpcp
    PythonOption wsgi.cleanup cherrypy::engine.stop
    PythonOption cherrysetup serverStarter::configureServer
    PythonOption sys.path 'yourPath/appName/lib'
    PythonAutoReload Off
    PythonDebug Off
    </Location>

    For the suggestion tool:
    Note: PHP must be installed on the server associated to 'anURL'.
    An example of suggest.php can be found in /appName/webapp/static/php/dojotree/
    ProxyRequests off
    ProxyPass /suggest/ http://anURL/php/suggest/suggest.php
    ProxyPassReverse /suggest/ http://anURL/php/suggest/suggest.php

Known Problems

  • The new portal is permanently improved. Update it regularly from the svn.

It has been tested on Windows XP Professional (SP 2), Debian 3.1 , and Ubuntu 6.06 LTS.
As client browsers, Internet Explorer 6.0, Mozilla Firefox 1.0 and Opera 7.54 have been found OK.

Download

BioCASE portal 2