
+++  BioACSE
+++  Provider Software


Version  : 2.4.2 build(817)
Date     : 2006-11-16
Author   : Markus Doering, m.doering@bgbm.org
           Javier de la Torre, j.torre@bgbm.org
           Wolfgang Lipp, w.lipp@bgbm.org
License  : Mozilla Public License
====================================================================

NOTE: Please read README.TXT first

NOTE: The former seperate pywrapper libraries are bundled with this BioCASE providersoftware v2. You dont need to install them seperately.

***** INSTALLATION *****
1 * unpack this archive into a place you like (-> INSTALLDIR)
2 * create a virtual directory (eg http//localhost/biocase -> WWWROOT) on your webserver that points to INSTALLDIR/www
    see INSTALLDIR/examples/apache2/httpd-biocase.conf for an apache configuration example
3 * allow python scripts (*.py AND *.cgi) to be executed in this virtual directory.
4 * make sure there are no old pywrapper libraries ( < version 2.0 )installed on your system! 
    This will create conflicts with the new version.
5 * run the INSTALLDIR/setup.py script with python from the terminal and follow the instructions:
    %> python setup.py 
6 * install basic python libraries (see WWWROOT/utilities/testlibs.cgi for latest details):
    - PyXML      -> http://pyxml.sourceforge.net/
    - libxml2    -> http://xmlsoft.org/python.html
    - mxDateTime -> http://www.egenix.com/files/python/eGenix-mx-Extensions.html#Download-mxBASE
    - your desired database drivers for python, eg winODBC -> http://www.egenix.com/files/python/eGenix-mx-Extensions.html#Download-mxCOMMERCIAL
    see WWWROOT/utilities/testlibs.cgi for further driver links or http://ww3.bgbm.org/biocase/utilities/testlibs.cgi



***** TESTING YOUR INSTALLATION *****
1 * try all the testing utilities in the first block of the utilities page:
    WWWROOT/utilities



***** CONFIGURATION *****
If you havent used the setup.py script you will need to provide some configuration parameters - 
otherwise you can skip this step, it should be configured already by the setup.py script!
In general all configuration files are kept at INSTALLDIR/configuration.

You can chose to manually edit the settings or use the system administration part of the configtool to update the settings.
See the BPS2 documentation for the configtool details; we will show the manual way here:
1 * Configure the server settings in INSTALLDIR/configuration/.configuration
    - "host"
      server name as seen from outside including the protocol ending without slash, e.g. http://www.bgbm.org
    - "webroot"
      webserver path to the root directory of the biocase provider software (biocase/www) starting with a slash.



***** IMPORT EXISTING PYWRAPPER DATASOURCES/DATABASES *****
To reuse existing PyWrapper configurations, follow this step by step guide.
You will have to use the configtool for this, which can be accessed online with a browser at:
http://WWWROOT/configtool
The default password is "ACDC" and currently can only be changed by modifying the "adminPassword" setting
in the global configtool configuration file at INSTALLDIR/configuration/configtool/.configuration

1 * Create a new empty datasource (DSA) with the configtool.
    Go to CfgTool->System Administration and do "Create DSA"
2 * manually copy your existing PSF (provider_setup_file.xml) into your new datasource directory replacing the existing one there:
    INSTALLDIR/configuration/datasources/XXX/provider_setup_file.xml
3 * Go to CfgTool->Datasource Administration (select the link to your DSA) to configure your datasource
4 * For each schema (CMF) you want to import, do the following:
    - Create a new empty schema (CMF) with the configtool
    - Run the script INSTALLDIR/tools/transferCMF.py from the command prompt to transfer your existing mappings to the new CMF.
      -> python transferCMF.py
      -> You will be asked by the script to enter the full absolute path to your existing CMF to be imported
      -> You will be asked by the script to enter the full absolute path to your new CMF to be updated with the imported mappings and filters
      -> YOu can delete the backup this script creates, cause it will be the empty CMF you created for your new DSA

Thats it.
    


***** TESTING YOUR DATASOURCE *****
You can test and use your datasource with the following tools:

1 * The querytool (not for SPICE):
    http://WWWROOT/querytool/
2 * The queryforms:
    http://WWWROOT/utilities/queryforms/
3 * The diagnostics analyser (not ready yet):
    http://WWWROOT/testingtool/


***** EXAMPLE DATASOURCE *****
7 * to immediately use the supplied training database do
    - windows: create an ODBC source called "biocase_training" which points to the access database (you will need MS Access on your system): INSTALLDIR/examples/trainingDB/TrainingDB.mdb
    - unix: create a new MySQL database from the SQL dumpfile INSTALLDIR/examples/trainingDB/trainingDB_mysql.sql
    

You can start now using the providersoftware. 
Enter http://WWWROOT to use the software.


Have fun,
BGBM BDI Team
support@biocase.org
