
############################################################################################################
/biocase

    #=======================================================================================================
    LICENSE.TXT
    README.html
    VERSIONS.html

    #=======================================================================================================
    configuration/

        #---------------------------------------------------------------------------------------------------
        .configuration      # global configuration
        
        #---------------------------------------------------------------------------------------------------
        datasources/
            #   Data sources configured by the provider. Each data source has its data source alias (dsa)
            #   for its name; it should be prohibited to use a dsa that also appears under schemas/
            #   (i.e. data source aliases and schema prefixes make up one single namespace, so 
            #   references like :xy:/foo/bar/baz are always uniquely resolveable). In order to publish
            #   a data source, an additional directory /biocase/www/datasources/${dsa} must be established.

            NoDIT2/
            pontaurus/
            rename_this_to_your_db/

        #---------------------------------------------------------------------------------------------------
        persistence/
            #   Datasources with graph descriptions of ABCD, :bion: and so on; session data etc. 
            #   Nothing the user will directly touch or change.

        #---------------------------------------------------------------------------------------------------
        schemas/
            #   Files particularly relating to a given schema, like the abcd.xsd and so on. Each schema
            #   gets its own directory with the conventional prefix as a name. 

            abcd12/
            .../
            cmf/        #   Mainly cmf.xsd for validity checking of ${dsa}_cmf.xml files
            psf/        #   Mainly psf.xsd for validity checking of ${dsa}_psf.xml files

        #---------------------------------------------------------------------------------------------------
        templates/

        #---------------------------------------------------------------------------------------------------
        configtool/
        querytool/
        pywrapper/
        apache2/        #   Sample configuration for Apache

    #=======================================================================================================
    lib/
        #   This is one more place that is added to sys.path and from where globally importable
        #   modules may be fetched; it is also an alternative location for people that cannot
        #   write to python/Lib/site-packages.
        
        biocase/            #   This corresponds to python/lib/site-packages/biocase.
            configtool/     #   Library of the configtool.
                utilities/  #   Files here probably move to lib/configtool and lib/utilities
            querytool/      #   Library of the querytool.

    #=======================================================================================================
    tools/      #   local scripts and apps for maintenance etc.
    log/        #   logfiles

    #=======================================================================================================
    www/
        #   Everything that should be world-readable


        #---------------------------------------------------------------------------------------------------
        datasources/
            #   Data sources that are actually published by the provider. 
            NoDIT2/
            pontaurus/

        #-------------------------------------------------------------------------------------------
        configtool/
            #   Cgi scripts, static pages etc. needed by the configtool,
            #   except libraries -- these are under /biocase/lib/

        #-------------------------------------------------------------------------------------------
        querytool/
            #   Cgi scripts, static pages etc. needed by the querytool,
            #   except libraries -- these are under /biocase/lib/

        #-------------------------------------------------------------------------------------------
        configuration/
            #   The 'public' or 'boot' configuration side -- only needed to set up a CGI
            #   context (i.e. find the private branch, append paths to sys.path, import
            #   globalNamebase.py). This directory should not be readable, but since it is
            #   on the web side of the application, we take the precaution of only keeping two
            #   essential paths in .configuration.

            fundamentals.py
            .configuration
            .htaccess

        #-------------------------------------------------------------------------------------------
        docs/       #   public documentation
        media/      #   Images, global stylesheets etc.
        tests/      #   test scripts

############################################################################################################
/biocase-internal
    #   files used for intermediary things and old files kept for reference
