Proposed new scheme for $SBEAMS/

Overview:

----------

cgi/       executable Perl

lib/       protected static files: libraries, source code, config files

servlet/   Java servlets processed by Tomcat

tmp/       downloadable dynamic files: autogen jars, autogen html

usr/       downloadable static files like jars, images, docs, includes

var/       protected dynamic files: resultsets, uploaded data, logs, data

In more detail:

------------

cgi/ [EXECUTABLE]

   /$MODULE/

lib/ [EXCLUDED] [nothing in here goes out via HTTP]

   /same structure as now

servlet/ [REMAP to Tomcat]

       /$MODULE/

tmp/ [OPEN]

   /images/ (instead of current /images/tmp)

   /jws/

   /$MODULE/ (module-specific dynamically generated files that need to be

              directly accessible like jnlps, data.jars, etc.)

   /Interactions/Cytoscape_upload/  (dynamically generated HTML describing

                                     the results of a bulk upload)

usr/ [OPEN]

   /images/ [move from root]

   /includes/ [move from root]

   /doc/ [move from root]

   /java/share/     (stable jars directly accessible)

   /java/$MODULE/   (module-specific stable jars directly accessible)

var/ [EXCLUDED] [nothing in here goes out via HTTP]

   /resultsets/ (instead of current /tmp/queries/)

   /logs/

   /upload/ (uploaded files via ManageTable)

   /$MODULE/ (module-specific data files that should be accessed via

             security-conscious cgi)