source: extensions/net.sf.basedb.reggie/trunk/README @ 1361

== Requirements ==

 1. BASE 2.17.1 or later.
 
== Introduction ==

This package is an extension package to BASE that can be used to
simplify biosource and sample registration.

 * The homepage for this extension: 
   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie

== Installation ==

 1. Download the reggie-*.tar.gz file.
 2. Unpack the downloaded file to a directory of your choice.
 3. Copy the 'reggie.jar' file and the 'lib' directory to your BASE extensions 
    directory: WEB-INF/extensions. 
 4. Run the 'Extensions->Manual scan' command if you have disabled automatic
    installation. Otherwise, just wait a bit and the automatic installation will
    find and install the new extension.
 5. Log in as a user with Administrator priviliges. 
 6. Create a project and set it as the active project. This step is
    optional but is recommended. Running Reggie without an active project
    will generate warning messages later on.
 7. Go to the Extensions->Reggie menu. Select the 'Installation wizard'
    If the 'Reggie' menu is not visible try BASE->Reload permissions menu.
 8. It should display a list with several error message about missing items.
    Click on the "Create missing items" button to create them. If no project
    was created in step 6, all annotatation types will be shared with the
    'PatientCurator' group, otherwise only some will be shared to the
    group and some will be shared to the active project.
 9. Done. 

 
== Using ==
 
Reggie appears as a menu entry in the Extensions menu. All operations
are available on that page. 

 * Installation wizard:
   This entry is available if the logged in user is an 'Administrator' and
   will perform some basic checks that items that are needed by Reggie
   exists and have been properly configured. Items that doesn't exists can
   be created automatically.
   
 * Personal information registration wizard:
   This entry is available for 'Administrators' and members of the 
   'PatientCurator' group. It is used to register new patients and
   cases and connect this information to (already existing) 
   specimen tubes. It can also be used to update missing information
   on existing cases and specimen tubes.
   
 * Referral form registration wizard:
   This entry is available for 'Administrators' and members of the 
   'PatientCurator' group. It is used to connect scanned referral
   forms (eg. pdf files) to already existing cases.

 * Consent form registration wizard:
    This entry is available for 'Administrators' and members of the 
   'PatientCurator' group. It is used to connect register consent
   for participating in the study. 

== Compiling ==

To compile this package you also need:
 
 1. Ant 1.6
 2. Java 1.6

Follow these instructions:

 1. Download the source code from the subversion repository. See
    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie for instructions.
 
 2. Type `ant download-lib` to automatically download the BASE core JAR files that
    are neeed for compilation. You can also do this manually by copying the 
    BASE2Core.jar, BASE2Webclient.jar and BASE2WSClient.jar
    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the 
    ./lib/compile directory.

 3. Type 'ant' to compile the code and generate the 'reggie.jar' file
    in the project directory.

 4. Use 'ant package' to create a downloadable tar.gz package.
 
Tip: If you need different values for any of the properties defined in
the 'build.xml' file, create a file named 'build.properties' and set
the values there.