source: extensions/net.sf.basedb.reggie/trunk/README @ 2290

== Requirements ==

 1. BASE 3.3 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 and updating ==

 1. Download the reggie-*.tar.gz file.
 2. Unpack the downloaded file to a directory of your choice.
 3. Copy the 'reggie.jar' file to your BASE plug-ins directory.
    Eg. the directory specified by the 'plugins.dir' setting in 'base.config'.
 4. Log in to BASE as a user with Administrator priviliges. 
 5. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
    Run the installation wizard and select to install/update 'reggie.jar'.
 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. Manual fixes. Check the release information if any manual changes are 
    needed to items that already exists in BASE.
10. 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.
 
 * Blood referral form registration wizard
   This entry is available for 'Administrators' and members of the 
   'PatientCurator' group. It is used to register blood samples
   and connect them with patients. The patient doesn't have to exists.
   If the blood sample already exists, the wizard can be used to update
   missing information.

 * 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.
   
 * Specimen tube registration wizard:
   This entry is available for those with permission to create samples.
   It is used to register new specimen tubes for cases that are not yet
   in BASE.
 
 * Partition registration wizard:
   This entry is available for those with permission to create samples
   and extracts. It is used to register new partitions of existing
   specimen tubes.
   
 * DNA/RNA extraction wizards
   Wizards for registering the extraction of DNA and RNA from the
   sample material.

 * Histology wizards
   Three wizards used in the process of creating H&E stained glass
   slides. The first wizard creates a printable lab tracking protocol
   for the current batch biomaterial items that are about to be
   processed. The second wizard records the paraffin embedding step,
   and the last wizard records the H&E staining step.

 * RNA quality control wizards
   Three wizards that are used in the RNA quality control workflow. The
   first wizard is used for placing the RNA aliquots on a Caliper or
   Bioanalyzer plate. The second wizard generates a sample name file that
   can be used by the Caliper software. The third wizard import the results
   from Caliper back into BASE.

== Compiling ==

To compile this package you also need:
 
 1. Ant 1.9
 2. Java 1.7

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 
    base-*.jar files 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.