source: extensions/net.sf.basedb.reggie/trunk/README @ 1485

Last change on this file since 1485 was 1463, checked in by Martin Svensson, 10 years ago

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Requirements

  1. BASE 3.0 or later.

Introduction

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

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. 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.

  • 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.

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.

  1. 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.
  1. Type 'ant' to compile the code and generate the 'reggie.jar' file in the project directory.
  1. 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.

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