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

Last change on this file was 6326, checked in by Nicklas Nordborg, 6 months ago

Merge Reggie 4.31.3 to the trunk

  • Property svn:mime-type set to text/x-trac-wiki
File size: 5.5 KB

Requirements

  1. BASE 3.18.1
  2. Open Grid Scheduler extension 1.4 must be installed
  3. Thumbnails extension 1.2 must be installed

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. Edit and copy configuration files to their correct location. See config/readme.txt for more information. If this is a first-time installation shut down BASE and run 'updatedb.sh' script so that additional reporter annotations and raw data columns are created.
  5. Log in to BASE as a user with Administrator priviliges.
  6. Go to 'Administrate->Plug-ins & Extensions->Overview' page. Run the installation wizard and select to install/update 'reggie.jar'.
  7. 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.
  8. Go to the Extensions->Reggie menu. Select the 'Installation wizard' If the 'Reggie' menu is not visible try BASE->Reload permissions menu.
  9. 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.
  1. Manual fixes. Check the release information if any manual changes are

needed to items that already exists in BASE.

  1. 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 (later versions may also work):

  1. Ant 1.10
  2. Java 11

Follow these instructions:

  1. Download the source code from the subversion repository. See https://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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