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DonorCheck Overview

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kaitlinrenee edited this page Mar 19, 2020 · 6 revisions

About

DonorCheck is a tool developed by the Division of Computational Pathology at the University of Minnesota, Twin Cities, to minimize data entry errors related to organ transplant.

This tool was created to address the workflow disconnect between organ donor typing data and the UNOS DonorNet system. DonorNet is a web interface into which all organ donors must be entered, with their HLA typing. But typing data can come from a variety of sources, which have no knowledge of DonorNet (and vice versa). Although the raw reports can be uploaded and attached to a donor's typing, ultimately all processing and interpretation is performed by a human. This presents the possibility for mistakes, which could pose serious risk to transplant recipients.

To address this risk, DonorCheck has two primary goals:

  1. To standardize the different formats of typing data, unifying instrument reports and DonorNet data into a common format for software-based comparison
  2. To create a user interface/experience facilitating consistent, reproducible comparison

Download and Installation

We currently provide pre-built installers for Windows only. Please select the appropriate download for your operating system:

Code use

This project is open source, distributed under the GPL v2 license. The application is free for use and redistribution.

Code Style

We use Google's java code format. Current version: 1.6

Support

Please join our Google group to keep up on the latest news and updates.

You are welcome to use GitHub issues and/or our Google group to:

  • Report bugs
  • Discuss feature requests
  • Contribute new donor formats

Build Instructions

Prerequisites

For the JFX Launcher (native installer)

  • Install (or confirm that you have installed) the JDK/JRE version that you want bundled in the native installer. For example, you may be using 64 bit JDK, but you may want a 32 bit JDK to be bundled in the native installer.
  • Install the specific packaging prerequisites for your native installer type. For a Windows .exe installer, this would mean installing Inno Setup 5 and adding it to your system's PATH environment variable.

Building the JFX Launcher (native installer)

  • The Java Runtime Environment (JRE) used to build the launcher will limit which machines can run the installer. Thus, you can only build launchers for computers that you share JRE compatibility with. If you will be creating a launcher for a system that is JRE-compatible, but not equivalent, (like building a launcher for 32 bit Windows from a 64 bit Windows machine), then you will need to download and install the compatible Java Development Kit (JDK) on your computer. The desired JDK must be used when running the Maven commands to build the native installer. If you are running Maven from the command line, you can simply change your JAVA_HOME(SET JAVA_HOME=my/java/directory) environment variable within your session. If you are running Maven from Eclipse, open your Maven run configuration and:

    1. Select the JRE tab, then select the necessary JDK from the Alternate JRE input (if you installed a JDK but it's not visible, click the Installed JREs button and add it).
    2. Select the Environment tab, click Select > Select All > OK, then find and remove the JAVA_HOME variable in the imported list. Finally, select the "Replace native environment with specified environment" radio button.
    3. Click Apply to save your changes.

  • From the pom Maven project (top-level/parent project) run

    C:\Users\JDoe\git\DonorCheck>mvn clean install -P jfx-installer -DskipTests
    • As mentioned above make sure this command is run using the appropriate JDK
    • Use the assemble profile to get a single executable jar found under ${base dir}/target
    • -DskipTests is important because you are running the command from the top-level pom, which means tests for the entire distribution would run (making the build take longer than necessary and may cause the build to fail if required distribution properties have not been set).

  • The output is a native installer (.exe for windows installers) that will be located in {$base dir}/target/jfx/native. If the native installer is not in this directory, then you may be missing the packaging prerequisites (see prerequisites section above).

  • Manually upload native installer to the remote download site (public_html > donornet>development or release). Choose between development or release based on the branch you are trying to push. Development for development branch and master for release. NOTE: in addition to using an ftp tool, the file can be downloaded by a user by navigating to genvisis.org/donorcheck/[development or release]/myFileName.exe (replacing "myFileName.exe" with the actual installer file name) from a web browser.

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