Introduction

platedecoder decodes 2D DataMatrix bar codes present on specimen tubes in a n sized well plate. Images containing the 2D bar codes can come from the file system or a flatbed scanner.

It can decode different sized plates such as plates containing 96, 81, 100 and 144 wells. The 2D bar code can be present on the top or bottoms of the tubes.

It can also send the decoded bar codes to an OpenSpecimen server to link tubes to patients or positions.

Run

A distributatble package can be built by using the following command:

gradle distZip

When the command completes, the directory build/distributions will contains ZIP file. Unzip this file to a location where you'd like to install it and then run it by using the Linux script or the MS Windows batch file present in the bin directory. The ZIP file comes bundled with the required libraries.

MS Windows

To use the app in MS Windows, you will first have to install the Microsoft Visual C++ 2010 SP1 Redistributable Package (x86). This only needs to be done once per computer.

Development

Maven repository

This app uses a custom maven repository to retrieve it's dependant libraries. This repository is hosted on GitHub at:

https://github.com/cbsrbiobank/biobank-maven-repo/

Build Environment

This project uses Gradle as the build tool. You will need to intsall it to build this application.

To build the project type the following at the project's root directory:

gradle build

To run the application, type:

gradle run

To generate the Javadoc.

gradle -q --console=plain javadoc

To build an installation, type:

gradle installDist

Then copy the DLLs (or Linux shared libraries) to build/install/platedecoder/lib. The build/install/platedecoder .

The fat jar is placed in the build/libs directory.

See also gradle distZip.

Future

See launch4j for how to generate a Windows EXE file.

Emacs

To build from Emacs type: TERM="dumb" gradle build or gradle --console=plain build.

Eclim

Use the Graphical Installer to install Eclim.

For tests to run, the native library folder has to be added to the JVM parameters as follows:

<path_to_eclim>/eclim -command project_setting -p platedecoder -s org.eclim.java.junit.jvmargs -v \[\"-Djava.library.path=./lib\"\]

The path to Eclim for me is:

/home/nelson/.eclipse/org.eclipse.platform_4.5.0_1473617060_linux_gtk_x86_64