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Notes For Developers

This classes and interfaces in this application are not (yet!) designed to be extended. They are subject to change at any time - in fact, you can bet on it!

Development Requirements

Library Dependencies

Building The MorphCX Application

  1. Insure that Java and Maven programs are installed.

  2. Download the ndex-object-model and ndndex-java-client dependencies from their respective GitHub repositories and place into their own project directories. From each respective project directory, enter the following command from a Terminal or Command shell. Start first with the ndex-object-model dependency, and follow that with the ndex-java-client dependency.

mvn clean install

This should result in both dependencies being installed into the Maven .M2 local repository.

  1. Clone or download this application's GitHub repository to yet another project directory.

  2. Then using a Terminal or Command shell from the project directory, enter the following command - just as you did with the ndex-object-model and ndex-java-client dependencies:

mvn clean package

The above command will compile and build this application's executable library (JAR) file, which is found in the ${project_dir/src/target} directory. The executable file named morphcx.jar contains a fully-formed executable packaged with all dependencies. This file should be placed in a directory pointed to by the Java CLASSPATH environment variable, or explicitedly pointed to when the application is invoked through the Java JVM.

Sample CX networks are provided in the ${project_dir/src/target/sample-networks} directory. It is possible -- even likely! -- that these networks are not the most up to-date CX network. The files are only intended to be used to quickly test the application and to verify a successful installation.

Test the application by making the target ${project_dir/src/target} directory the current directory, then enter the following command:

java -jar morphcx.jar -c tsv -i sample-networks/LUMINAL_BREAST_CANCER.json -o sample-networks/LUMINAL_BREAST_CANCER.tsv

The above command results in converting the input file into the tab-separated value file named LUMINAL_BREAST_CANCER.tsv in the sample-networks folder.

The -o output parameter can be altogether omitted, and this application will output tab-separated columns onto the console.

Finally, if a Microsoft Excel Workbook file (.xlsx) is desired, then enter this command:

java -jar morphcx.jar -c excel -i sample-networks/LUMINAL_BREAST_CANCER.json -o sample-networks/LUMINAL_BREAST_CANCER.tsv