GlyGen CFDE C2M2 data model generator

Purpose

This program is a maven/java project with the aim to generate the files needed to upload the GlyGen data to the CFDE data portal. This files have to follow the C2M2 specification. The Java program will download the GlyGen files according to the File configuration and generate the corresponding TSV files.

Prerequisite

To prepare the execution of the Java program two files have to be generated or update:

• File configuration with the list of all files to be integrated into the generation process. The default files.csv is available in the repository in folder data
• Property file containing the settings for the TSV metadata. The default glygen.properties is available in the repository in folder data

Run the application

To run the program it is necessary to download and install:

• Java 1.8+; either OpenJDK or Oracle Java
• Apache Maven

It is also necessary to checkout/clone or download the source code from the repository.

Before running the program the code needs to be compiled. Run the following commandline in the root folder of the source code (the pom.xml file is located there):

mvn compile

To finally run the program from commandline use the following command from the root folder of the source code (the pom.xml file is located there):

mvn exec:java -Dexec.mainClass=org.glygen.cfde.generator.App -Dexec.args="-c ./data/files.csv -o ./data/output/ -p ./data/glygen.properties -m ./data/mapping/"

The values in double quote are the commandline arguments that need to be adjusted according to the local system:

• -c location of the file with the File configuration
• -o folder that will be used to generate the output (GlyGen downloads, TSV files, error report)
• -p location of the Property file
• -m folder with the mapping files

The program runs successful it will generate a folder named tsv inside the output folder. This folder will contain all generated TSV files. Inside the output folder will also be a file log.csv which contains the error logging. Its important to check this file after the run to ensure now files or data rows where omitted.

Post run

After the execution was successful it is important to check the error file. After this the missing dictionary tables have to be generated using the presubmission prep tool from CFDE. Once this is successfully completed and data package can be submitted using the CFDE submission tool.