libSBOLj provides the core Java interfaces and their implementation for the Synthetic Biology Open Language (SBOL). The library provides an API to work with SBOL objects, the functionality to read and write SBOL documents as XML/RDF files, and a validator to check the correctness of SBOL models.

1. Create a GitHub account.
2. Setup Git on your machine.
3. Clone the libSBOLj GitHub repository to your machine.

1. Setup Apache Maven. A tutorial on using Apache Maven is provided here.

2. In the command line, change to the libSBOLj directory (e.g. cd /path/to/libSBOLj) and execute the following command

mvn package

This will compile the libSBOLj source files, package the compiled source into a libSBOLj JAR file (libSBOLj-core-2.0.0-SNAPSHOT.jar), and place the JAR file into the core/target sub-directory.

1. As first step, the libSBOLj JAR file must be added to the local Maven repository.

mvn install:install-file \ 
    -Dfile=/path/to/libSBOLj/core2/target/libSBOLj-core2-2.0.0-SNAPSHOT.jar \
    -DgroupId=org.sbolstandard \
    -DartifactId=libSBOLj-core2 \
    -Dversion=2.0.0-SNAPSHOT \
    -Dpackaging=jar

After libSBOLj is stored in the local Maven repository, it can be integrated into multiple Maven projects. That is, this step must be performed only after compiling and packaging the library.

2. In a Maven project that utilizes the libSBOLj library, add a dependency in the Maven project's pom.xml file.

<dependency>
	<groupId>org.sbolstandard</groupId>
	<artifactId>libSBOLj-core2</artifactId>
	<version>2.0.0-SNAPSHOT</version>
	<scope>compile</scope>
</dependency>

libSBOLj comes with a command-line interface (CLI) that can be used to validate SBOL files. After you build the libSBOLj-core-2.0.0-SNAPSHOT.jar as described above, you can use it to validate files as follows after changing to the core/target subdirectory:

cd core/target/
java -jar libSBOLj-core-2.0.0-SNAPSHOT.jar <inputFile>

If validation is successful, the program will print the contents of the SBOL document. You can also output the result to a file.

java -jar libSBOLj-core-1.0.0-SNAPSHOT.jar <inputFile> -o <outputFile>

If validation fails with an error, there will be a message printed about the validation error. In addition to checking all required validation rules, it will also check if the URIs are compliant and whether the SBOL document is complete (i.e., all referenced objects are contained within the file). These validation checks can be turned off with the -n and -i flags, respectively.

If the input file is an SBOL 1.1 file, then it will convert the file into an SBOL 2.0 file. This conversion should be provided a default URI prefix. It can also be provided a default version, if desired. Finally, the -t flag will insert the type of top level objects into the URI during conversion, if desired.

java -jar libSBOLj-core-1.0.0-SNAPSHOT.jar <inFile> -o <outFile> -p <URIprefix> -v <version>

1. Fork the libSBOLj repository. (link)