nanopub-java

This is a Java library for nanopublications (see http://nanopub.net) based on RDF4J.

It implements the formal structure defined in the official nanopublication guidelines.

Usage as Java Library

The easiest way to use this library in your project is to let Maven download it from The Central Repository, with an entry in your pom.xml file as shown here.

Alternatively, you might want to use one of the pre-built jar files.

Quickstart Java Instructions

In a nutshell, to create and publish nanopublications, you need to first make sure you have a local keypair. To create such a keypair, run just once:

MakeKeys.make("~/.nanopub/id", SignatureAlgorithm.RSA);

And then nanopublications can be created and published programmatically like this:

System.err.println("# Creating nanopub...");
NanopubCreator npCreator = new NanopubCreator(true);

final ValueFactory vf = SimpleValueFactory.getInstance();
final IRI anne = vf.createIRI("https://example.com/anne");

npCreator.addAssertionStatement(anne, RDF.TYPE, vf.createIRI("https://schema.org/Person"));
npCreator.addProvenanceStatement(PROV.WAS_ATTRIBUTED_TO, anne);
npCreator.addPubinfoStatement(RDF.TYPE, vf.createIRI("http://purl.org/nanopub/x/ExampleNanopub"));
Nanopub np = npCreator.finalizeNanopub(true);
System.err.println("# Nanopub before signing:");
NanopubUtils.writeToStream(np, System.err, RDFFormat.TRIG);

System.err.println("# Signing nanopub...");
Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());
System.err.println("# Final nanopub after signing:");
NanopubUtils.writeToStream(signedNp, System.err, RDFFormat.TRIG);

System.err.println("# Publishing to test server...");
PublishNanopub.publishToTestServer(signedNp);
//System.err.println("# Publishing to real server...");
//PublishNanopub.publish(signedNp);
System.err.println("# Published");

For the complete code checkout UsageExamples.java.

Documentation

See the JavaDocs for the API and source code documentation.

Here you can find more documentation.

Usage of Unix Command-Line

Check out this list of all command line commands.

To use this library on the command line, just run:

macOS, Linux, WSL:

curl -LsSf https://raw.githubusercontent.com/Nanopublication/nanopub-java/master/bin/install.sh | bash

Windows PowerShell:

irm https://raw.githubusercontent.com/Nanopublication/nanopub-java/master/bin/install.ps1 | iex

This automatically downloads the latest release as a jar file on the first run.

Usage with Docker

You can use this image from DockerHub.

Sign a nanopublication (nanopub.trig file in current dir here):

docker run -it --rm -v ~/.nanopub:/root/.nanopub -v $(pwd):/data nanopub/nanopub-java sign /data/nanopub.trig

Publish a signed nanopublication:

docker run -it --rm -v ~/.nanopub:/root/.nanopub -v $(pwd):/data nanopub/nanopub-java publish /data/signed.nanopub.trig

Build the Docker image:

docker build -t nanopub/nanopub-java .

Compilation

Maven has to be installed to compile the library:

./mvnw clean package

The library features can then be accessed by calling scripts/run.sh (with the same commands as for the np script above, but using the locally compiled code and not the jar file).

Test Coverage

Create the file target/jacoco.exec which includes the test coverage information in a binary format.

./mvnw clean verify

To create a HTML report out of jacoco.exec (target/site/jacoco/index.html) use:

./mvnw jacoco:report

Publication

• Tobias Kuhn. nanopub-java: A Java Library for Nanopublications. In Proceedings of the 5th Workshop on Linked Science (LISC 2015). 2015.

License

nanopub-java is free software under the MIT License. See LICENSE.

For an overview of the dependencies and their licenses, run ./mvnw project-info-reports:dependencies and then visit target/reports/dependencies.html.