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Make code easier to use; add quickstart example to README
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‎README.md

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Alternatively, you might want to use one of the [pre-built
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jar files](https://github.com/Nanopublication/nanopub-java/releases).
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## Quickstart Java Instructions
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In a nutshell, this is how nanopublications can be created and published
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programmatically:
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System.err.println("# Creating nanopub...");
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NanopubCreator npCreator = new NanopubCreator(true);
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final IRI anne = vf.createIRI("https://example.com/anne");
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npCreator.addAssertionStatement(anne, RDF.TYPE, vf.createIRI("https://schema.org/Person"));
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npCreator.addProvenanceStatement(PROV.WAS_ATTRIBUTED_TO, anne);
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npCreator.addPubinfoStatement(RDF.TYPE, vf.createIRI("http://purl.org/nanopub/x/ExampleNanopub"));
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Nanopub np = npCreator.finalizeNanopub(true);
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System.err.println("# Nanopub before signing:");
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NanopubUtils.writeToStream(np, System.err, RDFFormat.TRIG);
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Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());
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System.err.println("# Final nanopub after signing:");
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NanopubUtils.writeToStream(signedNp, System.err, RDFFormat.TRIG);
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System.err.println("# Publishing to test server...");
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PublishNanopub.publishToTestServer(signedNp);
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//System.err.println("# Publishing to real server...");
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//PublishNanopub.publish(signedNp);
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## Usage on Unix Command-Line
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‎src/main/java/org/nanopub/NanopubCreator.java

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@@ -47,6 +47,13 @@ public NanopubCreator() {
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init();
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}
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public NanopubCreator(boolean initWithTempNanopubIris) {
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this();
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if (initWithTempNanopubIris) {
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setNanopubUri(NanopubUtils.createTempNanopubIri());
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}
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}
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public NanopubCreator(IRI nanopubUri) {
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this();
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setNanopubUri(nanopubUri);

‎src/main/java/org/nanopub/NanopubUtils.java

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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Random;
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import java.util.Set;
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import org.apache.commons.lang3.tuple.Pair;
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return httpClient;
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}
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private static Random random = new Random();
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public static IRI createTempNanopubIri() {
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return vf.createIRI("http://purl.org/nanopub/temp/" + Math.abs(random.nextInt()) + "/");
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}
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}

‎src/main/java/org/nanopub/extra/security/TransformContext.java

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package org.nanopub.extra.security;
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import static org.nanopub.extra.security.SignatureAlgorithm.RSA;
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import java.security.KeyPair;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import org.eclipse.rdf4j.model.IRI;
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import org.eclipse.rdf4j.model.Resource;
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import org.eclipse.rdf4j.model.ValueFactory;
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import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
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import org.eclipse.rdf4j.rio.RDFFormat;
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import org.nanopub.NanopubProfile;
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import org.nanopub.trusty.CrossRefResolver;
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import net.trustyuri.TrustyUriUtils;
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// TODO: Use this also for MakeTrustyNanopub
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private static ValueFactory vf = SimpleValueFactory.getInstance();
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public static TransformContext makeDefault() {
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IRI signerIri = null;
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NanopubProfile profile = new NanopubProfile(NanopubProfile.IMPLICIT_PROFILE_FILE_NAME);
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if (profile.getOrcidId() != null) {
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signerIri = vf.createIRI(profile.getOrcidId());
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}
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KeyPair key = null;
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try {
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key = SignNanopub.loadKey("~/.nanopub/id_rsa", RSA);
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} catch (Exception ex) {
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ex.printStackTrace();
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}
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return new TransformContext(RSA, key, signerIri, false, false, false);
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}
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private SignatureAlgorithm algorithm;
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private KeyPair key;
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private IRI signer;

‎src/main/java/org/nanopub/extra/server/PublishNanopub.java

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return new PublishNanopub().publishNanopub(nanopub);
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}
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public static String publish(Nanopub nanopub, String serverUrl) throws IOException {
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return new PublishNanopub().publishNanopub(nanopub, serverUrl);
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}
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// TODO Make this dynamic/configureable:
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public static final String TEST_SERVER_URL = "https://test.registry.knowledgepixels.com/";
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public static String publishToTestServer(Nanopub nanopub) throws IOException {
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return new PublishNanopub().publishNanopub(nanopub, TEST_SERVER_URL);
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}
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private ServerIterator serverIterator = null;
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private RegistryInfo registryInfo = null;
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private Map<String,Integer> usedServers = new HashMap<>();

‎src/main/java/org/nanopub/op/Create.java

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package org.nanopub.op;
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import com.beust.jcommander.ParameterException;
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import net.trustyuri.TrustyUriException;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.util.zip.GZIPOutputStream;
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import org.eclipse.rdf4j.model.IRI;
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import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
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import org.eclipse.rdf4j.model.vocabulary.RDFS;
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import org.eclipse.rdf4j.rio.RDFFormat;
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import org.eclipse.rdf4j.rio.RDFHandlerException;
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import org.eclipse.rdf4j.rio.RDFParseException;
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import org.eclipse.rdf4j.rio.Rio;
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import org.nanopub.*;
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import org.nanopub.CliRunner;
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import org.nanopub.MalformedNanopubException;
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import org.nanopub.Nanopub;
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import org.nanopub.NanopubCreator;
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import org.nanopub.NanopubUtils;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.util.Random;
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import java.util.zip.GZIPOutputStream;
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import com.beust.jcommander.ParameterException;
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import net.trustyuri.TrustyUriException;
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public class Create extends CliRunner {
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private RDFFormat rdfOutFormat;
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private OutputStream outputStream = System.out;
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private Random random = new Random();
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private void run() throws IOException, RDFParseException, RDFHandlerException,
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MalformedNanopubException, TrustyUriException {
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}
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}
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String npUri = "http://purl.org/nanopub/temp/" + Math.abs(random.nextInt()) + "/";
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IRI nanopubIri = vf.createIRI(npUri);
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IRI creatorIri = vf.createIRI(npUri + "creator");
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IRI nanopubIri = NanopubUtils.createTempNanopubIri();
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IRI creatorIri = vf.createIRI(nanopubIri.stringValue() + "creator");
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NanopubCreator npCreator = new NanopubCreator(nanopubIri);
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npCreator.addAssertionStatement(npCreator.getAssertionUri(), RDFS.COMMENT, vf.createLiteral("Replace this with your assertion content."));
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npCreator.addProvenanceStatement(vf.createIRI("http://www.w3.org/ns/prov#hadPrimarySource"), creatorIri);

‎src/test/java/org/nanopub/NanopubUtilsTest.java

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package org.nanopub;
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import static org.assertj.core.api.Assertions.assertThat;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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import java.util.Set;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.eclipse.rdf4j.model.IRI;
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import org.eclipse.rdf4j.model.Statement;
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import org.eclipse.rdf4j.model.ValueFactory;
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import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
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import org.eclipse.rdf4j.model.vocabulary.DCTERMS;
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import org.eclipse.rdf4j.model.vocabulary.PROV;
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import org.eclipse.rdf4j.model.vocabulary.RDF;
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import org.eclipse.rdf4j.model.vocabulary.RDFS;
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import org.eclipse.rdf4j.rio.RDFFormat;
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import org.junit.jupiter.api.Test;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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import java.util.Set;
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import static org.assertj.core.api.Assertions.assertThat;
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import org.nanopub.extra.security.SignNanopub;
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import org.nanopub.extra.security.TransformContext;
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import org.nanopub.extra.server.PublishNanopub;
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public class NanopubUtilsTest {
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client = NanopubUtils.getHttpClient();
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assertThat(client).isNotNull();
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}
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// TODO: Using this as quickstart code in the README. Should probably be made executable somewhere, but not sure where...
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// @Test
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// void demoNanopubCreationExample() throws Exception {
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// System.err.println("==========");
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// System.err.println("# Creating nanopub...");
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// NanopubCreator npCreator = new NanopubCreator(true);
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// final IRI anne = vf.createIRI("https://example.com/anne");
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// npCreator.addAssertionStatement(anne, RDF.TYPE, vf.createIRI("https://schema.org/Person"));
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// npCreator.addProvenanceStatement(PROV.WAS_ATTRIBUTED_TO, anne);
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// npCreator.addPubinfoStatement(RDF.TYPE, vf.createIRI("http://purl.org/nanopub/x/ExampleNanopub"));
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// Nanopub np = npCreator.finalizeNanopub(true);
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// System.err.println("# Nanopub before signing:");
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// NanopubUtils.writeToStream(np, System.err, RDFFormat.TRIG);
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// Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());
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// System.err.println("# Final nanopub after signing:");
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// NanopubUtils.writeToStream(signedNp, System.err, RDFFormat.TRIG);
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// System.err.println("# Publishing to test server...");
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// PublishNanopub.publishToTestServer(signedNp);
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// //System.err.println("# Publishing to real server...");
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// //PublishNanopub.publish(signedNp);
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// System.err.println("==========");
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// }
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}

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