24823925845

Committed 23 Apr 2026 07:59AM UTC coverage: 52.15% (+0.5%) from 51.675%

Build # 24823925845

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #71 from Nanopublication/add-fdo-schema-enrichment

feat(fdo): schema enrichment, handle URLs, referentName label

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1133 of 3134 branches covered (36.15%)

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5429 of 9449 relevant lines covered (57.46%)

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0.0

src/main/java/org/nanopub/fdo/FdoCreate.java

package org.nanopub.fdo;

import com.beust.jcommander.ParameterException;
import net.trustyuri.TrustyUriException;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.CliRunner;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubAlreadyFinalizedException;
import org.nanopub.NanopubUtils;
import org.nanopub.extra.security.SignNanopub;
import org.nanopub.extra.security.TransformContext;
import org.nanopub.extra.server.PublishNanopub;

import java.io.IOException;
import java.net.URISyntaxException;
import java.security.InvalidKeyException;
import java.security.SignatureException;

/**
 * Create and optionally publish a nanopub for a handle-based FDO.
 */
public class FdoCreate extends CliRunner {

    @com.beust.jcommander.Parameter(description = "handle-id-or-url", required = true)
    private String handleId;

    @com.beust.jcommander.Parameter(names = "-u", description = "Unsigned, the Nanopub is not signed. Do not use with -p.")
    private boolean unsigned;

    @com.beust.jcommander.Parameter(names = "-p", description = "Directly publish the Nanopub.")
    private boolean publish;

    @com.beust.jcommander.Parameter(names = {"-s", "--enrich-from-schema"}, description = "Resolve the FDO profile's type registry entry and use property handles as predicates (with rdfs:label in pubinfo).")
    private boolean enrichFromSchema;

    /**
     * Main method to run the FdoCreate command-line tool.
     *
     * @param args command line arguments, expects a handle identifier
     */
    public static void main(String[] args) {
        try {
            FdoCreate obj = CliRunner.initJc(new FdoCreate(), args);
            obj.run();
        } catch (ParameterException ex) {
            System.exit(1);
        } catch (Exception ex) {
            ex.printStackTrace();
            System.exit(1);
        }
    }

    /**
     * Resolves the handle and creates a nanopub from it, then either prints or publishes it.
     *
     * @throws org.nanopub.MalformedNanopubException        if the nanopub is malformed
     * @throws java.io.IOException                          if there is an I/O error
     * @throws java.net.URISyntaxException                  if the handle identifier is not a valid URI
     * @throws java.lang.InterruptedException               if the thread is interrupted while resolving the handle
     * @throws net.trustyuri.TrustyUriException             if there is an issue with Trusty URI
     * @throws java.security.SignatureException             if there is an issue with signing the nanopub
     * @throws java.security.InvalidKeyException            if the signing key is invalid
     * @throws org.nanopub.NanopubAlreadyFinalizedException if the nanopub has already been finalized
     */
    public void run() throws MalformedNanopubException, IOException, URISyntaxException, InterruptedException,
            TrustyUriException, SignatureException, InvalidKeyException, NanopubAlreadyFinalizedException {

        if (unsigned && publish) {
            System.err.println("Do not use -u and -p together.");
            throw new ParameterException("Cannot use -u and -p together.");
        }

        String resolvedId = FdoUtils.extractHandleId(handleId);
        if (resolvedId == null) {
            System.err.println("Not a recognisable handle or handle/DOI URL: " + handleId);
            throw new ParameterException("Not a recognisable handle or handle/DOI URL: " + handleId);
        }

        Nanopub np = FdoNanopubCreator.createFromHandleSystem(resolvedId, enrichFromSchema);

        if (unsigned) {
            NanopubUtils.writeToStream(np, System.out, RDFFormat.TRIG);
        } else if (publish) {
            Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());
            PublishNanopub.publish(signedNp);
        } else {
            Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());
            NanopubUtils.writeToStream(signedNp, System.out, RDFFormat.TRIG);
        }
    }

}

1	package org.nanopub.fdo;
2
3	import com.beust.jcommander.ParameterException;
4	import net.trustyuri.TrustyUriException;
5	import org.eclipse.rdf4j.rio.RDFFormat;
6	import org.nanopub.CliRunner;
7	import org.nanopub.MalformedNanopubException;
8	import org.nanopub.Nanopub;
9	import org.nanopub.NanopubAlreadyFinalizedException;
10	import org.nanopub.NanopubUtils;
11	import org.nanopub.extra.security.SignNanopub;
12	import org.nanopub.extra.security.TransformContext;
13	import org.nanopub.extra.server.PublishNanopub;
14
15	import java.io.IOException;
16	import java.net.URISyntaxException;
17	import java.security.InvalidKeyException;
18	import java.security.SignatureException;
19
20	/**
21	* Create and optionally publish a nanopub for a handle-based FDO.
22	*/
23	public class FdoCreate extends CliRunner {	×
24
25	@com.beust.jcommander.Parameter(description = "handle-id-or-url", required = true)
26	private String handleId;
27
28	@com.beust.jcommander.Parameter(names = "-u", description = "Unsigned, the Nanopub is not signed. Do not use with -p.")
29	private boolean unsigned;
30
31	@com.beust.jcommander.Parameter(names = "-p", description = "Directly publish the Nanopub.")
32	private boolean publish;
33
34	@com.beust.jcommander.Parameter(names = {"-s", "--enrich-from-schema"}, description = "Resolve the FDO profile's type registry entry and use property handles as predicates (with rdfs:label in pubinfo).")
35	private boolean enrichFromSchema;
36
37	/**
38	* Main method to run the FdoCreate command-line tool.
39	*
40	* @param args command line arguments, expects a handle identifier
41	*/
42	public static void main(String[] args) {
43	try {
44	FdoCreate obj = CliRunner.initJc(new FdoCreate(), args);	×
45	obj.run();	×
46	} catch (ParameterException ex) {	×
47	System.exit(1);	×
48	} catch (Exception ex) {	×
49	ex.printStackTrace();	×
50	System.exit(1);	×
51	}	×
52	}	×
53
54	/**
55	* Resolves the handle and creates a nanopub from it, then either prints or publishes it.
56	*
57	* @throws org.nanopub.MalformedNanopubException if the nanopub is malformed
58	* @throws java.io.IOException if there is an I/O error
59	* @throws java.net.URISyntaxException if the handle identifier is not a valid URI
60	* @throws java.lang.InterruptedException if the thread is interrupted while resolving the handle
61	* @throws net.trustyuri.TrustyUriException if there is an issue with Trusty URI
62	* @throws java.security.SignatureException if there is an issue with signing the nanopub
63	* @throws java.security.InvalidKeyException if the signing key is invalid
64	* @throws org.nanopub.NanopubAlreadyFinalizedException if the nanopub has already been finalized
65	*/
66	public void run() throws MalformedNanopubException, IOException, URISyntaxException, InterruptedException,
67	TrustyUriException, SignatureException, InvalidKeyException, NanopubAlreadyFinalizedException {
68
69	if (unsigned && publish) {	×
70	System.err.println("Do not use -u and -p together.");	×
71	throw new ParameterException("Cannot use -u and -p together.");	×
72	}
73
74	String resolvedId = FdoUtils.extractHandleId(handleId);	×
75	if (resolvedId == null) {	×
76	System.err.println("Not a recognisable handle or handle/DOI URL: " + handleId);	×
77	throw new ParameterException("Not a recognisable handle or handle/DOI URL: " + handleId);	×
78	}
79
80	Nanopub np = FdoNanopubCreator.createFromHandleSystem(resolvedId, enrichFromSchema);	×
81
82	if (unsigned) {	×
83	NanopubUtils.writeToStream(np, System.out, RDFFormat.TRIG);	×
84	} else if (publish) {	×
85	Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());	×
86	PublishNanopub.publish(signedNp);	×
87	} else {	×
88	Nanopub signedNp = SignNanopub.signAndTransform(np, TransformContext.makeDefault());	×
89	NanopubUtils.writeToStream(signedNp, System.out, RDFFormat.TRIG);	×
90	}
91	}	×
92
93	}

Nanopublication / nanopub-java / 24823925845

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