17302137193

Committed 28 Aug 2025 04:35PM UTC coverage: 11.965% (-0.4%) from 12.355%

Build # 17302137193

Build Type

Pull #244

github

Committed by

web-flow

Commit Message

Merge 4e969b0ee into 3323a35f1

Pull Request Pull Request #244: Use vocabularies with latest version of `nanopub-java`

Run Details

331 of 3840 branches covered (8.62%)

Branch coverage included in aggregate %.

943 of 6808 relevant lines covered (13.85%)

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39.87

src/main/java/com/knowledgepixels/nanodash/component/NanodashLink.java

package com.knowledgepixels.nanodash.component;

import com.knowledgepixels.nanodash.User;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.connector.ios.DsConfig;
import com.knowledgepixels.nanodash.connector.ios.DsNanopubPage;
import com.knowledgepixels.nanodash.connector.pensoft.BdjConfig;
import com.knowledgepixels.nanodash.connector.pensoft.BdjNanopubPage;
import com.knowledgepixels.nanodash.connector.pensoft.RioConfig;
import com.knowledgepixels.nanodash.connector.pensoft.RioNanopubPage;
import com.knowledgepixels.nanodash.page.ExplorePage;
import com.knowledgepixels.nanodash.template.Template;
import com.knowledgepixels.nanodash.template.TemplateData;
import net.trustyuri.TrustyUriUtils;
import org.apache.commons.codec.Charsets;
import org.apache.wicket.Component;
import org.apache.wicket.behavior.AttributeAppender;
import org.apache.wicket.markup.html.basic.Label;
import org.apache.wicket.markup.html.link.BookmarkablePageLink;
import org.apache.wicket.markup.html.link.ExternalLink;
import org.apache.wicket.markup.html.panel.Panel;
import org.apache.wicket.model.Model;
import org.apache.wicket.request.mapper.parameter.PageParameters;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.RDFS;
import org.nanopub.Nanopub;
import org.nanopub.vocabulary.NP;
import org.nanopub.vocabulary.NTEMPLATE;

import java.net.URLEncoder;
import java.util.*;

/**
 * A Wicket component that creates a link to a nanopublication or an IRI.
 */
public class NanodashLink extends Panel {

    private static final long serialVersionUID = 1L;

    /**
     * Creates a link to a nanopublication or an IRI.
     *
     * @param id             the Wicket component ID
     * @param uri            the URI of the nanopublication or IRI
     * @param np             the nanopublication, or null if the link is not to a nanopublication
     * @param templateClass  the template class of the nanopublication, or null if the link is not to a nanopublication
     * @param objectPosition if true, the link is to an object position in a template, otherwise it is to a subject position
     * @param label          the label to display for the link, or null to derive it from the nanopublication or IRI
     */
    public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, boolean objectPosition, String label) {
        super(id);

        final List<Template> templates = new ArrayList<>();
        final Map<IRI, String> labels = new HashMap<>();
        if (np != null) {
            for (Statement st : np.getPubinfo()) {
                if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) || st.getPredicate().equals(RDFS.LABEL)) {
                    labels.put((IRI) st.getSubject(), st.getObject().stringValue());
                }
            }
        }

        final TemplateData td = TemplateData.get();

        if (NTEMPLATE.ASSERTION_TEMPLATE.equals(templateClass)) {
            IRI templateId = td.getTemplateId(np);
            if (templateId != null) {
                templates.add(td.getTemplate(templateId.stringValue()));
            }
        } else if (NTEMPLATE.PROVENANCE_TEMPLATE.equals(templateClass)) {
            IRI templateId = td.getProvenanceTemplateId(np);
            if (templateId != null) {
                templates.add(td.getTemplate(templateId.stringValue()));
            }
        } else if (NTEMPLATE.PUBINFO_TEMPLATE.equals(templateClass)) {
            Set<IRI> templateIds = td.getPubinfoTemplateIds(np);
            for (IRI templateId : templateIds) {
                templates.add(td.getTemplate(templateId.stringValue()));
            }
        }

        final IRI iriObj = vf.createIRI(uri);
        if (np != null && uri.equals(np.getUri().stringValue())) {
            ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this");
            add(link);
            add(new Label("description", "this specific nanopublication"));
        } else if (np != null && uri.equals(np.getAssertionUri().stringValue())) {
            ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this assertion");
            link.add(new AttributeAppender("class", " nanopub-assertion "));
            add(link);
            add(new Label("description", "the assertion of this specific nanopublication"));
        } else if (uri.equals(NP.HAS_ASSERTION.stringValue())) {
            ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "assertion");
            link.add(new AttributeAppender("class", " nanopub-assertion "));
            add(link);
            add(new Label("description", "links a nanopublication to its assertion"));
        } else if (uri.equals(NP.HAS_PROVENANCE.stringValue())) {
            ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "provenance");
            link.add(new AttributeAppender("class", " nanopub-provenance "));
            add(link);
            add(new Label("description", "links a nanopublication to its provenance"));
        } else if (uri.equals(NP.HAS_PUBINFO.stringValue())) {
            ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "pubinfo");
            link.add(new AttributeAppender("class", " nanopub-pubinfo "));
            add(link);
            add(new Label("description", "links a nanopublication to its pubinfo"));
        } else {
            if (label == null || label.isBlank()) {
                label = IriItem.getShortNameFromURI(uri);
                if (iriObj.equals(User.getSignatureOwnerIri(np))) {
                    if (objectPosition) {
                        label = "me (" + User.getShortDisplayName(iriObj) + ")";
                    } else {
                        label = "I (" + User.getShortDisplayName(iriObj) + ")";
                    }
                } else if (User.getName(iriObj) != null) {
                    label = User.getShortDisplayName(iriObj);
                } else {
                    for (Template template : templates) {
                        // TODO For pubinfo templates, we don't consider which triple came from which template (which is non-trivial):
                        String l = template.getLabel(iriObj);
                        if (l != null) {
                            label = l;
                            break;
                        }
                        l = labels.get(iriObj);
                        if (l != null) {
                            label = l;
                            break;
                        }
                    }
                }
            }
            String shortLabel = label.replaceFirst(" - [\\s\\S]*$", "");
            add(createLink("link", uri, shortLabel));
            String description = "";
            if (np != null && uri.startsWith(np.getUri().stringValue())) {
                description = "This is a local identifier that was minted when the nanopublication was created.";
            }
            if (label.contains(" - ")) description = label.replaceFirst("^.* - ", "");
            add(new Label("description", description));
        }
        add(Utils.getUriLink("uri", uri));
    }

    /**
     * <p>createLink.</p>
     *
     * @param markupId a {@link java.lang.String} object
     * @param uri      a {@link java.lang.String} object
     * @param label    a {@link java.lang.String} object
     * @return a {@link org.apache.wicket.Component} object
     */
    public static Component createLink(String markupId, String uri, String label) {
        boolean isNp = TrustyUriUtils.isPotentialTrustyUri(uri);
        // TODO Improve this
        if (isNp && uri.startsWith(DsConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, DsNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));
        } else if (isNp && uri.startsWith(BdjConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, BdjNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));
        } else if (isNp && uri.startsWith(RioConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, RioNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));
        } else {
            return new BookmarkablePageLink<Void>(markupId, ExplorePage.class, new PageParameters().add("id", uri).add("label", label)).setBody(Model.of(label));
        }
    }

    /**
     * Creates a link to a nanopublication or an IRI.
     *
     * @param id             the Wicket component ID
     * @param uri            the URI of the nanopublication or IRI
     * @param np             the nanopublication, or null if the link is not to a nanopublication
     * @param templateClass  the template class of the nanopublication, or null if the link is not to a nanopublication
     * @param objectPosition if true, the link is to an object position in a template, otherwise it is to a subject position
     */
    public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, boolean objectPosition) {
        this(id, uri, np, templateClass, objectPosition, null);
    }

    /**
     * Creates a link to a nanopublication or an IRI.
     *
     * @param id  the Wicket component ID
     * @param uri the URI of the nanopublication or IRI
     * @param np  the nanopublication, or null if the link is not to a nanopublication
     */
    public NanodashLink(String id, String uri, Nanopub np) {
        this(id, uri, np, null, false);
    }

    /**
     * Creates a link to a nanopublication or an IRI.
     *
     * @param id  the Wicket component ID
     * @param uri the URI of the nanopublication or IRI
     */
    public NanodashLink(String id, String uri) {
        this(id, uri, null, null, false);
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();

}

1	package com.knowledgepixels.nanodash.component;
2
3	import com.knowledgepixels.nanodash.User;
4	import com.knowledgepixels.nanodash.Utils;
5	import com.knowledgepixels.nanodash.connector.ios.DsConfig;
6	import com.knowledgepixels.nanodash.connector.ios.DsNanopubPage;
7	import com.knowledgepixels.nanodash.connector.pensoft.BdjConfig;
8	import com.knowledgepixels.nanodash.connector.pensoft.BdjNanopubPage;
9	import com.knowledgepixels.nanodash.connector.pensoft.RioConfig;
10	import com.knowledgepixels.nanodash.connector.pensoft.RioNanopubPage;
11	import com.knowledgepixels.nanodash.page.ExplorePage;
12	import com.knowledgepixels.nanodash.template.Template;
13	import com.knowledgepixels.nanodash.template.TemplateData;
14	import net.trustyuri.TrustyUriUtils;
15	import org.apache.commons.codec.Charsets;
16	import org.apache.wicket.Component;
17	import org.apache.wicket.behavior.AttributeAppender;
18	import org.apache.wicket.markup.html.basic.Label;
19	import org.apache.wicket.markup.html.link.BookmarkablePageLink;
20	import org.apache.wicket.markup.html.link.ExternalLink;
21	import org.apache.wicket.markup.html.panel.Panel;
22	import org.apache.wicket.model.Model;
23	import org.apache.wicket.request.mapper.parameter.PageParameters;
24	import org.eclipse.rdf4j.model.IRI;
25	import org.eclipse.rdf4j.model.Statement;
26	import org.eclipse.rdf4j.model.ValueFactory;
27	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
28	import org.eclipse.rdf4j.model.vocabulary.RDFS;
29	import org.nanopub.Nanopub;
30	import org.nanopub.vocabulary.NP;
31	import org.nanopub.vocabulary.NTEMPLATE;
32
33	import java.net.URLEncoder;
34	import java.util.*;
35
36	/**
37	* A Wicket component that creates a link to a nanopublication or an IRI.
38	*/
39	public class NanodashLink extends Panel {
40
41	private static final long serialVersionUID = 1L;
42
43	/**
44	* Creates a link to a nanopublication or an IRI.
45	*
46	* @param id the Wicket component ID
47	* @param uri the URI of the nanopublication or IRI
48	* @param np the nanopublication, or null if the link is not to a nanopublication
49	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
50	* @param objectPosition if true, the link is to an object position in a template, otherwise it is to a subject position
51	* @param label the label to display for the link, or null to derive it from the nanopublication or IRI
52	*/
53	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, boolean objectPosition, String label) {
54	super(id);	3✔
55
56	final List<Template> templates = new ArrayList<>();	4✔
57	final Map<IRI, String> labels = new HashMap<>();	4✔
58	if (np != null) {	2!
59	for (Statement st : np.getPubinfo()) {	11✔
60	if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) \|\| st.getPredicate().equals(RDFS.LABEL)) {	10!
61	labels.put((IRI) st.getSubject(), st.getObject().stringValue());	×
62	}
63	}	1✔
64	}
65
66	final TemplateData td = TemplateData.get();	2✔
67
68	if (NTEMPLATE.ASSERTION_TEMPLATE.equals(templateClass)) {	4!
69	IRI templateId = td.getTemplateId(np);	×
70	if (templateId != null) {	×
71	templates.add(td.getTemplate(templateId.stringValue()));	×
72	}
73	} else if (NTEMPLATE.PROVENANCE_TEMPLATE.equals(templateClass)) {	4!
74	IRI templateId = td.getProvenanceTemplateId(np);	×
75	if (templateId != null) {	×
76	templates.add(td.getTemplate(templateId.stringValue()));	×
77	}
78	} else if (NTEMPLATE.PUBINFO_TEMPLATE.equals(templateClass)) {	4!
79	Set<IRI> templateIds = td.getPubinfoTemplateIds(np);	×
80	for (IRI templateId : templateIds) {	×
81	templates.add(td.getTemplate(templateId.stringValue()));	×
82	}	×
83	}
84
85	final IRI iriObj = vf.createIRI(uri);	4✔
86	if (np != null && uri.equals(np.getUri().stringValue())) {	8!
87	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this");	×
88	add(link);	×
89	add(new Label("description", "this specific nanopublication"));	×
90	} else if (np != null && uri.equals(np.getAssertionUri().stringValue())) {	8!
91	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this assertion");	×
92	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
93	add(link);	×
94	add(new Label("description", "the assertion of this specific nanopublication"));	×
95	} else if (uri.equals(NP.HAS_ASSERTION.stringValue())) {	5!
96	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "assertion");	×
97	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
98	add(link);	×
99	add(new Label("description", "links a nanopublication to its assertion"));	×
100	} else if (uri.equals(NP.HAS_PROVENANCE.stringValue())) {	5!
101	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "provenance");	×
102	link.add(new AttributeAppender("class", " nanopub-provenance "));	×
103	add(link);	×
104	add(new Label("description", "links a nanopublication to its provenance"));	×
105	} else if (uri.equals(NP.HAS_PUBINFO.stringValue())) {	5!
106	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "pubinfo");	×
107	link.add(new AttributeAppender("class", " nanopub-pubinfo "));	×
108	add(link);	×
109	add(new Label("description", "links a nanopublication to its pubinfo"));	×
110	} else {	×
111	if (label == null \|\| label.isBlank()) {	2!
112	label = IriItem.getShortNameFromURI(uri);	3✔
113	if (iriObj.equals(User.getSignatureOwnerIri(np))) {	5!
114	if (objectPosition) {	×
115	label = "me (" + User.getShortDisplayName(iriObj) + ")";	×
116	} else {
117	label = "I (" + User.getShortDisplayName(iriObj) + ")";	×
118	}
119	} else if (User.getName(iriObj) != null) {	3!
120	label = User.getShortDisplayName(iriObj);	×
121	} else {
122	for (Template template : templates) {	6!
123	// TODO For pubinfo templates, we don't consider which triple came from which template (which is non-trivial):
124	String l = template.getLabel(iriObj);	×
125	if (l != null) {	×
126	label = l;	×
127	break;	×
128	}
129	l = labels.get(iriObj);	×
130	if (l != null) {	×
131	label = l;	×
132	break;	×
133	}
134	}	×
135	}
136	}
137	String shortLabel = label.replaceFirst(" - [\\s\\S]*$", "");	5✔
138	add(createLink("link", uri, shortLabel));	12✔
139	String description = "";	2✔
140	if (np != null && uri.startsWith(np.getUri().stringValue())) {	8!
141	description = "This is a local identifier that was minted when the nanopublication was created.";	×
142	}
143	if (label.contains(" - ")) description = label.replaceFirst("^.* - ", "");	4!
144	add(new Label("description", description));	13✔
145	}
146	add(Utils.getUriLink("uri", uri));	11✔
147	}	1✔
148
149	/**
150	* <p>createLink.</p>
151	*
152	* @param markupId a {@link java.lang.String} object
153	* @param uri a {@link java.lang.String} object
154	* @param label a {@link java.lang.String} object
155	* @return a {@link org.apache.wicket.Component} object
156	*/
157	public static Component createLink(String markupId, String uri, String label) {
158	boolean isNp = TrustyUriUtils.isPotentialTrustyUri(uri);	3✔
159	// TODO Improve this
160	if (isNp && uri.startsWith(DsConfig.get().getTargetNamespace())) {	2!
161	return new BookmarkablePageLink<Void>(markupId, DsNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));	×
162	} else if (isNp && uri.startsWith(BdjConfig.get().getTargetNamespace())) {	2!
163	return new BookmarkablePageLink<Void>(markupId, BdjNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));	×
164	} else if (isNp && uri.startsWith(RioConfig.get().getTargetNamespace())) {	2!
165	return new BookmarkablePageLink<Void>(markupId, RioNanopubPage.class, new PageParameters().add("id", uri).add("mode", "final")).setBody(Model.of(label));	×
166	} else {
167	return new BookmarkablePageLink<Void>(markupId, ExplorePage.class, new PageParameters().add("id", uri).add("label", label)).setBody(Model.of(label));	18✔
168	}
169	}
170
171	/**
172	* Creates a link to a nanopublication or an IRI.
173	*
174	* @param id the Wicket component ID
175	* @param uri the URI of the nanopublication or IRI
176	* @param np the nanopublication, or null if the link is not to a nanopublication
177	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
178	* @param objectPosition if true, the link is to an object position in a template, otherwise it is to a subject position
179	*/
180	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, boolean objectPosition) {
181	this(id, uri, np, templateClass, objectPosition, null);	8✔
182	}	1✔
183
184	/**
185	* Creates a link to a nanopublication or an IRI.
186	*
187	* @param id the Wicket component ID
188	* @param uri the URI of the nanopublication or IRI
189	* @param np the nanopublication, or null if the link is not to a nanopublication
190	*/
191	public NanodashLink(String id, String uri, Nanopub np) {
192	this(id, uri, np, null, false);	×
193	}	×
194
195	/**
196	* Creates a link to a nanopublication or an IRI.
197	*
198	* @param id the Wicket component ID
199	* @param uri the URI of the nanopublication or IRI
200	*/
201	public NanodashLink(String id, String uri) {
202	this(id, uri, null, null, false);	×
203	}	×
204
205	private static ValueFactory vf = SimpleValueFactory.getInstance();	3✔
206
207	}

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