20171903096

Committed 12 Dec 2025 03:42PM UTC coverage: 15.509% (-0.1%) from 15.633%

Build # 20171903096

Build Type

push

github

Committed by

tkuhn

Commit Message

feat(NanodashLink): Don't pass "^" label so it makes good nanopub links

Run Details

604 of 4976 branches covered (12.14%)

Branch coverage included in aggregate %.

1578 of 9093 relevant lines covered (17.35%)

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Source File
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41.94

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

package com.knowledgepixels.nanodash.component;

import com.knowledgepixels.nanodash.MaintainedResource;
import com.knowledgepixels.nanodash.Space;
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.page.MaintainedResourcePage;
import com.knowledgepixels.nanodash.page.ResourcePartPage;
import com.knowledgepixels.nanodash.page.SpacePage;
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 {

    public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, String label) {
        this(id, uri, np, templateClass, label, 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
     * @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
     * @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, String label, String contextId) {
        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 = Utils.getShortNameFromURI(uri);
                if (iriObj.equals(User.getSignatureOwnerIri(np))) {
                    // TODO We might want to introduce a "(you)" flag here at some point
                    label = 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, contextId));
            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, String contextId) {
        boolean isNp = TrustyUriUtils.isPotentialTrustyUri(uri);
        PageParameters params = new PageParameters().set("id", uri);
        if (contextId != null) params.set("context", contextId);
        // TODO Improve this
        if (isNp && uri.startsWith(DsConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, DsNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));
        } else if (isNp && uri.startsWith(BdjConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, BdjNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));
        } else if (isNp && uri.startsWith(RioConfig.get().getTargetNamespace())) {
            return new BookmarkablePageLink<Void>(markupId, RioNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));
        } else if (Space.get(uri) != null) {
            label = Space.get(uri).getLabel();
            return new BookmarkablePageLink<Void>(markupId, SpacePage.class, params).setBody(Model.of(label));
        } else if (MaintainedResource.get(uri) != null) {
            label = MaintainedResource.get(uri).getLabel();
            return new BookmarkablePageLink<Void>(markupId, MaintainedResourcePage.class, params).setBody(Model.of(label));
        } else {
            if (!"^".equals(label)) params.set("label", label);
            if (isPartOfResource(uri, contextId)) {
                return new BookmarkablePageLink<Void>(markupId, ResourcePartPage.class, params).setBody(Model.of(label));
            } else {
                return new BookmarkablePageLink<Void>(markupId, ExplorePage.class, params.set("forward-to-part", "true")).setBody(Model.of(label));
            }
        }
    }

    private static boolean isPartOfResource(String uri, String contextId) {
        if (contextId == null) return false;
        String uriNamespace = MaintainedResource.getNamespace(uri);
        MaintainedResource resource = MaintainedResource.getByNamespace(uriNamespace);
        if (resource == null) return false;
        return resource.getId().equals(contextId);
    }

    /**
     * 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
     */
    public NanodashLink(String id, String uri, Nanopub np, IRI templateClass) {
        this(id, uri, np, templateClass, 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);
    }

    /**
     * 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);
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();

}

1	package com.knowledgepixels.nanodash.component;
2
3	import com.knowledgepixels.nanodash.MaintainedResource;
4	import com.knowledgepixels.nanodash.Space;
5	import com.knowledgepixels.nanodash.User;
6	import com.knowledgepixels.nanodash.Utils;
7	import com.knowledgepixels.nanodash.connector.ios.DsConfig;
8	import com.knowledgepixels.nanodash.connector.ios.DsNanopubPage;
9	import com.knowledgepixels.nanodash.connector.pensoft.BdjConfig;
10	import com.knowledgepixels.nanodash.connector.pensoft.BdjNanopubPage;
11	import com.knowledgepixels.nanodash.connector.pensoft.RioConfig;
12	import com.knowledgepixels.nanodash.connector.pensoft.RioNanopubPage;
13	import com.knowledgepixels.nanodash.page.ExplorePage;
14	import com.knowledgepixels.nanodash.page.MaintainedResourcePage;
15	import com.knowledgepixels.nanodash.page.ResourcePartPage;
16	import com.knowledgepixels.nanodash.page.SpacePage;
17	import com.knowledgepixels.nanodash.template.Template;
18	import com.knowledgepixels.nanodash.template.TemplateData;
19	import net.trustyuri.TrustyUriUtils;
20	import org.apache.commons.codec.Charsets;
21	import org.apache.wicket.Component;
22	import org.apache.wicket.behavior.AttributeAppender;
23	import org.apache.wicket.markup.html.basic.Label;
24	import org.apache.wicket.markup.html.link.BookmarkablePageLink;
25	import org.apache.wicket.markup.html.link.ExternalLink;
26	import org.apache.wicket.markup.html.panel.Panel;
27	import org.apache.wicket.model.Model;
28	import org.apache.wicket.request.mapper.parameter.PageParameters;
29	import org.eclipse.rdf4j.model.IRI;
30	import org.eclipse.rdf4j.model.Statement;
31	import org.eclipse.rdf4j.model.ValueFactory;
32	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
33	import org.eclipse.rdf4j.model.vocabulary.RDFS;
34	import org.nanopub.Nanopub;
35	import org.nanopub.vocabulary.NP;
36	import org.nanopub.vocabulary.NTEMPLATE;
37
38	import java.net.URLEncoder;
39	import java.util.*;
40
41	/**
42	* A Wicket component that creates a link to a nanopublication or an IRI.
43	*/
44	public class NanodashLink extends Panel {
45
46	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, String label) {
47	this(id, uri, np, templateClass, label, null);	24✔
48	}	3✔
49
50	/**
51	* Creates a link to a nanopublication or an IRI.
52	*
53	* @param id the Wicket component ID
54	* @param uri the URI of the nanopublication or IRI
55	* @param np the nanopublication, or null if the link is not to a nanopublication
56	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
57	* @param label the label to display for the link, or null to derive it from the nanopublication or IRI
58	*/
59	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, String label, String contextId) {
60	super(id);	9✔
61
62	final List<Template> templates = new ArrayList<>();	12✔
63	final Map<IRI, String> labels = new HashMap<>();	12✔
64	if (np != null) {	6!
65	for (Statement st : np.getPubinfo()) {	33✔
66	if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) \|\| st.getPredicate().equals(RDFS.LABEL)) {	30!
67	labels.put((IRI) st.getSubject(), st.getObject().stringValue());	×
68	}
69	}	3✔
70	}
71
72	final TemplateData td = TemplateData.get();	6✔
73
74	if (NTEMPLATE.ASSERTION_TEMPLATE.equals(templateClass)) {	12!
75	IRI templateId = td.getTemplateId(np);	×
76	if (templateId != null) {	×
77	templates.add(td.getTemplate(templateId.stringValue()));	×
78	}
79	} else if (NTEMPLATE.PROVENANCE_TEMPLATE.equals(templateClass)) {	12!
80	IRI templateId = td.getProvenanceTemplateId(np);	×
81	if (templateId != null) {	×
82	templates.add(td.getTemplate(templateId.stringValue()));	×
83	}
84	} else if (NTEMPLATE.PUBINFO_TEMPLATE.equals(templateClass)) {	12!
85	Set<IRI> templateIds = td.getPubinfoTemplateIds(np);	×
86	for (IRI templateId : templateIds) {	×
87	templates.add(td.getTemplate(templateId.stringValue()));	×
88	}	×
89	}
90
91	final IRI iriObj = vf.createIRI(uri);	12✔
92	if (np != null && uri.equals(np.getUri().stringValue())) {	24!
93	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this");	×
94	add(link);	×
95	add(new Label("description", "this specific nanopublication"));	×
96	} else if (np != null && uri.equals(np.getAssertionUri().stringValue())) {	24!
97	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this assertion");	×
98	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
99	add(link);	×
100	add(new Label("description", "the assertion of this specific nanopublication"));	×
101	} else if (uri.equals(NP.HAS_ASSERTION.stringValue())) {	15!
102	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "assertion");	×
103	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
104	add(link);	×
105	add(new Label("description", "links a nanopublication to its assertion"));	×
106	} else if (uri.equals(NP.HAS_PROVENANCE.stringValue())) {	15!
107	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "provenance");	×
108	link.add(new AttributeAppender("class", " nanopub-provenance "));	×
109	add(link);	×
110	add(new Label("description", "links a nanopublication to its provenance"));	×
111	} else if (uri.equals(NP.HAS_PUBINFO.stringValue())) {	15!
112	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "pubinfo");	×
113	link.add(new AttributeAppender("class", " nanopub-pubinfo "));	×
114	add(link);	×
115	add(new Label("description", "links a nanopublication to its pubinfo"));	×
116	} else {	×
117	if (label == null \|\| label.isBlank()) {	6!
118	label = Utils.getShortNameFromURI(uri);	9✔
119	if (iriObj.equals(User.getSignatureOwnerIri(np))) {	15!
120	// TODO We might want to introduce a "(you)" flag here at some point
121	label = User.getShortDisplayName(iriObj);	×
122	} else if (User.getName(iriObj) != null) {	9!
123	label = User.getShortDisplayName(iriObj);	×
124	} else {
125	for (Template template : templates) {	18!
126	// TODO For pubinfo templates, we don't consider which triple came from which template (which is non-trivial):
127	String l = template.getLabel(iriObj);	×
128	if (l != null) {	×
129	label = l;	×
130	break;	×
131	}
132	l = labels.get(iriObj);	×
133	if (l != null) {	×
134	label = l;	×
135	break;	×
136	}
137	}	×
138	}
139	}
140	String shortLabel = label.replaceFirst(" - [\\s\\S]*$", "");	15✔
141	add(createLink("link", uri, shortLabel, contextId));	39✔
142	String description = "";	6✔
143	if (np != null && uri.startsWith(np.getUri().stringValue())) {	24!
144	description = "This is a local identifier that was minted when the nanopublication was created.";	×
145	}
146	if (label.contains(" - ")) description = label.replaceFirst("^.* - ", "");	12!
147	add(new Label("description", description));	39✔
148	}
149	add(Utils.getUriLink("uri", uri));	33✔
150	}	3✔
151
152	/**
153	* <p>createLink.</p>
154	*
155	* @param markupId a {@link java.lang.String} object
156	* @param uri a {@link java.lang.String} object
157	* @param label a {@link java.lang.String} object
158	* @return a {@link org.apache.wicket.Component} object
159	*/
160	public static Component createLink(String markupId, String uri, String label, String contextId) {
161	boolean isNp = TrustyUriUtils.isPotentialTrustyUri(uri);	9✔
162	PageParameters params = new PageParameters().set("id", uri);	21✔
163	if (contextId != null) params.set("context", contextId);	6!
164	// TODO Improve this
165	if (isNp && uri.startsWith(DsConfig.get().getTargetNamespace())) {	6!
166	return new BookmarkablePageLink<Void>(markupId, DsNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
167	} else if (isNp && uri.startsWith(BdjConfig.get().getTargetNamespace())) {	6!
168	return new BookmarkablePageLink<Void>(markupId, BdjNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
169	} else if (isNp && uri.startsWith(RioConfig.get().getTargetNamespace())) {	6!
170	return new BookmarkablePageLink<Void>(markupId, RioNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
171	} else if (Space.get(uri) != null) {	9!
172	label = Space.get(uri).getLabel();	×
173	return new BookmarkablePageLink<Void>(markupId, SpacePage.class, params).setBody(Model.of(label));	×
174	} else if (MaintainedResource.get(uri) != null) {	9!
175	label = MaintainedResource.get(uri).getLabel();	×
176	return new BookmarkablePageLink<Void>(markupId, MaintainedResourcePage.class, params).setBody(Model.of(label));	×
177	} else {
178	if (!"^".equals(label)) params.set("label", label);	27!
179	if (isPartOfResource(uri, contextId)) {	12!
180	return new BookmarkablePageLink<Void>(markupId, ResourcePartPage.class, params).setBody(Model.of(label));	×
181	} else {
182	return new BookmarkablePageLink<Void>(markupId, ExplorePage.class, params.set("forward-to-part", "true")).setBody(Model.of(label));	39✔
183	}
184	}
185	}
186
187	private static boolean isPartOfResource(String uri, String contextId) {
188	if (contextId == null) return false;	12!
189	String uriNamespace = MaintainedResource.getNamespace(uri);	×
190	MaintainedResource resource = MaintainedResource.getByNamespace(uriNamespace);	×
191	if (resource == null) return false;	×
192	return resource.getId().equals(contextId);	×
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	* @param np the nanopublication, or null if the link is not to a nanopublication
201	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
202	*/
203	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass) {
204	this(id, uri, np, templateClass, null);	21✔
205	}	3✔
206
207	/**
208	* Creates a link to a nanopublication or an IRI.
209	*
210	* @param id the Wicket component ID
211	* @param uri the URI of the nanopublication or IRI
212	* @param np the nanopublication, or null if the link is not to a nanopublication
213	*/
214	public NanodashLink(String id, String uri, Nanopub np) {
215	this(id, uri, np, null);	×
216	}	×
217
218	/**
219	* Creates a link to a nanopublication or an IRI.
220	*
221	* @param id the Wicket component ID
222	* @param uri the URI of the nanopublication or IRI
223	*/
224	public NanodashLink(String id, String uri) {
225	this(id, uri, null, null);	×
226	}	×
227
228	private static ValueFactory vf = SimpleValueFactory.getInstance();	9✔
229
230	}

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