22618039211

Committed 03 Mar 2026 10:05AM UTC coverage: 16.058% (+0.2%) from 15.884%

Build # 22618039211

Build Type

Pull #365

github

Committed by

web-flow

Commit Message

Merge 1e7e700f0 into a8c4b4a77

Pull Request Pull Request #365: Refactor of `ResourceWithProfile` and related classes

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

package com.knowledgepixels.nanodash.component;

import com.knowledgepixels.nanodash.domain.MaintainedResource;
import com.knowledgepixels.nanodash.domain.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.repository.MaintainedResourceRepository;
import com.knowledgepixels.nanodash.repository.SpaceRepository;
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 (SpaceRepository.get().findById(uri) != null) {
            label = SpaceRepository.get().findById(uri).getLabel();
            return new BookmarkablePageLink<Void>(markupId, SpacePage.class, params).setBody(Model.of(label));
        } else if (MaintainedResourceRepository.get().findById(uri) != null) {
            label = MaintainedResourceRepository.get().findById(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 = MaintainedResourceRepository.get().findByNamespace(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.domain.MaintainedResource;
4	import com.knowledgepixels.nanodash.domain.User;
5	import com.knowledgepixels.nanodash.Utils;
6	import com.knowledgepixels.nanodash.connector.ios.DsConfig;
7	import com.knowledgepixels.nanodash.connector.ios.DsNanopubPage;
8	import com.knowledgepixels.nanodash.connector.pensoft.BdjConfig;
9	import com.knowledgepixels.nanodash.connector.pensoft.BdjNanopubPage;
10	import com.knowledgepixels.nanodash.connector.pensoft.RioConfig;
11	import com.knowledgepixels.nanodash.connector.pensoft.RioNanopubPage;
12	import com.knowledgepixels.nanodash.page.ExplorePage;
13	import com.knowledgepixels.nanodash.page.MaintainedResourcePage;
14	import com.knowledgepixels.nanodash.page.ResourcePartPage;
15	import com.knowledgepixels.nanodash.page.SpacePage;
16	import com.knowledgepixels.nanodash.repository.MaintainedResourceRepository;
17	import com.knowledgepixels.nanodash.repository.SpaceRepository;
18	import com.knowledgepixels.nanodash.template.Template;
19	import com.knowledgepixels.nanodash.template.TemplateData;
20	import net.trustyuri.TrustyUriUtils;
21	import org.apache.commons.codec.Charsets;
22	import org.apache.wicket.Component;
23	import org.apache.wicket.behavior.AttributeAppender;
24	import org.apache.wicket.markup.html.basic.Label;
25	import org.apache.wicket.markup.html.link.BookmarkablePageLink;
26	import org.apache.wicket.markup.html.link.ExternalLink;
27	import org.apache.wicket.markup.html.panel.Panel;
28	import org.apache.wicket.model.Model;
29	import org.apache.wicket.request.mapper.parameter.PageParameters;
30	import org.eclipse.rdf4j.model.IRI;
31	import org.eclipse.rdf4j.model.Statement;
32	import org.eclipse.rdf4j.model.ValueFactory;
33	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
34	import org.eclipse.rdf4j.model.vocabulary.RDFS;
35	import org.nanopub.Nanopub;
36	import org.nanopub.vocabulary.NP;
37	import org.nanopub.vocabulary.NTEMPLATE;
38
39	import java.net.URLEncoder;
40	import java.util.*;
41
42	/**
43	* A Wicket component that creates a link to a nanopublication or an IRI.
44	*/
45	public class NanodashLink extends Panel {
46
47	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, String label) {
48	this(id, uri, np, templateClass, label, null);	24✔
49	}	3✔
50
51	/**
52	* Creates a link to a nanopublication or an IRI.
53	*
54	* @param id the Wicket component ID
55	* @param uri the URI of the nanopublication or IRI
56	* @param np the nanopublication, or null if the link is not to a nanopublication
57	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
58	* @param label the label to display for the link, or null to derive it from the nanopublication or IRI
59	*/
60	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass, String label, String contextId) {
61	super(id);	9✔
62
63	final List<Template> templates = new ArrayList<>();	12✔
64	final Map<IRI, String> labels = new HashMap<>();	12✔
65	if (np != null) {	6!
66	for (Statement st : np.getPubinfo()) {	33✔
67	if (st.getPredicate().equals(NTEMPLATE.HAS_LABEL_FROM_API) \|\| st.getPredicate().equals(RDFS.LABEL)) {	30!
68	labels.put((IRI) st.getSubject(), st.getObject().stringValue());	×
69	}
70	}	3✔
71	}
72
73	final TemplateData td = TemplateData.get();	6✔
74
75	if (NTEMPLATE.ASSERTION_TEMPLATE.equals(templateClass)) {	12!
76	IRI templateId = td.getTemplateId(np);	×
77	if (templateId != null) {	×
78	templates.add(td.getTemplate(templateId.stringValue()));	×
79	}
80	} else if (NTEMPLATE.PROVENANCE_TEMPLATE.equals(templateClass)) {	12!
81	IRI templateId = td.getProvenanceTemplateId(np);	×
82	if (templateId != null) {	×
83	templates.add(td.getTemplate(templateId.stringValue()));	×
84	}
85	} else if (NTEMPLATE.PUBINFO_TEMPLATE.equals(templateClass)) {	12!
86	Set<IRI> templateIds = td.getPubinfoTemplateIds(np);	×
87	for (IRI templateId : templateIds) {	×
88	templates.add(td.getTemplate(templateId.stringValue()));	×
89	}	×
90	}
91
92	final IRI iriObj = vf.createIRI(uri);	12✔
93	if (np != null && uri.equals(np.getUri().stringValue())) {	24!
94	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this");	×
95	add(link);	×
96	add(new Label("description", "this specific nanopublication"));	×
97	} else if (np != null && uri.equals(np.getAssertionUri().stringValue())) {	24!
98	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "this assertion");	×
99	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
100	add(link);	×
101	add(new Label("description", "the assertion of this specific nanopublication"));	×
102	} else if (uri.equals(NP.HAS_ASSERTION.stringValue())) {	15!
103	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "assertion");	×
104	link.add(new AttributeAppender("class", " nanopub-assertion "));	×
105	add(link);	×
106	add(new Label("description", "links a nanopublication to its assertion"));	×
107	} else if (uri.equals(NP.HAS_PROVENANCE.stringValue())) {	15!
108	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "provenance");	×
109	link.add(new AttributeAppender("class", " nanopub-provenance "));	×
110	add(link);	×
111	add(new Label("description", "links a nanopublication to its provenance"));	×
112	} else if (uri.equals(NP.HAS_PUBINFO.stringValue())) {	15!
113	ExternalLink link = new ExternalLink("link", ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(uri, Charsets.UTF_8), "pubinfo");	×
114	link.add(new AttributeAppender("class", " nanopub-pubinfo "));	×
115	add(link);	×
116	add(new Label("description", "links a nanopublication to its pubinfo"));	×
117	} else {	×
118	if (label == null \|\| label.isBlank()) {	6!
119	label = Utils.getShortNameFromURI(uri);	9✔
120	if (iriObj.equals(User.getSignatureOwnerIri(np))) {	15!
121	// TODO We might want to introduce a "(you)" flag here at some point
122	label = User.getShortDisplayName(iriObj);	×
123	} else if (User.getName(iriObj) != null) {	9!
124	label = User.getShortDisplayName(iriObj);	×
125	} else {
126	for (Template template : templates) {	18!
127	// TODO For pubinfo templates, we don't consider which triple came from which template (which is non-trivial):
128	String l = template.getLabel(iriObj);	×
129	if (l != null) {	×
130	label = l;	×
131	break;	×
132	}
133	l = labels.get(iriObj);	×
134	if (l != null) {	×
135	label = l;	×
136	break;	×
137	}
138	}	×
139	}
140	}
141	String shortLabel = label.replaceFirst(" - [\\s\\S]*$", "");	15✔
142	add(createLink("link", uri, shortLabel, contextId));	39✔
143	String description = "";	6✔
144	if (np != null && uri.startsWith(np.getUri().stringValue())) {	24!
145	description = "This is a local identifier that was minted when the nanopublication was created.";	×
146	}
147	if (label.contains(" - ")) description = label.replaceFirst("^.* - ", "");	12!
148	add(new Label("description", description));	39✔
149	}
150	add(Utils.getUriLink("uri", uri));	33✔
151	}	3✔
152
153	/**
154	* <p>createLink.</p>
155	*
156	* @param markupId a {@link java.lang.String} object
157	* @param uri a {@link java.lang.String} object
158	* @param label a {@link java.lang.String} object
159	* @return a {@link org.apache.wicket.Component} object
160	*/
161	public static Component createLink(String markupId, String uri, String label, String contextId) {
162	boolean isNp = TrustyUriUtils.isPotentialTrustyUri(uri);	9✔
163	PageParameters params = new PageParameters().set("id", uri);	21✔
164	if (contextId != null) params.set("context", contextId);	6!
165	// TODO Improve this
166	if (isNp && uri.startsWith(DsConfig.get().getTargetNamespace())) {	6!
167	return new BookmarkablePageLink<Void>(markupId, DsNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
168	} else if (isNp && uri.startsWith(BdjConfig.get().getTargetNamespace())) {	6!
169	return new BookmarkablePageLink<Void>(markupId, BdjNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
170	} else if (isNp && uri.startsWith(RioConfig.get().getTargetNamespace())) {	6!
171	return new BookmarkablePageLink<Void>(markupId, RioNanopubPage.class, params.set("mode", "final")).setBody(Model.of(label));	×
172	} else if (SpaceRepository.get().findById(uri) != null) {	12!
173	label = SpaceRepository.get().findById(uri).getLabel();	×
174	return new BookmarkablePageLink<Void>(markupId, SpacePage.class, params).setBody(Model.of(label));	×
175	} else if (MaintainedResourceRepository.get().findById(uri) != null) {	12!
176	label = MaintainedResourceRepository.get().findById(uri).getLabel();	×
177	return new BookmarkablePageLink<Void>(markupId, MaintainedResourcePage.class, params).setBody(Model.of(label));	×
178	} else {
179	if (!"^".equals(label)) params.set("label", label);	27!
180	if (isPartOfResource(uri, contextId)) {	12!
181	return new BookmarkablePageLink<Void>(markupId, ResourcePartPage.class, params).setBody(Model.of(label));	×
182	} else {
183	return new BookmarkablePageLink<Void>(markupId, ExplorePage.class, params.set("forward-to-part", "true")).setBody(Model.of(label));	39✔
184	}
185	}
186	}
187
188	private static boolean isPartOfResource(String uri, String contextId) {
189	if (contextId == null) return false;	12!
190	String uriNamespace = MaintainedResource.getNamespace(uri);	×
191	MaintainedResource resource = MaintainedResourceRepository.get().findByNamespace(uriNamespace);	×
192	if (resource == null) return false;	×
193	return resource.getId().equals(contextId);	×
194	}
195
196	/**
197	* Creates a link to a nanopublication or an IRI.
198	*
199	* @param id the Wicket component ID
200	* @param uri the URI of the nanopublication or IRI
201	* @param np the nanopublication, or null if the link is not to a nanopublication
202	* @param templateClass the template class of the nanopublication, or null if the link is not to a nanopublication
203	*/
204	public NanodashLink(String id, String uri, Nanopub np, IRI templateClass) {
205	this(id, uri, np, templateClass, null);	21✔
206	}	3✔
207
208	/**
209	* Creates a link to a nanopublication or an IRI.
210	*
211	* @param id the Wicket component ID
212	* @param uri the URI of the nanopublication or IRI
213	* @param np the nanopublication, or null if the link is not to a nanopublication
214	*/
215	public NanodashLink(String id, String uri, Nanopub np) {
216	this(id, uri, np, null);	×
217	}	×
218
219	/**
220	* Creates a link to a nanopublication or an IRI.
221	*
222	* @param id the Wicket component ID
223	* @param uri the URI of the nanopublication or IRI
224	*/
225	public NanodashLink(String id, String uri) {
226	this(id, uri, null, null);	×
227	}	×
228
229	private static ValueFactory vf = SimpleValueFactory.getInstance();	9✔
230
231	}

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