18939026354

Committed 30 Oct 2025 11:24AM UTC coverage: 14.184% (-0.1%) from 14.315%

Build # 18939026354

Build Type

push

github

Committed by

ashleycaselli

Commit Message

Merge branch 'master' of github.com:knowledgepixels/nanodash

Run Details

507 of 4504 branches covered (11.26%)

Branch coverage included in aggregate %.

1322 of 8391 relevant lines covered (15.75%)

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10.49

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

package com.knowledgepixels.nanodash.component;

import com.knowledgepixels.nanodash.LocalUri;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.StatementItem.RepetitionGroup;
import com.knowledgepixels.nanodash.page.ExplorePage;
import com.knowledgepixels.nanodash.template.ContextType;
import com.knowledgepixels.nanodash.template.Template;
import com.knowledgepixels.nanodash.template.UnificationException;
import org.apache.wicket.behavior.AttributeAppender;
import org.apache.wicket.markup.html.basic.Label;
import org.apache.wicket.markup.html.link.ExternalLink;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.PROV;
import org.nanopub.vocabulary.NTEMPLATE;

import java.net.URLDecoder;
import java.net.URLEncoder;

import static java.nio.charset.StandardCharsets.UTF_8;

/**
 * A panel that displays an IRI with a label and a link to explore it.
 */
public class IriItem extends AbstractContextComponent {

    private IRI iri;

    /**
     * Constructor for creating an IRI item with a given IRI and repetition group.
     *
     * @param id              the component ID
     * @param parentId        the parent ID (e.g., "subj", "obj")
     * @param iriP            the IRI to display
     * @param objectPosition  whether this is in the object position of a statement
     * @param statementPartId the ID of the statement part this IRI belongs to
     * @param rg              the repetition group context
     */
    public IriItem(String id, String parentId, IRI iriP, boolean objectPosition, IRI statementPartId, RepetitionGroup rg) {
        super(id, rg.getContext());
        this.iri = iriP;
        final Template template = context.getTemplate();
        String labelString = null;
        if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {
            if (context.getType() == ContextType.ASSERTION) {
                labelString = "this assertion";
            } else {
                labelString = "the assertion above";
            }
        } else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {
            labelString = "this nanopublication";
        }
        if (template.getLabel(iri) != null) {
            labelString = template.getLabel(iri);
        } else if (iri.equals(PROV.WAS_ATTRIBUTED_TO)) {
            // temporary solution until we have full provenance graph support
            labelString = "is attributed to";
        } else if (labelString == null) {
            labelString = getShortNameFromURI(iri.stringValue());
        }
        if (!statementPartId.equals(template.getFirstOccurence(iri))) {
            labelString = labelString.replaceFirst("^[aA]n? ", "the ");
        }
        if (!labelString.isEmpty() && parentId.equals("subj") && !labelString.matches("https?://.*")) {
            // Capitalize first letter of label if at subject position:
            labelString = labelString.substring(0, 1).toUpperCase() + labelString.substring(1);
        }
        labelString = labelString.replaceAll("%I%", "" + rg.getRepeatIndex());

        String iriString = iri.stringValue();
        String description = "";
        if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {
            if (this.context.getExistingNanopub() != null) {
                iriString = this.context.getExistingNanopub().getAssertionUri().stringValue();
            } else {
                iriString = LocalUri.PREFIX + "assertion";
            }
            description = "This is the identifier for the assertion of this nanopublication.";
        } else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {
            if (this.context.getExistingNanopub() != null) {
                iriString = this.context.getExistingNanopub().getUri().stringValue();
            } else {
                iriString = LocalUri.PREFIX + "nanopub";
            }
            description = "This is the identifier for this whole nanopublication.";
        } else if (template.isLocalResource(iri)) {
            if (this.context.getExistingNanopub() == null) {
                iriString = iriString.replace(Utils.getUriPrefix(iriString), LocalUri.PREFIX);
            }
        }
        if (iriString.startsWith(context.getTemplateId())) {
            iriString = iriString.replace(context.getTemplateId(), "");
            if (this.context.getExistingNanopub() != null) {
                iriString = this.context.getExistingNanopub().getUri().stringValue() + iriString;
            }
            description = "This is a local identifier minted within the nanopublication.";
        }
        if (labelString.contains(" - ")) description = labelString.replaceFirst("^.* - ", "");
        add(new Label("description", description));
        add(Utils.getUriLink("uri", iriString));

        String href = null;
        if (Utils.isLocalURI(iriString)) {
            href = "";
        } else {
            href = ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(iriString, UTF_8);
        }
        ExternalLink linkComp = new ExternalLink("link", href, labelString.replaceFirst(" - .*$", ""));
        if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {
            linkComp.add(new AttributeAppender("class", " this-assertion "));
            iri = vf.createIRI(LocalUri.PREFIX + "assertion");
        } else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {
            linkComp.add(new AttributeAppender("class", " this-nanopub "));
            iri = vf.createIRI(LocalUri.PREFIX + "nanopub");
        }
        add(linkComp);
        if (template.isIntroducedResource(iri) || template.isEmbeddedResource(iri)) {
            linkComp.add(AttributeAppender.append("class", "introduced"));
        }
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    // TODO Merge with Utils.getShortNameFromURI

    /**
     * <p>getShortNameFromURI.</p>
     *
     * @param uri a {@link java.lang.String} object
     * @return a {@link java.lang.String} object
     */
    public static String getShortNameFromURI(String uri) {
        if (uri.startsWith("https://doi.org/")) return uri.replace("https://doi.org/", "doi:");
        if (uri.startsWith("http://dx.doi.org/")) return uri.replace("http://dx.doi.org/", "doi:");
        uri = uri.replaceFirst("\\?.*$", "");
        uri = uri.replaceFirst("[/#]$", "");
        uri = uri.replaceFirst("^.*[/#]([^/#]*)[/#]([0-9]+)$", "$1/$2");
        if (uri.contains("#")) {
            uri = uri.replaceFirst("^.*#(.*[^0-9].*)$", "$1");
        } else {
            uri = uri.replaceFirst("^.*/([^/]*[^0-9/][^/]*)$", "$1");
        }
        uri = uri.replaceFirst("((^|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{8})[A-Za-z0-9\\-_]{35}$", "$1");
        uri = uri.replaceFirst("(^|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{43}[^A-Za-z0-9\\-_](.+)$", "$2");
        uri = URLDecoder.decode(uri, UTF_8);
        return uri;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void removeFromContext() {
        // Nothing to be done here.
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public boolean isUnifiableWith(Value v) {
        if (!(v instanceof IRI)) return false;
        // TODO: Check that template URIs don't have regex characters:
        String iriS = iri.stringValue().replaceFirst("^" + context.getTemplateId() + "[#/]?", LocalUri.PREFIX);
        if (context.isReadOnly()) {
            return iriS.equals(v.stringValue().replaceFirst("^" + context.getExistingNanopub().getUri() + "[#/]?", LocalUri.PREFIX));
        } else {
            return iriS.equals(v.stringValue());
        }
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void unifyWith(Value v) throws UnificationException {
        if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());
        // Nothing left to be done here.
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void fillFinished() {
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void finalizeValues() {
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public String toString() {
        return "[IRI item: " + iri + "]";
    }

}

1	package com.knowledgepixels.nanodash.component;
2
3	import com.knowledgepixels.nanodash.LocalUri;
4	import com.knowledgepixels.nanodash.Utils;
5	import com.knowledgepixels.nanodash.component.StatementItem.RepetitionGroup;
6	import com.knowledgepixels.nanodash.page.ExplorePage;
7	import com.knowledgepixels.nanodash.template.ContextType;
8	import com.knowledgepixels.nanodash.template.Template;
9	import com.knowledgepixels.nanodash.template.UnificationException;
10	import org.apache.wicket.behavior.AttributeAppender;
11	import org.apache.wicket.markup.html.basic.Label;
12	import org.apache.wicket.markup.html.link.ExternalLink;
13	import org.eclipse.rdf4j.model.IRI;
14	import org.eclipse.rdf4j.model.Value;
15	import org.eclipse.rdf4j.model.ValueFactory;
16	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
17	import org.eclipse.rdf4j.model.vocabulary.PROV;
18	import org.nanopub.vocabulary.NTEMPLATE;
19
20	import java.net.URLDecoder;
21	import java.net.URLEncoder;
22
23	import static java.nio.charset.StandardCharsets.UTF_8;
24
25	/**
26	* A panel that displays an IRI with a label and a link to explore it.
27	*/
28	public class IriItem extends AbstractContextComponent {
29
30	private IRI iri;
31
32	/**
33	* Constructor for creating an IRI item with a given IRI and repetition group.
34	*
35	* @param id the component ID
36	* @param parentId the parent ID (e.g., "subj", "obj")
37	* @param iriP the IRI to display
38	* @param objectPosition whether this is in the object position of a statement
39	* @param statementPartId the ID of the statement part this IRI belongs to
40	* @param rg the repetition group context
41	*/
42	public IriItem(String id, String parentId, IRI iriP, boolean objectPosition, IRI statementPartId, RepetitionGroup rg) {
43	super(id, rg.getContext());	×
44	this.iri = iriP;	×
45	final Template template = context.getTemplate();	×
46	String labelString = null;	×
47	if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {	×
48	if (context.getType() == ContextType.ASSERTION) {	×
49	labelString = "this assertion";	×
50	} else {
51	labelString = "the assertion above";	×
52	}
53	} else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {	×
54	labelString = "this nanopublication";	×
55	}
56	if (template.getLabel(iri) != null) {	×
57	labelString = template.getLabel(iri);	×
58	} else if (iri.equals(PROV.WAS_ATTRIBUTED_TO)) {	×
59	// temporary solution until we have full provenance graph support
60	labelString = "is attributed to";	×
61	} else if (labelString == null) {	×
62	labelString = getShortNameFromURI(iri.stringValue());	×
63	}
64	if (!statementPartId.equals(template.getFirstOccurence(iri))) {	×
65	labelString = labelString.replaceFirst("^[aA]n? ", "the ");	×
66	}
67	if (!labelString.isEmpty() && parentId.equals("subj") && !labelString.matches("https?://.*")) {	×
68	// Capitalize first letter of label if at subject position:
69	labelString = labelString.substring(0, 1).toUpperCase() + labelString.substring(1);	×
70	}
71	labelString = labelString.replaceAll("%I%", "" + rg.getRepeatIndex());	×
72
73	String iriString = iri.stringValue();	×
74	String description = "";	×
75	if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {	×
76	if (this.context.getExistingNanopub() != null) {	×
77	iriString = this.context.getExistingNanopub().getAssertionUri().stringValue();	×
78	} else {
79	iriString = LocalUri.PREFIX + "assertion";	×
80	}
81	description = "This is the identifier for the assertion of this nanopublication.";	×
82	} else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {	×
83	if (this.context.getExistingNanopub() != null) {	×
84	iriString = this.context.getExistingNanopub().getUri().stringValue();	×
85	} else {
86	iriString = LocalUri.PREFIX + "nanopub";	×
87	}
88	description = "This is the identifier for this whole nanopublication.";	×
89	} else if (template.isLocalResource(iri)) {	×
90	if (this.context.getExistingNanopub() == null) {	×
91	iriString = iriString.replace(Utils.getUriPrefix(iriString), LocalUri.PREFIX);	×
92	}
93	}
94	if (iriString.startsWith(context.getTemplateId())) {	×
95	iriString = iriString.replace(context.getTemplateId(), "");	×
96	if (this.context.getExistingNanopub() != null) {	×
97	iriString = this.context.getExistingNanopub().getUri().stringValue() + iriString;	×
98	}
99	description = "This is a local identifier minted within the nanopublication.";	×
100	}
101	if (labelString.contains(" - ")) description = labelString.replaceFirst("^.* - ", "");	×
102	add(new Label("description", description));	×
103	add(Utils.getUriLink("uri", iriString));	×
104
105	String href = null;	×
106	if (Utils.isLocalURI(iriString)) {	×
107	href = "";	×
108	} else {
109	href = ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(iriString, UTF_8);	×
110	}
111	ExternalLink linkComp = new ExternalLink("link", href, labelString.replaceFirst(" - .*$", ""));	×
112	if (iri.equals(NTEMPLATE.ASSERTION_PLACEHOLDER)) {	×
113	linkComp.add(new AttributeAppender("class", " this-assertion "));	×
114	iri = vf.createIRI(LocalUri.PREFIX + "assertion");	×
115	} else if (iri.equals(NTEMPLATE.NANOPUB_PLACEHOLDER)) {	×
116	linkComp.add(new AttributeAppender("class", " this-nanopub "));	×
117	iri = vf.createIRI(LocalUri.PREFIX + "nanopub");	×
118	}
119	add(linkComp);	×
120	if (template.isIntroducedResource(iri) \|\| template.isEmbeddedResource(iri)) {	×
121	linkComp.add(AttributeAppender.append("class", "introduced"));	×
122	}
123	}	×
124
125	private static ValueFactory vf = SimpleValueFactory.getInstance();	3✔
126
127	// TODO Merge with Utils.getShortNameFromURI
128
129	/**
130	* <p>getShortNameFromURI.</p>
131	*
132	* @param uri a {@link java.lang.String} object
133	* @return a {@link java.lang.String} object
134	*/
135	public static String getShortNameFromURI(String uri) {
136	if (uri.startsWith("https://doi.org/")) return uri.replace("https://doi.org/", "doi:");	4!
137	if (uri.startsWith("http://dx.doi.org/")) return uri.replace("http://dx.doi.org/", "doi:");	4!
138	uri = uri.replaceFirst("\\?.*$", "");	5✔
139	uri = uri.replaceFirst("[/#]$", "");	5✔
140	uri = uri.replaceFirst("^.[/#]([^/#])[/#]([0-9]+)$", "$1/$2");	5✔
141	if (uri.contains("#")) {	4!
142	uri = uri.replaceFirst("^.#(.[^0-9].*)$", "$1");	6✔
143	} else {
144	uri = uri.replaceFirst("^./([^/][^0-9/][^/]*)$", "$1");	×
145	}
146	uri = uri.replaceFirst("((^\|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{8})[A-Za-z0-9\\-_]{35}$", "$1");	5✔
147	uri = uri.replaceFirst("(^\|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{43}[^A-Za-z0-9\\-_](.+)$", "$2");	5✔
148	uri = URLDecoder.decode(uri, UTF_8);	4✔
149	return uri;	2✔
150	}
151
152	/**
153	* {@inheritDoc}
154	*/
155	@Override
156	public void removeFromContext() {
157	// Nothing to be done here.
158	}	×
159
160	/**
161	* {@inheritDoc}
162	*/
163	@Override
164	public boolean isUnifiableWith(Value v) {
165	if (!(v instanceof IRI)) return false;	×
166	// TODO: Check that template URIs don't have regex characters:
167	String iriS = iri.stringValue().replaceFirst("^" + context.getTemplateId() + "[#/]?", LocalUri.PREFIX);	×
168	if (context.isReadOnly()) {	×
169	return iriS.equals(v.stringValue().replaceFirst("^" + context.getExistingNanopub().getUri() + "[#/]?", LocalUri.PREFIX));	×
170	} else {
171	return iriS.equals(v.stringValue());	×
172	}
173	}
174
175	/**
176	* {@inheritDoc}
177	*/
178	@Override
179	public void unifyWith(Value v) throws UnificationException {
180	if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());	×
181	// Nothing left to be done here.
182	}	×
183
184	/**
185	* {@inheritDoc}
186	*/
187	@Override
188	public void fillFinished() {
189	}	×
190
191	/**
192	* {@inheritDoc}
193	*/
194	@Override
195	public void finalizeValues() {
196	}	×
197
198	/**
199	* {@inheritDoc}
200	*/
201	@Override
202	public String toString() {
203	return "[IRI item: " + iri + "]";	×
204	}
205
206	}

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