17267970789

Committed 27 Aug 2025 01:20PM UTC coverage: 12.355% (-0.007%) from 12.362%

Build # 17267970789

Build Type

push

github

Committed by

tkuhn

Commit Message

Add yellow border also for non-placeholder introduced resources

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989 of 6854 relevant lines covered (14.43%)

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10.42

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

package com.knowledgepixels.nanodash.component;

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.TemplateContext;
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.apache.wicket.markup.html.panel.Panel;
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.nanopub.SimpleCreatorPattern;

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 Panel implements ContextComponent {

    private static final long serialVersionUID = 1L;

    private IRI iri;
    private TemplateContext context;

    /**
     * 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);
        this.iri = iriP;
        this.context = rg.getContext();
        final Template template = context.getTemplate();
        String labelString = null;
        if (iri.equals(Template.ASSERTION_PLACEHOLDER)) {
            if (context.getType() == ContextType.ASSERTION) {
                labelString = "this assertion";
            } else {
                labelString = "the assertion above";
            }
        } else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {
            labelString = "this nanopublication";
        }
        if (template.getLabel(iri) != null) {
            labelString = template.getLabel(iri);
        } else if (iri.equals(SimpleCreatorPattern.PROV_WASATTRIBUTEDTO)) {
            // 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.length() > 0 && 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(Template.ASSERTION_PLACEHOLDER)) {
            if (rg.getContext().getExistingNanopub() != null) {
                iriString = rg.getContext().getExistingNanopub().getAssertionUri().stringValue();
            } else {
                iriString = "local:assertion";
            }
            description = "This is the identifier for the assertion of this nanopublication.";
        } else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {
            if (rg.getContext().getExistingNanopub() != null) {
                iriString = rg.getContext().getExistingNanopub().getUri().stringValue();
            } else {
                iriString = "local:nanopub";
            }
            description = "This is the identifier for this whole nanopublication.";
        } else if (template.isLocalResource(iri)) {
            if (rg.getContext().getExistingNanopub() == null) {
                iriString = iriString.replace(Utils.getUriPrefix(iriString), "local:");
            }
        }
        if (iriString.startsWith(context.getTemplateId())) {
            iriString = iriString.replace(context.getTemplateId(), "");
            if (rg.getContext().getExistingNanopub() != null) {
                iriString = rg.getContext().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 (iriString.startsWith("local:")) {
            href = "";
        } else {
            href = ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(iriString, UTF_8);
        }
        ExternalLink linkComp = new ExternalLink("link", href, labelString.replaceFirst(" - .*$", ""));
        if (iri.equals(Template.ASSERTION_PLACEHOLDER)) {
            linkComp.add(new AttributeAppender("class", " this-assertion "));
            iri = vf.createIRI("local:assertion");
        } else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {
            linkComp.add(new AttributeAppender("class", " this-nanopub "));
            iri = vf.createIRI("local: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() + "[#/]?", "local:");
        if (context.isReadOnly()) {
            return iriS.equals(v.stringValue().replaceFirst("^" + context.getExistingNanopub().getUri() + "[#/]?", "local:"));
        } 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.Utils;
4	import com.knowledgepixels.nanodash.component.StatementItem.RepetitionGroup;
5	import com.knowledgepixels.nanodash.page.ExplorePage;
6	import com.knowledgepixels.nanodash.template.ContextType;
7	import com.knowledgepixels.nanodash.template.Template;
8	import com.knowledgepixels.nanodash.template.TemplateContext;
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.apache.wicket.markup.html.panel.Panel;
14	import org.eclipse.rdf4j.model.IRI;
15	import org.eclipse.rdf4j.model.Value;
16	import org.eclipse.rdf4j.model.ValueFactory;
17	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
18	import org.nanopub.SimpleCreatorPattern;
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 Panel implements ContextComponent {
29
30	private static final long serialVersionUID = 1L;
31
32	private IRI iri;
33	private TemplateContext context;
34
35	/**
36	* Constructor for creating an IRI item with a given IRI and repetition group.
37	*
38	* @param id the component ID
39	* @param parentId the parent ID (e.g., "subj", "obj")
40	* @param iriP the IRI to display
41	* @param objectPosition whether this is in the object position of a statement
42	* @param statementPartId the ID of the statement part this IRI belongs to
43	* @param rg the repetition group context
44	*/
45	public IriItem(String id, String parentId, IRI iriP, boolean objectPosition, IRI statementPartId, RepetitionGroup rg) {
46	super(id);	×
47	this.iri = iriP;	×
48	this.context = rg.getContext();	×
49	final Template template = context.getTemplate();	×
50	String labelString = null;	×
51	if (iri.equals(Template.ASSERTION_PLACEHOLDER)) {	×
52	if (context.getType() == ContextType.ASSERTION) {	×
53	labelString = "this assertion";	×
54	} else {
55	labelString = "the assertion above";	×
56	}
57	} else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {	×
58	labelString = "this nanopublication";	×
59	}
60	if (template.getLabel(iri) != null) {	×
61	labelString = template.getLabel(iri);	×
62	} else if (iri.equals(SimpleCreatorPattern.PROV_WASATTRIBUTEDTO)) {	×
63	// temporary solution until we have full provenance graph support
64	labelString = "is attributed to";	×
65	} else if (labelString == null) {	×
66	labelString = getShortNameFromURI(iri.stringValue());	×
67	}
68	if (!statementPartId.equals(template.getFirstOccurence(iri))) {	×
69	labelString = labelString.replaceFirst("^[aA]n? ", "the ");	×
70	}
71	if (labelString.length() > 0 && parentId.equals("subj") && !labelString.matches("https?://.*")) {	×
72	// Capitalize first letter of label if at subject position:
73	labelString = labelString.substring(0, 1).toUpperCase() + labelString.substring(1);	×
74	}
75	labelString = labelString.replaceAll("%I%", "" + rg.getRepeatIndex());	×
76
77	String iriString = iri.stringValue();	×
78	String description = "";	×
79	if (iri.equals(Template.ASSERTION_PLACEHOLDER)) {	×
80	if (rg.getContext().getExistingNanopub() != null) {	×
81	iriString = rg.getContext().getExistingNanopub().getAssertionUri().stringValue();	×
82	} else {
83	iriString = "local:assertion";	×
84	}
85	description = "This is the identifier for the assertion of this nanopublication.";	×
86	} else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {	×
87	if (rg.getContext().getExistingNanopub() != null) {	×
88	iriString = rg.getContext().getExistingNanopub().getUri().stringValue();	×
89	} else {
90	iriString = "local:nanopub";	×
91	}
92	description = "This is the identifier for this whole nanopublication.";	×
93	} else if (template.isLocalResource(iri)) {	×
94	if (rg.getContext().getExistingNanopub() == null) {	×
95	iriString = iriString.replace(Utils.getUriPrefix(iriString), "local:");	×
96	}
97	}
98	if (iriString.startsWith(context.getTemplateId())) {	×
99	iriString = iriString.replace(context.getTemplateId(), "");	×
100	if (rg.getContext().getExistingNanopub() != null) {	×
101	iriString = rg.getContext().getExistingNanopub().getUri().stringValue() + iriString;	×
102	}
103	description = "This is a local identifier minted within the nanopublication.";	×
104	}
105	if (labelString.contains(" - ")) description = labelString.replaceFirst("^.* - ", "");	×
106	add(new Label("description", description));	×
107	add(Utils.getUriLink("uri", iriString));	×
108
109	String href = null;	×
110	if (iriString.startsWith("local:")) {	×
111	href = "";	×
112	} else {
113	href = ExplorePage.MOUNT_PATH + "?id=" + URLEncoder.encode(iriString, UTF_8);	×
114	}
115	ExternalLink linkComp = new ExternalLink("link", href, labelString.replaceFirst(" - .*$", ""));	×
116	if (iri.equals(Template.ASSERTION_PLACEHOLDER)) {	×
117	linkComp.add(new AttributeAppender("class", " this-assertion "));	×
118	iri = vf.createIRI("local:assertion");	×
119	} else if (iri.equals(Template.NANOPUB_PLACEHOLDER)) {	×
120	linkComp.add(new AttributeAppender("class", " this-nanopub "));	×
121	iri = vf.createIRI("local:nanopub");	×
122	}
123	add(linkComp);	×
124	if (template.isIntroducedResource(iri) \|\| template.isEmbeddedResource(iri)) {	×
125	linkComp.add(AttributeAppender.append("class", "introduced"));	×
126	}
127	}	×
128
129	private static ValueFactory vf = SimpleValueFactory.getInstance();	3✔
130
131	// TODO Merge with Utils.getShortNameFromURI
132
133	/**
134	* <p>getShortNameFromURI.</p>
135	*
136	* @param uri a {@link java.lang.String} object
137	* @return a {@link java.lang.String} object
138	*/
139	public static String getShortNameFromURI(String uri) {
140	if (uri.startsWith("https://doi.org/")) return uri.replace("https://doi.org/", "doi:");	4!
141	if (uri.startsWith("http://dx.doi.org/")) return uri.replace("http://dx.doi.org/", "doi:");	4!
142	uri = uri.replaceFirst("\\?.*$", "");	5✔
143	uri = uri.replaceFirst("[/#]$", "");	5✔
144	uri = uri.replaceFirst("^.[/#]([^/#])[/#]([0-9]+)$", "$1/$2");	5✔
145	if (uri.contains("#")) {	4!
146	uri = uri.replaceFirst("^.#(.[^0-9].*)$", "$1");	6✔
147	} else {
148	uri = uri.replaceFirst("^./([^/][^0-9/][^/]*)$", "$1");	×
149	}
150	uri = uri.replaceFirst("((^\|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{8})[A-Za-z0-9\\-_]{35}$", "$1");	5✔
151	uri = uri.replaceFirst("(^\|[^A-Za-z0-9\\-_])RA[A-Za-z0-9\\-_]{43}[^A-Za-z0-9\\-_](.+)$", "$2");	5✔
152	uri = URLDecoder.decode(uri, UTF_8);	4✔
153	return uri;	2✔
154	}
155
156	/**
157	* {@inheritDoc}
158	*/
159	@Override
160	public void removeFromContext() {
161	// Nothing to be done here.
162	}	×
163
164	/**
165	* {@inheritDoc}
166	*/
167	@Override
168	public boolean isUnifiableWith(Value v) {
169	if (!(v instanceof IRI)) return false;	×
170	// TODO: Check that template URIs don't have regex characters:
171	String iriS = iri.stringValue().replaceFirst("^" + context.getTemplateId() + "[#/]?", "local:");	×
172	if (context.isReadOnly()) {	×
173	return iriS.equals(v.stringValue().replaceFirst("^" + context.getExistingNanopub().getUri() + "[#/]?", "local:"));	×
174	} else {
175	return iriS.equals(v.stringValue());	×
176	}
177	}
178
179	/**
180	* {@inheritDoc}
181	*/
182	@Override
183	public void unifyWith(Value v) throws UnificationException {
184	if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());	×
185	// Nothing left to be done here.
186	}	×
187
188	/**
189	* {@inheritDoc}
190	*/
191	@Override
192	public void fillFinished() {
193	}	×
194
195	/**
196	* {@inheritDoc}
197	*/
198	@Override
199	public void finalizeValues() {
200	}	×
201
202	/**
203	* {@inheritDoc}
204	*/
205	@Override
206	public String toString() {
207	return "[IRI item: " + iri + "]";	×
208	}
209
210	}

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