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`

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331 of 3840 branches covered (8.62%)

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

package com.knowledgepixels.nanodash.component;

import com.knowledgepixels.nanodash.NanodashSession;
import com.knowledgepixels.nanodash.User;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.IriTextfieldItem.Validator;
import com.knowledgepixels.nanodash.page.ProfilePage;
import com.knowledgepixels.nanodash.template.Template;
import com.knowledgepixels.nanodash.template.TemplateContext;
import com.knowledgepixels.nanodash.template.UnificationException;
import org.apache.wicket.Component;
import org.apache.wicket.ajax.AjaxRequestTarget;
import org.apache.wicket.ajax.form.OnChangeAjaxBehavior;
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.apache.wicket.model.IModel;
import org.apache.wicket.model.Model;
import org.apache.wicket.validation.Validatable;
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.vocabulary.NTEMPLATE;
import org.wicketstuff.select2.ChoiceProvider;
import org.wicketstuff.select2.Response;
import org.wicketstuff.select2.Select2Choice;

import java.util.*;

/**
 * A component that allows users to select an agent (user) from a list or enter an ORCID or URL.
 */
public class AgentChoiceItem extends Panel implements ContextComponent {

    private static final long serialVersionUID = 1L;
    private TemplateContext context;
    private Select2Choice<String> textfield;
    private ExternalLink tooltipLink;
    private Label tooltipDescription;
    private IRI iri;
    private IModel<String> model;

    private String getChoiceLabel(String choiceId) {
        IRI iri = vf.createIRI(choiceId);
        String name = User.getName(iri);
        if (name != null) return name;
        return choiceId;
    }

    /**
     * Constructor for AgentChoiceItem.
     *
     * @param id       the component ID
     * @param parentId the parent component ID
     * @param iriP     the IRI of the agent choice item
     * @param optional whether the choice is optional
     * @param context  the template context
     */
    public AgentChoiceItem(String id, String parentId, final IRI iriP, boolean optional, final TemplateContext context) {
        super(id);
        this.context = context;
        this.iri = iriP;
        final Template template = context.getTemplate();
        model = context.getComponentModels().get(iri);
        if (model == null) {
            model = Model.of("");
            context.getComponentModels().put(iri, model);
        }
        String postfix = Utils.getUriPostfix(iri);
        if (context.hasParam(postfix)) {
            model.setObject(context.getParam(postfix));
        }
        final List<String> possibleValues = new ArrayList<>();
        for (Value v : template.getPossibleValues(iri)) {
            possibleValues.add(v.toString());
        }

        ChoiceProvider<String> choiceProvider = new ChoiceProvider<String>() {

            private static final long serialVersionUID = 1L;

            @Override
            public String getDisplayValue(String choiceId) {
                if (choiceId == null || choiceId.isEmpty()) return "";
                String label = getChoiceLabel(choiceId);
                if (label == null || label.isBlank()) {
                    return choiceId;
                }
                return label + " (" + choiceId + ")";
            }

            @Override
            public String getIdValue(String object) {
                return object;
            }

            // Getting strange errors with Tomcat if this method is not overridden:
            @Override
            public void detach() {
            }

            @Override
            public void query(String term, int page, Response<String> response) {
                if (term == null) {
                    if (possibleValues.isEmpty()) {
                        if (NanodashSession.get().getUserIri() != null) {
                            response.add(NanodashSession.get().getUserIri().stringValue());
                        }
                    } else {
                        response.addAll(possibleValues);
                    }
                    return;
                }
                if (term.startsWith("https://") || term.startsWith("http://")) {
                    response.add(term);
                } else if (term.matches(ProfilePage.ORCID_PATTERN)) {
                    response.add("https://orcid.org/" + term);
                }
                Map<String, Boolean> alreadyAddedMap = new HashMap<>();
                term = term.toLowerCase();
                for (String s : possibleValues) {
                    if (s.toLowerCase().contains(term) || getDisplayValue(s).toLowerCase().contains(term)) {
                        response.add(s);
                        alreadyAddedMap.put(s, true);
                    }
                }

                // TODO: We'll need some indexing to perform this more efficiently at some point:
                for (IRI iri : User.getUsers(true)) {
                    // Collect approved users
                    if (response.size() > 9) break;
                    if (response.getResults().contains(iri.stringValue())) continue;
                    String name = User.getName(iri);
                    if (iri.stringValue().contains(term)) {
                        response.add(iri.stringValue());
                    } else if (name != null && name.toLowerCase().contains(term)) {
                        response.add(iri.stringValue());
                    }
                }
                for (IRI iri : User.getUsers(false)) {
                    // Collect non-approved users
                    if (response.size() > 9) break;
                    if (response.getResults().contains(iri.stringValue())) continue;
                    String name = User.getName(iri);
                    if (iri.stringValue().contains(term)) {
                        response.add(iri.stringValue());
                    } else if (name != null && name.toLowerCase().contains(term)) {
                        response.add(iri.stringValue());
                    }
                }
            }

            @Override
            public Collection<String> toChoices(Collection<String> ids) {
                return ids;
            }

        };
        textfield = new Select2Choice<String>("textfield", model, choiceProvider);
        textfield.getSettings().getAjax(true).setDelay(500);
        textfield.getSettings().setCloseOnSelect(true);
        String placeholder = template.getLabel(iri);
        if (placeholder == null) placeholder = "select user or paste ORCID/URL";
        textfield.getSettings().setPlaceholder(placeholder);
        Utils.setSelect2ChoiceMinimalEscapeMarkup(textfield);
        textfield.getSettings().setAllowClear(true);

        if (!optional) textfield.setRequired(true);
        textfield.add(new AttributeAppender("class", " wide"));
        textfield.add(new Validator(iri, template, "", context));
        context.getComponents().add(textfield);

        tooltipDescription = new Label("description", new IModel<String>() {

            private static final long serialVersionUID = 1L;

            @Override
            public String getObject() {
                String obj = AgentChoiceItem.this.getModel().getObject();
                if (obj == null || obj.isEmpty()) return "choose a value";
                String label = getChoiceLabel(AgentChoiceItem.this.getModel().getObject());
                if (label == null || !label.contains(" - ")) return "";
                return label.substring(label.indexOf(" - ") + 3);
            }

        });
        tooltipDescription.setOutputMarkupId(true);
        add(tooltipDescription);

        tooltipLink = Utils.getUriLink("uri", model);
        tooltipLink.setOutputMarkupId(true);
        add(tooltipLink);

        textfield.add(new OnChangeAjaxBehavior() {

            private static final long serialVersionUID = 1L;

            @Override
            protected void onUpdate(AjaxRequestTarget target) {
                for (Component c : context.getComponents()) {
                    if (c == textfield) continue;
                    if (c.getDefaultModel() == textfield.getModel()) {
                        c.modelChanged();
                        target.add(c);
                    }
                }
                target.add(tooltipLink);
                target.add(tooltipDescription);
            }

        });
        add(textfield);
    }

    /**
     * Returns the IRI of the agent choice item.
     *
     * @return the IRI of the agent choice item
     */
    public IModel<String> getModel() {
        return model;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void removeFromContext() {
        context.getComponents().remove(textfield);
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public boolean isUnifiableWith(Value v) {
        if (v == null) return true;
        if (v instanceof IRI) {
            String vs = v.stringValue();
            if (vs.startsWith("local:")) vs = vs.replaceFirst("^local:", "");
            Validatable<String> validatable = new Validatable<>(vs);
            if (context.getTemplate().isLocalResource(iri) && !Utils.isUriPostfix(vs)) {
                vs = Utils.getUriPostfix(vs);
            }
            new Validator(iri, context.getTemplate(), "", context).validate(validatable);
            if (!validatable.isValid()) {
                return false;
            }
            if (textfield.getModelObject().isEmpty()) {
                return true;
            }
            return vs.equals(textfield.getModelObject());
        }
        return false;
    }

    /**
     * {@inheritDoc}
     */
    @Override
    public void unifyWith(Value v) throws UnificationException {
        if (v == null) return;
        if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());
        String vs = v.stringValue();
        if (vs.startsWith("local:")) {
            vs = vs.replaceFirst("^local:", "");
        }
        textfield.setModelObject(vs);
    }

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

    /**
     * {@inheritDoc}
     */
    @Override
    public void finalizeValues() {
        Value defaultValue = context.getTemplate().getDefault(iri);
        if (NTEMPLATE.CREATOR_PLACEHOLDER.equals(defaultValue)) {
            defaultValue = NanodashSession.get().getUserIri();
        }
        if (isUnifiableWith(defaultValue)) {
            try {
                unifyWith(defaultValue);
            } catch (UnificationException ex) {
                ex.printStackTrace();
            }
        }
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();

    /**
     * <p>toString.</p>
     *
     * @return a {@link java.lang.String} object
     */
    public String toString() {
        return "[Agent choiced item: " + iri + "]";
    }

}

1	package com.knowledgepixels.nanodash.component;
2
3	import com.knowledgepixels.nanodash.NanodashSession;
4	import com.knowledgepixels.nanodash.User;
5	import com.knowledgepixels.nanodash.Utils;
6	import com.knowledgepixels.nanodash.component.IriTextfieldItem.Validator;
7	import com.knowledgepixels.nanodash.page.ProfilePage;
8	import com.knowledgepixels.nanodash.template.Template;
9	import com.knowledgepixels.nanodash.template.TemplateContext;
10	import com.knowledgepixels.nanodash.template.UnificationException;
11	import org.apache.wicket.Component;
12	import org.apache.wicket.ajax.AjaxRequestTarget;
13	import org.apache.wicket.ajax.form.OnChangeAjaxBehavior;
14	import org.apache.wicket.behavior.AttributeAppender;
15	import org.apache.wicket.markup.html.basic.Label;
16	import org.apache.wicket.markup.html.link.ExternalLink;
17	import org.apache.wicket.markup.html.panel.Panel;
18	import org.apache.wicket.model.IModel;
19	import org.apache.wicket.model.Model;
20	import org.apache.wicket.validation.Validatable;
21	import org.eclipse.rdf4j.model.IRI;
22	import org.eclipse.rdf4j.model.Value;
23	import org.eclipse.rdf4j.model.ValueFactory;
24	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
25	import org.nanopub.vocabulary.NTEMPLATE;
26	import org.wicketstuff.select2.ChoiceProvider;
27	import org.wicketstuff.select2.Response;
28	import org.wicketstuff.select2.Select2Choice;
29
30	import java.util.*;
31
32	/**
33	* A component that allows users to select an agent (user) from a list or enter an ORCID or URL.
34	*/
35	public class AgentChoiceItem extends Panel implements ContextComponent {
36
37	private static final long serialVersionUID = 1L;
38	private TemplateContext context;
39	private Select2Choice<String> textfield;
40	private ExternalLink tooltipLink;
41	private Label tooltipDescription;
42	private IRI iri;
43	private IModel<String> model;
44
45	private String getChoiceLabel(String choiceId) {
46	IRI iri = vf.createIRI(choiceId);	×
47	String name = User.getName(iri);	×
48	if (name != null) return name;	×
49	return choiceId;	×
50	}
51
52	/**
53	* Constructor for AgentChoiceItem.
54	*
55	* @param id the component ID
56	* @param parentId the parent component ID
57	* @param iriP the IRI of the agent choice item
58	* @param optional whether the choice is optional
59	* @param context the template context
60	*/
61	public AgentChoiceItem(String id, String parentId, final IRI iriP, boolean optional, final TemplateContext context) {
62	super(id);	×
63	this.context = context;	×
64	this.iri = iriP;	×
65	final Template template = context.getTemplate();	×
66	model = context.getComponentModels().get(iri);	×
67	if (model == null) {	×
68	model = Model.of("");	×
69	context.getComponentModels().put(iri, model);	×
70	}
71	String postfix = Utils.getUriPostfix(iri);	×
72	if (context.hasParam(postfix)) {	×
73	model.setObject(context.getParam(postfix));	×
74	}
75	final List<String> possibleValues = new ArrayList<>();	×
76	for (Value v : template.getPossibleValues(iri)) {	×
77	possibleValues.add(v.toString());	×
78	}	×
79
80	ChoiceProvider<String> choiceProvider = new ChoiceProvider<String>() {	×
81
82	private static final long serialVersionUID = 1L;
83
84	@Override
85	public String getDisplayValue(String choiceId) {
86	if (choiceId == null \|\| choiceId.isEmpty()) return "";	×
87	String label = getChoiceLabel(choiceId);	×
88	if (label == null \|\| label.isBlank()) {	×
89	return choiceId;	×
90	}
91	return label + " (" + choiceId + ")";	×
92	}
93
94	@Override
95	public String getIdValue(String object) {
96	return object;	×
97	}
98
99	// Getting strange errors with Tomcat if this method is not overridden:
100	@Override
101	public void detach() {
102	}	×
103
104	@Override
105	public void query(String term, int page, Response<String> response) {
106	if (term == null) {	×
107	if (possibleValues.isEmpty()) {	×
108	if (NanodashSession.get().getUserIri() != null) {	×
109	response.add(NanodashSession.get().getUserIri().stringValue());	×
110	}
111	} else {
112	response.addAll(possibleValues);	×
113	}
114	return;	×
115	}
116	if (term.startsWith("https://") \|\| term.startsWith("http://")) {	×
117	response.add(term);	×
118	} else if (term.matches(ProfilePage.ORCID_PATTERN)) {	×
119	response.add("https://orcid.org/" + term);	×
120	}
121	Map<String, Boolean> alreadyAddedMap = new HashMap<>();	×
122	term = term.toLowerCase();	×
123	for (String s : possibleValues) {	×
124	if (s.toLowerCase().contains(term) \|\| getDisplayValue(s).toLowerCase().contains(term)) {	×
125	response.add(s);	×
126	alreadyAddedMap.put(s, true);	×
127	}
128	}	×
129
130	// TODO: We'll need some indexing to perform this more efficiently at some point:
131	for (IRI iri : User.getUsers(true)) {	×
132	// Collect approved users
133	if (response.size() > 9) break;	×
134	if (response.getResults().contains(iri.stringValue())) continue;	×
135	String name = User.getName(iri);	×
136	if (iri.stringValue().contains(term)) {	×
137	response.add(iri.stringValue());	×
138	} else if (name != null && name.toLowerCase().contains(term)) {	×
139	response.add(iri.stringValue());	×
140	}
141	}	×
142	for (IRI iri : User.getUsers(false)) {	×
143	// Collect non-approved users
144	if (response.size() > 9) break;	×
145	if (response.getResults().contains(iri.stringValue())) continue;	×
146	String name = User.getName(iri);	×
147	if (iri.stringValue().contains(term)) {	×
148	response.add(iri.stringValue());	×
149	} else if (name != null && name.toLowerCase().contains(term)) {	×
150	response.add(iri.stringValue());	×
151	}
152	}	×
153	}	×
154
155	@Override
156	public Collection<String> toChoices(Collection<String> ids) {
157	return ids;	×
158	}
159
160	};
161	textfield = new Select2Choice<String>("textfield", model, choiceProvider);	×
162	textfield.getSettings().getAjax(true).setDelay(500);	×
163	textfield.getSettings().setCloseOnSelect(true);	×
164	String placeholder = template.getLabel(iri);	×
165	if (placeholder == null) placeholder = "select user or paste ORCID/URL";	×
166	textfield.getSettings().setPlaceholder(placeholder);	×
167	Utils.setSelect2ChoiceMinimalEscapeMarkup(textfield);	×
168	textfield.getSettings().setAllowClear(true);	×
169
170	if (!optional) textfield.setRequired(true);	×
171	textfield.add(new AttributeAppender("class", " wide"));	×
172	textfield.add(new Validator(iri, template, "", context));	×
173	context.getComponents().add(textfield);	×
174
175	tooltipDescription = new Label("description", new IModel<String>() {	×
176
177	private static final long serialVersionUID = 1L;
178
179	@Override
180	public String getObject() {
181	String obj = AgentChoiceItem.this.getModel().getObject();	×
182	if (obj == null \|\| obj.isEmpty()) return "choose a value";	×
183	String label = getChoiceLabel(AgentChoiceItem.this.getModel().getObject());	×
184	if (label == null \|\| !label.contains(" - ")) return "";	×
185	return label.substring(label.indexOf(" - ") + 3);	×
186	}
187
188	});
189	tooltipDescription.setOutputMarkupId(true);	×
190	add(tooltipDescription);	×
191
192	tooltipLink = Utils.getUriLink("uri", model);	×
193	tooltipLink.setOutputMarkupId(true);	×
194	add(tooltipLink);	×
195
196	textfield.add(new OnChangeAjaxBehavior() {	×
197
198	private static final long serialVersionUID = 1L;
199
200	@Override
201	protected void onUpdate(AjaxRequestTarget target) {
202	for (Component c : context.getComponents()) {	×
203	if (c == textfield) continue;	×
204	if (c.getDefaultModel() == textfield.getModel()) {	×
205	c.modelChanged();	×
206	target.add(c);	×
207	}
208	}	×
209	target.add(tooltipLink);	×
210	target.add(tooltipDescription);	×
211	}	×
212
213	});
214	add(textfield);	×
215	}	×
216
217	/**
218	* Returns the IRI of the agent choice item.
219	*
220	* @return the IRI of the agent choice item
221	*/
222	public IModel<String> getModel() {
223	return model;	×
224	}
225
226	/**
227	* {@inheritDoc}
228	*/
229	@Override
230	public void removeFromContext() {
231	context.getComponents().remove(textfield);	×
232	}	×
233
234	/**
235	* {@inheritDoc}
236	*/
237	@Override
238	public boolean isUnifiableWith(Value v) {
239	if (v == null) return true;	×
240	if (v instanceof IRI) {	×
241	String vs = v.stringValue();	×
242	if (vs.startsWith("local:")) vs = vs.replaceFirst("^local:", "");	×
243	Validatable<String> validatable = new Validatable<>(vs);	×
244	if (context.getTemplate().isLocalResource(iri) && !Utils.isUriPostfix(vs)) {	×
245	vs = Utils.getUriPostfix(vs);	×
246	}
247	new Validator(iri, context.getTemplate(), "", context).validate(validatable);	×
248	if (!validatable.isValid()) {	×
249	return false;	×
250	}
251	if (textfield.getModelObject().isEmpty()) {	×
252	return true;	×
253	}
254	return vs.equals(textfield.getModelObject());	×
255	}
256	return false;	×
257	}
258
259	/**
260	* {@inheritDoc}
261	*/
262	@Override
263	public void unifyWith(Value v) throws UnificationException {
264	if (v == null) return;	×
265	if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());	×
266	String vs = v.stringValue();	×
267	if (vs.startsWith("local:")) {	×
268	vs = vs.replaceFirst("^local:", "");	×
269	}
270	textfield.setModelObject(vs);	×
271	}	×
272
273	/**
274	* {@inheritDoc}
275	*/
276	@Override
277	public void fillFinished() {
278	}	×
279
280	/**
281	* {@inheritDoc}
282	*/
283	@Override
284	public void finalizeValues() {
285	Value defaultValue = context.getTemplate().getDefault(iri);	×
286	if (NTEMPLATE.CREATOR_PLACEHOLDER.equals(defaultValue)) {	×
287	defaultValue = NanodashSession.get().getUserIri();	×
288	}
289	if (isUnifiableWith(defaultValue)) {	×
290	try {
291	unifyWith(defaultValue);	×
292	} catch (UnificationException ex) {	×
293	ex.printStackTrace();	×
294	}	×
295	}
296	}	×
297
298	private static ValueFactory vf = SimpleValueFactory.getInstance();	×
299
300	/**
301	* <p>toString.</p>
302	*
303	* @return a {@link java.lang.String} object
304	*/
305	public String toString() {
306	return "[Agent choiced item: " + iri + "]";	×
307	}
308
309	}

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