17380144000

Committed 01 Sep 2025 02:12PM UTC coverage: 12.03% (+0.05%) from 11.978%

Build # 17380144000

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: replace printStackTrace with logger.error for better error handling

Run Details

330 of 3850 branches covered (8.57%)

Branch coverage included in aggregate %.

958 of 6857 relevant lines covered (13.97%)

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0.0

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.slf4j.Logger;
import org.slf4j.LoggerFactory;
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 static final Logger logger = LoggerFactory.getLogger(AgentChoiceItem.class);

    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) {
                logger.error("Could not unify default value: {}", defaultValue, ex);
            }
        }
    }

    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.slf4j.Logger;
27	import org.slf4j.LoggerFactory;
28	import org.wicketstuff.select2.ChoiceProvider;
29	import org.wicketstuff.select2.Response;
30	import org.wicketstuff.select2.Select2Choice;
31
32	import java.util.*;
33
34	/**
35	* A component that allows users to select an agent (user) from a list or enter an ORCID or URL.
36	*/
37	public class AgentChoiceItem extends Panel implements ContextComponent {
38
39	private static final long serialVersionUID = 1L;
40	private TemplateContext context;
41	private Select2Choice<String> textfield;
42	private ExternalLink tooltipLink;
43	private Label tooltipDescription;
44	private IRI iri;
45	private IModel<String> model;
46	private static final Logger logger = LoggerFactory.getLogger(AgentChoiceItem.class);	×
47
48	private String getChoiceLabel(String choiceId) {
49	IRI iri = vf.createIRI(choiceId);	×
50	String name = User.getName(iri);	×
51	if (name != null) return name;	×
52	return choiceId;	×
53	}
54
55	/**
56	* Constructor for AgentChoiceItem.
57	*
58	* @param id the component ID
59	* @param parentId the parent component ID
60	* @param iriP the IRI of the agent choice item
61	* @param optional whether the choice is optional
62	* @param context the template context
63	*/
64	public AgentChoiceItem(String id, String parentId, final IRI iriP, boolean optional, final TemplateContext context) {
65	super(id);	×
66	this.context = context;	×
67	this.iri = iriP;	×
68	final Template template = context.getTemplate();	×
69	model = context.getComponentModels().get(iri);	×
70	if (model == null) {	×
71	model = Model.of("");	×
72	context.getComponentModels().put(iri, model);	×
73	}
74	String postfix = Utils.getUriPostfix(iri);	×
75	if (context.hasParam(postfix)) {	×
76	model.setObject(context.getParam(postfix));	×
77	}
78	final List<String> possibleValues = new ArrayList<>();	×
79	for (Value v : template.getPossibleValues(iri)) {	×
80	possibleValues.add(v.toString());	×
81	}	×
82
83	ChoiceProvider<String> choiceProvider = new ChoiceProvider<String>() {	×
84
85	private static final long serialVersionUID = 1L;
86
87	@Override
88	public String getDisplayValue(String choiceId) {
89	if (choiceId == null \|\| choiceId.isEmpty()) return "";	×
90	String label = getChoiceLabel(choiceId);	×
91	if (label == null \|\| label.isBlank()) {	×
92	return choiceId;	×
93	}
94	return label + " (" + choiceId + ")";	×
95	}
96
97	@Override
98	public String getIdValue(String object) {
99	return object;	×
100	}
101
102	// Getting strange errors with Tomcat if this method is not overridden:
103	@Override
104	public void detach() {
105	}	×
106
107	@Override
108	public void query(String term, int page, Response<String> response) {
109	if (term == null) {	×
110	if (possibleValues.isEmpty()) {	×
111	if (NanodashSession.get().getUserIri() != null) {	×
112	response.add(NanodashSession.get().getUserIri().stringValue());	×
113	}
114	} else {
115	response.addAll(possibleValues);	×
116	}
117	return;	×
118	}
119	if (term.startsWith("https://") \|\| term.startsWith("http://")) {	×
120	response.add(term);	×
121	} else if (term.matches(ProfilePage.ORCID_PATTERN)) {	×
122	response.add("https://orcid.org/" + term);	×
123	}
124	Map<String, Boolean> alreadyAddedMap = new HashMap<>();	×
125	term = term.toLowerCase();	×
126	for (String s : possibleValues) {	×
127	if (s.toLowerCase().contains(term) \|\| getDisplayValue(s).toLowerCase().contains(term)) {	×
128	response.add(s);	×
129	alreadyAddedMap.put(s, true);	×
130	}
131	}	×
132
133	// TODO: We'll need some indexing to perform this more efficiently at some point:
134	for (IRI iri : User.getUsers(true)) {	×
135	// Collect approved users
136	if (response.size() > 9) break;	×
137	if (response.getResults().contains(iri.stringValue())) continue;	×
138	String name = User.getName(iri);	×
139	if (iri.stringValue().contains(term)) {	×
140	response.add(iri.stringValue());	×
141	} else if (name != null && name.toLowerCase().contains(term)) {	×
142	response.add(iri.stringValue());	×
143	}
144	}	×
145	for (IRI iri : User.getUsers(false)) {	×
146	// Collect non-approved users
147	if (response.size() > 9) break;	×
148	if (response.getResults().contains(iri.stringValue())) continue;	×
149	String name = User.getName(iri);	×
150	if (iri.stringValue().contains(term)) {	×
151	response.add(iri.stringValue());	×
152	} else if (name != null && name.toLowerCase().contains(term)) {	×
153	response.add(iri.stringValue());	×
154	}
155	}	×
156	}	×
157
158	@Override
159	public Collection<String> toChoices(Collection<String> ids) {
160	return ids;	×
161	}
162
163	};
164	textfield = new Select2Choice<String>("textfield", model, choiceProvider);	×
165	textfield.getSettings().getAjax(true).setDelay(500);	×
166	textfield.getSettings().setCloseOnSelect(true);	×
167	String placeholder = template.getLabel(iri);	×
168	if (placeholder == null) placeholder = "select user or paste ORCID/URL";	×
169	textfield.getSettings().setPlaceholder(placeholder);	×
170	Utils.setSelect2ChoiceMinimalEscapeMarkup(textfield);	×
171	textfield.getSettings().setAllowClear(true);	×
172
173	if (!optional) textfield.setRequired(true);	×
174	textfield.add(new AttributeAppender("class", " wide"));	×
175	textfield.add(new Validator(iri, template, "", context));	×
176	context.getComponents().add(textfield);	×
177
178	tooltipDescription = new Label("description", new IModel<String>() {	×
179
180	private static final long serialVersionUID = 1L;
181
182	@Override
183	public String getObject() {
184	String obj = AgentChoiceItem.this.getModel().getObject();	×
185	if (obj == null \|\| obj.isEmpty()) return "choose a value";	×
186	String label = getChoiceLabel(AgentChoiceItem.this.getModel().getObject());	×
187	if (label == null \|\| !label.contains(" - ")) return "";	×
188	return label.substring(label.indexOf(" - ") + 3);	×
189	}
190
191	});
192	tooltipDescription.setOutputMarkupId(true);	×
193	add(tooltipDescription);	×
194
195	tooltipLink = Utils.getUriLink("uri", model);	×
196	tooltipLink.setOutputMarkupId(true);	×
197	add(tooltipLink);	×
198
199	textfield.add(new OnChangeAjaxBehavior() {	×
200
201	private static final long serialVersionUID = 1L;
202
203	@Override
204	protected void onUpdate(AjaxRequestTarget target) {
205	for (Component c : context.getComponents()) {	×
206	if (c == textfield) continue;	×
207	if (c.getDefaultModel() == textfield.getModel()) {	×
208	c.modelChanged();	×
209	target.add(c);	×
210	}
211	}	×
212	target.add(tooltipLink);	×
213	target.add(tooltipDescription);	×
214	}	×
215
216	});
217	add(textfield);	×
218	}	×
219
220	/**
221	* Returns the IRI of the agent choice item.
222	*
223	* @return the IRI of the agent choice item
224	*/
225	public IModel<String> getModel() {
226	return model;	×
227	}
228
229	/**
230	* {@inheritDoc}
231	*/
232	@Override
233	public void removeFromContext() {
234	context.getComponents().remove(textfield);	×
235	}	×
236
237	/**
238	* {@inheritDoc}
239	*/
240	@Override
241	public boolean isUnifiableWith(Value v) {
242	if (v == null) return true;	×
243	if (v instanceof IRI) {	×
244	String vs = v.stringValue();	×
245	if (vs.startsWith("local:")) vs = vs.replaceFirst("^local:", "");	×
246	Validatable<String> validatable = new Validatable<>(vs);	×
247	if (context.getTemplate().isLocalResource(iri) && !Utils.isUriPostfix(vs)) {	×
248	vs = Utils.getUriPostfix(vs);	×
249	}
250	new Validator(iri, context.getTemplate(), "", context).validate(validatable);	×
251	if (!validatable.isValid()) {	×
252	return false;	×
253	}
254	if (textfield.getModelObject().isEmpty()) {	×
255	return true;	×
256	}
257	return vs.equals(textfield.getModelObject());	×
258	}
259	return false;	×
260	}
261
262	/**
263	* {@inheritDoc}
264	*/
265	@Override
266	public void unifyWith(Value v) throws UnificationException {
267	if (v == null) return;	×
268	if (!isUnifiableWith(v)) throw new UnificationException(v.stringValue());	×
269	String vs = v.stringValue();	×
270	if (vs.startsWith("local:")) {	×
271	vs = vs.replaceFirst("^local:", "");	×
272	}
273	textfield.setModelObject(vs);	×
274	}	×
275
276	/**
277	* {@inheritDoc}
278	*/
279	@Override
280	public void fillFinished() {
281	}	×
282
283	/**
284	* {@inheritDoc}
285	*/
286	@Override
287	public void finalizeValues() {
288	Value defaultValue = context.getTemplate().getDefault(iri);	×
289	if (NTEMPLATE.CREATOR_PLACEHOLDER.equals(defaultValue)) {	×
290	defaultValue = NanodashSession.get().getUserIri();	×
291	}
292	if (isUnifiableWith(defaultValue)) {	×
293	try {
294	unifyWith(defaultValue);	×
295	} catch (UnificationException ex) {	×
296	logger.error("Could not unify default value: {}", defaultValue, ex);	×
297	}	×
298	}
299	}	×
300
301	private static ValueFactory vf = SimpleValueFactory.getInstance();	×
302
303	/**
304	* <p>toString.</p>
305	*
306	* @return a {@link java.lang.String} object
307	*/
308	public String toString() {
309	return "[Agent choiced item: " + iri + "]";	×
310	}
311
312	}

knowledgepixels / nanodash / 17380144000

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