20952016558

Committed 13 Jan 2026 09:42AM UTC coverage: 14.349% (-0.6%) from 14.953%

Build # 20952016558

Build Type

push

github

Committed by

tkuhn

Commit Message

fix(SearchPage): Search page tampered with cached list

Run Details

546 of 5034 branches covered (10.85%)

Branch coverage included in aggregate %.

1501 of 9232 relevant lines covered (16.26%)

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0.0

src/main/java/com/knowledgepixels/nanodash/page/SearchPage.java

package com.knowledgepixels.nanodash.page;

import java.time.Duration;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;

import org.apache.wicket.ajax.AjaxRequestTarget;
import org.apache.wicket.ajax.AjaxSelfUpdatingTimerBehavior;
import org.apache.wicket.extensions.ajax.markup.html.AjaxLazyLoadPanel;
import org.apache.wicket.markup.html.WebMarkupContainer;
import org.apache.wicket.markup.html.basic.Label;
import org.apache.wicket.markup.html.form.CheckBox;
import org.apache.wicket.markup.html.form.Form;
import org.apache.wicket.markup.html.form.RadioChoice;
import org.apache.wicket.markup.html.form.TextField;
import org.apache.wicket.model.Model;
import org.apache.wicket.request.mapper.parameter.PageParameters;
import org.nanopub.extra.services.ApiResponseEntry;
import org.nanopub.extra.services.QueryRef;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import com.knowledgepixels.nanodash.ApiCache;
import com.knowledgepixels.nanodash.NanodashPreferences;
import com.knowledgepixels.nanodash.NanodashSession;
import com.knowledgepixels.nanodash.NanopubElement;
import com.knowledgepixels.nanodash.User;
import com.knowledgepixels.nanodash.Utils;
import com.knowledgepixels.nanodash.component.NanopubResults;
import com.knowledgepixels.nanodash.component.TitleBar;

/**
 * SearchPage allows users to search for nanopublications by URI or free text.
 */
public class SearchPage extends NanodashPage {

    private static final Logger logger = LoggerFactory.getLogger(SearchPage.class);

    /**
     * The mount path for this page.
     */
    public static final String MOUNT_PATH = "/search";

    /**
     * {@inheritDoc}
     */
    @Override
    public String getMountPath() {
        return MOUNT_PATH;
    }

    private TextField<String> searchField;
    private CheckBox filterUser;
    private Model<String> progress;

    private Map<String, String> pubKeyMap;
    private RadioChoice<String> pubkeySelection;

    /**
     * Constructor for SearchPage.
     *
     * @param parameters Page parameters containing the search query, filter option, and public key.
     */
    public SearchPage(final PageParameters parameters) {
        super(parameters);

        add(new TitleBar("titlebar", this, "search"));

        final String searchText = parameters.get("query").toString();
        final Boolean filterCheck = Boolean.valueOf(parameters.get("filter").toString());
        final String pubkey = parameters.get("pubkey").toString();

        Form<?> form = new Form<Void>("form") {

            protected void onSubmit() {
                String searchText = searchField.getModelObject().trim();
                Boolean filterCheck = filterUser.getModelObject();
                String pubkey = pubkeySelection.getModelObject();
                PageParameters params = new PageParameters();
                params.set("query", searchText);
                params.set("filter", filterCheck);
                if (pubkey != null) params.set("pubkey", pubkey);
                setResponsePage(SearchPage.class, params);
            }
        };
        add(form);

        form.add(searchField = new TextField<String>("search", Model.of(searchText)));
        WebMarkupContainer ownFilter = new WebMarkupContainer("own-filter");
        ownFilter.add(filterUser = new CheckBox("filter", Model.of(filterCheck)));
        NanodashSession session = NanodashSession.get();
        ownFilter.setVisible(!NanodashPreferences.get().isReadOnlyMode() && session.getUserIri() != null);
        ArrayList<String> pubKeyList = new ArrayList<>();
        if (session.getUserIri() != null) {
            pubKeyMap = new HashMap<>();
            String lKeyShort = Utils.getShortPubkeyhashLabel(session.getPubkeyString(), session.getUserIri());
            pubKeyList.add(lKeyShort);
            pubKeyMap.put(lKeyShort, session.getPubkeyString());
            for (String pk : User.getPubkeyhashes(session.getUserIri(), null)) {
                String keyShort = Utils.getShortPubkeyhashLabel(pk, session.getUserIri());
                if (!pubKeyMap.containsKey(keyShort)) {
                    pubKeyList.add(keyShort);
                    pubKeyMap.put(keyShort, pk);
                }
            }
        }

        pubkeySelection = new RadioChoice<String>("pubkeygroup", Model.of(pubkey), pubKeyList);
        if (!pubKeyList.isEmpty() && pubkeySelection.getModelObject() == null) {
            pubkeySelection.setDefaultModelObject(pubKeyList.get(0));
        }
        ownFilter.add(pubkeySelection);

        form.add(ownFilter);

        // TODO: Progress bar doesn't update at the moment:
        progress = new Model<>();
        final Label progressLabel = new Label("progress", progress);
        progressLabel.setOutputMarkupId(true);
        progressLabel.add(new AjaxSelfUpdatingTimerBehavior(Duration.ofMillis(1000)));
        add(progressLabel);

        if (searchText == null || searchText.isEmpty()) {
            add(new Label("nanopubs", "Enter a search term above."));
        } else {
            add(new AjaxLazyLoadPanel<NanopubResults>("nanopubs") {

                @Override
                public NanopubResults getLazyLoadComponent(String markupId) {
                    Multimap<String, String> nanopubParams = ArrayListMultimap.create();
                    List<ApiResponseEntry> nanopubResults = new ArrayList<>();
                    String s = searchText;
                    if (s != null) {
                        s = s.trim();
                        if (s.matches("https?://[^\\s]+")) {
                            logger.info("URI QUERY: {}", s);
                            nanopubParams.put("ref", s);
                            if (Boolean.TRUE.equals(filterCheck)) {
                                String pubkey = pubKeyMap.get(pubkeySelection.getModelObject());
                                logger.info("Filter for PUBKEY: {}", pubkey);
                                nanopubParams.put("pubkey", pubkey);
                            }
                            try {
                                // nanopubResults = ApiAccess.getAll("find_nanopubs_with_uri", nanopubParams).getData();
                                nanopubResults = ApiCache.retrieveResponseSync(new QueryRef("find-uri-references", nanopubParams), false).getData();
                            } catch (Exception ex) {
                                logger.error("Error while running the query for URI", ex);
                            }
//                                                        nanopubResults = ApiAccess.getRecent("find_nanopubs_with_uri", nanopubParams, progress);
                        } else {
                            String freeTextQuery = getFreeTextQuery(s);
                            if (!freeTextQuery.isEmpty()) {
                                logger.info("FREE TEXT QUERY: {}", freeTextQuery);
                                nanopubParams.put("query", freeTextQuery);
                                if (filterCheck != null && Boolean.TRUE.equals(filterCheck)) {
                                    String pubkey = pubKeyMap.get(pubkeySelection.getModelObject());
                                    logger.info("Filter for PUBKEY: {}", pubkey);
                                    nanopubParams.put("pubkey", pubkey);
                                }
                                try {
                                    // nanopubResults = ApiAccess.getAll("find_nanopubs_with_text", nanopubParams).getData();
                                    nanopubResults = ApiCache.retrieveResponseSync(new QueryRef("fulltext-search-on-labels", nanopubParams), false).getData();
                                } catch (Exception ex) {
                                    logger.error("Error during search", ex);
                                }
                                logger.info("Results in: {}", nanopubResults.size());
//                                                                nanopubResults = ApiAccess.getRecent("find_nanopubs_with_text", nanopubParams, progress);
                            }
                        }
                    }
                    nanopubResults = new ArrayList<>(nanopubResults);
                    nanopubResults.sort(new ApiResponseEntry.DataComparator());
                    List<String> nanopubIds = new ArrayList<>();
                    while (!nanopubResults.isEmpty() && nanopubIds.size() < 100) {
                        String npUri = nanopubResults.remove(0).get("np");
                        if (!nanopubIds.contains(npUri)) nanopubIds.add(npUri);
                    }
                    progress.setObject("");
                    if (nanopubIds.isEmpty()) progress.setObject("nothing found");
                    List<NanopubElement> nanopubs = new ArrayList<>();
                    for (String id : nanopubIds) nanopubs.add(NanopubElement.get(id));
                    return NanopubResults.fromList(markupId, nanopubs, 20);
                }

                @Override
                protected void onContentLoaded(NanopubResults content, Optional<AjaxRequestTarget> target) {
                    super.onContentLoaded(content, target);
                    if (target.isPresent()) {
                        target.get().appendJavaScript("updateElements();");
                    }
                }

            });

        }
    }

    private static String getFreeTextQuery(String searchText) {
        String freeTextQuery = "";
        String previous = "AND";
        String preprocessed = "";
        boolean inQuote = true;
        for (String s : searchText.replaceAll("\\(\\s+", "(").replaceAll("\\s+\\)", ")").replaceAll("@", "").split("\"")) {
            inQuote = !inQuote;
            if (inQuote) {
                s = "\\\"" + String.join("@", s.split("[^\\p{L}0-9\\-_]+")) + "\\\"";
            }
            preprocessed += s;
        }
        preprocessed = preprocessed.trim();
        for (String s : preprocessed.split("[^\\p{L}0-9\\-_\\(\\)@\\\"\\\\]+")) {
            if (s.matches("[0-9].*")) continue;
            if (!s.matches("AND|OR|\\(+|\\)+|\\(?NOT")) {
                if (s.toLowerCase().matches("and|or|not")) {
                    // ignore lower-case and/or/not
                    continue;
                }
                if (!previous.matches("AND|OR|\\(?NOT")) {
                    freeTextQuery += " AND";
                }
            }
            freeTextQuery += " " + s.toLowerCase();
            previous = s;
        }
        freeTextQuery = freeTextQuery.replaceAll("@", " ").trim();
        return freeTextQuery;
    }

}

1	package com.knowledgepixels.nanodash.page;
2
3	import java.time.Duration;
4	import java.util.ArrayList;
5	import java.util.HashMap;
6	import java.util.List;
7	import java.util.Map;
8	import java.util.Optional;
9
10	import org.apache.wicket.ajax.AjaxRequestTarget;
11	import org.apache.wicket.ajax.AjaxSelfUpdatingTimerBehavior;
12	import org.apache.wicket.extensions.ajax.markup.html.AjaxLazyLoadPanel;
13	import org.apache.wicket.markup.html.WebMarkupContainer;
14	import org.apache.wicket.markup.html.basic.Label;
15	import org.apache.wicket.markup.html.form.CheckBox;
16	import org.apache.wicket.markup.html.form.Form;
17	import org.apache.wicket.markup.html.form.RadioChoice;
18	import org.apache.wicket.markup.html.form.TextField;
19	import org.apache.wicket.model.Model;
20	import org.apache.wicket.request.mapper.parameter.PageParameters;
21	import org.nanopub.extra.services.ApiResponseEntry;
22	import org.nanopub.extra.services.QueryRef;
23	import org.slf4j.Logger;
24	import org.slf4j.LoggerFactory;
25
26	import com.google.common.collect.ArrayListMultimap;
27	import com.google.common.collect.Multimap;
28	import com.knowledgepixels.nanodash.ApiCache;
29	import com.knowledgepixels.nanodash.NanodashPreferences;
30	import com.knowledgepixels.nanodash.NanodashSession;
31	import com.knowledgepixels.nanodash.NanopubElement;
32	import com.knowledgepixels.nanodash.User;
33	import com.knowledgepixels.nanodash.Utils;
34	import com.knowledgepixels.nanodash.component.NanopubResults;
35	import com.knowledgepixels.nanodash.component.TitleBar;
36
37	/**
38	* SearchPage allows users to search for nanopublications by URI or free text.
39	*/
40	public class SearchPage extends NanodashPage {
41
42	private static final Logger logger = LoggerFactory.getLogger(SearchPage.class);	×
43
44	/**
45	* The mount path for this page.
46	*/
47	public static final String MOUNT_PATH = "/search";
48
49	/**
50	* {@inheritDoc}
51	*/
52	@Override
53	public String getMountPath() {
54	return MOUNT_PATH;	×
55	}
56
57	private TextField<String> searchField;
58	private CheckBox filterUser;
59	private Model<String> progress;
60
61	private Map<String, String> pubKeyMap;
62	private RadioChoice<String> pubkeySelection;
63
64	/**
65	* Constructor for SearchPage.
66	*
67	* @param parameters Page parameters containing the search query, filter option, and public key.
68	*/
69	public SearchPage(final PageParameters parameters) {
70	super(parameters);	×
71
72	add(new TitleBar("titlebar", this, "search"));	×
73
74	final String searchText = parameters.get("query").toString();	×
75	final Boolean filterCheck = Boolean.valueOf(parameters.get("filter").toString());	×
76	final String pubkey = parameters.get("pubkey").toString();	×
77
78	Form<?> form = new Form<Void>("form") {	×
79
80	protected void onSubmit() {
81	String searchText = searchField.getModelObject().trim();	×
82	Boolean filterCheck = filterUser.getModelObject();	×
83	String pubkey = pubkeySelection.getModelObject();	×
84	PageParameters params = new PageParameters();	×
85	params.set("query", searchText);	×
86	params.set("filter", filterCheck);	×
87	if (pubkey != null) params.set("pubkey", pubkey);	×
88	setResponsePage(SearchPage.class, params);	×
89	}	×
90	};
91	add(form);	×
92
93	form.add(searchField = new TextField<String>("search", Model.of(searchText)));	×
94	WebMarkupContainer ownFilter = new WebMarkupContainer("own-filter");	×
95	ownFilter.add(filterUser = new CheckBox("filter", Model.of(filterCheck)));	×
96	NanodashSession session = NanodashSession.get();	×
97	ownFilter.setVisible(!NanodashPreferences.get().isReadOnlyMode() && session.getUserIri() != null);	×
98	ArrayList<String> pubKeyList = new ArrayList<>();	×
99	if (session.getUserIri() != null) {	×
100	pubKeyMap = new HashMap<>();	×
101	String lKeyShort = Utils.getShortPubkeyhashLabel(session.getPubkeyString(), session.getUserIri());	×
102	pubKeyList.add(lKeyShort);	×
103	pubKeyMap.put(lKeyShort, session.getPubkeyString());	×
104	for (String pk : User.getPubkeyhashes(session.getUserIri(), null)) {	×
105	String keyShort = Utils.getShortPubkeyhashLabel(pk, session.getUserIri());	×
106	if (!pubKeyMap.containsKey(keyShort)) {	×
107	pubKeyList.add(keyShort);	×
108	pubKeyMap.put(keyShort, pk);	×
109	}
110	}	×
111	}
112
113	pubkeySelection = new RadioChoice<String>("pubkeygroup", Model.of(pubkey), pubKeyList);	×
114	if (!pubKeyList.isEmpty() && pubkeySelection.getModelObject() == null) {	×
115	pubkeySelection.setDefaultModelObject(pubKeyList.get(0));	×
116	}
117	ownFilter.add(pubkeySelection);	×
118
119	form.add(ownFilter);	×
120
121	// TODO: Progress bar doesn't update at the moment:
122	progress = new Model<>();	×
123	final Label progressLabel = new Label("progress", progress);	×
124	progressLabel.setOutputMarkupId(true);	×
125	progressLabel.add(new AjaxSelfUpdatingTimerBehavior(Duration.ofMillis(1000)));	×
126	add(progressLabel);	×
127
128	if (searchText == null \|\| searchText.isEmpty()) {	×
129	add(new Label("nanopubs", "Enter a search term above."));	×
130	} else {
131	add(new AjaxLazyLoadPanel<NanopubResults>("nanopubs") {	×
132
133	@Override
134	public NanopubResults getLazyLoadComponent(String markupId) {
135	Multimap<String, String> nanopubParams = ArrayListMultimap.create();	×
136	List<ApiResponseEntry> nanopubResults = new ArrayList<>();	×
137	String s = searchText;	×
138	if (s != null) {	×
139	s = s.trim();	×
140	if (s.matches("https?://[^\\s]+")) {	×
141	logger.info("URI QUERY: {}", s);	×
142	nanopubParams.put("ref", s);	×
143	if (Boolean.TRUE.equals(filterCheck)) {	×
144	String pubkey = pubKeyMap.get(pubkeySelection.getModelObject());	×
145	logger.info("Filter for PUBKEY: {}", pubkey);	×
146	nanopubParams.put("pubkey", pubkey);	×
147	}
148	try {
149	// nanopubResults = ApiAccess.getAll("find_nanopubs_with_uri", nanopubParams).getData();
150	nanopubResults = ApiCache.retrieveResponseSync(new QueryRef("find-uri-references", nanopubParams), false).getData();	×
151	} catch (Exception ex) {	×
152	logger.error("Error while running the query for URI", ex);	×
153	}	×
154	// nanopubResults = ApiAccess.getRecent("find_nanopubs_with_uri", nanopubParams, progress);
155	} else {
156	String freeTextQuery = getFreeTextQuery(s);	×
157	if (!freeTextQuery.isEmpty()) {	×
158	logger.info("FREE TEXT QUERY: {}", freeTextQuery);	×
159	nanopubParams.put("query", freeTextQuery);	×
160	if (filterCheck != null && Boolean.TRUE.equals(filterCheck)) {	×
161	String pubkey = pubKeyMap.get(pubkeySelection.getModelObject());	×
162	logger.info("Filter for PUBKEY: {}", pubkey);	×
163	nanopubParams.put("pubkey", pubkey);	×
164	}
165	try {
166	// nanopubResults = ApiAccess.getAll("find_nanopubs_with_text", nanopubParams).getData();
167	nanopubResults = ApiCache.retrieveResponseSync(new QueryRef("fulltext-search-on-labels", nanopubParams), false).getData();	×
168	} catch (Exception ex) {	×
169	logger.error("Error during search", ex);	×
170	}	×
171	logger.info("Results in: {}", nanopubResults.size());	×
172	// nanopubResults = ApiAccess.getRecent("find_nanopubs_with_text", nanopubParams, progress);
173	}
174	}
175	}
176	nanopubResults = new ArrayList<>(nanopubResults);	×
177	nanopubResults.sort(new ApiResponseEntry.DataComparator());	×
178	List<String> nanopubIds = new ArrayList<>();	×
179	while (!nanopubResults.isEmpty() && nanopubIds.size() < 100) {	×
180	String npUri = nanopubResults.remove(0).get("np");	×
181	if (!nanopubIds.contains(npUri)) nanopubIds.add(npUri);	×
182	}	×
183	progress.setObject("");	×
184	if (nanopubIds.isEmpty()) progress.setObject("nothing found");	×
185	List<NanopubElement> nanopubs = new ArrayList<>();	×
186	for (String id : nanopubIds) nanopubs.add(NanopubElement.get(id));	×
187	return NanopubResults.fromList(markupId, nanopubs, 20);	×
188	}
189
190	@Override
191	protected void onContentLoaded(NanopubResults content, Optional<AjaxRequestTarget> target) {
192	super.onContentLoaded(content, target);	×
193	if (target.isPresent()) {	×
194	target.get().appendJavaScript("updateElements();");	×
195	}
196	}	×
197
198	});
199
200	}
201	}	×
202
203	private static String getFreeTextQuery(String searchText) {
204	String freeTextQuery = "";	×
205	String previous = "AND";	×
206	String preprocessed = "";	×
207	boolean inQuote = true;	×
208	for (String s : searchText.replaceAll("\\(\\s+", "(").replaceAll("\\s+\\)", ")").replaceAll("@", "").split("\"")) {	×
209	inQuote = !inQuote;	×
210	if (inQuote) {	×
211	s = "\\\"" + String.join("@", s.split("[^\\p{L}0-9\\-_]+")) + "\\\"";	×
212	}
213	preprocessed += s;	×
214	}
215	preprocessed = preprocessed.trim();	×
216	for (String s : preprocessed.split("[^\\p{L}0-9\\-_\\(\\)@\\\"\\\\]+")) {	×
217	if (s.matches("[0-9].*")) continue;	×
218	if (!s.matches("AND\|OR\|\\(+\|\\)+\|\\(?NOT")) {	×
219	if (s.toLowerCase().matches("and\|or\|not")) {	×
220	// ignore lower-case and/or/not
221	continue;	×
222	}
223	if (!previous.matches("AND\|OR\|\\(?NOT")) {	×
224	freeTextQuery += " AND";	×
225	}
226	}
227	freeTextQuery += " " + s.toLowerCase();	×
228	previous = s;	×
229	}
230	freeTextQuery = freeTextQuery.replaceAll("@", " ").trim();	×
231	return freeTextQuery;	×
232	}
233
234	}

knowledgepixels / nanodash / 20952016558

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