17837235071

Committed 18 Sep 2025 05:58PM UTC coverage: 13.87%. Remained the same

Build # 17837235071

Build Type

push

github

Committed by

tkuhn

Commit Message

chore: Remove serialVersionUIDs

Run Details

443 of 4022 branches covered (11.01%)

Branch coverage included in aggregate %.

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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.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.knowledgepixels.nanodash.NanodashPreferences;
import com.knowledgepixels.nanodash.NanodashSession;
import com.knowledgepixels.nanodash.NanopubElement;
import com.knowledgepixels.nanodash.QueryApiAccess;
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.add("query", searchText);
                params.add("filter", filterCheck);
                if (pubkey != null) params.add("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) {
                    Map<String, String> nanopubParams = new HashMap<>();
                    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 = QueryApiAccess.get("find-uri-references", nanopubParams).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 = QueryApiAccess.get("fulltext-search-on-labels", nanopubParams).getData();
                                } catch (Exception ex) {
                                    logger.error("Error during search", ex);
                                }
//                                                                nanopubResults = ApiAccess.getRecent("find_nanopubs_with_text", nanopubParams, progress);
                            }
                        }
                    }
                    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);
                }

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

knowledgepixels / nanodash / 17837235071

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