21766377938

Committed 06 Feb 2026 09:20PM UTC coverage: 14.086% (+0.2%) from 13.838%

Build # 21766377938

Build Type

push

github

Committed by

tkuhn

Commit Message

refactor: use nanopub URI as preview page id instead of random UUID

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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577 of 5266 branches covered (10.96%)

Branch coverage included in aggregate %.

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14.49

src/main/java/com/knowledgepixels/nanodash/NanodashSession.java

package com.knowledgepixels.nanodash;

import com.knowledgepixels.nanodash.component.NanopubResults;
import com.knowledgepixels.nanodash.component.PublishForm;
import com.knowledgepixels.nanodash.page.OrcidLoginPage;
import com.knowledgepixels.nanodash.page.ProfilePage;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpSession;
import jakarta.xml.bind.DatatypeConverter;
import org.apache.commons.io.FileUtils;
import org.apache.wicket.Session;
import org.apache.wicket.protocol.http.WebSession;
import org.apache.wicket.request.Request;
import org.apache.wicket.request.flow.RedirectToUrlException;
import org.apache.wicket.request.mapper.parameter.PageParameters;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.nanopub.extra.security.*;
import org.nanopub.extra.setting.IntroNanopub;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.security.KeyPair;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ConcurrentMap;

import org.apache.wicket.markup.html.WebPage;
import org.nanopub.Nanopub;

/**
 * Represents a session in the Nanodash application.
 */
public class NanodashSession extends WebSession {

    private transient HttpSession httpSession;
    private static final Logger logger = LoggerFactory.getLogger(NanodashSession.class);

    /**
     * Retrieves the current Nanodash session.
     *
     * @return The current NanodashSession instance.
     */
    public static NanodashSession get() {
        return (NanodashSession) Session.get();
    }

    /**
     * Constructs a new NanodashSession for the given request.
     * Initializes the HTTP session and loads profile information.
     *
     * @param request The HTTP request.
     */
    public NanodashSession(Request request) {
        super(request);
        httpSession = ((HttpServletRequest) request.getContainerRequest()).getSession();
        bind();
        loadProfileInfo();
    }

    private static ValueFactory vf = SimpleValueFactory.getInstance();

//        private IntroExtractor introExtractor;

    private String userDir = System.getProperty("user.home") + "/.nanopub/";
    private NanopubResults.ViewMode nanopubResultsViewMode = NanopubResults.ViewMode.LIST;

    private KeyPair keyPair;
    private IRI userIri;
    private ConcurrentMap<IRI, IntroNanopub> introNps;
//        private Boolean isOrcidLinked;
//        private String orcidLinkError;

    private Integer localIntroCount = null;
    private IntroNanopub localIntro = null;

    private Date lastTimeIntroPublished = null;

    // We should store here some sort of form model and not the forms themselves, but I couldn't figure
    // how to do it, so doing it like this for the moment...
    private ConcurrentMap<String, PublishForm> formMap = new ConcurrentHashMap<>();

    /**
     * Associates a form object with a specific ID.
     *
     * @param formObjId The ID of the form object.
     * @param formObj   The form object to associate.
     */
    public void setForm(String formObjId, PublishForm formObj) {
        formMap.put(formObjId, formObj);
    }

    /**
     * Checks if a form object with the given ID exists.
     *
     * @param formObjId The ID of the form object.
     * @return True if the form object exists, false otherwise.
     */
    public boolean hasForm(String formObjId) {
        return formMap.containsKey(formObjId);
    }

    /**
     * Retrieves the form object associated with the given ID.
     *
     * @param formObjId The ID of the form object.
     * @return The associated form object, or null if not found.
     */
    public PublishForm getForm(String formObjId) {
        return formMap.get(formObjId);
    }

    /**
     * Loads profile information for the user.
     * Initializes user-related data such as keys and introductions.
     */
    public void loadProfileInfo() {
        localIntroCount = null;
        localIntro = null;
        NanodashPreferences prefs = NanodashPreferences.get();
        if (prefs.isOrcidLoginMode()) {
            File usersDir = new File(System.getProperty("user.home") + "/.nanopub/nanodash-users/");
            if (!usersDir.exists()) usersDir.mkdir();
        }
        if (userIri == null && !prefs.isReadOnlyMode() && !prefs.isOrcidLoginMode()) {
            if (getOrcidFile().exists()) {
                try {
                    String orcid = FileUtils.readFileToString(getOrcidFile(), StandardCharsets.UTF_8).trim();
                    //String orcid = Files.readString(orcidFile.toPath(), StandardCharsets.UTF_8).trim();
                    if (orcid.matches(ProfilePage.ORCID_PATTERN)) {
                        userIri = vf.createIRI("https://orcid.org/" + orcid);
                        if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60);  // 24h
                    }
                } catch (IOException ex) {
                    logger.error("Couldn't read ORCID file", ex);
                }
            }
        }
        if (userIri != null && keyPair == null) {
            File keyFile = getKeyFile();
            if (keyFile.exists()) {
                try {
                    keyPair = SignNanopub.loadKey(keyFile.getPath(), SignatureAlgorithm.RSA);
                } catch (Exception ex) {
                    logger.error("Couldn't load key pair", ex);
                }
            } else {
                // Automatically generate new keys
                makeKeys();
            }
        }
        if (userIri != null && keyPair != null && introNps == null) {
            introNps = new ConcurrentHashMap<>(User.getIntroNanopubs(getPubkeyString()));
        }
//                checkOrcidLink();
    }

    /**
     * Checks if the user's profile is complete.
     *
     * @return True if the profile is complete, false otherwise.
     */
    public boolean isProfileComplete() {
        return userIri != null && keyPair != null && introNps != null;
    }

    /**
     * Redirects the user to the login page if their profile is incomplete.
     *
     * @param path       The path to redirect to after login.
     * @param parameters The page parameters for the redirect.
     */
    public void redirectToLoginIfNeeded(String path, PageParameters parameters) {
        String loginUrl = getLoginUrl(path, parameters);
        if (loginUrl == null) return;
        throw new RedirectToUrlException(loginUrl);
    }

    /**
     * Retrieves the login URL for the user.
     *
     * @param path       The path to redirect to after login.
     * @param parameters The page parameters for the redirect.
     * @return The login URL, or null if the user is already logged in.
     */
    public String getLoginUrl(String path, PageParameters parameters) {
        if (isProfileComplete()) return null;
        if (NanodashPreferences.get().isOrcidLoginMode()) {
            return OrcidLoginPage.getOrcidLoginUrl(path, parameters);
        } else {
            return ProfilePage.MOUNT_PATH;
        }
    }

    /**
     * Retrieves the public key as a Base64-encoded string.
     *
     * @return The public key string, or null if the key pair is not set.
     */
    public String getPubkeyString() {
        if (keyPair == null) return null;
        return DatatypeConverter.printBase64Binary(keyPair.getPublic().getEncoded()).replaceAll("\\s", "");
    }

    /**
     * Retrieves the public key hash for the user.
     *
     * @return The SHA-256 hash of the public key, or null if the public key is not set.
     */
    public String getPubkeyhash() {
        String pubkey = getPubkeyString();
        if (pubkey == null) return null;
        return Utils.createSha256HexHash(pubkey);
    }

    /**
     * Checks if the user's public key is approved.
     *
     * @return True if the public key is approved, false otherwise.
     */
    public boolean isPubkeyApproved() {
        if (keyPair == null || userIri == null) return false;
        return User.isApprovedPubkeyhashForUser(getPubkeyhash(), userIri);
    }

    /**
     * Retrieves the user's key pair.
     *
     * @return The key pair.
     */
    public KeyPair getKeyPair() {
        return keyPair;
    }

    /**
     * Generates a new key pair for the user.
     */
    public void makeKeys() {
        try {
            MakeKeys.make(getKeyFile().getAbsolutePath().replaceFirst("_rsa$", ""), SignatureAlgorithm.RSA);
            keyPair = SignNanopub.loadKey(getKeyFile().getPath(), SignatureAlgorithm.RSA);
        } catch (Exception ex) {
            logger.error("Couldn't create key pair", ex);
        }
    }

    /**
     * Retrieves the user's IRI.
     *
     * @return The user's IRI, or null if not set.
     */
    public IRI getUserIri() {
        return userIri;
    }

    /**
     * Retrieves the user's introduction nanopublications.
     *
     * @return A list of user's introduction nanopublications.
     */
    public List<IntroNanopub> getUserIntroNanopubs() {
        return User.getIntroNanopubs(userIri);
    }

    /**
     * Counts the number of local introduction nanopublications.
     *
     * @return The count of local introduction nanopublications.
     */
    public int getLocalIntroCount() {
        if (localIntroCount == null) {
            localIntroCount = 0;
            for (IntroNanopub inp : getUserIntroNanopubs()) {
                if (isIntroWithLocalKey(inp)) {
                    localIntroCount++;
                    localIntro = inp;
                }
            }
            if (localIntroCount > 1) localIntro = null;
        }
        return localIntroCount;
    }

    /**
     * Retrieves the local introduction nanopublication.
     *
     * @return The local introduction nanopublication, or null if not found.
     */
    public IntroNanopub getLocalIntro() {
        getLocalIntroCount();
        return localIntro;
    }

    /**
     * Checks if the given introduction nanopublication is associated with the local key.
     *
     * @param inp The introduction nanopublication.
     * @return True if associated with the local key, false otherwise.
     */
    public boolean isIntroWithLocalKey(IntroNanopub inp) {
        IRI location = Utils.getLocation(inp);
        NanopubSignatureElement el = Utils.getNanopubSignatureElement(inp);
        String siteUrl = NanodashPreferences.get().getWebsiteUrl();
        if (location != null && siteUrl != null) {
            String l = location.stringValue();
            // TODO: Solve the name change recognition in a better way:
            if (!l.equals(siteUrl) && !l.replace("nanobench", "nanodash").equals(siteUrl)) return false;
        }
        if (!getPubkeyString().equals(el.getPublicKeyString())) return false;
        for (KeyDeclaration kd : inp.getKeyDeclarations()) {
            if (getPubkeyString().equals(kd.getPublicKeyString())) return true;
        }
        return false;
    }

    /**
     * Sets the user's ORCID identifier.
     *
     * @param orcid The ORCID identifier.
     */
    public void setOrcid(String orcid) {
        if (!orcid.matches(ProfilePage.ORCID_PATTERN)) {
            throw new RuntimeException("Illegal ORCID identifier: " + orcid);
        }
        if (NanodashPreferences.get().isOrcidLoginMode()) {
            userDir = System.getProperty("user.home") + "/.nanopub/nanodash-users/" + orcid + "/";
            File f = new File(userDir);
            if (!f.exists()) f.mkdir();
        } else {
            try {
                FileUtils.writeStringToFile(getOrcidFile(), orcid + "\n", StandardCharsets.UTF_8);
                //                        Files.writeString(orcidFile.toPath(), orcid + "\n");
            } catch (IOException ex) {
                logger.error("Couldn't write ORCID file", ex);
            }
        }
        userIri = vf.createIRI("https://orcid.org/" + orcid);
        loadProfileInfo();
        if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60);  // 24h
    }

    /**
     * Logs out the user and invalidates the session.
     */
    public void logout() {
        userIri = null;
        invalidateNow();
    }

    /**
     * Retrieves the user's introduction nanopublications as a map.
     *
     * @return A map of introduction nanopublications.
     */
    public Map<IRI, IntroNanopub> getIntroNanopubs() {
        return introNps;
    }

//        public void checkOrcidLink() {
//                if (isOrcidLinked == null && userIri != null) {
//                        orcidLinkError = "";
//                        introExtractor = null;
//                        try {
//                                introExtractor = IntroNanopub.extract(userIri.stringValue(), null);
//                                if (introExtractor.getIntroNanopub() == null) {
//                                        orcidLinkError = "ORCID account is not linked.";
//                                        isOrcidLinked = false;
//                                } else {
//                                        IntroNanopub inp = IntroNanopub.get(userIri.stringValue(), introExtractor);
//                                        if (introNps != null && introNps.containsKey(inp.getNanopub().getUri())) {
//                                                // TODO: also check whether introduction contains local key
//                                                isOrcidLinked = true;
//                                        } else {
//                                                isOrcidLinked = false;
//                                                orcidLinkError = "Error: ORCID is linked to another introduction nanopublication.";
//                                        }
//                                }
//                        } catch (Exception ex) {
//                                logger.error("ORCID check failed");
//                                orcidLinkError = "ORCID check failed.";
//                        }
//                }
//        }
//
//        public void resetOrcidLinked() {
//                isOrcidLinked = null;
//        }
//
//        public boolean isOrcidLinked() {
//                checkOrcidLink();
//                return isOrcidLinked != null && isOrcidLinked == true;
//        }
//
//        public String getOrcidLinkError() {
//                return orcidLinkError;
//        }
//
//        public String getOrcidName() {
//                if (introExtractor == null || introExtractor.getName() == null) return null;
//                if (introExtractor.getName().trim().isEmpty()) return null;
//                return introExtractor.getName();
//        }

    /**
     * Retrieves the file for storing the user's ORCID identifier.
     *
     * @return The ORCID file.
     */
    private File getOrcidFile() {
        return new File(userDir + "orcid");
    }

    /**
     * Retrieves the file for storing the user's private key.
     *
     * @return The key file.
     */
    public File getKeyFile() {
        return new File(userDir + "id_rsa");
    }

    /**
     * Sets the time when the introduction was last published.
     */
    public void setIntroPublishedNow() {
        lastTimeIntroPublished = new Date();
    }

    /**
     * Checks if the introduction has been published.
     *
     * @return True if the introduction has been published, false otherwise.
     */
    public boolean hasIntroPublished() {
        return lastTimeIntroPublished != null;
    }

    /**
     * Calculates the time since the last introduction was published.
     *
     * @return The time in milliseconds since the last introduction was published, or Long.MAX_VALUE if it has never been published.
     */
    public long getTimeSinceLastIntroPublished() {
        if (lastTimeIntroPublished == null) return Long.MAX_VALUE;
        return new Date().getTime() - lastTimeIntroPublished.getTime();
    }

    /**
     * Sets the view mode for displaying nanopublication results.
     *
     * @param viewMode The desired view mode (e.g., GRID or LIST).
     */
    public void setNanopubResultsViewMode(NanopubResults.ViewMode viewMode) {
        this.nanopubResultsViewMode = viewMode;
    }

    /**
     * Retrieves the current view mode for displaying nanopublication results.
     *
     * @return The current view mode.
     */
    public NanopubResults.ViewMode getNanopubResultsViewMode() {
        return this.nanopubResultsViewMode;
    }

    // --- Preview nanopub support ---

    public static class PreviewNanopub implements Serializable {
        private final Nanopub nanopub;
        private final PageParameters pageParams;
        private final Class<? extends WebPage> confirmPageClass;

        public PreviewNanopub(Nanopub nanopub, PageParameters pageParams, Class<? extends WebPage> confirmPageClass) {
            this.nanopub = nanopub;
            this.pageParams = pageParams;
            this.confirmPageClass = confirmPageClass;
        }

        public Nanopub getNanopub() { return nanopub; }
        public PageParameters getPageParams() { return pageParams; }
        public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }
    }

    private ConcurrentMap<String, PreviewNanopub> previewMap = new ConcurrentHashMap<>();

    public void setPreviewNanopub(String id, PreviewNanopub preview) {
        previewMap.put(id, preview);
    }

    public PreviewNanopub getPreviewNanopub(String id) {
        return previewMap.get(id);
    }

    public PreviewNanopub removePreviewNanopub(String id) {
        return previewMap.remove(id);
    }

}

1	package com.knowledgepixels.nanodash;
2
3	import com.knowledgepixels.nanodash.component.NanopubResults;
4	import com.knowledgepixels.nanodash.component.PublishForm;
5	import com.knowledgepixels.nanodash.page.OrcidLoginPage;
6	import com.knowledgepixels.nanodash.page.ProfilePage;
7	import jakarta.servlet.http.HttpServletRequest;
8	import jakarta.servlet.http.HttpSession;
9	import jakarta.xml.bind.DatatypeConverter;
10	import org.apache.commons.io.FileUtils;
11	import org.apache.wicket.Session;
12	import org.apache.wicket.protocol.http.WebSession;
13	import org.apache.wicket.request.Request;
14	import org.apache.wicket.request.flow.RedirectToUrlException;
15	import org.apache.wicket.request.mapper.parameter.PageParameters;
16	import org.eclipse.rdf4j.model.IRI;
17	import org.eclipse.rdf4j.model.ValueFactory;
18	import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
19	import org.nanopub.extra.security.*;
20	import org.nanopub.extra.setting.IntroNanopub;
21	import org.slf4j.Logger;
22	import org.slf4j.LoggerFactory;
23
24	import java.io.File;
25	import java.io.IOException;
26	import java.io.Serializable;
27	import java.nio.charset.StandardCharsets;
28	import java.security.KeyPair;
29	import java.util.Date;
30	import java.util.List;
31	import java.util.Map;
32	import java.util.concurrent.ConcurrentHashMap;
33	import java.util.concurrent.ConcurrentMap;
34
35	import org.apache.wicket.markup.html.WebPage;
36	import org.nanopub.Nanopub;
37
38	/**
39	* Represents a session in the Nanodash application.
40	*/
41	public class NanodashSession extends WebSession {
42
43	private transient HttpSession httpSession;
44	private static final Logger logger = LoggerFactory.getLogger(NanodashSession.class);	9✔
45
46	/**
47	* Retrieves the current Nanodash session.
48	*
49	* @return The current NanodashSession instance.
50	*/
51	public static NanodashSession get() {
52	return (NanodashSession) Session.get();	×
53	}
54
55	/**
56	* Constructs a new NanodashSession for the given request.
57	* Initializes the HTTP session and loads profile information.
58	*
59	* @param request The HTTP request.
60	*/
61	public NanodashSession(Request request) {
62	super(request);	9✔
63	httpSession = ((HttpServletRequest) request.getContainerRequest()).getSession();	18✔
64	bind();	6✔
65	loadProfileInfo();	6✔
66	}	3✔
67
68	private static ValueFactory vf = SimpleValueFactory.getInstance();	9✔
69
70	// private IntroExtractor introExtractor;
71
72	private String userDir = System.getProperty("user.home") + "/.nanopub/";	15✔
73	private NanopubResults.ViewMode nanopubResultsViewMode = NanopubResults.ViewMode.LIST;	9✔
74
75	private KeyPair keyPair;
76	private IRI userIri;
77	private ConcurrentMap<IRI, IntroNanopub> introNps;
78	// private Boolean isOrcidLinked;
79	// private String orcidLinkError;
80
81	private Integer localIntroCount = null;	9✔
82	private IntroNanopub localIntro = null;	9✔
83
84	private Date lastTimeIntroPublished = null;	9✔
85
86	// We should store here some sort of form model and not the forms themselves, but I couldn't figure
87	// how to do it, so doing it like this for the moment...
88	private ConcurrentMap<String, PublishForm> formMap = new ConcurrentHashMap<>();	15✔
89
90	/**
91	* Associates a form object with a specific ID.
92	*
93	* @param formObjId The ID of the form object.
94	* @param formObj The form object to associate.
95	*/
96	public void setForm(String formObjId, PublishForm formObj) {
97	formMap.put(formObjId, formObj);	×
98	}	×
99
100	/**
101	* Checks if a form object with the given ID exists.
102	*
103	* @param formObjId The ID of the form object.
104	* @return True if the form object exists, false otherwise.
105	*/
106	public boolean hasForm(String formObjId) {
107	return formMap.containsKey(formObjId);	×
108	}
109
110	/**
111	* Retrieves the form object associated with the given ID.
112	*
113	* @param formObjId The ID of the form object.
114	* @return The associated form object, or null if not found.
115	*/
116	public PublishForm getForm(String formObjId) {
117	return formMap.get(formObjId);	×
118	}
119
120	/**
121	* Loads profile information for the user.
122	* Initializes user-related data such as keys and introductions.
123	*/
124	public void loadProfileInfo() {
125	localIntroCount = null;	9✔
126	localIntro = null;	9✔
127	NanodashPreferences prefs = NanodashPreferences.get();	6✔
128	if (prefs.isOrcidLoginMode()) {	9!
129	File usersDir = new File(System.getProperty("user.home") + "/.nanopub/nanodash-users/");	×
130	if (!usersDir.exists()) usersDir.mkdir();	×
131	}
132	if (userIri == null && !prefs.isReadOnlyMode() && !prefs.isOrcidLoginMode()) {	27!
133	if (getOrcidFile().exists()) {	12!
134	try {
135	String orcid = FileUtils.readFileToString(getOrcidFile(), StandardCharsets.UTF_8).trim();	×
136	//String orcid = Files.readString(orcidFile.toPath(), StandardCharsets.UTF_8).trim();
137	if (orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
138	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
139	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
140	}
141	} catch (IOException ex) {	×
142	logger.error("Couldn't read ORCID file", ex);	×
143	}	×
144	}
145	}
146	if (userIri != null && keyPair == null) {	9!
147	File keyFile = getKeyFile();	×
148	if (keyFile.exists()) {	×
149	try {
150	keyPair = SignNanopub.loadKey(keyFile.getPath(), SignatureAlgorithm.RSA);	×
151	} catch (Exception ex) {	×
152	logger.error("Couldn't load key pair", ex);	×
153	}	×
154	} else {
155	// Automatically generate new keys
156	makeKeys();	×
157	}
158	}
159	if (userIri != null && keyPair != null && introNps == null) {	9!
160	introNps = new ConcurrentHashMap<>(User.getIntroNanopubs(getPubkeyString()));	×
161	}
162	// checkOrcidLink();
163	}	3✔
164
165	/**
166	* Checks if the user's profile is complete.
167	*
168	* @return True if the profile is complete, false otherwise.
169	*/
170	public boolean isProfileComplete() {
171	return userIri != null && keyPair != null && introNps != null;	×
172	}
173
174	/**
175	* Redirects the user to the login page if their profile is incomplete.
176	*
177	* @param path The path to redirect to after login.
178	* @param parameters The page parameters for the redirect.
179	*/
180	public void redirectToLoginIfNeeded(String path, PageParameters parameters) {
181	String loginUrl = getLoginUrl(path, parameters);	×
182	if (loginUrl == null) return;	×
183	throw new RedirectToUrlException(loginUrl);	×
184	}
185
186	/**
187	* Retrieves the login URL for the user.
188	*
189	* @param path The path to redirect to after login.
190	* @param parameters The page parameters for the redirect.
191	* @return The login URL, or null if the user is already logged in.
192	*/
193	public String getLoginUrl(String path, PageParameters parameters) {
194	if (isProfileComplete()) return null;	×
195	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
196	return OrcidLoginPage.getOrcidLoginUrl(path, parameters);	×
197	} else {
198	return ProfilePage.MOUNT_PATH;	×
199	}
200	}
201
202	/**
203	* Retrieves the public key as a Base64-encoded string.
204	*
205	* @return The public key string, or null if the key pair is not set.
206	*/
207	public String getPubkeyString() {
208	if (keyPair == null) return null;	×
209	return DatatypeConverter.printBase64Binary(keyPair.getPublic().getEncoded()).replaceAll("\\s", "");	×
210	}
211
212	/**
213	* Retrieves the public key hash for the user.
214	*
215	* @return The SHA-256 hash of the public key, or null if the public key is not set.
216	*/
217	public String getPubkeyhash() {
218	String pubkey = getPubkeyString();	×
219	if (pubkey == null) return null;	×
220	return Utils.createSha256HexHash(pubkey);	×
221	}
222
223	/**
224	* Checks if the user's public key is approved.
225	*
226	* @return True if the public key is approved, false otherwise.
227	*/
228	public boolean isPubkeyApproved() {
229	if (keyPair == null \|\| userIri == null) return false;	×
230	return User.isApprovedPubkeyhashForUser(getPubkeyhash(), userIri);	×
231	}
232
233	/**
234	* Retrieves the user's key pair.
235	*
236	* @return The key pair.
237	*/
238	public KeyPair getKeyPair() {
239	return keyPair;	×
240	}
241
242	/**
243	* Generates a new key pair for the user.
244	*/
245	public void makeKeys() {
246	try {
247	MakeKeys.make(getKeyFile().getAbsolutePath().replaceFirst("_rsa$", ""), SignatureAlgorithm.RSA);	×
248	keyPair = SignNanopub.loadKey(getKeyFile().getPath(), SignatureAlgorithm.RSA);	×
249	} catch (Exception ex) {	×
250	logger.error("Couldn't create key pair", ex);	×
251	}	×
252	}	×
253
254	/**
255	* Retrieves the user's IRI.
256	*
257	* @return The user's IRI, or null if not set.
258	*/
259	public IRI getUserIri() {
260	return userIri;	×
261	}
262
263	/**
264	* Retrieves the user's introduction nanopublications.
265	*
266	* @return A list of user's introduction nanopublications.
267	*/
268	public List<IntroNanopub> getUserIntroNanopubs() {
269	return User.getIntroNanopubs(userIri);	×
270	}
271
272	/**
273	* Counts the number of local introduction nanopublications.
274	*
275	* @return The count of local introduction nanopublications.
276	*/
277	public int getLocalIntroCount() {
278	if (localIntroCount == null) {	×
279	localIntroCount = 0;	×
280	for (IntroNanopub inp : getUserIntroNanopubs()) {	×
281	if (isIntroWithLocalKey(inp)) {	×
282	localIntroCount++;	×
283	localIntro = inp;	×
284	}
285	}	×
286	if (localIntroCount > 1) localIntro = null;	×
287	}
288	return localIntroCount;	×
289	}
290
291	/**
292	* Retrieves the local introduction nanopublication.
293	*
294	* @return The local introduction nanopublication, or null if not found.
295	*/
296	public IntroNanopub getLocalIntro() {
297	getLocalIntroCount();	×
298	return localIntro;	×
299	}
300
301	/**
302	* Checks if the given introduction nanopublication is associated with the local key.
303	*
304	* @param inp The introduction nanopublication.
305	* @return True if associated with the local key, false otherwise.
306	*/
307	public boolean isIntroWithLocalKey(IntroNanopub inp) {
308	IRI location = Utils.getLocation(inp);	×
309	NanopubSignatureElement el = Utils.getNanopubSignatureElement(inp);	×
310	String siteUrl = NanodashPreferences.get().getWebsiteUrl();	×
311	if (location != null && siteUrl != null) {	×
312	String l = location.stringValue();	×
313	// TODO: Solve the name change recognition in a better way:
314	if (!l.equals(siteUrl) && !l.replace("nanobench", "nanodash").equals(siteUrl)) return false;	×
315	}
316	if (!getPubkeyString().equals(el.getPublicKeyString())) return false;	×
317	for (KeyDeclaration kd : inp.getKeyDeclarations()) {	×
318	if (getPubkeyString().equals(kd.getPublicKeyString())) return true;	×
319	}	×
320	return false;	×
321	}
322
323	/**
324	* Sets the user's ORCID identifier.
325	*
326	* @param orcid The ORCID identifier.
327	*/
328	public void setOrcid(String orcid) {
329	if (!orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
330	throw new RuntimeException("Illegal ORCID identifier: " + orcid);	×
331	}
332	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
333	userDir = System.getProperty("user.home") + "/.nanopub/nanodash-users/" + orcid + "/";	×
334	File f = new File(userDir);	×
335	if (!f.exists()) f.mkdir();	×
336	} else {	×
337	try {
338	FileUtils.writeStringToFile(getOrcidFile(), orcid + "\n", StandardCharsets.UTF_8);	×
339	// Files.writeString(orcidFile.toPath(), orcid + "\n");
340	} catch (IOException ex) {	×
341	logger.error("Couldn't write ORCID file", ex);	×
342	}	×
343	}
344	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
345	loadProfileInfo();	×
346	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
347	}	×
348
349	/**
350	* Logs out the user and invalidates the session.
351	*/
352	public void logout() {
353	userIri = null;	×
354	invalidateNow();	×
355	}	×
356
357	/**
358	* Retrieves the user's introduction nanopublications as a map.
359	*
360	* @return A map of introduction nanopublications.
361	*/
362	public Map<IRI, IntroNanopub> getIntroNanopubs() {
363	return introNps;	×
364	}
365
366	// public void checkOrcidLink() {
367	// if (isOrcidLinked == null && userIri != null) {
368	// orcidLinkError = "";
369	// introExtractor = null;
370	// try {
371	// introExtractor = IntroNanopub.extract(userIri.stringValue(), null);
372	// if (introExtractor.getIntroNanopub() == null) {
373	// orcidLinkError = "ORCID account is not linked.";
374	// isOrcidLinked = false;
375	// } else {
376	// IntroNanopub inp = IntroNanopub.get(userIri.stringValue(), introExtractor);
377	// if (introNps != null && introNps.containsKey(inp.getNanopub().getUri())) {
378	// // TODO: also check whether introduction contains local key
379	// isOrcidLinked = true;
380	// } else {
381	// isOrcidLinked = false;
382	// orcidLinkError = "Error: ORCID is linked to another introduction nanopublication.";
383	// }
384	// }
385	// } catch (Exception ex) {
386	// logger.error("ORCID check failed");
387	// orcidLinkError = "ORCID check failed.";
388	// }
389	// }
390	// }
391	//
392	// public void resetOrcidLinked() {
393	// isOrcidLinked = null;
394	// }
395	//
396	// public boolean isOrcidLinked() {
397	// checkOrcidLink();
398	// return isOrcidLinked != null && isOrcidLinked == true;
399	// }
400	//
401	// public String getOrcidLinkError() {
402	// return orcidLinkError;
403	// }
404	//
405	// public String getOrcidName() {
406	// if (introExtractor == null \|\| introExtractor.getName() == null) return null;
407	// if (introExtractor.getName().trim().isEmpty()) return null;
408	// return introExtractor.getName();
409	// }
410
411	/**
412	* Retrieves the file for storing the user's ORCID identifier.
413	*
414	* @return The ORCID file.
415	*/
416	private File getOrcidFile() {
417	return new File(userDir + "orcid");	21✔
418	}
419
420	/**
421	* Retrieves the file for storing the user's private key.
422	*
423	* @return The key file.
424	*/
425	public File getKeyFile() {
426	return new File(userDir + "id_rsa");	×
427	}
428
429	/**
430	* Sets the time when the introduction was last published.
431	*/
432	public void setIntroPublishedNow() {
433	lastTimeIntroPublished = new Date();	×
434	}	×
435
436	/**
437	* Checks if the introduction has been published.
438	*
439	* @return True if the introduction has been published, false otherwise.
440	*/
441	public boolean hasIntroPublished() {
442	return lastTimeIntroPublished != null;	×
443	}
444
445	/**
446	* Calculates the time since the last introduction was published.
447	*
448	* @return The time in milliseconds since the last introduction was published, or Long.MAX_VALUE if it has never been published.
449	*/
450	public long getTimeSinceLastIntroPublished() {
451	if (lastTimeIntroPublished == null) return Long.MAX_VALUE;	×
452	return new Date().getTime() - lastTimeIntroPublished.getTime();	×
453	}
454
455	/**
456	* Sets the view mode for displaying nanopublication results.
457	*
458	* @param viewMode The desired view mode (e.g., GRID or LIST).
459	*/
460	public void setNanopubResultsViewMode(NanopubResults.ViewMode viewMode) {
461	this.nanopubResultsViewMode = viewMode;	×
462	}	×
463
464	/**
465	* Retrieves the current view mode for displaying nanopublication results.
466	*
467	* @return The current view mode.
468	*/
469	public NanopubResults.ViewMode getNanopubResultsViewMode() {
470	return this.nanopubResultsViewMode;	×
471	}
472
473	// --- Preview nanopub support ---
474
475	public static class PreviewNanopub implements Serializable {
476	private final Nanopub nanopub;
477	private final PageParameters pageParams;
478	private final Class<? extends WebPage> confirmPageClass;
479
480	public PreviewNanopub(Nanopub nanopub, PageParameters pageParams, Class<? extends WebPage> confirmPageClass) {	×
481	this.nanopub = nanopub;	×
482	this.pageParams = pageParams;	×
483	this.confirmPageClass = confirmPageClass;	×
484	}	×
485
486	public Nanopub getNanopub() { return nanopub; }	×
487	public PageParameters getPageParams() { return pageParams; }	×
488	public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }	×
489	}
490
491	private ConcurrentMap<String, PreviewNanopub> previewMap = new ConcurrentHashMap<>();	15✔
492
493	public void setPreviewNanopub(String id, PreviewNanopub preview) {
494	previewMap.put(id, preview);	×
495	}	×
496
497	public PreviewNanopub getPreviewNanopub(String id) {
498	return previewMap.get(id);	×
499	}
500
501	public PreviewNanopub removePreviewNanopub(String id) {
502	return previewMap.remove(id);	×
503	}
504
505	}

knowledgepixels / nanodash / 21766377938

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