25386070558

Committed 05 May 2026 03:34PM UTC coverage: 18.296% (+0.009%) from 18.287%

Build # 25386070558

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push

github

Committed by

tkuhn

Commit Message

Merge branch 'master' of github.com:knowledgepixels/nanodash

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

package com.knowledgepixels.nanodash;

import com.knowledgepixels.nanodash.component.NanopubResults;
import com.knowledgepixels.nanodash.domain.User;
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.PageReference;
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.Locale;
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);
        setLocale(Locale.US);
        httpSession = ((HttpServletRequest) request.getContainerRequest()).getSession();
        bind();
        loadProfileInfo();
    }

    @Override
    public Session setLocale(Locale locale) {
        return super.setLocale(Locale.US);
    }

    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;

    /**
     * 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;
        private final boolean consentChecked;
        private final PageReference sourcePageRef;

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

        public Nanopub getNanopub() { return nanopub; }
        public PageParameters getPageParams() { return pageParams; }
        public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }
        public boolean isConsentChecked() { return consentChecked; }
        public PageReference getSourcePageRef() { return sourcePageRef; }
    }

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

knowledgepixels / nanodash / 25386070558

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