24787247242

Committed 22 Apr 2026 03:31PM UTC coverage: 17.496% (+0.03%) from 17.465%

Build # 24787247242

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push

github

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web-flow

Commit Message

Merge pull request #449 from knowledgepixels/remove-formobj-use-pagereference

refactor: drop formobj, use PageReference for preview Back

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15.02

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.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;

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

knowledgepixels / nanodash / 24787247242

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