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24785731352

Committed 22 Apr 2026 03:01PM UTC coverage: 17.46% (-0.005%) from 17.465%

Build # 24785731352

Build Type

Pull #449

github

Committed by

web-flow

Commit Message

Merge e4d6d022c into c9b9c0de8

Pull Request Pull Request #449: refactor: drop formobj, use PageReference for preview Back

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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.Collections;
import java.util.Date;
import java.util.LinkedHashMap;
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;

    // Small LRU of formObjId -> PageReference so that browser-back to
    // /publish?...&formobj=Y can recover the live PublishPage instance from
    // the page store. Holds PageReferences only, so entries are cheap and the
    // cap can stay generous.
    private static final int MAX_FORM_PAGE_REFS = 50;
    private final Map<String, PageReference> formPageRefMap = Collections.synchronizedMap(new LinkedHashMap<>(16, 0.75f, true) {
        @Override
        protected boolean removeEldestEntry(Map.Entry<String, PageReference> eldest) {
            return size() > MAX_FORM_PAGE_REFS;
        }
    });

    public void setFormPageRef(String formObjId, PageReference ref) {
        formPageRefMap.put(formObjId, ref);
    }

    public PageReference getFormPageRef(String formObjId) {
        return formPageRefMap.get(formObjId);
    }

    public void removeFormPageRef(String formObjId) {
        formPageRefMap.remove(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;
        private final boolean consentChecked;
        private final String formObj;

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

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

    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.Collections;
31	import java.util.Date;
32	import java.util.LinkedHashMap;
33	import java.util.List;
34	import java.util.Map;
35	import java.util.concurrent.ConcurrentHashMap;
36	import java.util.concurrent.ConcurrentMap;
37
38	import org.apache.wicket.markup.html.WebPage;
39	import org.nanopub.Nanopub;
40
41	/**
42	* Represents a session in the Nanodash application.
43	*/
44	public class NanodashSession extends WebSession {
45
46	private transient HttpSession httpSession;
47	private static final Logger logger = LoggerFactory.getLogger(NanodashSession.class);	9✔
48
49	/**
50	* Retrieves the current Nanodash session.
51	*
52	* @return The current NanodashSession instance.
53	*/
54	public static NanodashSession get() {
55	return (NanodashSession) Session.get();	9✔
56	}
57
58	/**
59	* Constructs a new NanodashSession for the given request.
60	* Initializes the HTTP session and loads profile information.
61	*
62	* @param request The HTTP request.
63	*/
64	public NanodashSession(Request request) {
65	super(request);	9✔
66	httpSession = ((HttpServletRequest) request.getContainerRequest()).getSession();	18✔
67	bind();	6✔
68	loadProfileInfo();	6✔
69	}	3✔
70
71	private static ValueFactory vf = SimpleValueFactory.getInstance();	9✔
72
73	// private IntroExtractor introExtractor;
74
75	private String userDir = System.getProperty("user.home") + "/.nanopub/";	15✔
76	private NanopubResults.ViewMode nanopubResultsViewMode = NanopubResults.ViewMode.LIST;	9✔
77
78	private KeyPair keyPair;
79	private IRI userIri;
80	private ConcurrentMap<IRI, IntroNanopub> introNps;
81	// private Boolean isOrcidLinked;
82	// private String orcidLinkError;
83
84	private Integer localIntroCount = null;	9✔
85	private IntroNanopub localIntro = null;	9✔
86
87	private Date lastTimeIntroPublished = null;	9✔
88
89	// Small LRU of formObjId -> PageReference so that browser-back to
90	// /publish?...&formobj=Y can recover the live PublishPage instance from
91	// the page store. Holds PageReferences only, so entries are cheap and the
92	// cap can stay generous.
93	private static final int MAX_FORM_PAGE_REFS = 50;
94	private final Map<String, PageReference> formPageRefMap = Collections.synchronizedMap(new LinkedHashMap<>(16, 0.75f, true) {	57✔
95	@Override
96	protected boolean removeEldestEntry(Map.Entry<String, PageReference> eldest) {
97	return size() > MAX_FORM_PAGE_REFS;	×
98	}
99	});
100
101	public void setFormPageRef(String formObjId, PageReference ref) {
102	formPageRefMap.put(formObjId, ref);	×
103	}	×
104
105	public PageReference getFormPageRef(String formObjId) {
106	return formPageRefMap.get(formObjId);	×
107	}
108
109	public void removeFormPageRef(String formObjId) {
110	formPageRefMap.remove(formObjId);	×
111	}	×
112
113	/**
114	* Loads profile information for the user.
115	* Initializes user-related data such as keys and introductions.
116	*/
117	public void loadProfileInfo() {
118	localIntroCount = null;	9✔
119	localIntro = null;	9✔
120	NanodashPreferences prefs = NanodashPreferences.get();	6✔
121	if (prefs.isOrcidLoginMode()) {	9!
122	File usersDir = new File(System.getProperty("user.home") + "/.nanopub/nanodash-users/");	×
123	if (!usersDir.exists()) usersDir.mkdir();	×
124	}
125	if (userIri == null && !prefs.isReadOnlyMode() && !prefs.isOrcidLoginMode()) {	27!
126	if (getOrcidFile().exists()) {	12!
127	try {
128	String orcid = FileUtils.readFileToString(getOrcidFile(), StandardCharsets.UTF_8).trim();	×
129	//String orcid = Files.readString(orcidFile.toPath(), StandardCharsets.UTF_8).trim();
130	if (orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
131	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
132	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
133	}
134	} catch (IOException ex) {	×
135	logger.error("Couldn't read ORCID file", ex);	×
136	}	×
137	}
138	}
139	if (userIri != null && keyPair == null) {	9!
140	File keyFile = getKeyFile();	×
141	if (keyFile.exists()) {	×
142	try {
143	keyPair = SignNanopub.loadKey(keyFile.getPath(), SignatureAlgorithm.RSA);	×
144	} catch (Exception ex) {	×
145	logger.error("Couldn't load key pair", ex);	×
146	}	×
147	} else {
148	// Automatically generate new keys
149	makeKeys();	×
150	}
151	}
152	if (userIri != null && keyPair != null && introNps == null) {	9!
153	introNps = new ConcurrentHashMap<>(User.getIntroNanopubs(getPubkeyString()));	×
154	}
155	// checkOrcidLink();
156	}	3✔
157
158	/**
159	* Checks if the user's profile is complete.
160	*
161	* @return True if the profile is complete, false otherwise.
162	*/
163	public boolean isProfileComplete() {
164	return userIri != null && keyPair != null && introNps != null;	×
165	}
166
167	/**
168	* Redirects the user to the login page if their profile is incomplete.
169	*
170	* @param path The path to redirect to after login.
171	* @param parameters The page parameters for the redirect.
172	*/
173	public void redirectToLoginIfNeeded(String path, PageParameters parameters) {
174	String loginUrl = getLoginUrl(path, parameters);	×
175	if (loginUrl == null) return;	×
176	throw new RedirectToUrlException(loginUrl);	×
177	}
178
179	/**
180	* Retrieves the login URL for the user.
181	*
182	* @param path The path to redirect to after login.
183	* @param parameters The page parameters for the redirect.
184	* @return The login URL, or null if the user is already logged in.
185	*/
186	public String getLoginUrl(String path, PageParameters parameters) {
187	if (isProfileComplete()) return null;	×
188	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
189	return OrcidLoginPage.getOrcidLoginUrl(path, parameters);	×
190	} else {
191	return ProfilePage.MOUNT_PATH;	×
192	}
193	}
194
195	/**
196	* Retrieves the public key as a Base64-encoded string.
197	*
198	* @return The public key string, or null if the key pair is not set.
199	*/
200	public String getPubkeyString() {
201	if (keyPair == null) return null;	×
202	return DatatypeConverter.printBase64Binary(keyPair.getPublic().getEncoded()).replaceAll("\\s", "");	×
203	}
204
205	/**
206	* Retrieves the public key hash for the user.
207	*
208	* @return The SHA-256 hash of the public key, or null if the public key is not set.
209	*/
210	public String getPubkeyhash() {
211	String pubkey = getPubkeyString();	×
212	if (pubkey == null) return null;	×
213	return Utils.createSha256HexHash(pubkey);	×
214	}
215
216	/**
217	* Checks if the user's public key is approved.
218	*
219	* @return True if the public key is approved, false otherwise.
220	*/
221	public boolean isPubkeyApproved() {
222	if (keyPair == null \|\| userIri == null) return false;	×
223	return User.isApprovedPubkeyhashForUser(getPubkeyhash(), userIri);	×
224	}
225
226	/**
227	* Retrieves the user's key pair.
228	*
229	* @return The key pair.
230	*/
231	public KeyPair getKeyPair() {
232	return keyPair;	×
233	}
234
235	/**
236	* Generates a new key pair for the user.
237	*/
238	public void makeKeys() {
239	try {
240	MakeKeys.make(getKeyFile().getAbsolutePath().replaceFirst("_rsa$", ""), SignatureAlgorithm.RSA);	×
241	keyPair = SignNanopub.loadKey(getKeyFile().getPath(), SignatureAlgorithm.RSA);	×
242	} catch (Exception ex) {	×
243	logger.error("Couldn't create key pair", ex);	×
244	}	×
245	}	×
246
247	/**
248	* Retrieves the user's IRI.
249	*
250	* @return The user's IRI, or null if not set.
251	*/
252	public IRI getUserIri() {
253	return userIri;	9✔
254	}
255
256	/**
257	* Retrieves the user's introduction nanopublications.
258	*
259	* @return A list of user's introduction nanopublications.
260	*/
261	public List<IntroNanopub> getUserIntroNanopubs() {
262	return User.getIntroNanopubs(userIri);	×
263	}
264
265	/**
266	* Counts the number of local introduction nanopublications.
267	*
268	* @return The count of local introduction nanopublications.
269	*/
270	public int getLocalIntroCount() {
271	if (localIntroCount == null) {	×
272	localIntroCount = 0;	×
273	for (IntroNanopub inp : getUserIntroNanopubs()) {	×
274	if (isIntroWithLocalKey(inp)) {	×
275	localIntroCount++;	×
276	localIntro = inp;	×
277	}
278	}	×
279	if (localIntroCount > 1) localIntro = null;	×
280	}
281	return localIntroCount;	×
282	}
283
284	/**
285	* Retrieves the local introduction nanopublication.
286	*
287	* @return The local introduction nanopublication, or null if not found.
288	*/
289	public IntroNanopub getLocalIntro() {
290	getLocalIntroCount();	×
291	return localIntro;	×
292	}
293
294	/**
295	* Checks if the given introduction nanopublication is associated with the local key.
296	*
297	* @param inp The introduction nanopublication.
298	* @return True if associated with the local key, false otherwise.
299	*/
300	public boolean isIntroWithLocalKey(IntroNanopub inp) {
301	IRI location = Utils.getLocation(inp);	×
302	NanopubSignatureElement el = Utils.getNanopubSignatureElement(inp);	×
303	String siteUrl = NanodashPreferences.get().getWebsiteUrl();	×
304	if (location != null && siteUrl != null) {	×
305	String l = location.stringValue();	×
306	// TODO: Solve the name change recognition in a better way:
307	if (!l.equals(siteUrl) && !l.replace("nanobench", "nanodash").equals(siteUrl)) return false;	×
308	}
309	if (!getPubkeyString().equals(el.getPublicKeyString())) return false;	×
310	for (KeyDeclaration kd : inp.getKeyDeclarations()) {	×
311	if (getPubkeyString().equals(kd.getPublicKeyString())) return true;	×
312	}	×
313	return false;	×
314	}
315
316	/**
317	* Sets the user's ORCID identifier.
318	*
319	* @param orcid The ORCID identifier.
320	*/
321	public void setOrcid(String orcid) {
322	if (!orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
323	throw new RuntimeException("Illegal ORCID identifier: " + orcid);	×
324	}
325	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
326	userDir = System.getProperty("user.home") + "/.nanopub/nanodash-users/" + orcid + "/";	×
327	File f = new File(userDir);	×
328	if (!f.exists()) f.mkdir();	×
329	} else {	×
330	try {
331	FileUtils.writeStringToFile(getOrcidFile(), orcid + "\n", StandardCharsets.UTF_8);	×
332	// Files.writeString(orcidFile.toPath(), orcid + "\n");
333	} catch (IOException ex) {	×
334	logger.error("Couldn't write ORCID file", ex);	×
335	}	×
336	}
337	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
338	loadProfileInfo();	×
339	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
340	}	×
341
342	/**
343	* Logs out the user and invalidates the session.
344	*/
345	public void logout() {
346	userIri = null;	×
347	invalidateNow();	×
348	}	×
349
350	/**
351	* Retrieves the user's introduction nanopublications as a map.
352	*
353	* @return A map of introduction nanopublications.
354	*/
355	public Map<IRI, IntroNanopub> getIntroNanopubs() {
356	return introNps;	×
357	}
358
359	// public void checkOrcidLink() {
360	// if (isOrcidLinked == null && userIri != null) {
361	// orcidLinkError = "";
362	// introExtractor = null;
363	// try {
364	// introExtractor = IntroNanopub.extract(userIri.stringValue(), null);
365	// if (introExtractor.getIntroNanopub() == null) {
366	// orcidLinkError = "ORCID account is not linked.";
367	// isOrcidLinked = false;
368	// } else {
369	// IntroNanopub inp = IntroNanopub.get(userIri.stringValue(), introExtractor);
370	// if (introNps != null && introNps.containsKey(inp.getNanopub().getUri())) {
371	// // TODO: also check whether introduction contains local key
372	// isOrcidLinked = true;
373	// } else {
374	// isOrcidLinked = false;
375	// orcidLinkError = "Error: ORCID is linked to another introduction nanopublication.";
376	// }
377	// }
378	// } catch (Exception ex) {
379	// logger.error("ORCID check failed");
380	// orcidLinkError = "ORCID check failed.";
381	// }
382	// }
383	// }
384	//
385	// public void resetOrcidLinked() {
386	// isOrcidLinked = null;
387	// }
388	//
389	// public boolean isOrcidLinked() {
390	// checkOrcidLink();
391	// return isOrcidLinked != null && isOrcidLinked == true;
392	// }
393	//
394	// public String getOrcidLinkError() {
395	// return orcidLinkError;
396	// }
397	//
398	// public String getOrcidName() {
399	// if (introExtractor == null \|\| introExtractor.getName() == null) return null;
400	// if (introExtractor.getName().trim().isEmpty()) return null;
401	// return introExtractor.getName();
402	// }
403
404	/**
405	* Retrieves the file for storing the user's ORCID identifier.
406	*
407	* @return The ORCID file.
408	*/
409	private File getOrcidFile() {
410	return new File(userDir + "orcid");	21✔
411	}
412
413	/**
414	* Retrieves the file for storing the user's private key.
415	*
416	* @return The key file.
417	*/
418	public File getKeyFile() {
419	return new File(userDir + "id_rsa");	×
420	}
421
422	/**
423	* Sets the time when the introduction was last published.
424	*/
425	public void setIntroPublishedNow() {
426	lastTimeIntroPublished = new Date();	×
427	}	×
428
429	/**
430	* Checks if the introduction has been published.
431	*
432	* @return True if the introduction has been published, false otherwise.
433	*/
434	public boolean hasIntroPublished() {
435	return lastTimeIntroPublished != null;	×
436	}
437
438	/**
439	* Calculates the time since the last introduction was published.
440	*
441	* @return The time in milliseconds since the last introduction was published, or Long.MAX_VALUE if it has never been published.
442	*/
443	public long getTimeSinceLastIntroPublished() {
444	if (lastTimeIntroPublished == null) return Long.MAX_VALUE;	×
445	return new Date().getTime() - lastTimeIntroPublished.getTime();	×
446	}
447
448	/**
449	* Sets the view mode for displaying nanopublication results.
450	*
451	* @param viewMode The desired view mode (e.g., GRID or LIST).
452	*/
453	public void setNanopubResultsViewMode(NanopubResults.ViewMode viewMode) {
454	this.nanopubResultsViewMode = viewMode;	×
455	}	×
456
457	/**
458	* Retrieves the current view mode for displaying nanopublication results.
459	*
460	* @return The current view mode.
461	*/
462	public NanopubResults.ViewMode getNanopubResultsViewMode() {
463	return this.nanopubResultsViewMode;	×
464	}
465
466	// --- Preview nanopub support ---
467
468	public static class PreviewNanopub implements Serializable {
469	private final Nanopub nanopub;
470	private final PageParameters pageParams;
471	private final Class<? extends WebPage> confirmPageClass;
472	private final boolean consentChecked;
473	private final String formObj;
474
475	public PreviewNanopub(Nanopub nanopub, PageParameters pageParams, Class<? extends WebPage> confirmPageClass, boolean consentChecked, String formObj) {	×
476	this.nanopub = nanopub;	×
477	this.pageParams = pageParams;	×
478	this.confirmPageClass = confirmPageClass;	×
479	this.consentChecked = consentChecked;	×
480	this.formObj = formObj;	×
481	}	×
482
483	public Nanopub getNanopub() { return nanopub; }	×
484	public PageParameters getPageParams() { return pageParams; }	×
485	public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }	×
486	public boolean isConsentChecked() { return consentChecked; }	×
487	public String getFormObj() { return formObj; }	×
488	}
489
490	private ConcurrentMap<String, PreviewNanopub> previewMap = new ConcurrentHashMap<>();	15✔
491
492	public void setPreviewNanopub(String id, PreviewNanopub preview) {
493	previewMap.put(id, preview);	×
494	}	×
495
496	public PreviewNanopub getPreviewNanopub(String id) {
497	return previewMap.get(id);	×
498	}
499
500	public PreviewNanopub removePreviewNanopub(String id) {
501	return previewMap.remove(id);	×
502	}
503
504	}

knowledgepixels / nanodash / 24785731352

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