22618039211

Committed 03 Mar 2026 10:05AM UTC coverage: 16.058% (+0.2%) from 15.884%

Build # 22618039211

Build Type

Pull #365

github

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web-flow

Commit Message

Merge 1e7e700f0 into a8c4b4a77

Pull Request Pull Request #365: Refactor of `ResourceWithProfile` and related classes

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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.component.PublishForm;
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.Session;
import org.apache.wicket.protocol.http.WebSession;
import org.apache.wicket.request.Request;
import org.apache.wicket.request.flow.RedirectToUrlException;
import org.apache.wicket.request.mapper.parameter.PageParameters;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.nanopub.extra.security.*;
import org.nanopub.extra.setting.IntroNanopub;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

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

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

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

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

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

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

    private static ValueFactory vf = SimpleValueFactory.getInstance();

//        private IntroExtractor introExtractor;

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

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

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

    private Date lastTimeIntroPublished = null;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    // --- Preview nanopub support ---

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

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

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

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

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

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

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

}

1	package com.knowledgepixels.nanodash;
2
3	import com.knowledgepixels.nanodash.component.NanopubResults;
4	import com.knowledgepixels.nanodash.component.PublishForm;
5	import com.knowledgepixels.nanodash.domain.User;
6	import com.knowledgepixels.nanodash.page.OrcidLoginPage;
7	import com.knowledgepixels.nanodash.page.ProfilePage;
8	import jakarta.servlet.http.HttpServletRequest;
9	import jakarta.servlet.http.HttpSession;
10	import jakarta.xml.bind.DatatypeConverter;
11	import org.apache.commons.io.FileUtils;
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();	×
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	// We should store here some sort of form model and not the forms themselves, but I couldn't figure
88	// how to do it, so doing it like this for the moment...
89	private ConcurrentMap<String, PublishForm> formMap = new ConcurrentHashMap<>();	15✔
90
91	/**
92	* Associates a form object with a specific ID.
93	*
94	* @param formObjId The ID of the form object.
95	* @param formObj The form object to associate.
96	*/
97	public void setForm(String formObjId, PublishForm formObj) {
98	formMap.put(formObjId, formObj);	×
99	}	×
100
101	/**
102	* Checks if a form object with the given ID exists.
103	*
104	* @param formObjId The ID of the form object.
105	* @return True if the form object exists, false otherwise.
106	*/
107	public boolean hasForm(String formObjId) {
108	return formMap.containsKey(formObjId);	×
109	}
110
111	/**
112	* Retrieves the form object associated with the given ID.
113	*
114	* @param formObjId The ID of the form object.
115	* @return The associated form object, or null if not found.
116	*/
117	public PublishForm getForm(String formObjId) {
118	return formMap.get(formObjId);	×
119	}
120
121	/**
122	* Loads profile information for the user.
123	* Initializes user-related data such as keys and introductions.
124	*/
125	public void loadProfileInfo() {
126	localIntroCount = null;	9✔
127	localIntro = null;	9✔
128	NanodashPreferences prefs = NanodashPreferences.get();	6✔
129	if (prefs.isOrcidLoginMode()) {	9!
130	File usersDir = new File(System.getProperty("user.home") + "/.nanopub/nanodash-users/");	×
131	if (!usersDir.exists()) usersDir.mkdir();	×
132	}
133	if (userIri == null && !prefs.isReadOnlyMode() && !prefs.isOrcidLoginMode()) {	27!
134	if (getOrcidFile().exists()) {	12!
135	try {
136	String orcid = FileUtils.readFileToString(getOrcidFile(), StandardCharsets.UTF_8).trim();	×
137	//String orcid = Files.readString(orcidFile.toPath(), StandardCharsets.UTF_8).trim();
138	if (orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
139	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
140	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
141	}
142	} catch (IOException ex) {	×
143	logger.error("Couldn't read ORCID file", ex);	×
144	}	×
145	}
146	}
147	if (userIri != null && keyPair == null) {	9!
148	File keyFile = getKeyFile();	×
149	if (keyFile.exists()) {	×
150	try {
151	keyPair = SignNanopub.loadKey(keyFile.getPath(), SignatureAlgorithm.RSA);	×
152	} catch (Exception ex) {	×
153	logger.error("Couldn't load key pair", ex);	×
154	}	×
155	} else {
156	// Automatically generate new keys
157	makeKeys();	×
158	}
159	}
160	if (userIri != null && keyPair != null && introNps == null) {	9!
161	introNps = new ConcurrentHashMap<>(User.getIntroNanopubs(getPubkeyString()));	×
162	}
163	// checkOrcidLink();
164	}	3✔
165
166	/**
167	* Checks if the user's profile is complete.
168	*
169	* @return True if the profile is complete, false otherwise.
170	*/
171	public boolean isProfileComplete() {
172	return userIri != null && keyPair != null && introNps != null;	×
173	}
174
175	/**
176	* Redirects the user to the login page if their profile is incomplete.
177	*
178	* @param path The path to redirect to after login.
179	* @param parameters The page parameters for the redirect.
180	*/
181	public void redirectToLoginIfNeeded(String path, PageParameters parameters) {
182	String loginUrl = getLoginUrl(path, parameters);	×
183	if (loginUrl == null) return;	×
184	throw new RedirectToUrlException(loginUrl);	×
185	}
186
187	/**
188	* Retrieves the login URL for the user.
189	*
190	* @param path The path to redirect to after login.
191	* @param parameters The page parameters for the redirect.
192	* @return The login URL, or null if the user is already logged in.
193	*/
194	public String getLoginUrl(String path, PageParameters parameters) {
195	if (isProfileComplete()) return null;	×
196	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
197	return OrcidLoginPage.getOrcidLoginUrl(path, parameters);	×
198	} else {
199	return ProfilePage.MOUNT_PATH;	×
200	}
201	}
202
203	/**
204	* Retrieves the public key as a Base64-encoded string.
205	*
206	* @return The public key string, or null if the key pair is not set.
207	*/
208	public String getPubkeyString() {
209	if (keyPair == null) return null;	×
210	return DatatypeConverter.printBase64Binary(keyPair.getPublic().getEncoded()).replaceAll("\\s", "");	×
211	}
212
213	/**
214	* Retrieves the public key hash for the user.
215	*
216	* @return The SHA-256 hash of the public key, or null if the public key is not set.
217	*/
218	public String getPubkeyhash() {
219	String pubkey = getPubkeyString();	×
220	if (pubkey == null) return null;	×
221	return Utils.createSha256HexHash(pubkey);	×
222	}
223
224	/**
225	* Checks if the user's public key is approved.
226	*
227	* @return True if the public key is approved, false otherwise.
228	*/
229	public boolean isPubkeyApproved() {
230	if (keyPair == null \|\| userIri == null) return false;	×
231	return User.isApprovedPubkeyhashForUser(getPubkeyhash(), userIri);	×
232	}
233
234	/**
235	* Retrieves the user's key pair.
236	*
237	* @return The key pair.
238	*/
239	public KeyPair getKeyPair() {
240	return keyPair;	×
241	}
242
243	/**
244	* Generates a new key pair for the user.
245	*/
246	public void makeKeys() {
247	try {
248	MakeKeys.make(getKeyFile().getAbsolutePath().replaceFirst("_rsa$", ""), SignatureAlgorithm.RSA);	×
249	keyPair = SignNanopub.loadKey(getKeyFile().getPath(), SignatureAlgorithm.RSA);	×
250	} catch (Exception ex) {	×
251	logger.error("Couldn't create key pair", ex);	×
252	}	×
253	}	×
254
255	/**
256	* Retrieves the user's IRI.
257	*
258	* @return The user's IRI, or null if not set.
259	*/
260	public IRI getUserIri() {
261	return userIri;	×
262	}
263
264	/**
265	* Retrieves the user's introduction nanopublications.
266	*
267	* @return A list of user's introduction nanopublications.
268	*/
269	public List<IntroNanopub> getUserIntroNanopubs() {
270	return User.getIntroNanopubs(userIri);	×
271	}
272
273	/**
274	* Counts the number of local introduction nanopublications.
275	*
276	* @return The count of local introduction nanopublications.
277	*/
278	public int getLocalIntroCount() {
279	if (localIntroCount == null) {	×
280	localIntroCount = 0;	×
281	for (IntroNanopub inp : getUserIntroNanopubs()) {	×
282	if (isIntroWithLocalKey(inp)) {	×
283	localIntroCount++;	×
284	localIntro = inp;	×
285	}
286	}	×
287	if (localIntroCount > 1) localIntro = null;	×
288	}
289	return localIntroCount;	×
290	}
291
292	/**
293	* Retrieves the local introduction nanopublication.
294	*
295	* @return The local introduction nanopublication, or null if not found.
296	*/
297	public IntroNanopub getLocalIntro() {
298	getLocalIntroCount();	×
299	return localIntro;	×
300	}
301
302	/**
303	* Checks if the given introduction nanopublication is associated with the local key.
304	*
305	* @param inp The introduction nanopublication.
306	* @return True if associated with the local key, false otherwise.
307	*/
308	public boolean isIntroWithLocalKey(IntroNanopub inp) {
309	IRI location = Utils.getLocation(inp);	×
310	NanopubSignatureElement el = Utils.getNanopubSignatureElement(inp);	×
311	String siteUrl = NanodashPreferences.get().getWebsiteUrl();	×
312	if (location != null && siteUrl != null) {	×
313	String l = location.stringValue();	×
314	// TODO: Solve the name change recognition in a better way:
315	if (!l.equals(siteUrl) && !l.replace("nanobench", "nanodash").equals(siteUrl)) return false;	×
316	}
317	if (!getPubkeyString().equals(el.getPublicKeyString())) return false;	×
318	for (KeyDeclaration kd : inp.getKeyDeclarations()) {	×
319	if (getPubkeyString().equals(kd.getPublicKeyString())) return true;	×
320	}	×
321	return false;	×
322	}
323
324	/**
325	* Sets the user's ORCID identifier.
326	*
327	* @param orcid The ORCID identifier.
328	*/
329	public void setOrcid(String orcid) {
330	if (!orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
331	throw new RuntimeException("Illegal ORCID identifier: " + orcid);	×
332	}
333	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
334	userDir = System.getProperty("user.home") + "/.nanopub/nanodash-users/" + orcid + "/";	×
335	File f = new File(userDir);	×
336	if (!f.exists()) f.mkdir();	×
337	} else {	×
338	try {
339	FileUtils.writeStringToFile(getOrcidFile(), orcid + "\n", StandardCharsets.UTF_8);	×
340	// Files.writeString(orcidFile.toPath(), orcid + "\n");
341	} catch (IOException ex) {	×
342	logger.error("Couldn't write ORCID file", ex);	×
343	}	×
344	}
345	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
346	loadProfileInfo();	×
347	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
348	}	×
349
350	/**
351	* Logs out the user and invalidates the session.
352	*/
353	public void logout() {
354	userIri = null;	×
355	invalidateNow();	×
356	}	×
357
358	/**
359	* Retrieves the user's introduction nanopublications as a map.
360	*
361	* @return A map of introduction nanopublications.
362	*/
363	public Map<IRI, IntroNanopub> getIntroNanopubs() {
364	return introNps;	×
365	}
366
367	// public void checkOrcidLink() {
368	// if (isOrcidLinked == null && userIri != null) {
369	// orcidLinkError = "";
370	// introExtractor = null;
371	// try {
372	// introExtractor = IntroNanopub.extract(userIri.stringValue(), null);
373	// if (introExtractor.getIntroNanopub() == null) {
374	// orcidLinkError = "ORCID account is not linked.";
375	// isOrcidLinked = false;
376	// } else {
377	// IntroNanopub inp = IntroNanopub.get(userIri.stringValue(), introExtractor);
378	// if (introNps != null && introNps.containsKey(inp.getNanopub().getUri())) {
379	// // TODO: also check whether introduction contains local key
380	// isOrcidLinked = true;
381	// } else {
382	// isOrcidLinked = false;
383	// orcidLinkError = "Error: ORCID is linked to another introduction nanopublication.";
384	// }
385	// }
386	// } catch (Exception ex) {
387	// logger.error("ORCID check failed");
388	// orcidLinkError = "ORCID check failed.";
389	// }
390	// }
391	// }
392	//
393	// public void resetOrcidLinked() {
394	// isOrcidLinked = null;
395	// }
396	//
397	// public boolean isOrcidLinked() {
398	// checkOrcidLink();
399	// return isOrcidLinked != null && isOrcidLinked == true;
400	// }
401	//
402	// public String getOrcidLinkError() {
403	// return orcidLinkError;
404	// }
405	//
406	// public String getOrcidName() {
407	// if (introExtractor == null \|\| introExtractor.getName() == null) return null;
408	// if (introExtractor.getName().trim().isEmpty()) return null;
409	// return introExtractor.getName();
410	// }
411
412	/**
413	* Retrieves the file for storing the user's ORCID identifier.
414	*
415	* @return The ORCID file.
416	*/
417	private File getOrcidFile() {
418	return new File(userDir + "orcid");	21✔
419	}
420
421	/**
422	* Retrieves the file for storing the user's private key.
423	*
424	* @return The key file.
425	*/
426	public File getKeyFile() {
427	return new File(userDir + "id_rsa");	×
428	}
429
430	/**
431	* Sets the time when the introduction was last published.
432	*/
433	public void setIntroPublishedNow() {
434	lastTimeIntroPublished = new Date();	×
435	}	×
436
437	/**
438	* Checks if the introduction has been published.
439	*
440	* @return True if the introduction has been published, false otherwise.
441	*/
442	public boolean hasIntroPublished() {
443	return lastTimeIntroPublished != null;	×
444	}
445
446	/**
447	* Calculates the time since the last introduction was published.
448	*
449	* @return The time in milliseconds since the last introduction was published, or Long.MAX_VALUE if it has never been published.
450	*/
451	public long getTimeSinceLastIntroPublished() {
452	if (lastTimeIntroPublished == null) return Long.MAX_VALUE;	×
453	return new Date().getTime() - lastTimeIntroPublished.getTime();	×
454	}
455
456	/**
457	* Sets the view mode for displaying nanopublication results.
458	*
459	* @param viewMode The desired view mode (e.g., GRID or LIST).
460	*/
461	public void setNanopubResultsViewMode(NanopubResults.ViewMode viewMode) {
462	this.nanopubResultsViewMode = viewMode;	×
463	}	×
464
465	/**
466	* Retrieves the current view mode for displaying nanopublication results.
467	*
468	* @return The current view mode.
469	*/
470	public NanopubResults.ViewMode getNanopubResultsViewMode() {
471	return this.nanopubResultsViewMode;	×
472	}
473
474	// --- Preview nanopub support ---
475
476	public static class PreviewNanopub implements Serializable {
477	private final Nanopub nanopub;
478	private final PageParameters pageParams;
479	private final Class<? extends WebPage> confirmPageClass;
480	private final boolean consentChecked;
481
482	public PreviewNanopub(Nanopub nanopub, PageParameters pageParams, Class<? extends WebPage> confirmPageClass, boolean consentChecked) {	×
483	this.nanopub = nanopub;	×
484	this.pageParams = pageParams;	×
485	this.confirmPageClass = confirmPageClass;	×
486	this.consentChecked = consentChecked;	×
487	}	×
488
489	public Nanopub getNanopub() { return nanopub; }	×
490	public PageParameters getPageParams() { return pageParams; }	×
491	public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }	×
492	public boolean isConsentChecked() { return consentChecked; }	×
493	}
494
495	private ConcurrentMap<String, PreviewNanopub> previewMap = new ConcurrentHashMap<>();	15✔
496
497	public void setPreviewNanopub(String id, PreviewNanopub preview) {
498	previewMap.put(id, preview);	×
499	}	×
500
501	public PreviewNanopub getPreviewNanopub(String id) {
502	return previewMap.get(id);	×
503	}
504
505	public PreviewNanopub removePreviewNanopub(String id) {
506	return previewMap.remove(id);	×
507	}
508
509	}

knowledgepixels / nanodash / 22618039211

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