23133101585

Committed 16 Mar 2026 07:45AM UTC coverage: 15.984% (+0.2%) from 15.811%

Build # 23133101585

Build Type

Pull #402

github

Committed by

web-flow

Commit Message

Merge bd8288c47 into 39c6ac11c

Pull Request Pull Request #402: Fix unbounded memory growth and resource exhaustion

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14.03

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.Collections;
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;

    // 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 static final int MAX_FORMS = 20;
    private final Map<String, PublishForm> formMap = Collections.synchronizedMap(new LinkedHashMap<>(16, 0.75f, true) {
        @Override
        protected boolean removeEldestEntry(Map.Entry<String, PublishForm> eldest) {
            return size() > MAX_FORMS;
        }
    });

    /**
     * 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);
    }

    /**
     * Removes the form object associated with the given ID.
     *
     * @param formObjId The ID of the form object to remove.
     */
    public void removeForm(String formObjId) {
        formMap.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;

        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.Collections;
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();	×
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	// We should store here some sort of form model and not the forms themselves, but I couldn't figure
90	// how to do it, so doing it like this for the moment...
91	private static final int MAX_FORMS = 20;
92	private final Map<String, PublishForm> formMap = Collections.synchronizedMap(new LinkedHashMap<>(16, 0.75f, true) {	57✔
93	@Override
94	protected boolean removeEldestEntry(Map.Entry<String, PublishForm> eldest) {
95	return size() > MAX_FORMS;	×
96	}
97	});
98
99	/**
100	* Associates a form object with a specific ID.
101	*
102	* @param formObjId The ID of the form object.
103	* @param formObj The form object to associate.
104	*/
105	public void setForm(String formObjId, PublishForm formObj) {
106	formMap.put(formObjId, formObj);	×
107	}	×
108
109	/**
110	* Checks if a form object with the given ID exists.
111	*
112	* @param formObjId The ID of the form object.
113	* @return True if the form object exists, false otherwise.
114	*/
115	public boolean hasForm(String formObjId) {
116	return formMap.containsKey(formObjId);	×
117	}
118
119	/**
120	* Retrieves the form object associated with the given ID.
121	*
122	* @param formObjId The ID of the form object.
123	* @return The associated form object, or null if not found.
124	*/
125	public PublishForm getForm(String formObjId) {
126	return formMap.get(formObjId);	×
127	}
128
129	/**
130	* Removes the form object associated with the given ID.
131	*
132	* @param formObjId The ID of the form object to remove.
133	*/
134	public void removeForm(String formObjId) {
135	formMap.remove(formObjId);	×
136	}	×
137
138	/**
139	* Loads profile information for the user.
140	* Initializes user-related data such as keys and introductions.
141	*/
142	public void loadProfileInfo() {
143	localIntroCount = null;	9✔
144	localIntro = null;	9✔
145	NanodashPreferences prefs = NanodashPreferences.get();	6✔
146	if (prefs.isOrcidLoginMode()) {	9!
147	File usersDir = new File(System.getProperty("user.home") + "/.nanopub/nanodash-users/");	×
148	if (!usersDir.exists()) usersDir.mkdir();	×
149	}
150	if (userIri == null && !prefs.isReadOnlyMode() && !prefs.isOrcidLoginMode()) {	27!
151	if (getOrcidFile().exists()) {	12!
152	try {
153	String orcid = FileUtils.readFileToString(getOrcidFile(), StandardCharsets.UTF_8).trim();	×
154	//String orcid = Files.readString(orcidFile.toPath(), StandardCharsets.UTF_8).trim();
155	if (orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
156	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
157	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
158	}
159	} catch (IOException ex) {	×
160	logger.error("Couldn't read ORCID file", ex);	×
161	}	×
162	}
163	}
164	if (userIri != null && keyPair == null) {	9!
165	File keyFile = getKeyFile();	×
166	if (keyFile.exists()) {	×
167	try {
168	keyPair = SignNanopub.loadKey(keyFile.getPath(), SignatureAlgorithm.RSA);	×
169	} catch (Exception ex) {	×
170	logger.error("Couldn't load key pair", ex);	×
171	}	×
172	} else {
173	// Automatically generate new keys
174	makeKeys();	×
175	}
176	}
177	if (userIri != null && keyPair != null && introNps == null) {	9!
178	introNps = new ConcurrentHashMap<>(User.getIntroNanopubs(getPubkeyString()));	×
179	}
180	// checkOrcidLink();
181	}	3✔
182
183	/**
184	* Checks if the user's profile is complete.
185	*
186	* @return True if the profile is complete, false otherwise.
187	*/
188	public boolean isProfileComplete() {
189	return userIri != null && keyPair != null && introNps != null;	×
190	}
191
192	/**
193	* Redirects the user to the login page if their profile is incomplete.
194	*
195	* @param path The path to redirect to after login.
196	* @param parameters The page parameters for the redirect.
197	*/
198	public void redirectToLoginIfNeeded(String path, PageParameters parameters) {
199	String loginUrl = getLoginUrl(path, parameters);	×
200	if (loginUrl == null) return;	×
201	throw new RedirectToUrlException(loginUrl);	×
202	}
203
204	/**
205	* Retrieves the login URL for the user.
206	*
207	* @param path The path to redirect to after login.
208	* @param parameters The page parameters for the redirect.
209	* @return The login URL, or null if the user is already logged in.
210	*/
211	public String getLoginUrl(String path, PageParameters parameters) {
212	if (isProfileComplete()) return null;	×
213	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
214	return OrcidLoginPage.getOrcidLoginUrl(path, parameters);	×
215	} else {
216	return ProfilePage.MOUNT_PATH;	×
217	}
218	}
219
220	/**
221	* Retrieves the public key as a Base64-encoded string.
222	*
223	* @return The public key string, or null if the key pair is not set.
224	*/
225	public String getPubkeyString() {
226	if (keyPair == null) return null;	×
227	return DatatypeConverter.printBase64Binary(keyPair.getPublic().getEncoded()).replaceAll("\\s", "");	×
228	}
229
230	/**
231	* Retrieves the public key hash for the user.
232	*
233	* @return The SHA-256 hash of the public key, or null if the public key is not set.
234	*/
235	public String getPubkeyhash() {
236	String pubkey = getPubkeyString();	×
237	if (pubkey == null) return null;	×
238	return Utils.createSha256HexHash(pubkey);	×
239	}
240
241	/**
242	* Checks if the user's public key is approved.
243	*
244	* @return True if the public key is approved, false otherwise.
245	*/
246	public boolean isPubkeyApproved() {
247	if (keyPair == null \|\| userIri == null) return false;	×
248	return User.isApprovedPubkeyhashForUser(getPubkeyhash(), userIri);	×
249	}
250
251	/**
252	* Retrieves the user's key pair.
253	*
254	* @return The key pair.
255	*/
256	public KeyPair getKeyPair() {
257	return keyPair;	×
258	}
259
260	/**
261	* Generates a new key pair for the user.
262	*/
263	public void makeKeys() {
264	try {
265	MakeKeys.make(getKeyFile().getAbsolutePath().replaceFirst("_rsa$", ""), SignatureAlgorithm.RSA);	×
266	keyPair = SignNanopub.loadKey(getKeyFile().getPath(), SignatureAlgorithm.RSA);	×
267	} catch (Exception ex) {	×
268	logger.error("Couldn't create key pair", ex);	×
269	}	×
270	}	×
271
272	/**
273	* Retrieves the user's IRI.
274	*
275	* @return The user's IRI, or null if not set.
276	*/
277	public IRI getUserIri() {
278	return userIri;	×
279	}
280
281	/**
282	* Retrieves the user's introduction nanopublications.
283	*
284	* @return A list of user's introduction nanopublications.
285	*/
286	public List<IntroNanopub> getUserIntroNanopubs() {
287	return User.getIntroNanopubs(userIri);	×
288	}
289
290	/**
291	* Counts the number of local introduction nanopublications.
292	*
293	* @return The count of local introduction nanopublications.
294	*/
295	public int getLocalIntroCount() {
296	if (localIntroCount == null) {	×
297	localIntroCount = 0;	×
298	for (IntroNanopub inp : getUserIntroNanopubs()) {	×
299	if (isIntroWithLocalKey(inp)) {	×
300	localIntroCount++;	×
301	localIntro = inp;	×
302	}
303	}	×
304	if (localIntroCount > 1) localIntro = null;	×
305	}
306	return localIntroCount;	×
307	}
308
309	/**
310	* Retrieves the local introduction nanopublication.
311	*
312	* @return The local introduction nanopublication, or null if not found.
313	*/
314	public IntroNanopub getLocalIntro() {
315	getLocalIntroCount();	×
316	return localIntro;	×
317	}
318
319	/**
320	* Checks if the given introduction nanopublication is associated with the local key.
321	*
322	* @param inp The introduction nanopublication.
323	* @return True if associated with the local key, false otherwise.
324	*/
325	public boolean isIntroWithLocalKey(IntroNanopub inp) {
326	IRI location = Utils.getLocation(inp);	×
327	NanopubSignatureElement el = Utils.getNanopubSignatureElement(inp);	×
328	String siteUrl = NanodashPreferences.get().getWebsiteUrl();	×
329	if (location != null && siteUrl != null) {	×
330	String l = location.stringValue();	×
331	// TODO: Solve the name change recognition in a better way:
332	if (!l.equals(siteUrl) && !l.replace("nanobench", "nanodash").equals(siteUrl)) return false;	×
333	}
334	if (!getPubkeyString().equals(el.getPublicKeyString())) return false;	×
335	for (KeyDeclaration kd : inp.getKeyDeclarations()) {	×
336	if (getPubkeyString().equals(kd.getPublicKeyString())) return true;	×
337	}	×
338	return false;	×
339	}
340
341	/**
342	* Sets the user's ORCID identifier.
343	*
344	* @param orcid The ORCID identifier.
345	*/
346	public void setOrcid(String orcid) {
347	if (!orcid.matches(ProfilePage.ORCID_PATTERN)) {	×
348	throw new RuntimeException("Illegal ORCID identifier: " + orcid);	×
349	}
350	if (NanodashPreferences.get().isOrcidLoginMode()) {	×
351	userDir = System.getProperty("user.home") + "/.nanopub/nanodash-users/" + orcid + "/";	×
352	File f = new File(userDir);	×
353	if (!f.exists()) f.mkdir();	×
354	} else {	×
355	try {
356	FileUtils.writeStringToFile(getOrcidFile(), orcid + "\n", StandardCharsets.UTF_8);	×
357	// Files.writeString(orcidFile.toPath(), orcid + "\n");
358	} catch (IOException ex) {	×
359	logger.error("Couldn't write ORCID file", ex);	×
360	}	×
361	}
362	userIri = vf.createIRI("https://orcid.org/" + orcid);	×
363	loadProfileInfo();	×
364	if (httpSession != null) httpSession.setMaxInactiveInterval(24 * 60 * 60); // 24h	×
365	}	×
366
367	/**
368	* Logs out the user and invalidates the session.
369	*/
370	public void logout() {
371	userIri = null;	×
372	invalidateNow();	×
373	}	×
374
375	/**
376	* Retrieves the user's introduction nanopublications as a map.
377	*
378	* @return A map of introduction nanopublications.
379	*/
380	public Map<IRI, IntroNanopub> getIntroNanopubs() {
381	return introNps;	×
382	}
383
384	// public void checkOrcidLink() {
385	// if (isOrcidLinked == null && userIri != null) {
386	// orcidLinkError = "";
387	// introExtractor = null;
388	// try {
389	// introExtractor = IntroNanopub.extract(userIri.stringValue(), null);
390	// if (introExtractor.getIntroNanopub() == null) {
391	// orcidLinkError = "ORCID account is not linked.";
392	// isOrcidLinked = false;
393	// } else {
394	// IntroNanopub inp = IntroNanopub.get(userIri.stringValue(), introExtractor);
395	// if (introNps != null && introNps.containsKey(inp.getNanopub().getUri())) {
396	// // TODO: also check whether introduction contains local key
397	// isOrcidLinked = true;
398	// } else {
399	// isOrcidLinked = false;
400	// orcidLinkError = "Error: ORCID is linked to another introduction nanopublication.";
401	// }
402	// }
403	// } catch (Exception ex) {
404	// logger.error("ORCID check failed");
405	// orcidLinkError = "ORCID check failed.";
406	// }
407	// }
408	// }
409	//
410	// public void resetOrcidLinked() {
411	// isOrcidLinked = null;
412	// }
413	//
414	// public boolean isOrcidLinked() {
415	// checkOrcidLink();
416	// return isOrcidLinked != null && isOrcidLinked == true;
417	// }
418	//
419	// public String getOrcidLinkError() {
420	// return orcidLinkError;
421	// }
422	//
423	// public String getOrcidName() {
424	// if (introExtractor == null \|\| introExtractor.getName() == null) return null;
425	// if (introExtractor.getName().trim().isEmpty()) return null;
426	// return introExtractor.getName();
427	// }
428
429	/**
430	* Retrieves the file for storing the user's ORCID identifier.
431	*
432	* @return The ORCID file.
433	*/
434	private File getOrcidFile() {
435	return new File(userDir + "orcid");	21✔
436	}
437
438	/**
439	* Retrieves the file for storing the user's private key.
440	*
441	* @return The key file.
442	*/
443	public File getKeyFile() {
444	return new File(userDir + "id_rsa");	×
445	}
446
447	/**
448	* Sets the time when the introduction was last published.
449	*/
450	public void setIntroPublishedNow() {
451	lastTimeIntroPublished = new Date();	×
452	}	×
453
454	/**
455	* Checks if the introduction has been published.
456	*
457	* @return True if the introduction has been published, false otherwise.
458	*/
459	public boolean hasIntroPublished() {
460	return lastTimeIntroPublished != null;	×
461	}
462
463	/**
464	* Calculates the time since the last introduction was published.
465	*
466	* @return The time in milliseconds since the last introduction was published, or Long.MAX_VALUE if it has never been published.
467	*/
468	public long getTimeSinceLastIntroPublished() {
469	if (lastTimeIntroPublished == null) return Long.MAX_VALUE;	×
470	return new Date().getTime() - lastTimeIntroPublished.getTime();	×
471	}
472
473	/**
474	* Sets the view mode for displaying nanopublication results.
475	*
476	* @param viewMode The desired view mode (e.g., GRID or LIST).
477	*/
478	public void setNanopubResultsViewMode(NanopubResults.ViewMode viewMode) {
479	this.nanopubResultsViewMode = viewMode;	×
480	}	×
481
482	/**
483	* Retrieves the current view mode for displaying nanopublication results.
484	*
485	* @return The current view mode.
486	*/
487	public NanopubResults.ViewMode getNanopubResultsViewMode() {
488	return this.nanopubResultsViewMode;	×
489	}
490
491	// --- Preview nanopub support ---
492
493	public static class PreviewNanopub implements Serializable {
494	private final Nanopub nanopub;
495	private final PageParameters pageParams;
496	private final Class<? extends WebPage> confirmPageClass;
497	private final boolean consentChecked;
498
499	public PreviewNanopub(Nanopub nanopub, PageParameters pageParams, Class<? extends WebPage> confirmPageClass, boolean consentChecked) {	×
500	this.nanopub = nanopub;	×
501	this.pageParams = pageParams;	×
502	this.confirmPageClass = confirmPageClass;	×
503	this.consentChecked = consentChecked;	×
504	}	×
505
506	public Nanopub getNanopub() { return nanopub; }	×
507	public PageParameters getPageParams() { return pageParams; }	×
508	public Class<? extends WebPage> getConfirmPageClass() { return confirmPageClass; }	×
509	public boolean isConsentChecked() { return consentChecked; }	×
510	}
511
512	private ConcurrentMap<String, PreviewNanopub> previewMap = new ConcurrentHashMap<>();	15✔
513
514	public void setPreviewNanopub(String id, PreviewNanopub preview) {
515	previewMap.put(id, preview);	×
516	}	×
517
518	public PreviewNanopub getPreviewNanopub(String id) {
519	return previewMap.get(id);	×
520	}
521
522	public PreviewNanopub removePreviewNanopub(String id) {
523	return previewMap.remove(id);	×
524	}
525
526	}

knowledgepixels / nanodash / 23133101585

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