Sanitize URLs in file fields to handle invalid pipe characters ('|')

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -1,10 +1,10 @@
 package org.jabref.gui.entryeditor.citationrelationtab.semanticscholar;
 
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.util.List;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.fetcher.CustomizableKeyFetcher;
@@ -38,7 +38,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
 
         URL citationsUrl;
         try {
-            citationsUrl = URI.create(getAPIUrl("citations", entry)).toURL();
+            citationsUrl = URLUtil.create(getAPIUrl("citations", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }
@@ -62,7 +62,7 @@ public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
 
         URL referencesUrl;
         try {
-            referencesUrl = URI.create(getAPIUrl("references", entry)).toURL();
+            referencesUrl = URLUtil.create(getAPIUrl("references", entry));
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java

@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -242,7 +241,7 @@ private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
 
     public boolean downloadFile(String urlText) {
         try {
-            URL url = URI.create(urlText).toURL();
+            URL url = URLUtil.create(urlText);
             addFromURLAndDownload(url);
             return true;
         } catch (MalformedURLException exception) {

src/main/java/org/jabref/gui/fieldeditors/URLUtil.java

@@ -2,6 +2,7 @@
 
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
@@ -22,10 +23,9 @@ private URLUtil() {
 
     /**
      * Cleans URLs returned by Google search.
-     *
      * <example>
-     *  If you copy links from search results from Google, all links will be enriched with search meta data, e.g.
-     *  https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&&url=http%3A%2F%2Fwww.inrg.csie.ntu.edu.tw%2Falgorithm2014%2Fhomework%2FWagner-74.pdf&ei=DifeVYHkDYWqU5W0j6gD&usg=AFQjCNFl638rl5KVta1jIMWLyb4CPSZidg&sig2=0hSSMw9XZXL3HJWwEcJtOg
+     * If you copy links from search results from Google, all links will be enriched with search meta data, e.g.
+     * https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&&url=http%3A%2F%2Fwww.inrg.csie.ntu.edu.tw%2Falgorithm2014%2Fhomework%2FWagner-74.pdf&ei=DifeVYHkDYWqU5W0j6gD&usg=AFQjCNFl638rl5KVta1jIMWLyb4CPSZidg&sig2=0hSSMw9XZXL3HJWwEcJtOg
      * </example>
      *
      * @param url the Google search URL string
@@ -39,7 +39,7 @@ public static String cleanGoogleSearchURL(String url) {
         }
         // Extract destination URL
         try {
-            URL searchURL = URI.create(url).toURL();
+            URL searchURL = URLUtil.create(url);
             // URL parameters
             String query = searchURL.getQuery();
             // no parameters
@@ -77,7 +77,7 @@ public static String cleanGoogleSearchURL(String url) {
      */
     public static boolean isURL(String url) {
         try {
-            URI.create(url).toURL();
+            URLUtil.create(url);
             return true;
         } catch (MalformedURLException | IllegalArgumentException e) {
             return false;
@@ -96,7 +96,7 @@ public static Optional<String> getSuffix(final String link, ExternalApplications
         String strippedLink = link;
         try {
             // Try to strip the query string, if any, to get the correct suffix:
-            URL url = URI.create(link).toURL();
+            URL url = URLUtil.create(link);
             if ((url.getQuery() != null) && (url.getQuery().length() < (link.length() - 1))) {
                 strippedLink = link.substring(0, link.length() - url.getQuery().length() - 1);
             }
@@ -138,4 +138,37 @@ public static Optional<String> getSuffix(final String link, ExternalApplications
             return Optional.ofNullable(suffix);
         }
     }
+
+    /**
+     * Creates a {@link URL} object from the given string URL.
+     *
+     * @param url the URL string to be converted into a {@link URL}.
+     * @return the {@link URL} object created from the string URL.
+     * @throws MalformedURLException if the URL is malformed and cannot be converted to a {@link URL}.
+     */
+    public static URL create(String url) throws MalformedURLException {
+        return URLUtil.createUri(url).toURL();
+    }
+
+    /**
+     * Creates a {@link URI} object from the given string URL.
+     * This method attempts to convert the given URL string into a {@link URI} object.
+     * The pipe character ('|') is replaced with its percent-encoded equivalent ("%7C") because the pipe character
+     * is not a valid character in certain parts of a URI (specifically, in the path or query components).
+     * According to the URI specification (RFC 3986), certain characters must be percent-encoded when used in specific contexts.
+     *
+     * @param url the URL string to be converted into a {@link URI}.
+     * @return the {@link URI} object created from the string URL.
+     * @throws IllegalArgumentException if the string URL is not a valid URI or if the URI format is incorrect.
+     * @throws URISyntaxException if the string URL has an invalid syntax and cannot be converted into a {@link URI}.
+     */
+    public static URI createUri(String url) {
+        try {
+            // Replace '|' character with its percent-encoded representation '%7C'.
+            String urlFormat = url.replace("|", "%7C");
+            return new URI(urlFormat);
+        } catch (URISyntaxException e) {
+            throw new IllegalArgumentException(e);
+        }
+    }
 }

src/main/java/org/jabref/gui/linkedfile/AttachFileFromURLAction.java

@@ -1,7 +1,6 @@
 package org.jabref.gui.linkedfile;
 
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.util.Optional;
 
@@ -11,6 +10,7 @@
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.TaskExecutor;
@@ -61,7 +61,7 @@ public void execute() {
         }
 
         try {
-            URL url = URI.create(urlforDownload.get()).toURL();
+            URL url = URLUtil.create(urlforDownload.get());
             LinkedFileViewModel onlineFile = new LinkedFileViewModel(
                              new LinkedFile(url, ""),
                              entry,

src/main/java/org/jabref/gui/linkedfile/LinkedFileEditDialogViewModel.java

@@ -19,6 +19,7 @@
 import org.jabref.gui.externalfiletype.ExternalFileType;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.externalfiletype.UnknownExternalFileType;
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.gui.frame.ExternalApplicationsPreferences;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.FilePreferences;
@@ -139,7 +140,7 @@ public LinkedFile getNewLinkedFile() {
 
         if (LinkedFile.isOnlineLink(link.getValue())) {
             try {
-                return new LinkedFile(description.getValue(), URI.create(link.getValue()).toURL(), fileType, sourceUrl.getValue());
+                return new LinkedFile(description.getValue(), URLUtil.create(link.getValue()), fileType, sourceUrl.getValue());
             } catch (MalformedURLException e) {
                 return new LinkedFile(description.getValue(), link.getValue(), fileType, sourceUrl.getValue());
             }

src/main/java/org/jabref/gui/theme/StyleSheetFile.java

@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.URI;
 import java.net.URL;
 import java.net.URLConnection;
 import java.nio.file.Files;
@@ -11,6 +10,8 @@
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicReference;
 
+import org.jabref.gui.fieldeditors.URLUtil;
+
 import com.google.common.base.Strings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -54,7 +55,7 @@ final class StyleSheetFile extends StyleSheet {
 
     StyleSheetFile(URL url) {
         this.url = url;
-        this.path = Path.of(URI.create(url.toExternalForm()));
+        this.path = Path.of(URLUtil.createUri(url.toExternalForm()));
         reload();
     }
 

src/main/java/org/jabref/logic/importer/fetcher/ACS.java

@@ -1,11 +1,11 @@
 package org.jabref.logic.importer.fetcher;
 
 import java.io.IOException;
-import java.net.URI;
 import java.net.URL;
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.importer.FulltextFetcher;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
@@ -45,7 +45,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException {
 
         if (link != null) {
             LOGGER.info("Fulltext PDF found @ ACS.");
-            return Optional.of(URI.create(source.replaceFirst("/abs/", "/pdf/")).toURL());
+            return Optional.of(URLUtil.create(source.replaceFirst("/abs/", "/pdf/")));
         }
         return Optional.empty();
     }

src/main/java/org/jabref/logic/importer/fetcher/ApsFetcher.java

@@ -2,12 +2,12 @@
 
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.net.URLConnection;
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.importer.FulltextFetcher;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
@@ -48,7 +48,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException {
             if (code == 200) {
                 LOGGER.info("Fulltext PDF found @ APS.");
                 try {
-                    return Optional.of(URI.create(pdfRequestUrl).toURL());
+                    return Optional.of(URLUtil.create(pdfRequestUrl));
                 } catch (MalformedURLException e) {
                     LOGGER.warn("APS returned malformed URL, cannot find PDF.");
                 }
@@ -77,7 +77,7 @@ private Optional<String> getId(String doi) {
 
         URLConnection con;
         try {
-            con = URI.create(doiRequest).toURL().openConnection();
+            con = URLUtil.create(doiRequest).openConnection();
             con.connect();
             con.getInputStream();
             String[] urlParts = con.getURL().toString().split("abstract/");

src/main/java/org/jabref/logic/importer/fetcher/ArXivFetcher.java

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.ArrayList;
@@ -24,6 +23,7 @@
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.cleanup.EprintCleanup;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.FetcherException;
@@ -710,7 +710,7 @@ public ArXivEntry(Node item) {
                     if (linkTitle.equals(Optional.of("pdf"))) {
                         pdfUrlParsed = XMLUtil.getAttributeContent(linkNode, "href").map(url -> {
                             try {
-                                return URI.create(url).toURL();
+                                return URLUtil.create(url);
                             } catch (MalformedURLException e) {
                                 return null;
                             }

src/main/java/org/jabref/logic/importer/fetcher/BibsonomyScraper.java

@@ -1,10 +1,10 @@
 package org.jabref.logic.importer.fetcher;
 
 import java.io.IOException;
-import java.net.URI;
 import java.net.URL;
 import java.util.Optional;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ParseException;
@@ -37,7 +37,7 @@ public static Optional<BibEntry> getEntry(String entryUrl, ImportFormatPreferenc
             String cleanURL = entryUrl.replace("%", "%25").replace(":", "%3A").replace("/", "%2F").replace("?", "%3F")
                                       .replace("&", "%26").replace("=", "%3D");
 
-            URL url = URI.create(BibsonomyScraper.BIBSONOMY_SCRAPER + cleanURL + BibsonomyScraper.BIBSONOMY_SCRAPER_POST).toURL();
+            URL url = URLUtil.create(BibsonomyScraper.BIBSONOMY_SCRAPER + cleanURL + BibsonomyScraper.BIBSONOMY_SCRAPER_POST);
             String bibtex = new URLDownload(url).asString();
             return BibtexParser.singleFromString(bibtex, importFormatPreferences);
         } catch (IOException | FetcherException ex) {

src/main/java/org/jabref/logic/importer/fetcher/CiteSeer.java

@@ -1,12 +1,12 @@
 package org.jabref.logic.importer.fetcher;
 
 import java.io.IOException;
-import java.net.URI;
 import java.net.URL;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.http.dto.SimpleHttpResponse;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.FetcherException;
@@ -103,13 +103,13 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException, FetcherExc
         Optional<String> id = entry.getField(StandardField.DOI);
         if (id.isPresent()) {
             String source = PDF_URL.formatted(id.get());
-            return Optional.of(URI.create(source).toURL());
+            return Optional.of(URLUtil.create(source));
         }
 
         // if using id fails, we can try the source URL
         Optional<String> urlString = entry.getField(StandardField.URL);
         if (urlString.isPresent()) {
-            return Optional.of(URI.create(urlString.get()).toURL());
+            return Optional.of(URLUtil.create(urlString.get()));
         }
 
         return Optional.empty();

src/main/java/org/jabref/logic/importer/fetcher/DoiFetcher.java

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URL;
 import java.net.URLConnection;
 import java.util.Collections;
@@ -13,6 +12,7 @@
 import java.util.concurrent.CompletionException;
 import java.util.regex.Pattern;
 
+import org.jabref.gui.fieldeditors.URLUtil;
 import org.jabref.logic.cleanup.FieldFormatterCleanup;
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
 import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
@@ -122,7 +122,7 @@ public Optional<BibEntry> performSearchById(String identifier) throws FetcherExc
 
         URL doiURL;
         try {
-            doiURL = URI.create(doi.get().getURIAsASCIIString()).toURL();
+            doiURL = URLUtil.create(doi.get().getURIAsASCIIString());
         } catch (MalformedURLException e) {
             throw new FetcherException("Malformed URL", e);
         }
@@ -219,7 +219,7 @@ public List<BibEntry> performSearch(BibEntry entry) throws FetcherException {
     public Optional<String> getAgency(DOI doi) throws FetcherException, MalformedURLException {
         Optional<String> agency = Optional.empty();
         try {
-            URLDownload download = getUrlDownload(URI.create(DOI.AGENCY_RESOLVER + "/" + doi.asString()).toURL());
+            URLDownload download = getUrlDownload(URLUtil.create(DOI.AGENCY_RESOLVER + "/" + doi.asString()));
             JSONObject response = new JSONArray(download.asString()).getJSONObject(0);
             if (response != null) {
                 agency = Optional.ofNullable(response.optString("RA"));