Fix modernizer and refactor protected terms

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -10,7 +10,6 @@
 import java.util.Locale;
 import java.util.Optional;
 import java.util.Set;
-import java.util.Vector;
 import java.util.prefs.BackingStoreException;
 
 import org.jabref.gui.Globals;
@@ -288,8 +287,8 @@ private void writeMetadatatoPdf(List<ParserResult> loaded, String filesAndCiteke
             return;
         }
 
-        Vector<String> citeKeys = new Vector<>();
-        Vector<String> pdfs = new Vector<>();
+        List<String> citeKeys = new ArrayList<>();
+        List<String> pdfs = new ArrayList<>();
         for (String fileOrCiteKey : filesAndCitekeys.split(",")) {
             if (fileOrCiteKey.toLowerCase(Locale.ROOT).endsWith(".pdf")) {
                 pdfs.add(fileOrCiteKey);
@@ -323,7 +322,7 @@ private void writeMetadatatoPDFsOfEntry(BibDatabaseContext databaseContext, Stri
         }
     }
 
-    private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
+    private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, List<String> citeKeys, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
         for (String citeKey : citeKeys) {
             List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
             if (bibEntryList.isEmpty()) {
@@ -336,8 +335,8 @@ private void writeMetadatatoPdfByCitekey(BibDatabaseContext databaseContext, Bib
         }
     }
 
-    private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
-        for (String fileName : fileNames) {
+    private void writeMetadatatoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, List<String> pdfs, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter, EmbeddedBibFilePdfExporter embeddedBibFilePdfExporter, boolean writeXMP, boolean embeddBibfile) {
+        for (String fileName : pdfs) {
             Path filePath = Path.of(fileName);
             if (!filePath.isAbsolute()) {
                 filePath = FileHelper.find(fileName, databaseContext.getFileDirectories(filePreferences)).orElse(FileHelper.find(fileName, List.of(Path.of("").toAbsolutePath())).orElse(filePath));

src/main/java/org/jabref/gui/maintable/columns/FieldColumn.java

@@ -11,7 +11,7 @@
 import org.jabref.model.entry.field.OrFields;
 import org.jabref.model.entry.field.UnknownField;
 
-import com.google.common.collect.Iterables;
+import com.google.common.collect.MoreCollectors;
 
 /**
  * A column that displays the text-value of the field
@@ -33,9 +33,9 @@ public FieldColumn(MainTableColumnModel model) {
 
         if (fields.size() == 1) {
             // comparator can't parse more than one value
-            Field field = Iterables.getOnlyElement(fields);
+            Field field = fields.stream().collect(MoreCollectors.onlyElement());
 
-            if (field instanceof UnknownField || field.isNumeric()) {
+            if ((field instanceof UnknownField) || field.isNumeric()) {
                 this.setComparator(new NumericFieldComparator());
             }
         }

src/main/java/org/jabref/gui/preferences/protectedterms/ProtectedTermsTabViewModel.java

@@ -1,8 +1,7 @@
 package org.jabref.gui.preferences.protectedterms;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
@@ -57,6 +56,7 @@ public void setValues() {
         termsFilesProperty.addAll(termsLoader.getProtectedTermsLists().stream().map(ProtectedTermsListItemModel::new).toList());
     }
 
+    @Override
     public void storeSettings() {
         List<String> enabledExternalList = new ArrayList<>();
         List<String> disabledExternalList = new ArrayList<>();
@@ -97,12 +97,8 @@ public void addFile() {
 
         dialogService.showFileOpenDialog(fileDialogConfiguration)
                      .ifPresent(file -> {
-                         String fileName = file.toAbsolutePath().toString();
-                         try {
-                             termsFilesProperty.add(new ProtectedTermsListItemModel(ProtectedTermsLoader.readProtectedTermsListFromFile(new File(fileName), true)));
-                         } catch (FileNotFoundException e) {
-                             LOGGER.warn("Cannot find protected terms file " + fileName, e);
-                         }
+                         Path fileName = file.toAbsolutePath();
+                         termsFilesProperty.add(new ProtectedTermsListItemModel(ProtectedTermsLoader.readProtectedTermsListFromFile(fileName, true)));
                      });
     }
 
@@ -155,16 +151,12 @@ public void displayContent(ProtectedTermsListItemModel itemModel) {
 
     public void reloadList(ProtectedTermsListItemModel oldItemModel) {
         ProtectedTermsList oldList = oldItemModel.getTermsList();
-        try {
-            ProtectedTermsList newList = ProtectedTermsLoader.readProtectedTermsListFromFile(new File(oldList.getLocation()), oldList.isEnabled());
-            int index = termsFilesProperty.indexOf(oldItemModel);
-            if (index >= 0) {
-                termsFilesProperty.set(index, new ProtectedTermsListItemModel(newList));
-            } else {
-                LOGGER.warn("Problem reloading protected terms file {}.", oldList.getLocation());
-            }
-        } catch (IOException e) {
-            LOGGER.warn("Problem reloading protected terms file {}.", oldList.getLocation(), e);
+        ProtectedTermsList newList = ProtectedTermsLoader.readProtectedTermsListFromFile(Path.of(oldList.getLocation()), oldList.isEnabled());
+        int index = termsFilesProperty.indexOf(oldItemModel);
+        if (index >= 0) {
+            termsFilesProperty.set(index, new ProtectedTermsListItemModel(newList));
+        } else {
+            LOGGER.warn("Problem reloading protected terms file {}.", oldList.getLocation());
         }
     }
 

src/main/java/org/jabref/logic/cleanup/DoiCleanup.java

@@ -1,7 +1,7 @@
 package org.jabref.logic.cleanup;
 
-import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -34,11 +34,7 @@ public List<FieldChange> cleanup(BibEntry entry) {
             String doiFieldValue = entry.getField(StandardField.DOI).orElse(null);
 
             String decodeDoiFieldValue = "";
-            try {
-                decodeDoiFieldValue = URLDecoder.decode(doiFieldValue, "UTF-8");
-            } catch (UnsupportedEncodingException e) {
-                decodeDoiFieldValue = doiFieldValue;
-            }
+            decodeDoiFieldValue = URLDecoder.decode(doiFieldValue, StandardCharsets.UTF_8);
             doiFieldValue = decodeDoiFieldValue;
 
             Optional<DOI> doi = DOI.parse(doiFieldValue);

src/main/java/org/jabref/logic/exporter/TemplateExporter.java

@@ -1,14 +1,13 @@
 package org.jabref.logic.exporter;
 
-import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.io.Reader;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -156,28 +155,24 @@ private Reader getReader(String filename) throws IOException {
         } else {
             dir = LAYOUT_PREFIX + (directory == null ? "" : directory + '/');
         }
-
         // Attempt to get a Reader for the file path given, either by
         // loading it as a resource (from within JAR), or as a normal file. If
         // unsuccessful (e.g. file not found), an IOException is thrown.
         String name = dir + filename;
-        Reader reader;
         // Try loading as a resource first. This works for files inside the JAR:
-        URL reso = TemplateExporter.class.getResource(name);
-
         // If that did not work, try loading as a normal file URL:
         try {
-            if (reso == null) {
-                File f = new File(name);
-                reader = new FileReader(f);
+            URL res = TemplateExporter.class.getResource(name);
+            Path reso;
+            if (res == null) {
+                reso = Path.of(name);
             } else {
-                reader = new InputStreamReader(reso.openStream());
+                reso = Path.of(res.toURI());
             }
-        } catch (FileNotFoundException ex) {
+            return Files.newBufferedReader(reso, StandardCharsets.UTF_8);
+        } catch (FileNotFoundException | URISyntaxException ex) {
             throw new IOException("Cannot find layout file: '" + name + "'.");
         }
-
-        return reader;
     }
 
     @Override
@@ -280,7 +275,6 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
             }
 
             // Print footer
-
             // changed section - begin (arudert)
             Layout endLayout = null;
             try (Reader reader = getReader(lfFileName + END_INFIX + LAYOUT_EXTENSION)) {
@@ -313,9 +307,9 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
      * If so, read all the name formatters so they can be used by the filter layouts.
      */
     private void readFormatterFile() {
-        File formatterFile = new File(lfFileName + FORMATTERS_EXTENSION);
-        if (formatterFile.exists()) {
-            try (Reader in = new FileReader(formatterFile)) {
+        Path formatterFile = Path.of(lfFileName + FORMATTERS_EXTENSION);
+        if (Files.exists(formatterFile)) {
+            try (Reader in = Files.newBufferedReader(formatterFile, StandardCharsets.UTF_8)) {
                 // Ok, we found and opened the file. Read all contents:
                 StringBuilder sb = new StringBuilder();
                 int c;

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

@@ -47,7 +47,6 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.OptionalUtil;
 
-import com.google.common.collect.ImmutableMap;
 import org.apache.http.client.utils.URIBuilder;
 import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
 import org.slf4j.Logger;
@@ -93,9 +92,9 @@ public class ArXivFetcher implements FulltextFetcher, PagedSearchBasedFetcher, I
      */
     private static final Set<Field> CHOSEN_MANUAL_DOI_FIELDS = Set.of(StandardField.DOI, StandardField.PUBLISHER, InternalField.KEY_FIELD);
 
-    private static final Map<String, String> ARXIV_KEYWORDS_WITH_COMMA_REPLACEMENTS = ImmutableMap.of(
+    private static final Map<String, String> ARXIV_KEYWORDS_WITH_COMMA_REPLACEMENTS = Collections.unmodifiableMap(Map.of(
             "Computational Engineering, Finance, and Science", "Computational Engineering / Finance / Science",
-            "Distributed, Parallel, and Cluster Computing", "Distributed / Parallel / Cluster Computing");
+            "Distributed, Parallel, and Cluster Computing", "Distributed / Parallel / Cluster Computing"));
 
     private final ArXiv arXiv;
     private final DoiFetcher doiFetcher;
@@ -607,8 +606,8 @@ private List<BibEntry> filterYears(List<BibEntry> searchResult, ArXivQueryTransf
             return searchResult.stream()
                                .filter(entry -> entry.getField(StandardField.DATE).isPresent())
                                // Filter the date field for year only
-                               .filter(entry -> transformer.getEndYear().isEmpty() || Integer.parseInt(entry.getField(StandardField.DATE).get().substring(0, 4)) <= transformer.getEndYear().get())
-                               .filter(entry -> transformer.getStartYear().isEmpty() || Integer.parseInt(entry.getField(StandardField.DATE).get().substring(0, 4)) >= transformer.getStartYear().get())
+                               .filter(entry -> transformer.getEndYear().isEmpty() || (Integer.parseInt(entry.getField(StandardField.DATE).get().substring(0, 4)) <= transformer.getEndYear().get()))
+                               .filter(entry -> transformer.getStartYear().isEmpty() || (Integer.parseInt(entry.getField(StandardField.DATE).get().substring(0, 4)) >= transformer.getStartYear().get()))
                                .collect(Collectors.toList());
         }