Some Globals.prefs injection in logic and model

CHANGELOG.md

@@ -27,6 +27,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Fixed [#1592](https://github.com/JabRef/jabref/issues/1592): LibreOffice: wrong numbers in citation labels
 
 ### Removed
+- It is not longer possible to choose to convert HTML sub- and superscripts to equations
 
 
 

src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java

@@ -122,7 +122,7 @@ public String htmlToLatexConversion() {
     @Benchmark
     public boolean keywordGroupContains() throws ParseException {
         KeywordGroup group = new KeywordGroup("testGroup", "keyword", "testkeyword", false, false,
-                GroupHierarchyType.INDEPENDENT);
+                GroupHierarchyType.INDEPENDENT, Globals.prefs);
         return group.containsAll(database.getEntries());
     }
 

src/main/java/net/sf/jabref/JabRefMain.java

@@ -61,12 +61,12 @@ private static void start(String[] args) {
         Globals.prefs.setLanguageDependentDefaultValues();
 
         // Update which fields should be treated as numeric, based on preferences:
-        InternalBibtexFields.setNumericFieldsFromPrefs();
+        InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
 
         /* Build list of Import and Export formats */
         Globals.IMPORT_FORMAT_READER.resetImportFormats();
         CustomEntryTypesManager.loadCustomEntryTypes(preferences);
-        ExportFormats.initAllExports();
+        ExportFormats.initAllExports(Globals.prefs.customExports.getCustomExportFormats(Globals.prefs));
 
         // Read list(s) of journal names and abbreviations
         Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();

src/main/java/net/sf/jabref/MetaData.java

@@ -178,7 +178,7 @@ public void putData(String key, List<String> orderedData) {
      */
     private void putGroups(List<String> orderedData) throws ParseException {
         try {
-            groupsRoot = GroupTreeNode.parse(orderedData);
+            groupsRoot = GroupTreeNode.parse(orderedData, Globals.prefs);
         } catch (ParseException e) {
             throw new ParseException(Localization.lang(
                     "Group tree could not be parsed. If you save the BibTeX database, all groups will be lost."), e);
@@ -238,7 +238,7 @@ public AbstractLabelPattern getLabelPattern() {
             return labelPattern;
         }
 
-        labelPattern = new DatabaseLabelPattern();
+        labelPattern = new DatabaseLabelPattern(Globals.prefs);
 
         // read the data from the metadata and store it into the labelPattern
         for (String key : this) {

src/main/java/net/sf/jabref/cli/ArgumentProcessor.java

@@ -390,7 +390,7 @@ private void importPreferences() {
         try {
             Globals.prefs.importPreferences(cli.getPreferencesImport());
             CustomEntryTypesManager.loadCustomEntryTypes(Globals.prefs);
-            ExportFormats.initAllExports();
+            ExportFormats.initAllExports(Globals.prefs.customExports.getCustomExportFormats(Globals.prefs));
         } catch (JabRefException ex) {
             LOGGER.error("Cannot import preferences", ex);
         }
@@ -435,7 +435,7 @@ private void regenerateBibtexKeys(List<ParserResult> loaded) {
                 LOGGER.info(Localization.lang("Regenerating BibTeX keys according to metadata"));
                 for (BibEntry entry : database.getEntries()) {
                     // try to make a new label
-                    LabelPatternUtil.makeLabel(metaData, database, entry);
+                    LabelPatternUtil.makeLabel(metaData, database, entry, Globals.prefs);
                 }
             } else {
                 LOGGER.info(Localization.lang("No meta data present in bibfile. Cannot regenerate BibTeX keys"));

src/main/java/net/sf/jabref/external/AutoSetLinks.java

@@ -104,7 +104,7 @@ public void run() {
                     String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
                     result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
                 } else {
-                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs);
+                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs, Globals.prefs);
                 }
 
                 boolean foundAny = false;

src/main/java/net/sf/jabref/external/DownloadExternalFile.java

@@ -270,7 +270,8 @@ private void downloadFinished() {
     // FIXME: will break download if no bibtexkey is present!
     private String getSuggestedFileName(String suffix) {
         String plannedName = FileUtil.createFileNameFromPattern(databaseContext.getDatabase(),
-                frame.getCurrentBasePanel().getSelectedEntries().get(0), Globals.journalAbbreviationLoader);
+                frame.getCurrentBasePanel().getSelectedEntries().get(0), Globals.journalAbbreviationLoader,
+                Globals.prefs);
 
         if (!suffix.isEmpty()) {
             plannedName += "." + suffix;

src/main/java/net/sf/jabref/external/DroppedFileHandler.java

@@ -233,7 +233,7 @@ private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCo
 
         List<BibEntry> xmpEntriesInFile;
         try {
-            xmpEntriesInFile = XMPUtil.readXMP(fileName);
+            xmpEntriesInFile = XMPUtil.readXMP(fileName, Globals.prefs);
         } catch (IOException e) {
             LOGGER.warn("Problem reading XMP", e);
             return false;
@@ -350,7 +350,8 @@ private boolean showLinkMoveCopyRenameDialog(String linkFileName, ExternalFileTy
         renameCheckBox.setText(Localization.lang("Rename file to").concat(": "));
 
         // Determine which name to suggest:
-        String targetName = FileUtil.createFileNameFromPattern(database, entry, Globals.journalAbbreviationLoader);
+        String targetName = FileUtil.createFileNameFromPattern(database, entry, Globals.journalAbbreviationLoader,
+                Globals.prefs);
 
         renameToTextBox.setText(targetName.concat(".").concat(fileType.getExtension()));
 

src/main/java/net/sf/jabref/external/MoveFileAction.java

@@ -112,7 +112,7 @@ public void actionPerformed(ActionEvent event) {
                     // Determine which name to suggest:
                     String suggName = FileUtil
                             .createFileNameFromPattern(eEditor.getDatabase(), eEditor.getEntry(),
-                                    Globals.journalAbbreviationLoader)
+                                    Globals.journalAbbreviationLoader, Globals.prefs)
                             .concat(entry.type.isPresent() ? "." + entry.type.get().getExtension() : "");
                     CheckBoxMessage cbm = new CheckBoxMessage(Localization.lang("Move file to file directory?"),
                             Localization.lang("Rename to '%0'", suggName),

src/main/java/net/sf/jabref/gui/BasePanel.java

@@ -575,7 +575,7 @@ public void run() {
                 // Finally, set the new keys:
                 for (BibEntry entry : entries) {
                     bes = entry;
-                    LabelPatternUtil.makeLabel(bibDatabaseContext.getMetaData(), database, bes);
+                    LabelPatternUtil.makeLabel(bibDatabaseContext.getMetaData(), database, bes, Globals.prefs);
                     ce.addEdit(new UndoableKeyChange(database, bes, (String) oldvals.get(bes),
                             bes.getCiteKey()));
                 }
@@ -990,7 +990,7 @@ private void copyKeyAndTitle() {
                     "\\bibtexkey - \\begin{title}\\format[RemoveBrackets]{\\title}\\end{title}\n");
             Layout layout;
             try {
-                layout = new LayoutHelper(sr, Globals.journalAbbreviationLoader).getLayoutFromText();
+                layout = new LayoutHelper(sr, Globals.prefs, Globals.journalAbbreviationLoader).getLayoutFromText();
             } catch (IOException e) {
                 LOGGER.info("Could not get layout", e);
                 return;
@@ -1987,7 +1987,7 @@ public void autoGenerateKeysBeforeSaving() {
             for (BibEntry bes : database.getEntries()) {
                 String oldKey = bes.getCiteKey();
                 if ((oldKey == null) || oldKey.isEmpty()) {
-                    LabelPatternUtil.makeLabel(bibDatabaseContext.getMetaData(), database, bes);
+                    LabelPatternUtil.makeLabel(bibDatabaseContext.getMetaData(), database, bes, Globals.prefs);
                     ce.addEdit(new UndoableKeyChange(database, bes, null, bes.getCiteKey()));
                     any = true;
                 }
@@ -2425,7 +2425,7 @@ public Optional<String> searchAndOpen() {
                 String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
                 result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
             } else {
-                result = FileUtil.findAssociatedFiles(entries, extensions, dirs);
+                result = FileUtil.findAssociatedFiles(entries, extensions, dirs, Globals.prefs);
             }
             if (result.containsKey(entry)) {
                 final List<File> res = result.get(entry);

src/main/java/net/sf/jabref/gui/ImportInspectionDialog.java

@@ -461,7 +461,7 @@ private void generateKeySelectedEntry() {
             database.insertEntry(entry);
 
             // Generate a unique key:
-            LabelPatternUtil.makeLabel(localMetaData, database, entry);
+            LabelPatternUtil.makeLabel(localMetaData, database, entry, Globals.prefs);
             // Remove the entry from the database again, since we only added it in
             // order to
             // make sure the key was unique:
@@ -502,7 +502,7 @@ private void generateKeys() {
                 entry.setId(IdGenerator.next());
                 database.insertEntry(entry);
 
-                LabelPatternUtil.makeLabel(localMetaData, database, entry);
+                LabelPatternUtil.makeLabel(localMetaData, database, entry, Globals.prefs);
                 // Add the generated key to our list:
                 keys.add(entry.getCiteKey());
             }

src/main/java/net/sf/jabref/gui/JabRefFrame.java

@@ -776,7 +776,7 @@ private void tearDownJabRef(List<String> filenames) {
         }
 
         fileHistory.storeHistory();
-        prefs.customExports.store();
+        prefs.customExports.store(Globals.prefs);
         prefs.customImports.store();
         CustomEntryTypesManager.saveCustomEntryTypes(prefs);
 

src/main/java/net/sf/jabref/gui/PreviewPanel.java

@@ -261,7 +261,8 @@ public void updateLayout(String layoutFormat) {
     private void updateLayout() {
         StringReader sr = new StringReader(layoutFile.replace("__NEWLINE__", "\n"));
         try {
-            layout = Optional.of(new LayoutHelper(sr, Globals.journalAbbreviationLoader).getLayoutFromText());
+            layout = Optional
+                    .of(new LayoutHelper(sr, Globals.prefs, Globals.journalAbbreviationLoader).getLayoutFromText());
         } catch (IOException e) {
             layout = Optional.empty();
             LOGGER.debug("no layout could be set", e);

src/main/java/net/sf/jabref/gui/StringDialog.java

@@ -55,6 +55,7 @@
 import net.sf.jabref.gui.undo.UndoableStringChange;
 import net.sf.jabref.gui.util.PositionWindow;
 import net.sf.jabref.logic.bibtex.LatexFieldFormatter;
+import net.sf.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import net.sf.jabref.logic.bibtex.comparator.BibtexStringComparator;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.database.BibDatabase;
@@ -266,7 +267,8 @@ public void setValueAt(Object value, int row, int col) {
 
                 if (!value.equals(subject.getContent())) {
                     try {
-                        new LatexFieldFormatter().format((String) value, "__dummy");
+                        new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs))
+                                .format((String) value, "__dummy");
                     } catch (IllegalArgumentException ex) {
                         return;
                     }

src/main/java/net/sf/jabref/gui/TransferableBibtexEntry.java

@@ -24,8 +24,10 @@
 
 import javax.swing.JOptionPane;
 
+import net.sf.jabref.Globals;
 import net.sf.jabref.logic.bibtex.BibEntryWriter;
 import net.sf.jabref.logic.bibtex.LatexFieldFormatter;
+import net.sf.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.entry.BibEntry;
@@ -63,7 +65,8 @@ public Object getTransferData(DataFlavor flavor)
         } else if (flavor.equals(DataFlavor.stringFlavor)) {
             try {
                 StringWriter sw = new StringWriter();
-                BibEntryWriter bibtexEntryWriter = new BibEntryWriter(new LatexFieldFormatter(), false);
+                BibEntryWriter bibtexEntryWriter = new BibEntryWriter(
+                        new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs)), false);
                 for (BibEntry entry : data) {
                     bibtexEntryWriter.write(entry, sw, BibDatabaseMode.BIBTEX);
                 }

src/main/java/net/sf/jabref/gui/actions/CleanupAction.java

@@ -161,7 +161,7 @@ private int showDialog(CleanupPresetPanel presetPanel) {
     private void doCleanup(CleanupPreset preset, BibEntry entry, NamedCompound ce) {
         // Create and run cleaner
         BibDatabaseContext bibDatabaseContext = panel.getBibDatabaseContext();
-        CleanupWorker cleaner = new CleanupWorker(bibDatabaseContext, Globals.journalAbbreviationLoader);
+        CleanupWorker cleaner = new CleanupWorker(bibDatabaseContext, Globals.journalAbbreviationLoader, Globals.prefs);
         List<FieldChange> changes = cleaner.cleanup(preset, entry);
 
         unsuccessfulRenames = cleaner.getUnsuccessfulRenames();

src/main/java/net/sf/jabref/gui/actions/ManageKeywordsAction.java

@@ -54,6 +54,7 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.entry.BibEntry;
+import net.sf.jabref.preferences.JabRefPreferences;
 import net.sf.jabref.specialfields.Printed;
 import net.sf.jabref.specialfields.Priority;
 import net.sf.jabref.specialfields.Quality;
@@ -321,7 +322,8 @@ private NamedCompound updateKeywords(List<BibEntry> entries, Set<String> keyword
             keywords.addAll(keywordsToAdd);
 
             // put keywords back
-            Optional<FieldChange> change = entry.putKeywords(keywords);
+            Optional<FieldChange> change = entry.putKeywords(keywords,
+                    Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
             if (change.isPresent()) {
                 ce.addEdit(new UndoableFieldChange(change.get()));
             }

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditor.java

@@ -96,6 +96,7 @@
 import net.sf.jabref.logic.autocompleter.AutoCompleter;
 import net.sf.jabref.logic.bibtex.BibEntryWriter;
 import net.sf.jabref.logic.bibtex.LatexFieldFormatter;
+import net.sf.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.labelpattern.LabelPatternUtil;
 import net.sf.jabref.logic.search.SearchQueryHighlightListener;
@@ -592,7 +593,8 @@ public void updateSource() {
 
     public static String getSourceString(BibEntry entry, BibDatabaseMode type) throws IOException {
         StringWriter stringWriter = new StringWriter(200);
-        LatexFieldFormatter formatter = LatexFieldFormatter.buildIgnoreHashes();
+        LatexFieldFormatter formatter = LatexFieldFormatter
+                .buildIgnoreHashes(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs));
         new BibEntryWriter(formatter, false).writeWithoutPrependedNewlines(entry, stringWriter, type);
 
         return stringWriter.getBuffer().toString();
@@ -813,7 +815,8 @@ private boolean storeSource() {
                 String newValue = newEntry.getField(field);
                 if (!Objects.equals(oldValue, newValue)) {
                     // Test if the field is legally set.
-                    new LatexFieldFormatter().format(newValue, field);
+                    new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs))
+                            .format(newValue, field);
 
                     compound.addEdit(new UndoableFieldChange(entry, field, oldValue, newValue));
                     entry.setField(field, newValue);
@@ -1167,7 +1170,8 @@ public void actionPerformed(ActionEvent event) {
                         // properly formatted. If that happens, the field
                         // is not stored and the textarea turns red.
                         if (toSet != null) {
-                            new LatexFieldFormatter().format(toSet, fieldEditor.getFieldName());
+                            new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs))
+                                    .format(toSet, fieldEditor.getFieldName());
                         }
 
                         String oldValue = entry.getField(fieldEditor.getFieldName());
@@ -1362,7 +1366,8 @@ public void actionPerformed(ActionEvent e) {
                 }
             }
 
-            LabelPatternUtil.makeLabel(panel.getBibDatabaseContext().getMetaData(), panel.getDatabase(), entry);
+            LabelPatternUtil.makeLabel(panel.getBibDatabaseContext().getMetaData(), panel.getDatabase(), entry,
+                    Globals.prefs);
 
             // Store undo information:
             panel.getUndoManager().addEdit(new UndoableKeyChange(panel.getDatabase(), entry, (String) oldValue, entry.getCiteKey()));

src/main/java/net/sf/jabref/gui/entryeditor/FieldExtraComponents.java

@@ -45,6 +45,7 @@
 import net.sf.jabref.gui.fieldeditors.FieldEditor;
 import net.sf.jabref.gui.mergeentries.MergeEntryDOIDialog;
 import net.sf.jabref.gui.undo.UndoableFieldChange;
+import net.sf.jabref.logic.journals.JournalAbbreviationPreferences;
 import net.sf.jabref.logic.journals.JournalAbbreviationRepository;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.net.URLUtil;
@@ -93,7 +94,8 @@ public static Optional<JComponent> getJournalExtraComponent(JabRefFrame frame, B
         button.setToolTipText(ABBREVIATION_TOOLTIP_TEXT);
         button.addActionListener(actionEvent -> {
             String text = editor.getText();
-            JournalAbbreviationRepository abbreviationRepository = Globals.journalAbbreviationLoader.getRepository();
+            JournalAbbreviationRepository abbreviationRepository = Globals.journalAbbreviationLoader
+                    .getRepository(JournalAbbreviationPreferences.fromPreferences(Globals.prefs));
             if (abbreviationRepository.isKnownName(text)) {
                 String s = abbreviationRepository.getNextAbbreviation(text).orElse(text);
 

src/main/java/net/sf/jabref/gui/exporter/ExportAction.java

@@ -59,7 +59,7 @@ public InternalExportAction(JabRefFrame frame, boolean selectedOnly) {
 
             @Override
             public void actionPerformed(ActionEvent e) {
-                ExportFormats.initAllExports();
+                ExportFormats.initAllExports(Globals.prefs.customExports.getCustomExportFormats(Globals.prefs));
                 JFileChooser fc = ExportAction
                         .createExportFileChooser(Globals.prefs.get(JabRefPreferences.EXPORT_WORKING_DIRECTORY));
                 fc.showSaveDialog(frame);