Probably the last injections for now

JabRef · Jul 18, 2016 · fc2b5fa · fc2b5fa
1 parent ac3158e
commit fc2b5fa
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Showing 45 changed files with 213 additions and 149 deletions.
diff --git a/src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java b/src/jmh/java/net/sf/jabref/benchmarks/Benchmarks.java
@@ -60,7 +60,8 @@ public void init() throws Exception {
             entry.setField("rnd", "2" + randomizer.nextInt());
             database.insertEntry(entry);
         }
-        BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
+        BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new,
+                Globals.prefs);
         StringSaveSession saveSession = databaseWriter.savePartOfDatabase(
                 new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries(),
                 new SavePreferences());
@@ -80,7 +81,8 @@ public ParserResult parse() throws IOException {
 
     @Benchmark
     public String write() throws Exception {
-        BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
+        BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new,
+                Globals.prefs);
         StringSaveSession saveSession = databaseWriter.savePartOfDatabase(
                 new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries(),
                 new SavePreferences());
@@ -115,14 +117,15 @@ public String latexToHTMLConversion() {
 
     @Benchmark
     public String htmlToLatexConversion() {
-        HtmlToLatexFormatter f = new HtmlToLatexFormatter();
+        HtmlToLatexFormatter f = new HtmlToLatexFormatter(
+                Globals.prefs.getBoolean(JabRefPreferences.USE_CONVERT_TO_EQUATION));
         return f.format(htmlConversionString);
     }
 
     @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());
     }
 

diff --git a/src/main/java/net/sf/jabref/JabRefMain.java b/src/main/java/net/sf/jabref/JabRefMain.java
@@ -60,7 +60,7 @@ private static void start(String[] args) {
         Globals.prefs.setLanguageDependentDefaultValues();
 
         // Update which fields should be treated as numeric, based on preferences:
-        InternalBibtexFields.setNumericFieldsFromPrefs(Globals.prefs);
+        InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
 
         /* Build list of Import and Export formats */
         Globals.IMPORT_FORMAT_READER.resetImportFormats();

diff --git a/src/main/java/net/sf/jabref/JabRefPreferences.java b/src/main/java/net/sf/jabref/JabRefPreferences.java
@@ -360,7 +360,7 @@ public class JabRefPreferences {
         activeFormatterCleanups.add(new FieldFormatterCleanup("title", new ProtectTermsFormatter()));
         activeFormatterCleanups.add(new FieldFormatterCleanup("title", new UnitsToLatexFormatter()));
         activeFormatterCleanups.add(new FieldFormatterCleanup("title", new LatexCleanupFormatter()));
-        activeFormatterCleanups.add(new FieldFormatterCleanup("title", new HtmlToLatexFormatter()));
+        activeFormatterCleanups.add(new FieldFormatterCleanup("title", new HtmlToLatexFormatter(false))); // TODO: Get the actual value USE_CONVERT_TO_EQUATION
         FieldFormatterCleanups formatterCleanups = new FieldFormatterCleanups(true, activeFormatterCleanups);
         CLEANUP_DEFAULT_PRESET = new CleanupPreset(EnumSet.complementOf(deactivedJobs), formatterCleanups);
     }

diff --git a/src/main/java/net/sf/jabref/cli/ArgumentProcessor.java b/src/main/java/net/sf/jabref/cli/ArgumentProcessor.java
@@ -288,7 +288,7 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
                 try {
                     System.out.println(Localization.lang("Saving") + ": " + subName);
                     SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs);
-                    BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+                    BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new, Globals.prefs);
                     Defaults defaults = new Defaults(BibDatabaseMode
                             .fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_DEFAULT_MODE)));
                     SaveSession session = databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults),
@@ -332,7 +332,8 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
                         SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs);
                         Defaults defaults = new Defaults(BibDatabaseMode.fromPreference(
                                 Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_DEFAULT_MODE)));
-                        BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+                        BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new,
+                                Globals.prefs);
                         SaveSession session = databaseWriter.saveDatabase(
                                 new BibDatabaseContext(pr.getDatabase(), pr.getMetaData(), defaults), prefs);
 

diff --git a/src/main/java/net/sf/jabref/collab/ChangeScanner.java b/src/main/java/net/sf/jabref/collab/ChangeScanner.java
@@ -167,7 +167,7 @@ private void storeTempDatabase() {
 
                 Defaults defaults = new Defaults(BibDatabaseMode
                         .fromPreference(Globals.prefs.getBoolean(JabRefPreferences.BIBLATEX_DEFAULT_MODE)));
-                BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+                BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new, Globals.prefs);
                 SaveSession ss = databaseWriter.saveDatabase(new BibDatabaseContext(inTemp, mdInTemp, defaults), prefs);
                 ss.commit(Globals.getFileUpdateMonitor().getTempFile(panel.fileMonitorHandle()));
             } catch (SaveException ex) {

diff --git a/src/main/java/net/sf/jabref/gui/BasePanel.java b/src/main/java/net/sf/jabref/gui/BasePanel.java
@@ -1105,7 +1105,7 @@ private boolean saveDatabase(File file, boolean selectedOnly, Charset enc,
         try {
             SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs).withEncoding(enc)
                     .withSaveType(saveType);
-            BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+            BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new, Globals.prefs);
             if (selectedOnly) {
                 session = databaseWriter.savePartOfDatabase(bibDatabaseContext, mainTable.getSelectedEntries(), prefs);
             } else {
@@ -1572,7 +1572,7 @@ public void setupMainPanel() {
         // Set up AutoCompleters for this panel:
         if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_COMPLETE)) {
             autoCompleters = new ContentAutoCompleters(getDatabase(), bibDatabaseContext.getMetaData(),
-                    autoCompletePreferences, Globals.journalAbbreviationLoader);
+                    autoCompletePreferences, Globals.journalAbbreviationLoader, Globals.prefs);
             // ensure that the autocompleters are in sync with entries
             this.getDatabase().registerListener(new AutoCompleteListener());
         } else {
@@ -1598,7 +1598,7 @@ public void updateSearchManager() {
     private void instantiateSearchAutoCompleter() {
         AutoCompletePreferences autoCompletePreferences = new AutoCompletePreferences(Globals.prefs);
         AutoCompleterFactory autoCompleterFactory = new AutoCompleterFactory(autoCompletePreferences,
-                Globals.journalAbbreviationLoader);
+                Globals.journalAbbreviationLoader, Globals.prefs);
         searchAutoCompleter = autoCompleterFactory.getPersonAutoCompleter();
         for (BibEntry entry : database.getEntries()) {
             searchAutoCompleter.addBibtexEntry(entry);

diff --git a/src/main/java/net/sf/jabref/gui/entryeditor/FieldExtraComponents.java b/src/main/java/net/sf/jabref/gui/entryeditor/FieldExtraComponents.java
@@ -93,7 +93,8 @@ 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(Globals.prefs);
             if (abbreviationRepository.isKnownName(text)) {
                 String s = abbreviationRepository.getNextAbbreviation(text).orElse(text);
 

diff --git a/src/main/java/net/sf/jabref/gui/exporter/AutoSaveManager.java b/src/main/java/net/sf/jabref/gui/exporter/AutoSaveManager.java
@@ -102,7 +102,7 @@ private static boolean autoSave(BasePanel panel) {
                     .withMakeBackup(false)
                     .withEncoding(panel.getBibDatabaseContext().getMetaData().getEncoding());
 
-            BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+            BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new, Globals.prefs);
             SaveSession ss = databaseWriter.saveDatabase(panel.getBibDatabaseContext(), prefs);
             ss.commit(backupFile.toPath());
         } catch (SaveException e) {

diff --git a/src/main/java/net/sf/jabref/gui/exporter/SaveDatabaseAction.java b/src/main/java/net/sf/jabref/gui/exporter/SaveDatabaseAction.java
@@ -173,7 +173,7 @@ private boolean saveDatabase(File file, boolean selectedOnly, Charset encoding)
         frame.block();
         try {
             SavePreferences prefs = SavePreferences.loadForSaveFromPreferences(Globals.prefs).withEncoding(encoding);
-            BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new);
+            BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(FileSaveSession::new, Globals.prefs);
             if (selectedOnly) {
                 session = databaseWriter.savePartOfDatabase(panel.getBibDatabaseContext(), panel.getSelectedEntries(),
                         prefs);

diff --git a/src/main/java/net/sf/jabref/gui/groups/AutoGroupDialog.java b/src/main/java/net/sf/jabref/gui/groups/AutoGroupDialog.java
@@ -94,7 +94,8 @@ public void actionPerformed(ActionEvent e) {
 
                 try {
                     GroupTreeNode autoGroupsRoot = GroupTreeNode.fromGroup(
-                            new ExplicitGroup(Localization.lang("Automatically created groups"), GroupHierarchyType.INCLUDING));
+                            new ExplicitGroup(Localization.lang("Automatically created groups"),
+                                    GroupHierarchyType.INCLUDING, Globals.prefs));
                     Set<String> hs;
                     String fieldText = field.getText();
                     if (keywords.isSelected()) {
@@ -120,7 +121,7 @@ public void actionPerformed(ActionEvent e) {
 
                     for (String keyword : hs) {
                         KeywordGroup group = new KeywordGroup(keyword, fieldText, keyword, false, false,
-                                GroupHierarchyType.INDEPENDENT);
+                                GroupHierarchyType.INDEPENDENT, Globals.prefs);
                         autoGroupsRoot.addChild(GroupTreeNode.fromGroup(group));
                     }
 

diff --git a/src/main/java/net/sf/jabref/gui/groups/GroupDialog.java b/src/main/java/net/sf/jabref/gui/groups/GroupDialog.java
@@ -279,21 +279,21 @@ public void actionPerformed(ActionEvent e) {
                 isOkPressed = true;
             try {
                 if (explicitRadioButton.isSelected()) {
-                    resultingGroup = new ExplicitGroup(nameField.getText().trim(), getContext());
+                    resultingGroup = new ExplicitGroup(nameField.getText().trim(), getContext(), Globals.prefs);
                 } else if (keywordsRadioButton.isSelected()) {
                     // regex is correct, otherwise OK would have been disabled
                     // therefore I don't catch anything here
                     resultingGroup = new KeywordGroup(nameField.getText().trim(), keywordGroupSearchField.getText().trim(),
                             keywordGroupSearchTerm.getText().trim(), keywordGroupCaseSensitive.isSelected(), keywordGroupRegExp
                             .isSelected(),
-                            getContext());
+                            getContext(), Globals.prefs);
                 } else if (searchRadioButton.isSelected()) {
                     try {
                         // regex is correct, otherwise OK would have been
                         // disabled
                         // therefore I don't catch anything here
                         resultingGroup = new SearchGroup(nameField.getText().trim(), searchGroupSearchExpression.getText().trim(),
-                                isCaseSensitive(), isRegex(), getContext());
+                                isCaseSensitive(), isRegex(), getContext(), Globals.prefs);
                     } catch (Exception e1) {
                         // should never happen
                     }
@@ -317,7 +317,7 @@ public void actionPerformed(ActionEvent e) {
         searchGroupCaseSensitive.addItemListener(itemListener);
 
         // configure for current type
-        if (editedGroup != null && editedGroup.getClass() == KeywordGroup.class) {
+        if ((editedGroup != null) && (editedGroup.getClass() == KeywordGroup.class)) {
             KeywordGroup group = (KeywordGroup) editedGroup;
             nameField.setText(group.getName());
             keywordGroupSearchField.setText(group.getSearchField());
@@ -326,15 +326,15 @@ public void actionPerformed(ActionEvent e) {
             keywordGroupRegExp.setSelected(group.isRegExp());
             keywordsRadioButton.setSelected(true);
             setContext(editedGroup.getHierarchicalContext());
-        } else if (editedGroup != null && editedGroup.getClass() == SearchGroup.class) {
+        } else if ((editedGroup != null) && (editedGroup.getClass() == SearchGroup.class)) {
             SearchGroup group = (SearchGroup) editedGroup;
             nameField.setText(group.getName());
             searchGroupSearchExpression.setText(group.getSearchExpression());
             searchGroupCaseSensitive.setSelected(group.isCaseSensitive());
             searchGroupRegExp.setSelected(group.isRegExp());
             searchRadioButton.setSelected(true);
             setContext(editedGroup.getHierarchicalContext());
-        } else if (editedGroup != null && editedGroup.getClass() == ExplicitGroup.class) {
+        } else if ((editedGroup != null) && (editedGroup.getClass() == ExplicitGroup.class)) {
             nameField.setText(editedGroup.getName());
             explicitRadioButton.setSelected(true);
             setContext(editedGroup.getHierarchicalContext());

diff --git a/src/main/java/net/sf/jabref/gui/journals/AbbreviateAction.java b/src/main/java/net/sf/jabref/gui/journals/AbbreviateAction.java
@@ -52,7 +52,7 @@ public void run() {
         }
 
         UndoableAbbreviator undoableAbbreviator = new UndoableAbbreviator(
-                Globals.journalAbbreviationLoader.getRepository(), iso);
+                Globals.journalAbbreviationLoader.getRepository(Globals.prefs), iso);
 
         NamedCompound ce = new NamedCompound(Localization.lang("Abbreviate journal names"));
         int count = 0;

diff --git a/src/main/java/net/sf/jabref/gui/journals/ManageJournalsPanel.java b/src/main/java/net/sf/jabref/gui/journals/ManageJournalsPanel.java
@@ -185,7 +185,7 @@ public ManageJournalsPanel(final JabRefFrame frame) {
 
         viewBuiltin.addActionListener(e -> {
             JTable table = new JTable(JournalAbbreviationsUtil
-                    .getTableModel(Globals.journalAbbreviationLoader.getRepository().getAbbreviations()));
+                    .getTableModel(Globals.journalAbbreviationLoader.getRepository(Globals.prefs).getAbbreviations()));
             JScrollPane pane = new JScrollPane(table);
             JOptionPane.showMessageDialog(null, pane, Localization.lang("Journal list preview"),
                     JOptionPane.INFORMATION_MESSAGE);

diff --git a/src/main/java/net/sf/jabref/gui/journals/UnabbreviateAction.java b/src/main/java/net/sf/jabref/gui/journals/UnabbreviateAction.java
@@ -50,7 +50,7 @@ public void run() {
         }
 
         UndoableUnabbreviator undoableAbbreviator = new UndoableUnabbreviator(
-                Globals.journalAbbreviationLoader.getRepository());
+                Globals.journalAbbreviationLoader.getRepository(Globals.prefs));
 
         NamedCompound ce = new NamedCompound(Localization.lang("Unabbreviate journal names"));
         int count = 0;

diff --git a/src/main/java/net/sf/jabref/gui/preftabs/TablePrefsTab.java b/src/main/java/net/sf/jabref/gui/preftabs/TablePrefsTab.java
@@ -301,7 +301,7 @@ public void storeSettings() {
         }
         if (!Objects.equals(oldVal, newVal)) {
             prefs.put(JabRefPreferences.NUMERIC_FIELDS, newVal);
-            InternalBibtexFields.setNumericFieldsFromPrefs(Globals.prefs);
+            InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
         }
 
     }

diff --git a/src/main/java/net/sf/jabref/importer/AppendDatabaseAction.java b/src/main/java/net/sf/jabref/importer/AppendDatabaseAction.java
@@ -168,7 +168,7 @@ private static void mergeFromBibtex(JabRefFrame frame, BasePanel panel, ParserRe
                     // create a dummy group
                     ExplicitGroup group = null;
                     try {
-                        group = new ExplicitGroup("Imported", GroupHierarchyType.INDEPENDENT);
+                        group = new ExplicitGroup("Imported", GroupHierarchyType.INDEPENDENT, Globals.prefs);
                     } catch (ParseException e) {
                         LOGGER.error(e);
                     }

diff --git a/src/main/java/net/sf/jabref/importer/fetcher/ACMPortalFetcher.java b/src/main/java/net/sf/jabref/importer/fetcher/ACMPortalFetcher.java
@@ -62,7 +62,8 @@ public class ACMPortalFetcher implements PreviewEntryFetcher {
 
     private static final Log LOGGER = LogFactory.getLog(ACMPortalFetcher.class);
 
-    private final HtmlToLatexFormatter htmlToLatexFormatter = new HtmlToLatexFormatter();
+    private final HtmlToLatexFormatter htmlToLatexFormatter = new HtmlToLatexFormatter(
+            Globals.prefs.getBoolean(JabRefPreferences.USE_CONVERT_TO_EQUATION));
     private final ProtectTermsFormatter protectTermsFormatter = new ProtectTermsFormatter();
     private final UnitsToLatexFormatter unitsToLatexFormatter = new UnitsToLatexFormatter();
     private String terms;

diff --git a/src/main/java/net/sf/jabref/importer/fetcher/IEEEXploreFetcher.java b/src/main/java/net/sf/jabref/importer/fetcher/IEEEXploreFetcher.java
@@ -81,7 +81,8 @@ public class IEEEXploreFetcher implements EntryFetcher {
 
     private final ProtectTermsFormatter protectTermsFormatter = new ProtectTermsFormatter();
     private final UnitsToLatexFormatter unitsToLatexFormatter = new UnitsToLatexFormatter();
-    private final HtmlToLatexFormatter htmlToLatexFormatter = new HtmlToLatexFormatter();
+    private final HtmlToLatexFormatter htmlToLatexFormatter = new HtmlToLatexFormatter(
+            Globals.prefs.getBoolean(JabRefPreferences.USE_CONVERT_TO_EQUATION));
     private final JCheckBox absCheckBox = new JCheckBox(Localization.lang("Include abstracts"), false);
 
     private boolean shouldContinue;
@@ -444,7 +445,8 @@ private BibEntry cleanup(BibEntry entry) {
 
                 fullName = fullName.trim();
                 if (Globals.prefs.getBoolean(JabRefPreferences.USE_IEEE_ABRV)) {
-                    fullName = abbreviationLoader.getRepository().getMedlineAbbreviation(fullName).orElse(fullName);
+                    fullName = abbreviationLoader.getRepository(Globals.prefs).getMedlineAbbreviation(fullName)
+                            .orElse(fullName);
                 }
             }
             if ("inproceedings".equals(type)) {

diff --git a/src/main/java/net/sf/jabref/logic/autocompleter/AutoCompleterFactory.java b/src/main/java/net/sf/jabref/logic/autocompleter/AutoCompleterFactory.java
@@ -18,6 +18,7 @@
 import java.util.Arrays;
 import java.util.Objects;
 
+import net.sf.jabref.JabRefPreferences;
 import net.sf.jabref.logic.journals.JournalAbbreviationLoader;
 import net.sf.jabref.model.entry.FieldProperties;
 import net.sf.jabref.model.entry.InternalBibtexFields;
@@ -31,10 +32,13 @@ public class AutoCompleterFactory {
 
     private final AutoCompletePreferences preferences;
     private final JournalAbbreviationLoader abbreviationLoader;
+    private final JabRefPreferences jabRefPreferences;
 
-    public AutoCompleterFactory(AutoCompletePreferences preferences, JournalAbbreviationLoader abbreviationLoader) {
+    public AutoCompleterFactory(AutoCompletePreferences preferences, JournalAbbreviationLoader abbreviationLoader,
+            JabRefPreferences jabRefPreferences) {
         this.preferences = Objects.requireNonNull(preferences);
         this.abbreviationLoader = Objects.requireNonNull(abbreviationLoader);
+        this.jabRefPreferences = Objects.requireNonNull(jabRefPreferences);
     }
 
     public AutoCompleter<String> getFor(String fieldName) {
@@ -45,7 +49,7 @@ public AutoCompleter<String> getFor(String fieldName) {
         } else if ("crossref".equals(fieldName)) {
             return new BibtexKeyAutoCompleter(preferences);
         } else if ("journal".equals(fieldName) || "publisher".equals(fieldName)) {
-            return new JournalAutoCompleter(fieldName, preferences, abbreviationLoader);
+            return new JournalAutoCompleter(fieldName, preferences, abbreviationLoader, jabRefPreferences);
         } else {
             return new DefaultAutoCompleter(fieldName, preferences);
         }