Removed last Globals dependency in MetaData (#1867)

* Removed last Globals dependency in MetaData

* Removed Globals from logic tests

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

@@ -123,7 +123,7 @@ public String htmlToLatexConversion() {
     @Benchmark
     public boolean keywordGroupContains() throws ParseException {
         KeywordGroup group = new KeywordGroup("testGroup", "keyword", "testkeyword", false, false,
-                GroupHierarchyType.INDEPENDENT, Globals.prefs);
+                GroupHierarchyType.INDEPENDENT, Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
         return group.containsAll(database.getEntries());
     }
 

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

@@ -66,12 +66,13 @@ public class MetaData implements Iterable<String> {
      * must simply make sure the appropriate changes are reflected in the Vector
      * it has been passed.
      */
-    private MetaData(Map<String, String> inData) throws ParseException {
+    private MetaData(Map<String, String> inData, String keywordSeparator) throws ParseException {
         Objects.requireNonNull(inData);
-        setData(inData);
+        setData(inData, keywordSeparator);
     }
-    private MetaData(Map<String, String> inData, Charset encoding) throws ParseException {
-        this(inData);
+
+    private MetaData(Map<String, String> inData, Charset encoding, String keywordSeparator) throws ParseException {
+        this(inData, keywordSeparator);
         this.encoding = Objects.requireNonNull(encoding);
     }
 
@@ -86,15 +87,16 @@ public MetaData(Charset encoding) {
         this.encoding = encoding;
     }
 
-    public static MetaData parse(Map<String, String> data) throws ParseException {
-        return new MetaData(data);
+    public static MetaData parse(Map<String, String> data, String keywordSeparator) throws ParseException {
+        return new MetaData(data, keywordSeparator);
     }
 
-    public static MetaData parse(Map<String, String> data, Charset encoding) throws ParseException {
-        return new MetaData(data, encoding);
+    public static MetaData parse(Map<String, String> data, Charset encoding, String keywordSeparator)
+            throws ParseException {
+        return new MetaData(data, encoding, keywordSeparator);
     }
 
-    public void setData(Map<String, String> inData) throws ParseException {
+    public void setData(Map<String, String> inData, String keywordSeparator) throws ParseException {
         clearMetaData();
         for (Map.Entry<String, String> entry : inData.entrySet()) {
             StringReader data = new StringReader(entry.getValue());
@@ -109,7 +111,7 @@ public void setData(Map<String, String> inData) throws ParseException {
                 LOGGER.error("Weird error while parsing meta data.", ex);
             }
             if (GROUPSTREE.equals(entry.getKey())) {
-                putGroups(orderedData);
+                putGroups(orderedData, keywordSeparator);
                 // the keys "groupsversion" and "groups" were used in JabRef versions around 1.3, we will not support them anymore
                 eventBus.post(new GroupUpdatedEvent(this));
             } else if (SAVE_ACTIONS.equals(entry.getKey())) {
@@ -186,9 +188,9 @@ public void putData(String key, List<String> orderedData) {
      *
      * @param orderedData The vector of metadata strings
      */
-    private void putGroups(List<String> orderedData) throws ParseException {
+    private void putGroups(List<String> orderedData, String keywordSeparator) throws ParseException {
         try {
-            groupsRoot = GroupTreeNode.parse(orderedData, Globals.prefs);
+            groupsRoot = GroupTreeNode.parse(orderedData, keywordSeparator);
             eventBus.post(new GroupUpdatedEvent(this));
         } catch (ParseException e) {
             throw new ParseException(Localization.lang(

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

@@ -286,7 +286,7 @@ public void actionPerformed(ActionEvent e) {
             return;
         }
 
-        if (SpecialFieldsUtils.keywordSyncEnabled() && !keywordsToAdd.isEmpty()) {
+        if (Globals.prefs.isKeywordSyncEnabled() && !keywordsToAdd.isEmpty()) {
             synchronizeSpecialFields(keywordsToAdd, keywordsToRemove);
         }
 
@@ -312,7 +312,7 @@ private NamedCompound updateKeywords(List<BibEntry> entries, Set<String> keyword
                 ce.addEdit(new UndoableFieldChange(change.get()));
             }
 
-            if (SpecialFieldsUtils.keywordSyncEnabled()) {
+            if (Globals.prefs.isKeywordSyncEnabled()) {
                 SpecialFieldsUtils.syncSpecialFieldsFromKeywords(entry, ce);
             }
         }

src/main/java/net/sf/jabref/gui/groups/AutoGroupDialog.java

@@ -36,6 +36,7 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.layout.format.LatexToUnicodeFormatter;
 import net.sf.jabref.model.entry.FieldName;
+import net.sf.jabref.preferences.JabRefPreferences;
 
 import com.jgoodies.forms.builder.ButtonBarBuilder;
 import com.jgoodies.forms.builder.FormBuilder;
@@ -82,7 +83,8 @@ public void actionPerformed(ActionEvent e) {
                 try {
                     GroupTreeNode autoGroupsRoot = GroupTreeNode.fromGroup(
                             new ExplicitGroup(Localization.lang("Automatically created groups"),
-                                    GroupHierarchyType.INCLUDING, Globals.prefs));
+                                    GroupHierarchyType.INCLUDING,
+                                    Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR)));
                     Set<String> hs;
                     String fieldText = field.getText();
                     if (keywords.isSelected()) {
@@ -110,7 +112,7 @@ public void actionPerformed(ActionEvent e) {
 
                     for (String keyword : hs) {
                         KeywordGroup group = new KeywordGroup(formatter.format(keyword), fieldText, keyword, false, false,
-                                GroupHierarchyType.INDEPENDENT, Globals.prefs);
+                                GroupHierarchyType.INDEPENDENT, Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
                         autoGroupsRoot.addChild(GroupTreeNode.fromGroup(group));
                     }
 

src/main/java/net/sf/jabref/gui/groups/GroupDialog.java

@@ -265,14 +265,15 @@ public void actionPerformed(ActionEvent e) {
                 isOkPressed = true;
             try {
                 if (explicitRadioButton.isSelected()) {
-                    resultingGroup = new ExplicitGroup(nameField.getText().trim(), getContext(), Globals.prefs);
+                    resultingGroup = new ExplicitGroup(nameField.getText().trim(), getContext(),
+                            Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
                 } 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(), Globals.prefs);
+                    resultingGroup = new KeywordGroup(nameField.getText().trim(),
+                            keywordGroupSearchField.getText().trim(), keywordGroupSearchTerm.getText().trim(),
+                            keywordGroupCaseSensitive.isSelected(), keywordGroupRegExp.isSelected(), getContext(),
+                            Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
                 } else if (searchRadioButton.isSelected()) {
                     try {
                         // regex is correct, otherwise OK would have been

src/main/java/net/sf/jabref/gui/importer/actions/AppendDatabaseAction.java

@@ -141,7 +141,7 @@ private static void mergeFromBibtex(JabRefFrame frame, BasePanel panel, ParserRe
                     // create a dummy group
                     try {
                         ExplicitGroup group = new ExplicitGroup("Imported", GroupHierarchyType.INDEPENDENT,
-                                Globals.prefs);
+                                Globals.prefs.get(JabRefPreferences.KEYWORD_SEPARATOR));
                         newGroups.setGroup(group);
                         group.add(appendedEntries);
                     } catch (ParseException e) {

src/main/java/net/sf/jabref/logic/groups/AbstractGroup.java

@@ -8,7 +8,6 @@
 import net.sf.jabref.logic.search.SearchMatcher;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.entry.BibEntry;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 /**
  * A group of BibtexEntries.
@@ -48,9 +47,9 @@ public abstract class AbstractGroup implements SearchMatcher {
      * @throws ParseException If an error occurred and a group could not be created,
      *                        e.g. due to a malformed regular expression.
      */
-    public static AbstractGroup fromString(String s, JabRefPreferences jabRefPreferences) throws ParseException {
+    public static AbstractGroup fromString(String s, String keywordSeparator) throws ParseException {
         if (s.startsWith(KeywordGroup.ID)) {
-            return KeywordGroup.fromString(s, jabRefPreferences);
+            return KeywordGroup.fromString(s, keywordSeparator);
         }
         if (s.startsWith(AllEntriesGroup.ID)) {
             return AllEntriesGroup.fromString(s);
@@ -59,7 +58,7 @@ public static AbstractGroup fromString(String s, JabRefPreferences jabRefPrefere
             return SearchGroup.fromString(s);
         }
         if (s.startsWith(ExplicitGroup.ID)) {
-            return ExplicitGroup.fromString(s, jabRefPreferences);
+            return ExplicitGroup.fromString(s, keywordSeparator);
         }
         return null; // unknown group
     }

src/main/java/net/sf/jabref/logic/groups/ExplicitGroup.java

@@ -11,7 +11,6 @@
 import net.sf.jabref.logic.util.strings.QuotedStringTokenizer;
 import net.sf.jabref.logic.util.strings.StringUtil;
 import net.sf.jabref.model.entry.FieldName;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -29,12 +28,13 @@ public class ExplicitGroup extends KeywordGroup {
 
     private static final Log LOGGER = LogFactory.getLog(ExplicitGroup.class);
 
-    public ExplicitGroup(String name, GroupHierarchyType context, JabRefPreferences jabRefPreferences)
+
+    public ExplicitGroup(String name, GroupHierarchyType context, String keywordSeparator)
             throws ParseException {
-        super(name, FieldName.GROUPS, name, true, false, context, jabRefPreferences);
+        super(name, FieldName.GROUPS, name, true, false, context, keywordSeparator);
     }
 
-    public static ExplicitGroup fromString(String s, JabRefPreferences jabRefPreferences) throws ParseException {
+    public static ExplicitGroup fromString(String s, String keywordSeparator) throws ParseException {
         if (!s.startsWith(ExplicitGroup.ID)) {
             throw new IllegalArgumentException("ExplicitGroup cannot be created from \"" + s + "\".");
         }
@@ -43,7 +43,7 @@ public static ExplicitGroup fromString(String s, JabRefPreferences jabRefPrefere
 
         String name = tok.nextToken();
         int context = Integer.parseInt(tok.nextToken());
-        ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumber(context), jabRefPreferences);
+        ExplicitGroup newGroup = new ExplicitGroup(name, GroupHierarchyType.getByNumber(context), keywordSeparator);
         newGroup.addLegacyEntryKeys(tok);
         return newGroup;
     }
@@ -68,7 +68,7 @@ public void addLegacyEntryKey(String key) {
     @Override
     public AbstractGroup deepCopy() {
         try {
-            ExplicitGroup copy = new ExplicitGroup(getName(), getContext(), jabRefPreferences);
+            ExplicitGroup copy = new ExplicitGroup(getName(), getContext(), keywordSeparator);
             copy.legacyEntryKeys.addAll(legacyEntryKeys);
             return copy;
         } catch (ParseException exception) {

src/main/java/net/sf/jabref/logic/groups/GroupTreeNode.java

@@ -12,7 +12,6 @@
 import net.sf.jabref.logic.search.matchers.MatcherSets;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.entry.BibEntry;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 /**
  * A node in the groups tree that holds exactly one AbstractGroup.
@@ -234,9 +233,9 @@ public GroupTreeNode copyNode() {
         return GroupTreeNode.fromGroup(group);
     }
 
-    public static GroupTreeNode parse(List<String> orderedData, JabRefPreferences jabRefPreferences)
+    public static GroupTreeNode parse(List<String> orderedData, String keywordSeparator)
             throws ParseException {
-        return GroupsParser.importGroups(orderedData, jabRefPreferences);
+        return GroupsParser.importGroups(orderedData, keywordSeparator);
     }
 
     /**

src/main/java/net/sf/jabref/logic/groups/GroupsParser.java

@@ -4,14 +4,13 @@
 
 import net.sf.jabref.logic.importer.util.ParseException;
 import net.sf.jabref.logic.l10n.Localization;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 /**
  * Converts string representation of groups to a parsed {@link GroupTreeNode}.
  */
 class GroupsParser {
 
-    public static GroupTreeNode importGroups(List<String> orderedData, JabRefPreferences jabRefPreferences)
+    public static GroupTreeNode importGroups(List<String> orderedData, String keywordSeparator)
             throws ParseException {
         GroupTreeNode cursor = null;
         GroupTreeNode root = null;
@@ -27,7 +26,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, JabRefPrefere
                 throw new ParseException(Localization.lang("Expected \"%0\" to contain whitespace", string));
             }
             int level = Integer.parseInt(string.substring(0, spaceIndex));
-            AbstractGroup group = AbstractGroup.fromString(string.substring(spaceIndex + 1), jabRefPreferences);
+            AbstractGroup group = AbstractGroup.fromString(string.substring(spaceIndex + 1), keywordSeparator);
             GroupTreeNode newNode = GroupTreeNode.fromGroup(group);
             if (cursor == null) {
                 // create new root

src/main/java/net/sf/jabref/logic/groups/KeywordGroup.java

@@ -14,7 +14,6 @@
 import net.sf.jabref.model.FieldChange;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.model.entry.EntryUtil;
-import net.sf.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -32,7 +31,7 @@ public class KeywordGroup extends AbstractGroup {
     private final boolean regExp;
     private Pattern pattern;
     private final List<String> searchWords;
-    protected final JabRefPreferences jabRefPreferences;
+    protected final String keywordSeparator;
 
     private static final Log LOGGER = LogFactory.getLog(KeywordGroup.class);
 
@@ -42,7 +41,7 @@ public class KeywordGroup extends AbstractGroup {
      */
     public KeywordGroup(String name, String searchField,
                         String searchExpression, boolean caseSensitive, boolean regExp,
-            GroupHierarchyType context, JabRefPreferences jabRefPreferences) throws ParseException {
+            GroupHierarchyType context, String keywordSeparator) throws ParseException {
         super(name, context);
         this.searchField = searchField;
         this.searchExpression = searchExpression;
@@ -51,7 +50,7 @@ public KeywordGroup(String name, String searchField,
         if (this.regExp) {
             compilePattern();
         }
-        this.jabRefPreferences = jabRefPreferences;
+        this.keywordSeparator = keywordSeparator;
         this.searchWords = EntryUtil.getStringAsWords(searchExpression);
     }
 
@@ -70,7 +69,7 @@ private void compilePattern() throws ParseException {
      * @param s The String representation obtained from
      *          KeywordGroup.toString()
      */
-    public static AbstractGroup fromString(String s, JabRefPreferences jabRefPreferences) throws ParseException {
+    public static AbstractGroup fromString(String s, String keywordSeparator) throws ParseException {
         if (!s.startsWith(KeywordGroup.ID)) {
             throw new IllegalArgumentException("KeywordGroup cannot be created from \"" + s + "\".");
         }
@@ -86,7 +85,7 @@ public static AbstractGroup fromString(String s, JabRefPreferences jabRefPrefere
         return new KeywordGroup(StringUtil.unquote(name, AbstractGroup.QUOTE_CHAR),
                 StringUtil.unquote(field, AbstractGroup.QUOTE_CHAR),
                 StringUtil.unquote(expression, AbstractGroup.QUOTE_CHAR), caseSensitive, regExp,
-                GroupHierarchyType.getByNumber(context), jabRefPreferences);
+                GroupHierarchyType.getByNumber(context), keywordSeparator);
     }
 
     /**
@@ -125,9 +124,8 @@ public Optional<EntriesGroupChange> add(List<BibEntry> entriesToAdd) {
             for (BibEntry entry : entriesToAdd) {
                 if (!contains(entry)) {
                     String oldContent = entry.getFieldOptional(searchField).orElse(null);
-                    String pre = jabRefPreferences.get(JabRefPreferences.KEYWORD_SEPARATOR);
                     String newContent = (oldContent == null ? "" : oldContent
-                            + pre)
+                            + keywordSeparator)
                             + searchExpression;
                     entry.setField(searchField, newContent);
 
@@ -263,21 +261,20 @@ private void removeMatches(BibEntry entry) {
             int i;
             int j;
             int k;
-            final String separator = jabRefPreferences.get(JabRefPreferences.KEYWORD_SEPARATOR);
             while ((i = haystack.indexOf(needle)) >= 0) {
                 sbOrig.replace(i, i + needle.length(), "");
                 sbLower.replace(i, i + needle.length(), "");
                 // reduce spaces at i to 1
                 j = i;
                 k = i;
-                while (((j - 1) >= 0) && (separator.indexOf(haystack.charAt(j - 1)) >= 0)) {
+                while (((j - 1) >= 0) && (keywordSeparator.indexOf(haystack.charAt(j - 1)) >= 0)) {
                     --j;
                 }
-                while ((k < haystack.length()) && (separator.indexOf(haystack.charAt(k)) >= 0)) {
+                while ((k < haystack.length()) && (keywordSeparator.indexOf(haystack.charAt(k)) >= 0)) {
                     ++k;
                 }
-                sbOrig.replace(j, k, (j >= 0) && (k < sbOrig.length()) ? separator : "");
-                sbLower.replace(j, k, (j >= 0) && (k < sbOrig.length()) ? separator : "");
+                sbOrig.replace(j, k, (j >= 0) && (k < sbOrig.length()) ? keywordSeparator : "");
+                sbLower.replace(j, k, (j >= 0) && (k < sbOrig.length()) ? keywordSeparator : "");
             }
 
             String result = sbOrig.toString().trim();
@@ -293,7 +290,7 @@ private void removeMatches(BibEntry entry) {
     public AbstractGroup deepCopy() {
         try {
             return new KeywordGroup(getName(), searchField, searchExpression,
-                    caseSensitive, regExp, getContext(), jabRefPreferences);
+                    caseSensitive, regExp, getContext(), keywordSeparator);
         } catch (ParseException exception) {
             // this should never happen, because the constructor obviously succeeded in creating _this_ instance!
             LOGGER.error("Internal error in KeywordGroup.deepCopy(). "