Mark some methods as deprecated in BibEntry and BibDatabase

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

@@ -58,7 +58,7 @@ public void init() throws Exception {
             entry.setField("keyword", "testkeyword");
             entry.setField("year", "1" + i);
             entry.setField("rnd", "2" + randomizer.nextInt());
-            database.insertEntry(entry);
+            database.insertEntryWithDuplicationCheck(entry);
         }
         BibtexDatabaseWriter<StringSaveSession> databaseWriter = new BibtexDatabaseWriter<>(StringSaveSession::new);
         StringSaveSession saveSession = databaseWriter.savePartOfDatabase(

src/main/java/net/sf/jabref/collab/EntryAddChange.java

@@ -31,8 +31,8 @@ public EntryAddChange(BibEntry diskEntry) {
     @Override
     public boolean makeChange(BasePanel panel, BibDatabase secondary, NamedCompound undoEdit) {
         diskEntry.setId(IdGenerator.next());
-        panel.getDatabase().insertEntry(diskEntry);
-        secondary.insertEntry(diskEntry);
+        panel.getDatabase().insertEntryWithDuplicationCheck(diskEntry);
+        secondary.insertEntryWithDuplicationCheck(diskEntry);
         undoEdit.addEdit(new UndoableInsertEntry(panel.getDatabase(), diskEntry, panel));
         return true;
     }

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

@@ -291,7 +291,7 @@ private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCo
 
                 aXmpEntriesInFile.setId(IdGenerator.next());
                 edits.addEdit(new UndoableInsertEntry(panel.getDatabase(), aXmpEntriesInFile, panel));
-                panel.getDatabase().insertEntry(aXmpEntriesInFile);
+                panel.getDatabase().insertEntryWithDuplicationCheck(aXmpEntriesInFile);
                 doLink(aXmpEntriesInFile, fileType, destFilename, true, edits);
 
             }

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

@@ -466,7 +466,7 @@ public void run() {
                         bes = entry;
                         // Store the old value:
                         oldvals.put(bes, bes.getCiteKeyOptional().orElse(null));
-                        bibDatabaseContext.getDatabase().setCiteKeyForEntry(bes, null);
+                        bes.clearCiteKey();
                     }
                 }
 
@@ -824,7 +824,7 @@ private void paste() {
                 // independently of the copied
                 // ones.
                 be.setId(IdGenerator.next());
-                bibDatabaseContext.getDatabase().insertEntry(be);
+                bibDatabaseContext.getDatabase().insertEntryWithDuplicationCheck(be);
 
                 ce.addEdit(new UndoableInsertEntry(bibDatabaseContext.getDatabase(), be, BasePanel.this));
 
@@ -1136,7 +1136,7 @@ public BibEntry newEntry(EntryType type) {
             String id = IdGenerator.next();
             final BibEntry be = new BibEntry(id, actualType.getName());
             try {
-                bibDatabaseContext.getDatabase().insertEntry(be);
+                bibDatabaseContext.getDatabase().insertEntryWithDuplicationCheck(be);
                 // Set owner/timestamp if options are enabled:
                 List<BibEntry> list = new ArrayList<>();
                 list.add(be);
@@ -1290,7 +1290,7 @@ public void listen(EntryChangedEvent entryChangedEvent) {
     public void insertEntry(final BibEntry bibEntry) {
         if (bibEntry != null) {
             try {
-                bibDatabaseContext.getDatabase().insertEntry(bibEntry);
+                bibDatabaseContext.getDatabase().insertEntryWithDuplicationCheck(bibEntry);
                 if (Globals.prefs.getBoolean(JabRefPreferences.USE_OWNER)) {
                     // Set owner field to default value
                     UpdateField.setAutomaticFields(bibEntry, true, true, Globals.prefs.getUpdateFieldPreferences());

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

@@ -124,7 +124,7 @@ public void run() {
                 // and adding merged entries:
                 if (!toAdd.isEmpty()) {
                     for (BibEntry entry : toAdd) {
-                        panel.getDatabase().insertEntry(entry);
+                        panel.getDatabase().insertEntryWithDuplicationCheck(entry);
                         ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry, panel));
                     }
                     panel.markBaseChanged();

src/main/java/net/sf/jabref/gui/importer/EntryFromFileCreatorManager.java

@@ -147,7 +147,7 @@ public int addEntriesFromFiles(List<File> files,
                 if (!database.containsEntryWithId(entry.get().getId())) {
                     // Work around SIDE EFFECT of creator.createEntry. The EntryFromPDFCreator also creates the entry in the table
                     // Therefore, we only insert the entry if it is not already present
-                    if (database.insertEntry(entry.get())) {
+                    if (database.insertEntryWithDuplicationCheck(entry.get())) {
                         importGUIMessages.add("Problem importing " + f.getPath() + ": Insert into BibDatabase failed.");
                     } else {
                         count++;

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

@@ -458,7 +458,7 @@ private void generateKeyForEntry(BibEntry entry) {
 
             entry.setId(IdGenerator.next());
             // Add the entry to the database we are working with:
-            database.insertEntry(entry);
+            database.insertEntryWithDuplicationCheck(entry);
 
             // Generate a unique key:
             BibtexKeyPatternUtil.makeLabel(localMetaData, database, entry,
@@ -501,7 +501,7 @@ private void generateKeys() {
             for (BibEntry entry : entries) {
 
                 entry.setId(IdGenerator.next());
-                database.insertEntry(entry);
+                database.insertEntryWithDuplicationCheck(entry);
 
                 BibtexKeyPatternUtil.makeLabel(localMetaData, database, entry,
                         Globals.prefs.getBibtexKeyPatternPreferences());
@@ -735,7 +735,7 @@ private void addSelectedEntries(NamedCompound ce, final List<BibEntry> selected)
                 }
 
                 entry.setId(IdGenerator.next());
-                panel.getDatabase().insertEntry(entry);
+                panel.getDatabase().insertEntryWithDuplicationCheck(entry);
                 ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), entry, panel));
 
             }

src/main/java/net/sf/jabref/gui/importer/ImportMenuItem.java

@@ -206,7 +206,7 @@ private ParserResult mergeImportResults(List<ImportFormatReader.UnknownFormatImp
 
                 // Merge entries:
                 for (BibEntry entry : pr.getDatabase().getEntries()) {
-                    database.insertEntry(entry);
+                    database.insertEntryWithDuplicationCheck(entry);
                 }
 
                 // Merge strings:
@@ -233,7 +233,7 @@ private ParserResult mergeImportResults(List<ImportFormatReader.UnknownFormatImp
                     if (markEntries) {
                         EntryMarker.markEntry(entry, EntryMarker.IMPORT_MARK_LEVEL, false, new NamedCompound(""));
                     }
-                    database.insertEntry(entry);
+                    database.insertEntryWithDuplicationCheck(entry);
                 }
             }
         }

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

@@ -118,7 +118,7 @@ private static void mergeFromBibtex(JabRefFrame frame, BasePanel panel, ParserRe
                 be.setId(IdGenerator.next());
                 UpdateField.setAutomaticFields(be, overwriteOwner, overwriteTimeStamp,
                         Globals.prefs.getUpdateFieldPreferences());
-                database.insertEntry(be);
+                database.insertEntryWithDuplicationCheck(be);
                 appendedEntries.add(be);
                 originalEntries.add(originalEntry);
                 ce.addEdit(new UndoableInsertEntry(database, be, panel));

src/main/java/net/sf/jabref/gui/maintable/MainTableColumn.java

@@ -94,7 +94,7 @@ public Object getColumnValue(BibEntry entry) {
 
         Optional<String> content = Optional.empty();
         for (String field : bibtexFields) {
-            content = BibDatabase.getResolvedField(field, entry, database.orElse(null));
+            content = entry.getResolvedFieldOrAlias(field, database.orElse(null));
             if (content.isPresent()) {
                 isNameColumn = InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES);
                 break;
@@ -127,7 +127,7 @@ public JLabel getHeaderLabel() {
      * The reasons for being different are (combinations may also happen):
      * - The entry has a crossref where the field content is obtained from
      * - The field has a string in it (which getColumnValue() resolves)
-     * - There are some alias fields. For example, if the entry has a date field but no year field, getResolvedField()
+     * - There are some alias fields. For example, if the entry has a date field but no year field, getResolvedFieldOrAlias()
      *   will return the year value from the date field when queried for year
      *
      *
@@ -148,7 +148,7 @@ public boolean isResolved(BibEntry entry) {
                 return false;
             } else {
                 plainFieldContent = entry.getField(field);
-                resolvedFieldContent = BibDatabase.getResolvedField(field, entry, database.orElse(null));
+                resolvedFieldContent = entry.getResolvedFieldOrAlias(field, database.orElse(null));
             }
 
             if (resolvedFieldContent.isPresent()) {

src/main/java/net/sf/jabref/gui/openoffice/OOBibBase.java

@@ -1366,13 +1366,13 @@ public BibDatabase generateDatabase(List<BibDatabase> databases)
                     BibEntry clonedEntry = (BibEntry) entry.get().clone();
                     clonedEntry.setId(IdGenerator.next());
                     // Insert a copy of the entry
-                    resultDatabase.insertEntry(clonedEntry);
+                    resultDatabase.insertEntryWithDuplicationCheck(clonedEntry);
                     // Check if the cloned entry has a crossref field
                     clonedEntry.getField(FieldName.CROSSREF).ifPresent(crossref -> {
                         // If the crossref entry is not already in the database
                         if (!resultDatabase.getEntryByKey(crossref).isPresent()) {
                             // Add it if it is in the current database
-                            loopDatabase.getEntryByKey(crossref).ifPresent(resultDatabase::insertEntry);
+                            loopDatabase.getEntryByKey(crossref).ifPresent(resultDatabase::insertEntryWithDuplicationCheck);
                         }
                     });
 

src/main/java/net/sf/jabref/gui/undo/UndoableInsertEntry.java

@@ -54,7 +54,7 @@ public void undo() {
     @Override
     public void redo() {
         super.redo();
-        base.insertEntry(entry);
+        base.insertEntryWithDuplicationCheck(entry);
     }
 
 }

src/main/java/net/sf/jabref/logic/auxparser/AuxParser.java

@@ -173,6 +173,6 @@ private void resolveCrossReferences(BibEntry entry, AuxParserResult result) {
     private void insertEntry(BibEntry entry, AuxParserResult result) {
         BibEntry clonedEntry = (BibEntry) entry.clone();
         clonedEntry.setId(IdGenerator.next());
-        result.getGeneratedBibDatabase().insertEntry(clonedEntry);
+        result.getGeneratedBibDatabase().insertEntryWithDuplicationCheck(clonedEntry);
     }
 }

src/main/java/net/sf/jabref/logic/exporter/OpenDocumentRepresentation.java

@@ -199,7 +199,7 @@ public Document getDOMrepresentation() {
     }
 
     private String getField(BibEntry e, String field) {
-        return BibDatabase.getResolvedField(field, e, database).orElse("");
+        return e.getResolvedFieldOrAlias(field, database).orElse("");
     }
 
     private void addTableCell(Document doc, Element parent, String content) {

src/main/java/net/sf/jabref/logic/importer/fileformat/BibtexParser.java

@@ -220,7 +220,7 @@ private void parseAndAddEntry(String type) {
             // store complete parsed serialization (comments, type definition + type contents)
             entry.setParsedSerialization(commentsAndEntryTypeDefinition + dumpTextReadSoFarToString());
 
-            boolean duplicateKey = database.insertEntry(entry);
+            boolean duplicateKey = database.insertEntryWithDuplicationCheck(entry);
             if (duplicateKey) {
                 parserResult.addDuplicateKey(entry.getCiteKey());
             } else if (!entry.getCiteKeyOptional().isPresent() || entry.getCiteKeyOptional().get().isEmpty()) {

src/main/java/net/sf/jabref/logic/importer/fileformat/PdfContentImporter.java

@@ -209,7 +209,7 @@ public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
                 ParserResult parserResult = new ParserResult(result);
                 Optional<BibEntry> entry = DOItoBibTeX.getEntryFromDOI(doi.get().getDOI(), parserResult,
                         importFormatPreferences);
-                entry.ifPresent(parserResult.getDatabase()::insertEntry);
+                entry.ifPresent(parserResult.getDatabase()::insertEntryWithDuplicationCheck);
                 return parserResult;
             }
 

src/main/java/net/sf/jabref/logic/layout/LayoutEntry.java

@@ -193,7 +193,7 @@ public String doLayout(BibEntry bibtex, BibDatabase database, Optional<Pattern>
         case LayoutHelper.IS_LAYOUT_TEXT:
             return text;
         case LayoutHelper.IS_SIMPLE_FIELD:
-            String value = BibDatabase.getResolvedField(text, bibtex, database).orElse("");
+            String value = bibtex.getResolvedFieldOrAlias(text, database).orElse("");
 
             // If a post formatter has been set, call it:
             if (postFormatter != null) {
@@ -212,7 +212,7 @@ public String doLayout(BibEntry bibtex, BibDatabase database, Optional<Pattern>
             // Printing the encoding name is not supported in entry layouts, only
             // in begin/end layouts. This prevents breakage if some users depend
             // on a field called "encoding". We simply return this field instead:
-            return BibDatabase.getResolvedField("encoding", bibtex, database).orElse(null);
+            return bibtex.getResolvedFieldOrAlias("encoding", database).orElse(null);
         default:
             return "";
         }
@@ -231,8 +231,8 @@ private String handleOptionField(BibEntry bibtex, BibDatabase database) {
         } else {
             // changed section begin - arudert
             // resolve field (recognized by leading backslash) or text
-            fieldEntry = text.startsWith("\\") ? BibDatabase
-                    .getResolvedField(text.substring(1), bibtex, database)
+            fieldEntry = text.startsWith("\\") ? bibtex
+                    .getResolvedFieldOrAlias(text.substring(1), database)
                     .orElse("") : BibDatabase.getText(text, database);
             // changed section end - arudert
         }
@@ -254,13 +254,13 @@ private String handleOptionField(BibEntry bibtex, BibDatabase database) {
     private String handleFieldOrGroupStart(BibEntry bibtex, BibDatabase database, Optional<Pattern> highlightPattern) {
         Optional<String> field;
         if (type == LayoutHelper.IS_GROUP_START) {
-            field = BibDatabase.getResolvedField(text, bibtex, database);
+            field = bibtex.getResolvedFieldOrAlias(text, database);
         } else if (text.matches(".*(;|(\\&+)).*")) {
             // split the strings along &, && or ; for AND formatter
             String[] parts = text.split("\\s*(;|(\\&+))\\s*");
             field = Optional.empty();
             for (String part : parts) {
-                field = BibDatabase.getResolvedField(part, bibtex, database);
+                field = bibtex.getResolvedFieldOrAlias(part, database);
                 if (!field.isPresent()) {
                     break;
                 }
@@ -270,7 +270,7 @@ private String handleFieldOrGroupStart(BibEntry bibtex, BibDatabase database, Op
             String[] parts = text.split("\\s*(\\|+)\\s*");
             field = Optional.empty();
             for (String part : parts) {
-                field = BibDatabase.getResolvedField(part, bibtex, database);
+                field = bibtex.getResolvedFieldOrAlias(part, database);
                 if (field.isPresent()) {
                     break;
                 }

src/main/java/net/sf/jabref/logic/openoffice/OOBibStyle.java

@@ -717,7 +717,7 @@ private String getCitationMarkerField(BibEntry entry, BibDatabase database, Stri
         String authorField = getStringCitProperty(AUTHOR_FIELD);
         String[] fields = field.split(FieldName.FIELD_SEPARATOR);
         for (String s : fields) {
-            Optional<String> content = BibDatabase.getResolvedField(s, entry, database);
+            Optional<String> content = entry.getResolvedFieldOrAlias(s, database);
 
             if ((content.isPresent()) && !content.get().trim().isEmpty()) {
                 if (field.equals(authorField) && StringUtil.isInCurlyBrackets(content.get())) {

src/main/java/net/sf/jabref/logic/util/io/RegExpFileSearch.java

@@ -316,7 +316,7 @@ public static String getFieldAndFormat(String fieldAndFormat, BibEntry entry, Bi
         }
 
         // If no field value was found, try to interpret it as a key generator field marker:
-        String fieldValue = BibDatabase.getResolvedField(beforeColon, entry, database)
+        String fieldValue = entry.getResolvedFieldOrAlias(beforeColon, database)
                 .orElse(BibtexKeyPatternUtil.makeLabel(entry, beforeColon));
 
         if (fieldValue == null) {

src/main/java/net/sf/jabref/logic/xmp/XMPSchemaBibtex.java

@@ -279,7 +279,7 @@ public void setBibtexEntry(BibEntry entry, BibDatabase database, XMPPreferences
         }
 
         for (String field : fields) {
-            String value = BibDatabase.getResolvedField(field, entry, database).orElse("");
+            String value = entry.getResolvedFieldOrAlias(field, database).orElse("");
             if (InternalBibtexFields.getFieldProperties(field).contains(FieldProperty.PERSON_NAMES)) {
                 setPersonList(field, value);
             } else {