Code refinements (#11851)

* Refine JavaDoc

* OpenRewrite: OptionalNotEmptyToIsPresent and OptionalNotPresentToIsEmpty

rewrite.yml

@@ -102,6 +102,8 @@ recipeList:
   - org.openrewrite.java.migrate.io.ReplaceFileInOrOutputStreamFinalizeWithClose
   - org.openrewrite.java.migrate.net.JavaNetAPIs
   - org.openrewrite.java.migrate.net.URLConstructorsToURIRecipes
+  - org.openrewrite.java.migrate.util.OptionalNotEmptyToIsPresent
+  - org.openrewrite.java.migrate.util.OptionalNotPresentToIsEmpty
   - org.openrewrite.java.migrate.util.SequencedCollection
   - org.openrewrite.java.migrate.lang.StringFormatted
 

src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java

@@ -68,7 +68,7 @@ protected SequencedSet<Field> determineFieldsToShow(BibEntry entry) {
         BibDatabaseMode mode = databaseContext.getMode();
         Optional<BibEntryType> entryType = entryTypesManager.enrich(entry.getType(), mode);
         if (entryType.isPresent()) {
-            return entryType.get().getDeprecatedFields(mode).stream().filter(field -> !entry.getField(field).isEmpty()).collect(Collectors.toCollection(LinkedHashSet::new));
+            return entryType.get().getDeprecatedFields(mode).stream().filter(field -> entry.getField(field).isPresent()).collect(Collectors.toCollection(LinkedHashSet::new));
         } else {
             // Entry type unknown -> treat all fields as required (thus no optional fields)
             return new LinkedHashSet<>();

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -33,7 +33,7 @@ public String getAPIUrl(String entry_point, BibEntry entry) {
 
     @Override
     public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
-        if (!entry.getDOI().isPresent()) {
+        if (entry.getDOI().isEmpty()) {
             return List.of();
         }
 
@@ -59,7 +59,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
 
     @Override
     public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
-        if (!entry.getDOI().isPresent()) {
+        if (entry.getDOI().isEmpty()) {
             return List.of();
         }
 

src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java

@@ -126,7 +126,7 @@ private void resolveTags(AuxParserResult result) {
         List<BibEntry> entriesToInsert = new ArrayList<>();
 
         for (String key : result.getUniqueKeys()) {
-            if (!result.getGeneratedBibDatabase().getEntryByCitationKey(key).isPresent()) {
+            if (result.getGeneratedBibDatabase().getEntryByCitationKey(key).isEmpty()) {
                 Optional<BibEntry> entry = masterDatabase.getEntryByCitationKey(key);
                 if (entry.isPresent()) {
                     entriesToInsert.add(entry.get());
@@ -155,7 +155,7 @@ private void resolveCrossReferences(List<BibEntry> entries, AuxParserResult resu
         List<BibEntry> entriesToInsert = new ArrayList<>();
         for (BibEntry entry : entries) {
             entry.getField(StandardField.CROSSREF).ifPresent(crossref -> {
-                if (!result.getGeneratedBibDatabase().getEntryByCitationKey(crossref).isPresent()) {
+                if (result.getGeneratedBibDatabase().getEntryByCitationKey(crossref).isEmpty()) {
                     Optional<BibEntry> refEntry = masterDatabase.getEntryByCitationKey(crossref);
 
                     if (refEntry.isPresent()) {

src/main/java/org/jabref/logic/bibtex/comparator/BibDatabaseDiff.java

@@ -41,7 +41,7 @@ private BibDatabaseDiff(BibDatabaseContext originalDatabase, BibDatabaseContext
     }
 
     private boolean isEmpty() {
-        return !metaDataDiff.isPresent() && !preambleDiff.isPresent() && bibStringDiffs.isEmpty() && entryDiffs.isEmpty();
+        return metaDataDiff.isEmpty() && preambleDiff.isEmpty() && bibStringDiffs.isEmpty() && entryDiffs.isEmpty();
     }
 
     private List<BibEntryDiff> getBibEntryDiffs(BibDatabaseContext originalDatabase, BibDatabaseContext newDatabase) {

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

@@ -25,7 +25,7 @@ public List<FieldChange> cleanup(BibEntry entry) {
             Field oldField = alias.getKey();
             Field newField = alias.getValue();
             entry.getField(oldField).ifPresent(oldValue -> {
-                if (!oldValue.isEmpty() && (!entry.getField(newField).isPresent())) {
+                if (!oldValue.isEmpty() && (entry.getField(newField).isEmpty())) {
                     // There is content in the old field and no value in the new, so just copy
                     entry.setField(newField, oldValue).ifPresent(changes::add);
                     entry.clearField(oldField).ifPresent(changes::add);

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

@@ -40,7 +40,7 @@ public List<FieldChange> cleanup(BibEntry entry) {
             Field oldField = alias.getValue();
             Field newField = alias.getKey();
             entry.getField(oldField).ifPresent(oldValue -> {
-                if (!oldValue.isEmpty() && (!entry.getField(newField).isPresent())) {
+                if (!oldValue.isEmpty() && (entry.getField(newField).isEmpty())) {
                     // There is content in the old field and no value in the new, so just copy
                     entry.setField(newField, oldValue).ifPresent(changes::add);
                     entry.clearField(oldField).ifPresent(changes::add);

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

@@ -18,7 +18,7 @@ public class FileLinksCleanup implements CleanupJob {
     @Override
     public List<FieldChange> cleanup(BibEntry entry) {
         Optional<String> oldValue = entry.getField(StandardField.FILE);
-        if (!oldValue.isPresent()) {
+        if (oldValue.isEmpty()) {
             return Collections.emptyList();
         }
 

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

@@ -14,7 +14,7 @@ public class ISSNCleanup implements CleanupJob {
     @Override
     public List<FieldChange> cleanup(BibEntry entry) {
         Optional<String> issnString = entry.getField(StandardField.ISSN);
-        if (!issnString.isPresent()) {
+        if (issnString.isEmpty()) {
             return Collections.emptyList();
         }
 

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

@@ -26,23 +26,15 @@ public class ACS implements FulltextFetcher {
     private static final String SOURCE = "https://pubs.acs.org/doi/abs/%s";
 
     /**
-     * Tries to find a fulltext URL for a given BibTex entry.
-     * <p>
-     * Currently only uses the DOI if found.
-     *
-     * @param entry The Bibtex entry
-     * @return The fulltext PDF URL Optional, if found, or an empty Optional if not found.
-     * @throws NullPointerException if no BibTex entry is given
-     * @throws java.io.IOException
+     * Tries to find a fulltext URL for a given BibTeX entry.
+     * Requires the entry to have a DOI field.
+     * In case no DOI is present, an empty Optional is returned.
      */
     @Override
     public Optional<URL> findFullText(BibEntry entry) throws IOException {
         Objects.requireNonNull(entry);
-
-        // DOI search
         Optional<DOI> doi = entry.getField(StandardField.DOI).flatMap(DOI::parse);
-
-        if (!doi.isPresent()) {
+        if (doi.isEmpty()) {
             return Optional.empty();
         }
 

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

@@ -35,7 +35,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException {
 
         Optional<DOI> doi = entry.getField(StandardField.DOI).flatMap(DOI::parse);
 
-        if (!doi.isPresent()) {
+        if (doi.isEmpty()) {
             return Optional.empty();
         }
 

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

@@ -54,7 +54,7 @@ public String getName() {
     @Override
     public List<BibEntry> performSearch(BibEntry entry) throws FetcherException {
         Optional<String> title = entry.getFieldLatexFree(StandardField.TITLE);
-        if (!title.isPresent()) {
+        if (title.isEmpty()) {
             // without a title there is no reason to ask MrDLib
             return List.of();
         }

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

@@ -36,7 +36,7 @@ public Optional<URL> findFullText(BibEntry entry) throws IOException {
         Optional<DOI> doi = entry.getField(StandardField.DOI)
                                  .flatMap(DOI::parse);
 
-        if (!doi.isPresent()) {
+        if (doi.isEmpty()) {
             return Optional.empty();
         }
 

src/main/java/org/jabref/logic/integrity/DateChecker.java

@@ -15,7 +15,7 @@ public Optional<String> checkValue(String value) {
         }
 
         Optional<Date> parsedDate = Date.parse(value);
-        if (!parsedDate.isPresent()) {
+        if (parsedDate.isEmpty()) {
             return Optional.of(Localization.lang("incorrect format"));
         }
 

src/main/java/org/jabref/logic/integrity/FileChecker.java

@@ -36,7 +36,7 @@ public Optional<String> checkValue(String value) {
 
         for (LinkedFile file : linkedFiles) {
             Optional<Path> linkedFile = file.findIn(context, filePreferences);
-            if ((!linkedFile.isPresent()) || !Files.exists(linkedFile.get())) {
+            if ((linkedFile.isEmpty()) || !Files.exists(linkedFile.get())) {
                 return Optional.of(Localization.lang("link should refer to a correct file path"));
             }
         }

src/main/java/org/jabref/logic/msbib/MSBibConverter.java

@@ -67,7 +67,7 @@ public static MSBibEntry convert(BibEntry entry) {
         result.day = entry.getFieldOrAliasLatexFree(StandardField.DAY).orElse(null);
         result.month = entry.getMonth().map(Month::getFullName).orElse(null);
 
-        if (!entry.getFieldLatexFree(StandardField.YEAR).isPresent()) {
+        if (entry.getFieldLatexFree(StandardField.YEAR).isEmpty()) {
             result.year = entry.getFieldOrAliasLatexFree(StandardField.YEAR).orElse(null);
         }
         result.journalName = entry.getFieldOrAliasLatexFree(StandardField.JOURNAL).orElse(null);

src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java

@@ -327,7 +327,7 @@ public void pullChanges() {
      * Synchronizes local BibEntries only if last entry changes still remain
      */
     public void pullLastEntryChanges() {
-        if (!lastEntryChanged.isEmpty()) {
+        if (lastEntryChanged.isPresent()) {
             if (!checkCurrentConnection()) {
                 return;
             }
@@ -342,7 +342,7 @@ public void pullLastEntryChanges() {
      * Synchronizes local BibEntries and pulls remaining last entry changes
      */
     private void pullWithLastEntry() {
-        if (!lastEntryChanged.isEmpty() && isPresentLocalBibEntry(lastEntryChanged.get())) {
+        if (lastEntryChanged.isPresent() && isPresentLocalBibEntry(lastEntryChanged.get())) {
             synchronizeSharedEntry(lastEntryChanged.get());
         }
         lastEntryChanged = Optional.empty();

src/main/java/org/jabref/migrations/ConvertLegacyExplicitGroups.java

@@ -18,7 +18,7 @@ public class ConvertLegacyExplicitGroups implements PostOpenMigration {
     @Override
     public void performMigration(ParserResult parserResult) {
         Objects.requireNonNull(parserResult);
-        if (!parserResult.getMetaData().getGroups().isPresent()) {
+        if (parserResult.getMetaData().getGroups().isEmpty()) {
             return;
         }
 

src/main/java/org/jabref/migrations/ConvertMarkingToGroups.java

@@ -49,7 +49,7 @@ public void performMigration(ParserResult parserResult) {
                 markingGroup.addEntriesToGroup(markingMatchedEntries);
             }
 
-            if (!parserResult.getMetaData().getGroups().isPresent()) {
+            if (parserResult.getMetaData().getGroups().isEmpty()) {
                 parserResult.getMetaData().setGroups(GroupTreeNode.fromGroup(DefaultGroupsFactory.getAllEntriesGroup()));
             }
             GroupTreeNode root = parserResult.getMetaData().getGroups().get();
@@ -68,7 +68,7 @@ private Multimap<String, BibEntry> getMarkingWithEntries(List<BibEntry> entries)
 
         for (BibEntry entry : entries) {
             Optional<String> marking = entry.getField(InternalField.MARKED_INTERNAL);
-            if (!marking.isPresent()) {
+            if (marking.isEmpty()) {
                 continue;
             }
 

src/main/java/org/jabref/model/util/OptionalUtil.java

@@ -13,8 +13,8 @@
 public class OptionalUtil {
 
     public static <T, U> boolean equals(Optional<T> left, Optional<U> right, BiPredicate<T, U> equality) {
-        if (!left.isPresent()) {
-            return !right.isPresent();
+        if (left.isEmpty()) {
+            return right.isEmpty();
         } else {
             if (right.isPresent()) {
                 return equality.test(left.get(), right.get());