Fix Nullwarnings

jablib/src/main/java/org/jabref/logic/ai/AiPreferences.java

@@ -116,6 +116,9 @@ public AiPreferences(boolean enableAi,
         this.ragMaxResultsCount = new SimpleIntegerProperty(ragMaxResultsCount);
         this.ragMinScore = new SimpleDoubleProperty(ragMinScore);
 
+        this.apiKeyChangeListener = () -> {
+        };
+
         this.templates = Map.of(
                 AiTemplate.CHATTING_SYSTEM_MESSAGE, new SimpleStringProperty(templates.get(AiTemplate.CHATTING_SYSTEM_MESSAGE)),
                 AiTemplate.CHATTING_USER_MESSAGE, new SimpleStringProperty(templates.get(AiTemplate.CHATTING_USER_MESSAGE)),
@@ -550,14 +553,14 @@ public void apiKeyUpdated() {
     }
 
     public void setTemplate(AiTemplate aiTemplate, String template) {
-        templates.get(aiTemplate).set(template);
+        templateProperty(aiTemplate).set(template);
     }
 
     public String getTemplate(AiTemplate aiTemplate) {
-        return templates.get(aiTemplate).get();
+        return templateProperty(aiTemplate).get();
     }
 
     public StringProperty templateProperty(AiTemplate aiTemplate) {
-        return templates.get(aiTemplate);
+        return templates.getOrDefault(aiTemplate, new SimpleStringProperty(""));
     }
 }

jablib/src/main/java/org/jabref/logic/ai/ingestion/MVStoreEmbeddingStore.java

@@ -125,7 +125,7 @@ public EmbeddingSearchResult<TextSegment> search(EmbeddingSearchRequest request)
         PriorityQueue<EmbeddingMatch<TextSegment>> matches = new PriorityQueue<>(comparator);
 
         applyFilter(request.filter()).forEach(id -> {
-            EmbeddingRecord eRecord = embeddingsMap.get(id);
+            EmbeddingRecord eRecord = embeddingsMap.getOrDefault(id, new EmbeddingRecord(null, "", new float[0]));
 
             double cosineSimilarity = CosineSimilarity.between(Embedding.from(eRecord.embeddingVector), request.queryEmbedding());
             double score = RelevanceScore.fromCosineSimilarity(cosineSimilarity);

jablib/src/main/java/org/jabref/logic/ai/ingestion/model/JabRefEmbeddingModel.java

@@ -74,15 +74,15 @@ public void startRebuildingTask() {
         predictorProperty.set(Optional.empty());
 
         new UpdateEmbeddingModelTask(aiPreferences, predictorProperty)
-                .onSuccess(v -> {
+                .onSuccess(_ -> {
                     LOGGER.info("Embedding model was successfully updated");
                     errorWhileBuildingModel = "";
                     eventBus.post(new EmbeddingModelBuiltEvent());
                 })
                 .onFailure(e -> {
                     LOGGER.error("An error occurred while building the embedding model", e);
                     notificationService.notify(Localization.lang("An error occurred while building the embedding model"));
-                    errorWhileBuildingModel = e.getMessage();
+                    errorWhileBuildingModel = e.getMessage() == null ? "" : e.getMessage();
                     eventBus.post(new EmbeddingModelBuildingErrorEvent());
                 })
                 .executeWith(taskExecutor);

jablib/src/main/java/org/jabref/logic/ai/util/MVStoreBase.java

@@ -8,7 +8,7 @@
 
 import org.h2.mvstore.MVStore;
 import org.h2.mvstore.MVStoreException;
-import org.jspecify.annotations.Nullable;
+import org.jspecify.annotations.NonNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -17,7 +17,7 @@ public abstract class MVStoreBase implements AutoCloseable {
 
     protected MVStore mvStore;
 
-    public MVStoreBase(@Nullable Path path, NotificationService dialogService) {
+    public MVStoreBase(@NonNull Path path, NotificationService dialogService) {
         Path mvStorePath = path;
 
         try {

jablib/src/main/java/org/jabref/logic/importer/FetcherException.java

@@ -9,6 +9,7 @@
 import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.http.SimpleHttpResponse;
 
+import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -18,10 +19,13 @@ public class FetcherException extends JabRefException {
     private static final Pattern API_KEY_PATTERN = Pattern.compile("(?i)(?<" + API_KEY_PARAM_NAME + ">api|key|api[-_]?key)=[^&]*");
     private static final String REDACTED_STRING = "[REDACTED]";
 
+    @Nullable
     private final String url;
+
+    @Nullable
     private final SimpleHttpResponse httpResponse;
 
-    public FetcherException(String url, SimpleHttpResponse httpResponse) {
+    public FetcherException(@Nullable String url, @Nullable SimpleHttpResponse httpResponse) {
         // Empty string handled at org.jabref.logic.importer.FetcherException.getPrefix.
         super("");
         this.url = url;
@@ -87,7 +91,7 @@ public String getLocalizedMessage() {
     }
 
     String getRedactedUrl() {
-        return getRedactedUrl(url);
+        return getRedactedUrl(url == null ? "" : url);
     }
 
     public static String getRedactedUrl(String source) {

jablib/src/main/java/org/jabref/logic/importer/fetcher/ISIDOREFetcher.java

@@ -82,7 +82,7 @@ public Parser getParser() {
             } catch (ParserConfigurationException | IOException | SAXException e) {
                 Unchecked.throwChecked(new FetcherException("Issue with parsing link", e));
             }
-            return null;
+            return List.of();
         };
     }
 

jablib/src/main/java/org/jabref/logic/importer/fetcher/ResearchGate.java

@@ -221,7 +221,7 @@ public List<BibEntry> performSearch(BaseQueryNode queryNode) throws FetcherExcep
             html = getPage(url);
             // ResearchGate's server blocks when too many request are made
             if (!html.getElementsByClass("nova-legacy-v-publication-item__title").hasText()) {
-                throw new FetcherException(url, "Required HTML element not found", null);
+                throw new FetcherException(url, "Required HTML element not found", new IllegalStateException("Missing element"));
             }
         } catch (IOException e) {
             throw new FetcherException(url, e);
@@ -230,11 +230,13 @@ public List<BibEntry> performSearch(BaseQueryNode queryNode) throws FetcherExcep
         Elements sol = html.getElementsByClass("nova-legacy-v-publication-item__title");
         List<String> urls = sol.select("a").eachAttr("href").stream()
                                .filter(stream -> stream.contains("publication/"))
-                               .map(resultStream -> resultStream.substring(resultStream.indexOf("publication/") + 12, resultStream.indexOf("_")))
+                               .map(resultStream -> resultStream.substring(
+                                       resultStream.indexOf("publication/") + 12,
+                                       resultStream.indexOf("_")))
                                .map(idStream -> SEARCH_FOR_BIB_ENTRY + idStream)
                                .map(this::getInputStream)
-                               .filter(Objects::nonNull)
-                               .map(stream -> stream.lines().collect(Collectors.joining(OS.NEWLINE)))
+                               .flatMap(Optional::stream)
+                               .map(reader -> reader.lines().collect(Collectors.joining(OS.NEWLINE)))
                                .toList();
 
         List<BibEntry> list = new ArrayList<>();
@@ -251,14 +253,14 @@ public List<BibEntry> performSearch(BaseQueryNode queryNode) throws FetcherExcep
         return list;
     }
 
-    private BufferedReader getInputStream(String urlString) {
+    private Optional<BufferedReader> getInputStream(String urlString) {
         try {
             URL url = URLUtil.create(urlString);
-            return new BufferedReader(new InputStreamReader(url.openStream()));
+            return Optional.of(new BufferedReader(new InputStreamReader(url.openStream())));
         } catch (IOException e) {
             LOGGER.debug("Wrong URL", e);
+            return Optional.empty();
         }
-        return null;
     }
 
     @Override

jablib/src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -32,6 +32,7 @@
 import org.jabref.model.study.Study;
 
 import org.jspecify.annotations.NonNull;
+import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -62,9 +63,12 @@ public class BibDatabaseContext {
     /**
      * The path where this database was last saved to.
      */
+    @Nullable
     private Path path;
 
+    @Nullable
     private DatabaseSynchronizer dbmsSynchronizer;
+    @Nullable
     private CoarseChangeFilter dbmsListener;
     private DatabaseLocation location;
 
@@ -223,10 +227,15 @@ private Path getFileDirectoryPath(String directory) {
 
         // If this path is relative, we try to interpret it as relative to the file path of this BIB file:
         return getDatabasePath()
-                .map(databaseFile -> databaseFile.getParent().resolve(path).normalize().toAbsolutePath())
+                .map(databaseFile -> Optional.ofNullable(databaseFile.getParent())
+                                             .orElse(Path.of(""))
+                                             .resolve(path)
+                                             .normalize()
+                                             .toAbsolutePath())
                 .orElse(path);
     }
 
+    @Nullable
     public DatabaseSynchronizer getDBMSSynchronizer() {
         return this.dbmsSynchronizer;
     }
@@ -250,7 +259,9 @@ public void convertToSharedDatabase(DatabaseSynchronizer dmbsSynchronizer) {
 
     public void convertToLocalDatabase() {
         if (dbmsListener != null && (location == DatabaseLocation.SHARED)) {
-            dbmsListener.unregisterListener(dbmsSynchronizer);
+            if (dbmsSynchronizer != null) {
+                dbmsListener.unregisterListener(dbmsSynchronizer);
+            }
             dbmsListener.shutdown();
         }
 

jablib/src/main/java/org/jabref/model/entry/field/StandardField.java

@@ -34,7 +34,7 @@ public enum StandardField implements Field {
     DATE("date", FieldProperty.DATE),
     DAY("day"),
     DAYFILED("dayfiled"),
-    DOI("doi", "DOI", FieldProperty.VERBATIM, FieldProperty.IDENTIFIER),
+    DOI("doi", FieldProperty.VERBATIM, FieldProperty.IDENTIFIER),
     EDITION("edition", FieldProperty.NUMERIC),
     EDITOR("editor", FieldProperty.PERSON_NAMES),
     EDITORA("editora", FieldProperty.PERSON_NAMES),
@@ -64,9 +64,9 @@ public enum StandardField implements Field {
     IDS("ids", FieldProperty.MULTIPLE_ENTRY_LINK),
     INSTITUTION("institution"),
     INTRODUCTION("introduction", FieldProperty.PERSON_NAMES),
-    ISBN("isbn", "ISBN", FieldProperty.VERBATIM),
-    ISRN("isrn", "ISRN", FieldProperty.VERBATIM),
-    ISSN("issn", "ISSN", FieldProperty.VERBATIM),
+    ISBN("isbn", FieldProperty.VERBATIM),
+    ISRN("isrn", FieldProperty.VERBATIM),
+    ISSN("issn", FieldProperty.VERBATIM),
     ISSUE("issue"),
     ISSUETITLE("issuetitle"),
     ISSUESUBTITLE("issuesubtitle"),
@@ -96,9 +96,9 @@ public enum StandardField implements Field {
     PAGETOTAL("pagetotal", FieldProperty.NUMERIC),
     PAGINATION("pagination", FieldProperty.PAGINATION),
     PART("part"),
-    PDF("pdf", "PDF"),
-    PMID("pmid", "PMID", FieldProperty.NUMERIC, FieldProperty.IDENTIFIER),
-    PS("ps", "PS"),
+    PDF("pdf"),
+    PMID("pmid", FieldProperty.NUMERIC, FieldProperty.IDENTIFIER),
+    PS("ps"),
     PUBLISHER("publisher"),
     PUBSTATE("pubstate"),
     PRIMARYCLASS("primaryclass"),
@@ -118,8 +118,8 @@ public enum StandardField implements Field {
     TITLEADDON("titleaddon"),
     TRANSLATOR("translator", FieldProperty.PERSON_NAMES),
     TYPE("type"),
-    URI("uri", "URI", FieldProperty.EXTERNAL, FieldProperty.VERBATIM),
-    URL("url", "URL", FieldProperty.EXTERNAL, FieldProperty.VERBATIM),
+    URI("uri", FieldProperty.EXTERNAL, FieldProperty.VERBATIM),
+    URL("url", FieldProperty.EXTERNAL, FieldProperty.VERBATIM),
     URLDATE("urldate", FieldProperty.DATE),
     VENUE("venue"),
     VERSION("version"),
@@ -152,7 +152,6 @@ public enum StandardField implements Field {
     private static final Map<String, StandardField> NAME_TO_STANDARD_FIELD = new HashMap<>();
 
     private final String name;
-    private final String displayName;
     private final EnumSet<FieldProperty> properties;
 
     static {
@@ -163,25 +162,11 @@ public enum StandardField implements Field {
 
     StandardField(String name) {
         this.name = name;
-        this.displayName = null;
         this.properties = EnumSet.noneOf(FieldProperty.class);
     }
 
-    StandardField(String name, String displayName) {
-        this.name = name;
-        this.displayName = displayName;
-        this.properties = EnumSet.noneOf(FieldProperty.class);
-    }
-
-    StandardField(String name, String displayName, FieldProperty first, FieldProperty... rest) {
-        this.name = name;
-        this.displayName = displayName;
-        this.properties = EnumSet.of(first, rest);
-    }
-
     StandardField(String name, FieldProperty first, FieldProperty... rest) {
         this.name = name;
-        this.displayName = null;
         this.properties = EnumSet.of(first, rest);
     }