Miscellaneous refactoring - II

jabgui/src/main/java/org/jabref/gui/exporter/WriteMetadataToLinkedPdfsAction.java

@@ -1,17 +1,22 @@
 package org.jabref.gui.exporter;
 
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
+
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.fieldeditors.WriteMetadataToSinglePdfAction;
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.bibtex.FieldPreferences;
+import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.BackgroundTask;
@@ -178,7 +183,10 @@ public Void call() {
                                         filePreferences,
                                         xmpPreferences);
                                 entriesChanged++;
-                            } catch (Exception e) {
+                            } catch (IOException
+                                     | TransformerException
+                                     | SaveException
+                                     | ParserConfigurationException e) {
                                 LOGGER.error("Error while writing XMP data to pdf '{}'", file, e);
                                 failedWrittenFiles.add(file);
                                 errors++;

jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBaseConnect.java

@@ -27,6 +27,7 @@
 import com.sun.star.lang.XComponent;
 import com.sun.star.lang.XMultiComponentFactory;
 import com.sun.star.text.XTextDocument;
+import com.sun.star.uno.Exception;
 import com.sun.star.uno.XComponentContext;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -73,7 +74,7 @@ private XDesktop simpleBootstrap(Path loPath)
         Object desktop;
         try {
             desktop = sem.createInstanceWithContext("com.sun.star.frame.Desktop", context);
-        } catch (com.sun.star.uno.Exception e) {
+        } catch (Exception e) {
             throw new CreationException(e.getMessage());
         }
         return UnoCast.cast(XDesktop.class, desktop).get();

jabgui/src/main/java/org/jabref/gui/slr/ManageStudyDefinitionViewModel.java

@@ -34,6 +34,7 @@
 import org.jabref.model.study.StudyDatabase;
 import org.jabref.model.study.StudyQuery;
 
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -195,7 +196,7 @@ public SlrStudyAndDirectory saveStudy() {
 
         try {
             new GitHandler(studyDirectory).createCommitOnCurrentBranch("Update study definition", false);
-        } catch (Exception e) {
+        } catch (IOException | GitAPIException e) {
             LOGGER.error("Could not commit study definition file in directory {}", studyDirectory, e);
             dialogService.notify(Localization.lang("Please enter a valid file path.") +
                     ": " + studyDirectory);

jabgui/src/main/java/org/jabref/gui/util/FilteredListProxy.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.util;
 
 import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.util.Arrays;
 import java.util.ListIterator;
@@ -34,7 +35,10 @@ public static void refilterListReflection(FilteredList<BibEntryTableViewModel> f
                 initReflection();
             }
             REFILTER_METHOD.invoke(filteredList);
-        } catch (Exception e) {
+        } catch (IllegalAccessException
+                 | InvocationTargetException
+                 | NoSuchMethodException
+                 | NoSuchFieldException e) {
             LOGGER.warn("Could not refilter list", e);
         }
     }

jabkit/src/main/java/module-info.java

@@ -20,4 +20,5 @@
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     requires org.tinylog.impl;
+    requires java.xml;
 }

jabkit/src/main/java/org/jabref/cli/Convert.java

@@ -1,11 +1,16 @@
 package org.jabref.cli;
 
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Optional;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
+
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
+import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
@@ -102,7 +107,10 @@ protected void exportFile(@NonNull ParserResult parserResult, @NonNull Path outp
                     parserResult.getDatabaseContext().getDatabase().getEntries(),
                     fileDirForDatabase,
                     Injector.instantiateModelOrService(JournalAbbreviationRepository.class));
-        } catch (Exception ex) {
+        } catch (IOException
+                | SaveException
+                | ParserConfigurationException
+                | TransformerException ex) {
             LOGGER.error("Could not export file '{}'.", outputFile, ex);
         }
     }

jabkit/src/main/java/org/jabref/cli/PdfUpdate.java

@@ -1,13 +1,18 @@
 package org.jabref.cli;
 
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Optional;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
+
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
+import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.exporter.XmpPdfExporter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
@@ -180,7 +185,10 @@ private static void writeMetadataToPDFsOfEntry(BibDatabaseContext databaseContex
                     System.out.println(Localization.lang("Cannot embed metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
                 }
             }
-        } catch (Exception e) {
+        } catch (IOException
+                 | ParserConfigurationException
+                 | SaveException
+                 | TransformerException e) {
             LOGGER.error("Failed writing metadata on a linked file of {}.", citeKey);
         }
     }
@@ -248,7 +256,10 @@ private static void writeMetadataToPdfByFileNames(BibDatabaseContext databaseCon
                         System.out.println(Localization.lang("File %0 is not linked to any entry in library.", filePath));
                     }
                 }
-            } catch (Exception e) {
+            } catch (IOException
+                     | ParserConfigurationException
+                     | SaveException
+                     | TransformerException e) {
                 LOGGER.error("Error writing entry to {}.", filePath);
             }
         }

jabkit/src/main/java/org/jabref/cli/Search.java

@@ -5,8 +5,12 @@
 import java.util.List;
 import java.util.Optional;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerException;
+
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
+import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
@@ -123,7 +127,10 @@ public void run() {
                         matches,
                         List.of(),
                         Injector.instantiateModelOrService(JournalAbbreviationRepository.class));
-            } catch (Exception ex) {
+            } catch (IOException
+                     | SaveException
+                     | ParserConfigurationException
+                     | TransformerException ex) {
                 LOGGER.error("Could not export file '{}}'", outputFile.toAbsolutePath(), ex);
             }
         }

jablib/src/main/java/org/jabref/generators/CitationStyleCatalogGenerator.java

@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -49,7 +50,7 @@ public static void generateCitationStyleCatalog() {
             List<CitationStyle> styles = discoverStyles(stylesDirectory);
 
             generateCatalog(styles);
-        } catch (Exception e) {
+        } catch (URISyntaxException | IOException e) {
             LOGGER.error("Error generating citation style catalog", e);
         }
     }

jablib/src/main/java/org/jabref/generators/LtwaListMvGenerator.java

@@ -57,14 +57,14 @@ public static void main(String[] args) {
      */
     private static Path downloadLtwaFile() throws IOException, URISyntaxException {
         LOGGER.info("Downloading LTWA file from {}.", LtwaListMvGenerator.LTWA_URL);
-        InputStream inputStream = new URI(LTWA_URL).toURL().openStream();
-        Path path = Files.writeString(
-                Files.createTempFile("ltwa", ".csv"),
-                new String(inputStream.readAllBytes()),
-                StandardOpenOption.CREATE,
-                StandardOpenOption.TRUNCATE_EXISTING);
-        inputStream.close();
-        return path;
+        try (InputStream inputStream = new URI(LTWA_URL).toURL().openStream()) {
+            Path path = Files.writeString(
+                    Files.createTempFile("ltwa", ".csv"),
+                    new String(inputStream.readAllBytes()),
+                    StandardOpenOption.CREATE,
+                    StandardOpenOption.TRUNCATE_EXISTING);
+            return path;
+        }
     }
 
     /**

jablib/src/main/java/org/jabref/logic/ai/chatting/model/Gpt4AllModel.java

@@ -1,5 +1,6 @@
 package org.jabref.logic.ai.chatting.model;
 
+import java.io.IOException;
 import java.net.http.HttpClient;
 import java.net.http.HttpRequest;
 import java.net.http.HttpResponse;
@@ -88,7 +89,7 @@ public ChatResponse chat(List<ChatMessage> list) {
                                              .tokenUsage(new TokenUsage(0, 0))
                                              .finishReason(FinishReason.OTHER)
                                              .build();
-        } catch (Exception e) {
+        } catch (IOException | InterruptedException e) {
             LOGGER.error("Error generating message from Gpt4All", e);
             throw new RuntimeException("Failed to generate AI message", e);
         }

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

@@ -1,5 +1,6 @@
 package org.jabref.logic.ai.ingestion;
 
+import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.file.Path;
 import java.util.Optional;
@@ -51,7 +52,7 @@ private Optional<Document> fromPdfFile(Path path) {
             }
 
             return fromString(writer.toString());
-        } catch (Exception e) {
+        } catch (IOException e) {
             LOGGER.error("An error occurred while reading the PDF file: {}", path, e);
             return Optional.empty();
         }

jablib/src/main/java/org/jabref/logic/bst/BstPreviewLayout.java

@@ -44,7 +44,7 @@ public BstPreviewLayout(Path path) {
         }
         try {
             bstVM = new BstVM(path);
-        } catch (Exception e) {
+        } catch (IOException e) {
             LOGGER.error("Could not read {}.", path.toAbsolutePath(), e);
             error = Localization.lang("Error opening file '%0'", path.toString());
         }

jablib/src/main/java/org/jabref/logic/citationstyle/CSLStyleLoader.java

@@ -110,12 +110,8 @@ private void loadExternalStyles() {
 
         List<String> stylePaths = openOfficePreferences.getExternalCslStyles();
         for (String stylePath : stylePaths) {
-            try {
-                Optional<CitationStyle> style = CSLStyleUtils.createCitationStyleFromFile(stylePath);
-                style.ifPresent(EXTERNAL_STYLES::add);
-            } catch (Exception e) {
-                LOGGER.info("Problem reading external style file {}", stylePath, e);
-            }
+            Optional<CitationStyle> style = CSLStyleUtils.createCitationStyleFromFile(stylePath);
+            style.ifPresent(EXTERNAL_STYLES::add);
         }
     }
 

jablib/src/main/java/org/jabref/logic/exporter/AtomicFileOutputStream.java

@@ -214,7 +214,7 @@ public void close() throws IOException {
             if (Files.exists(targetFile)) {
                 try {
                     Files.copy(targetFile, backupFile, StandardCopyOption.REPLACE_EXISTING);
-                } catch (Exception e) {
+                } catch (IOException e) {
                     LOGGER.warn("Could not create backup file {}", backupFile);
                 }
                 if (FileUtil.IS_POSIX_COMPLIANT) {
@@ -229,7 +229,7 @@ public void close() throws IOException {
             try {
                 // Move temporary file (replace original if it exists)
                 Files.move(temporaryFile, targetFile, StandardCopyOption.ATOMIC_MOVE, StandardCopyOption.REPLACE_EXISTING);
-            } catch (Exception e) {
+            } catch (IOException e) {
                 LOGGER.warn("Could not move temporary file", e);
                 throw e;
             }

jablib/src/main/java/org/jabref/logic/exporter/OOCalcDatabase.java

@@ -2,10 +2,10 @@
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.bibtex.comparator.FieldComparatorStack;
@@ -34,7 +34,7 @@ class OOCalcDatabase {
 
     private final List<BibEntry> entries = new ArrayList<>();
     private final List<Field> toExportFields = Stream.concat(FieldFactory.getStandardFieldsWithCitationKey().stream(), Stream.of(REPORT_TYPE_FIELD))
-                                                     .collect(Collectors.toList());
+                                                     .toList();
 
     public OOCalcDatabase(BibDatabase bibtex, List<BibEntry> entries) {
         this.entries.addAll(entries != null ? entries : bibtex.getEntries());
@@ -68,7 +68,7 @@ public Document getDOMrepresentation() {
             for (BibEntry entry : entries) {
                 addEntryRow(entry, table, document);
             }
-        } catch (Exception e) {
+        } catch (ParserConfigurationException e) {
             LOGGER.warn("Exception caught...", e);
         }
         return document;

jablib/src/main/java/org/jabref/logic/exporter/OpenDocumentRepresentation.java

@@ -5,6 +5,7 @@
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.bibtex.comparator.FieldComparatorStack;
@@ -190,7 +191,7 @@ public Document getDOMrepresentation() {
             collection.appendChild(body);
 
             result.appendChild(collection);
-        } catch (Exception e) {
+        } catch (ParserConfigurationException e) {
             LOGGER.warn("Exception caught...", e);
         }
         return result;

jablib/src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java

@@ -19,6 +19,7 @@
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
@@ -113,7 +114,7 @@ private static void exportOpenDocumentSpreadsheetXML(File tmpFile, BibDatabase d
             Transformer trans = TransformerFactory.newInstance().newTransformer();
             trans.setOutputProperty(OutputKeys.INDENT, "yes");
             trans.transform(source, result);
-        } catch (Exception e) {
+        } catch (TransformerException | IOException e) {
             throw new Error(e);
         }
     }

jablib/src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java

@@ -18,6 +18,7 @@
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
@@ -95,7 +96,7 @@ private static void exportOpenOfficeCalcXML(File tmpFile, BibDatabase database,
             Transformer trans = TransformerFactory.newInstance().newTransformer();
             trans.setOutputProperty(OutputKeys.INDENT, "yes");
             trans.transform(source, result);
-        } catch (Exception e) {
+        } catch (TransformerException | IOException e) {
             throw new Error(e);
         }
     }