fix most of the stuff

JabRef · Jan 27, 2025 · 62a9339 · 62a9339
1 parent c380706
commit 62a9339
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Showing 8 changed files with 98 additions and 64 deletions.
diff --git a/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java b/src/main/java/org/jabref/logic/crawler/StudyYamlParser.java
@@ -3,6 +3,7 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
 import java.nio.file.Path;
 
 import org.jabref.model.study.Study;
@@ -21,7 +22,7 @@ public class StudyYamlParser {
      */
     public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
         ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory());
-        try (InputStream fileInputStream = new FileInputStream(studyYamlFile.toFile())) {
+        try (InputStream fileInputStream = Files.newInputStream(studyYamlFile)) {
             return yamlMapper.readValue(fileInputStream, Study.class);
         }
     }

diff --git a/src/main/java/org/jabref/logic/exporter/AtomicFileOutputStream.java b/src/main/java/org/jabref/logic/exporter/AtomicFileOutputStream.java
@@ -80,7 +80,7 @@ public class AtomicFileOutputStream extends FilterOutputStream {
      */
     public AtomicFileOutputStream(Path path, boolean keepBackup) throws IOException {
         // Files.newOutputStream(getPathOfTemporaryFile(path)) leads to a "sun.nio.ch.ChannelOutputStream", which does not offer "lock"
-        this(path, getPathOfTemporaryFile(path), new FileOutputStream(getPathOfTemporaryFile(path).toFile()), keepBackup);
+        this(path, getPathOfTemporaryFile(path), Files.newOutputStream(getPathOfTemporaryFile(path)), keepBackup);
     }
 
     /**

diff --git a/src/main/java/org/jabref/logic/exporter/CffExporter.java b/src/main/java/org/jabref/logic/exporter/CffExporter.java
@@ -2,7 +2,9 @@
 
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.Writer;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -18,6 +20,7 @@
 import org.jabref.model.entry.AuthorList;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.Date;
+import org.jabref.model.entry.ParsedEntryLink;
 import org.jabref.model.entry.field.BiblatexSoftwareField;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.StandardField;
@@ -141,7 +144,7 @@ public void export(BibDatabaseContext databaseContext, Path file, List<BibEntry>
         if (main.hasField(StandardField.RELATED)) {
             main.getEntryLinkList(StandardField.RELATED, databaseContext.getDatabase())
                 .stream()
-                .map(link -> link.getLinkedEntry())
+                .map(ParsedEntryLink::getLinkedEntry)
                 .filter(Optional::isPresent)
                 .map(Optional::get)
                 .forEach(entry -> {
@@ -158,7 +161,7 @@ public void export(BibDatabaseContext databaseContext, Path file, List<BibEntry>
             cffData.put("references", related);
         }
 
-        try (FileWriter writer = new FileWriter(file.toFile(), StandardCharsets.UTF_8)) {
+        try (Writer writer = Files.newBufferedWriter(file, StandardCharsets.UTF_8)) {
             yaml.dump(cffData, writer);
         } catch (IOException ex) {
             throw new SaveException(ex);

diff --git a/src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java b/src/main/java/org/jabref/logic/exporter/OpenDocumentSpreadsheetCreator.java
@@ -4,11 +4,9 @@
 import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 import java.io.Writer;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
@@ -33,6 +31,7 @@
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
 
 public class OpenDocumentSpreadsheetCreator extends Exporter {
 
@@ -83,15 +82,15 @@ private static void exportOpenDocumentSpreadsheet(Path file, BibDatabase databas
             throws IOException {
 
         // First store the xml formatted content to a temporary file.
-        File tmpFile = File.createTempFile("opendocument", null);
+        Path tmpFile = Files.createTempFile("opendocument", null);
         OpenDocumentSpreadsheetCreator.exportOpenDocumentSpreadsheetXML(tmpFile, database, entries);
 
         // Then add the content to the zip file:
-        try (BufferedInputStream in = new BufferedInputStream(new FileInputStream(tmpFile))) {
+        try (InputStream in = Files.newInputStream(file)) {
             OpenDocumentSpreadsheetCreator.storeOpenDocumentSpreadsheetFile(file, in);
         }
         // Delete the temporary file:
-        if (!tmpFile.delete()) {
+        if (!Files.deleteIfExists(tmpFile)) {
             LOGGER.info("Cannot delete temporary export file");
         }
     }
@@ -106,11 +105,14 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
         }
     }
 
-    private static void exportOpenDocumentSpreadsheetXML(File tmpFile, BibDatabase database, List<BibEntry> entries) {
+    private static void exportOpenDocumentSpreadsheetXML(Path tmpFile, BibDatabase database, List<BibEntry> entries) {
         OpenDocumentRepresentation od = new OpenDocumentRepresentation(database, entries);
+        writeDomtoFile(tmpFile, od.getDOMrepresentation(), od);
+    }
 
-        try (Writer ps = new OutputStreamWriter(new FileOutputStream(tmpFile), StandardCharsets.UTF_8)) {
-            DOMSource source = new DOMSource(od.getDOMrepresentation());
+    static void writeDomtoFile(Path tmpFile, Document domRepresentation, OpenDocumentRepresentation od) {
+        try (Writer ps = Files.newBufferedWriter(tmpFile, StandardCharsets.UTF_8)) {
+            DOMSource source = new DOMSource(domRepresentation);
             StreamResult result = new StreamResult(ps);
             Transformer trans = TransformerFactory.newInstance().newTransformer();
             trans.setOutputProperty(OutputKeys.INDENT, "yes");

diff --git a/src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java b/src/main/java/org/jabref/logic/exporter/OpenOfficeDocumentCreator.java
@@ -1,14 +1,9 @@
 package org.jabref.logic.exporter;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.io.OutputStreamWriter;
 import java.io.Writer;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
@@ -64,18 +59,16 @@ private static void storeOpenOfficeFile(Path file, InputStream source) throws Ex
 
     private static void exportOpenOfficeCalc(Path file, BibDatabase database, List<BibEntry> entries) throws Exception {
         // First store the xml formatted content to a temporary file.
-        File tmpFile = File.createTempFile("oocalc", null);
+        Path tmpFile = Files.createTempFile("oocalc", null);
         OpenOfficeDocumentCreator.exportOpenOfficeCalcXML(tmpFile, database, entries);
 
         // Then add the content to the zip file:
-        try (BufferedInputStream in = new BufferedInputStream(new FileInputStream(tmpFile))) {
+        try (InputStream in = Files.newInputStream(file)) {
             OpenOfficeDocumentCreator.storeOpenOfficeFile(file, in);
         }
 
         // Delete the temporary file:
-        if (!tmpFile.delete()) {
-            LOGGER.info("Cannot delete temporary export file");
-        }
+        Files.deleteIfExists(tmpFile);
     }
 
     @Override
@@ -88,10 +81,10 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
         }
     }
 
-    private static void exportOpenOfficeCalcXML(File tmpFile, BibDatabase database, List<BibEntry> entries) {
+    private static void exportOpenOfficeCalcXML(Path tmpFile, BibDatabase database, List<BibEntry> entries) {
         OOCalcDatabase od = new OOCalcDatabase(database, entries);
 
-        try (Writer ps = new OutputStreamWriter(new FileOutputStream(tmpFile), StandardCharsets.UTF_8)) {
+        try (Writer ps =  Files.newBufferedWriter(tmpFile, StandardCharsets.UTF_8)) {
             DOMSource source = new DOMSource(od.getDOMrepresentation());
             StreamResult result = new StreamResult(ps);
             Transformer trans = TransformerFactory.newInstance().newTransformer();

diff --git a/src/main/java/org/jabref/logic/net/ssl/SSLCertificate.java b/src/main/java/org/jabref/logic/net/ssl/SSLCertificate.java
@@ -2,6 +2,8 @@
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.cert.CertificateEncodingException;
 import java.security.cert.CertificateException;
@@ -87,11 +89,13 @@ public static Optional<SSLCertificate> fromPath(Path certPath) {
         Objects.requireNonNull(certPath);
         try {
             CertificateFactory certificateFactory = CertificateFactory.getInstance("X509");
-            return fromX509((X509Certificate) certificateFactory.generateCertificate(new FileInputStream(certPath.toFile())));
+            return fromX509((X509Certificate) certificateFactory.generateCertificate(Files.newInputStream(certPath)));
         } catch (CertificateException e) {
             LOGGER.warn("Certificate doesn't follow X.509 format", e);
         } catch (FileNotFoundException e) {
             LOGGER.warn("Bad Certificate path: {}", certPath, e);
+        } catch (IOException e) {
+           LOGGER.warn("Error while reading certificate", e);
         }
         return Optional.empty();
     }

diff --git a/src/main/java/org/jabref/logic/net/ssl/TrustStoreManager.java b/src/main/java/org/jabref/logic/net/ssl/TrustStoreManager.java
@@ -44,7 +44,7 @@ public TrustStoreManager(Path storePath) {
         createTruststoreFileIfNotExist(storePath);
         try {
             store = KeyStore.getInstance(KeyStore.getDefaultType());
-            store.load(new FileInputStream(storePath.toFile()), STORE_PASSWORD.toCharArray());
+            store.load(Files.newInputStream(storePath), STORE_PASSWORD.toCharArray());
         } catch (CertificateException | IOException | NoSuchAlgorithmException | KeyStoreException e) {
             LOGGER.warn("Error while loading trust store from: {}", storePath.toAbsolutePath(), e);
         }
@@ -56,7 +56,7 @@ public void addCertificate(String alias, Path certPath) {
 
         try {
             CertificateFactory certificateFactory = CertificateFactory.getInstance("X509");
-            store.setCertificateEntry(alias, certificateFactory.generateCertificate(new FileInputStream(certPath.toFile())));
+            store.setCertificateEntry(alias, certificateFactory.generateCertificate(Files.newInputStream(certPath)));
         } catch (KeyStoreException | CertificateException | IOException e) {
             LOGGER.warn("Error while adding a new certificate to the truststore: {}", alias, e);
         }