Merge branch 'master' into file-based-bibtex-mode

src/main/java/net/sf/jabref/exporter/AutoSaveManager.java

@@ -25,15 +25,19 @@
 
 import java.util.Timer;
 import java.util.TimerTask;
-import java.util.List;
-import java.util.ArrayList;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import java.io.File;
 
 /**
  * Background task and utilities for autosave feature.
  */
 public class AutoSaveManager {
 
+    private static final Log LOGGER = LogFactory.getLog(AutoSaveManager.class);
+
     private final JabRefFrame frame;
     private Timer t;
 
@@ -65,12 +69,7 @@ public void run() {
             // Since this method is running in the background, we must be prepared that
             // there could be changes done by the user while this method is running.
 
-            List<BasePanel> panels = new ArrayList<>();
-            for (int i = 0; i < frame.getBasePanelCount(); i++) {
-                panels.add(frame.getBasePanelAt(i));
-            }
-
-            for (BasePanel panel : panels) {
+            for (BasePanel panel : frame.getBasePanelList()) {
                 if (panel.isModified() && (panel.getBibDatabaseContext().getDatabaseFile() != null)) {
                         AutoSaveManager.autoSave(panel);
                 }
@@ -101,10 +100,7 @@ private static boolean autoSave(BasePanel panel) {
                     backupFile, Globals.prefs, false, false, panel.getEncoding(), true);
             ss.commit();
         } catch (SaveException e) {
-            e.printStackTrace();
-            return false;
-        } catch (Throwable ex) {
-            ex.printStackTrace();
+            LOGGER.error("Problem with automatic save", e);
             return false;
         }
         return true;
@@ -132,11 +128,7 @@ public static boolean deleteAutoSaveFile(BasePanel panel) {
      * if they exist.
      */
     public void clearAutoSaves() {
-        List<BasePanel> panels = new ArrayList<>();
-        for (int i = 0; i < frame.getBasePanelCount(); i++) {
-            panels.add(frame.getBasePanelAt(i));
-        }
-        for (BasePanel panel : panels) {
+        for (BasePanel panel : frame.getBasePanelList()) {
             AutoSaveManager.deleteAutoSaveFile(panel);
         }
     }

src/main/java/net/sf/jabref/exporter/ExportFormat.java

@@ -174,9 +174,8 @@ private Reader getReader(String filename) throws IOException {
      *      net.sf.jabref.MetaData, java.lang.String, java.lang.String, java.util.Set)
      */
     @Override
-    public void performExport(final BibDatabase database,
-            final MetaData metaData, final String file,
-            final Charset enc, Set<String> entryIds) throws Exception {
+    public void performExport(final BibDatabase database, final MetaData metaData, final String file, final Charset enc,
+            Set<String> entryIds) throws Exception {
 
         File outFile = new File(file);
         SaveSession ss = null;
@@ -363,7 +362,7 @@ public FileFilter getFileFilter() {
         return fileFilter;
     }
 
-    public void finalizeSaveSession(final SaveSession ss) throws Exception {
+    public void finalizeSaveSession(final SaveSession ss) throws SaveException, IOException {
         ss.getWriter().flush();
         ss.getWriter().close();
 

src/main/java/net/sf/jabref/exporter/ExportFormats.java

@@ -26,6 +26,9 @@
 import javax.swing.JOptionPane;
 import javax.swing.filechooser.FileFilter;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import net.sf.jabref.*;
 import net.sf.jabref.gui.JabRefFrame;
 import net.sf.jabref.gui.actions.MnemonicAwareAction;
@@ -42,6 +45,8 @@
  */
 public class ExportFormats {
 
+    private static final Log LOGGER = LogFactory.getLog(ExportFormats.class);
+
     private static final Map<String, IExportFormat> EXPORT_FORMATS = new TreeMap<>();
 
     // Global variable that is used for counting output entries when exporting:
@@ -232,7 +237,7 @@ public void run() {
                                         finFile.getPath(), frame
                                                 .getCurrentBasePanel().getEncoding(), finEntryIDs);
                             } catch (Exception ex) {
-                                ex.printStackTrace();
+                                LOGGER.warn("Problem exporting", ex);
                                 if (ex.getMessage() == null) {
                                     errorMessage = ex.toString();
                                 } else {

src/main/java/net/sf/jabref/exporter/FileActions.java

@@ -137,7 +137,9 @@ private static void writeString(Writer fw, BibtexString bs, Map<String, BibtexSt
         String suffix = suffixSB.toString();
 
         fw.write("@String { " + bs.getName() + suffix + " = ");
-        if (!bs.getContent().isEmpty()) {
+        if (bs.getContent().isEmpty()) {
+            fw.write("{}");
+        } else {
             try {
                 String formatted = new LatexFieldFormatter().format(bs.getContent(), LatexFieldFormatter.BIBTEX_STRING);
                 fw.write(formatted);
@@ -146,9 +148,6 @@ private static void writeString(Writer fw, BibtexString bs, Map<String, BibtexSt
                         "The # character is not allowed in BibTeX strings unless escaped as in '\\#'.\n"
                                 + "Before saving, please edit any strings containing the # character.");
             }
-
-        } else {
-            fw.write("{}");
         }
 
         fw.write(" }" + Globals.NEWLINE);
@@ -283,10 +282,7 @@ public static SaveSession saveDatabase(BibDatabaseContext bibDatabaseContext, Fi
     }
 
     private static List<BibEntry> applySaveActions(List<BibEntry> toChange, MetaData metaData) {
-        if (metaData.getData(SaveActions.META_KEY) != null) {
-            // no save actions defined -> do nothing
-            return toChange;
-        } else {
+        if (metaData.getData(SaveActions.META_KEY) == null) {
             // save actions defined -> apply for every entry
             List<BibEntry> result = new ArrayList<>(toChange.size());
 
@@ -297,6 +293,9 @@ private static List<BibEntry> applySaveActions(List<BibEntry> toChange, MetaData
             }
 
             return result;
+        } else {
+            // no save actions defined -> do nothing
+            return toChange;
         }
     }
 
@@ -477,16 +476,16 @@ public static Reader getReader(String name) throws IOException {
         URL reso = Globals.class.getResource(name);
 
         // If that didn't work, try loading as a normal file URL:
-        if (reso != null) {
+        if (reso == null) {
+            File f = new File(name);
             try {
-                reader = new InputStreamReader(reso.openStream());
+                reader = new FileReader(f);
             } catch (FileNotFoundException ex) {
                 throw new IOException("Cannot find layout file: '" + name + "'.");
             }
         } else {
-            File f = new File(name);
             try {
-                reader = new FileReader(f);
+                reader = new InputStreamReader(reso.openStream());
             } catch (FileNotFoundException ex) {
                 throw new IOException("Cannot find layout file: '" + name + "'.");
             }

src/main/java/net/sf/jabref/exporter/IExportFormat.java

@@ -59,6 +59,7 @@ public interface IExportFormat {
      */
     void performExport(BibDatabase database, MetaData metaData,
  String file, Charset encoding,
-            Set<String> entryIds) throws Exception;
+ Set<String> entryIds)
+            throws Exception;
 
 }

src/main/java/net/sf/jabref/exporter/MSBibExportFormat.java

@@ -23,7 +23,9 @@
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerFactoryConfigurationError;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
@@ -58,11 +60,11 @@ public void performExport(final BibDatabase database, final MetaData metaData, f
                 Transformer trans = TransformerFactory.newInstance().newTransformer();
                 trans.setOutputProperty(OutputKeys.INDENT, "yes");
                 trans.transform(source, result);
-            } catch (Exception e) {
+            } catch (TransformerException | IllegalArgumentException | TransformerFactoryConfigurationError e) {
                 throw new Error(e);
             }
             finalizeSaveSession(ss);
-        } catch (Exception ex) {
+        } catch (SaveException | IOException ex) {
             throw new IOException(ex.getMessage());
         }
     }

src/main/java/net/sf/jabref/exporter/ModsExportFormat.java

@@ -23,7 +23,9 @@
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerFactoryConfigurationError;
 import javax.xml.transform.OutputKeys;
 import java.util.Set;
 import java.io.IOException;
@@ -54,11 +56,11 @@ public void performExport(final BibDatabase database, final MetaData metaData,
                 Transformer trans = TransformerFactory.newInstance().newTransformer();
                 trans.setOutputProperty(OutputKeys.INDENT, "yes");
                 trans.transform(source, result);
-            } catch (Exception e) {
+            } catch (TransformerException | IllegalArgumentException | TransformerFactoryConfigurationError e) {
                 throw new Error(e);
             }
             finalizeSaveSession(ss);
-        } catch (Exception ex) {
+        } catch (SaveException | IOException ex) {
             throw new IOException(ex.getMessage());
         }
     }

src/main/java/net/sf/jabref/exporter/OpenDocumentSpreadsheetCreator.java

@@ -24,6 +24,10 @@
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import java.io.*;
 import java.net.URL;
 import java.nio.charset.Charset;
@@ -38,6 +42,9 @@
  */
 public class OpenDocumentSpreadsheetCreator extends ExportFormat {
 
+    private static final Log LOGGER = LogFactory.getLog(OpenDocumentSpreadsheetCreator.class);
+
+
     /**
      * Creates a new instance of OpenOfficeDocumentCreator
      */
@@ -137,7 +144,7 @@ private static void addFromResource(String resource, OutputStream out) {
                 }
             }
         } catch (IOException e) {
-            e.printStackTrace();
+            LOGGER.warn("Cannot get resource", e);
         }
     }
 }

src/main/java/net/sf/jabref/exporter/OpenOfficeDocumentCreator.java

@@ -24,6 +24,10 @@
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import java.io.*;
 import java.net.URL;
 import java.nio.charset.Charset;
@@ -37,6 +41,9 @@
  */
 public class OpenOfficeDocumentCreator extends ExportFormat {
 
+    private static final Log LOGGER = LogFactory.getLog(OpenOfficeDocumentCreator.class);
+
+
     /**
      * Creates a new instance of OpenOfficeDocumentCreator
      */
@@ -121,7 +128,7 @@ private static void addFromResource(String resource, OutputStream out) {
                 }
             }
         } catch (IOException e) {
-            e.printStackTrace();
+            LOGGER.warn("Cannot get resource", e);
         }
     }
 }

src/main/java/net/sf/jabref/exporter/RtfSelection.java

@@ -21,8 +21,13 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 class RtfSelection implements Transferable {
 
+    private static final Log LOGGER = LogFactory.getLog(RtfSelection.class);
+
     private DataFlavor rtfFlavor;
     private DataFlavor[] supportedFlavors;
     private final String content;
@@ -34,7 +39,7 @@ public RtfSelection(String s) {
             rtfFlavor = new DataFlavor("text/rtf; class=java.io.InputStream");
             supportedFlavors = new DataFlavor[] {rtfFlavor, DataFlavor.stringFlavor};
         } catch (ClassNotFoundException ex) {
-            ex.printStackTrace();
+            LOGGER.warn("Cannot find class", ex);
         }
     }
 

src/main/java/net/sf/jabref/exporter/SaveActions.java

@@ -10,10 +10,11 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 public class SaveActions {
 
-    private HashMap<String, Formatter> actions;
+    private final Map<String, Formatter> actions;
 
     private List<Formatter> availableFormatters;