Moved the main part of XMPUtil to jabref.XMPUtilMain and injected a b…

src/main/java/net/sf/jabref/cli/XMPUtilMain.java

@@ -0,0 +1,175 @@
+package net.sf.jabref.cli;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.nio.charset.StandardCharsets;
+import java.util.Collection;
+import java.util.List;
+import java.util.Optional;
+
+import javax.xml.transform.TransformerException;
+
+import net.sf.jabref.Globals;
+import net.sf.jabref.importer.ParserResult;
+import net.sf.jabref.importer.fileformat.BibtexParser;
+import net.sf.jabref.logic.bibtex.BibEntryWriter;
+import net.sf.jabref.logic.bibtex.LatexFieldFormatter;
+import net.sf.jabref.logic.bibtex.LatexFieldFormatterPreferences;
+import net.sf.jabref.logic.xmp.XMPPreferences;
+import net.sf.jabref.logic.xmp.XMPUtil;
+import net.sf.jabref.model.database.BibDatabaseMode;
+import net.sf.jabref.model.entry.BibEntry;
+import net.sf.jabref.preferences.JabRefPreferences;
+
+import org.apache.jempbox.impl.XMLUtil;
+import org.apache.jempbox.xmp.XMPMetadata;
+
+public class XMPUtilMain {
+
+    /**
+     * Command-line tool for working with XMP-data.
+     *
+     * Read or write XMP-metadata from or to pdf file.
+     *
+     * Usage:
+     * <dl>
+     * <dd>Read from PDF and print as bibtex:</dd>
+     * <dt>xmpUtil PDF</dt>
+     * <dd>Read from PDF and print raw XMP:</dd>
+     * <dt>xmpUtil -x PDF</dt>
+     * <dd>Write the entry in BIB given by KEY to the PDF:</dd>
+     * <dt>xmpUtil KEY BIB PDF</dt>
+     * <dd>Write all entries in BIB to the PDF:</dd>
+     * <dt>xmpUtil BIB PDF</dt>
+     * </dl>
+     *
+     * @param args
+     *            Command line strings passed to utility.
+     * @throws IOException
+     *             If any of the given files could not be read or written.
+     * @throws TransformerException
+     *             If the given BibEntry is malformed.
+     */
+    public static void main(String[] args) throws IOException, TransformerException {
+
+        // Don't forget to initialize the preferences
+        if (Globals.prefs == null) {
+            Globals.prefs = JabRefPreferences.getInstance();
+        }
+
+        XMPPreferences xmpPreferences = XMPPreferences.fromPreferences(Globals.prefs);
+
+        switch (args.length) {
+        case 0:
+            usage();
+            break;
+        case 1:
+
+            if (args[0].endsWith(".pdf")) {
+                // Read from pdf and write as BibTex
+                List<BibEntry> l = XMPUtil.readXMP(new File(args[0]), xmpPreferences);
+
+                BibEntryWriter bibtexEntryWriter = new BibEntryWriter(
+                        new LatexFieldFormatter(LatexFieldFormatterPreferences.fromPreferences(Globals.prefs)), false);
+
+                for (BibEntry entry : l) {
+                    StringWriter sw = new StringWriter();
+                    bibtexEntryWriter.write(entry, sw, BibDatabaseMode.BIBTEX);
+                    System.out.println(sw.getBuffer());
+                }
+
+            } else if (args[0].endsWith(".bib")) {
+                // Read from BIB and write as XMP
+                try (FileReader fr = new FileReader(args[0])) {
+                    ParserResult result = BibtexParser.parse(fr);
+                    Collection<BibEntry> entries = result.getDatabase().getEntries();
+
+                    if (entries.isEmpty()) {
+                        System.err.println("Could not find BibEntry in " + args[0]);
+                    } else {
+                        System.out.println(XMPUtil.toXMP(entries, result.getDatabase(), xmpPreferences));
+                    }
+                }
+            } else {
+                usage();
+            }
+            break;
+        case 2:
+            if ("-x".equals(args[0]) && args[1].endsWith(".pdf")) {
+                // Read from pdf and write as BibTex
+                Optional<XMPMetadata> meta = XMPUtil.readRawXMP(new File(args[1]));
+
+                if (meta.isPresent()) {
+                    XMLUtil.save(meta.get().getXMPDocument(), System.out, StandardCharsets.UTF_8.name());
+                } else {
+                    System.err.println("The given pdf does not contain any XMP-metadata.");
+                }
+                break;
+            }
+
+            if (args[0].endsWith(".bib") && args[1].endsWith(".pdf")) {
+                ParserResult result = BibtexParser.parse(new FileReader(args[0]));
+
+                Collection<BibEntry> entries = result.getDatabase().getEntries();
+
+                if (entries.isEmpty()) {
+                    System.err.println("Could not find BibEntry in " + args[0]);
+                } else {
+                    XMPUtil.writeXMP(new File(args[1]), entries, result.getDatabase(), false, xmpPreferences);
+                    System.out.println("XMP written.");
+                }
+                break;
+            }
+
+            usage();
+            break;
+        case 3:
+            if (!args[1].endsWith(".bib") && !args[2].endsWith(".pdf")) {
+                usage();
+                break;
+            }
+
+            ParserResult result = BibtexParser.parse(new FileReader(args[1]));
+
+            Optional<BibEntry> bibEntry = result.getDatabase().getEntryByKey(args[0]);
+
+            if (bibEntry.isPresent()) {
+                XMPUtil.writeXMP(new File(args[2]), bibEntry.get(), result.getDatabase(), xmpPreferences);
+
+                System.out.println("XMP written.");
+            } else {
+                System.err.println("Could not find BibEntry " + args[0] + " in " + args[0]);
+            }
+            break;
+
+        default:
+            usage();
+        }
+    }
+
+    /**
+     * Print usage information for the command line tool xmpUtil.
+     *
+     * @see XMPUtil#main(String[])
+     */
+    private static void usage() {
+        System.out.println("Read or write XMP-metadata from or to pdf file.");
+        System.out.println("");
+        System.out.println("Usage:");
+        System.out.println("Read from PDF and print as bibtex:");
+        System.out.println("  xmpUtil <pdf>");
+        System.out.println("Read from PDF and print raw XMP:");
+        System.out.println("  xmpUtil -x <pdf>");
+        System.out
+        .println("Write the entry in <bib> given by <key> to the PDF:");
+        System.out.println("  xmpUtil <key> <bib> <pdf>");
+        System.out.println("Write all entries in <bib> to the PDF:");
+        System.out.println("  xmpUtil <bib> <pdf>");
+        System.out.println("");
+        System.out
+        .println("To report bugs visit http://jabref.sourceforge.net");
+    }
+
+}

src/main/java/net/sf/jabref/external/DroppedFileHandler.java

@@ -42,6 +42,7 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.io.FileUtil;
+import net.sf.jabref.logic.xmp.XMPPreferences;
 import net.sf.jabref.logic.xmp.XMPUtil;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.entry.BibEntry;
@@ -235,7 +236,7 @@ private boolean tryXmpImport(String fileName, ExternalFileType fileType, NamedCo
 
         List<BibEntry> xmpEntriesInFile;
         try {
-            xmpEntriesInFile = XMPUtil.readXMP(fileName, Globals.prefs);
+            xmpEntriesInFile = XMPUtil.readXMP(fileName, XMPPreferences.fromPreferences(Globals.prefs));
         } catch (IOException e) {
             LOGGER.warn("Problem reading XMP", e);
             return false;

src/main/java/net/sf/jabref/external/WriteXMPAction.java

@@ -46,6 +46,7 @@
 import net.sf.jabref.gui.worker.AbstractWorker;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.util.io.FileUtil;
+import net.sf.jabref.logic.xmp.XMPPreferences;
 import net.sf.jabref.logic.xmp.XMPUtil;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.entry.BibEntry;
@@ -159,7 +160,7 @@ public void run() {
                 for (File file : files) {
                     if (file.exists()) {
                         try {
-                            XMPUtil.writeXMP(file, entry, database);
+                            XMPUtil.writeXMP(file, entry, database, XMPPreferences.fromPreferences(Globals.prefs));
                             optDiag.getProgressArea().append("  " + Localization.lang("OK") + ".\n");
                             entriesChanged++;
                         } catch (Exception e) {

src/main/java/net/sf/jabref/external/WriteXMPEntryEditorAction.java

@@ -25,6 +25,7 @@
 import javax.swing.Action;
 import javax.xml.transform.TransformerException;
 
+import net.sf.jabref.Globals;
 import net.sf.jabref.gui.BasePanel;
 import net.sf.jabref.gui.FileListEntry;
 import net.sf.jabref.gui.FileListTableModel;
@@ -33,6 +34,7 @@
 import net.sf.jabref.gui.worker.AbstractWorker;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.util.io.FileUtil;
+import net.sf.jabref.logic.xmp.XMPPreferences;
 import net.sf.jabref.logic.xmp.XMPUtil;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.model.entry.FieldName;
@@ -126,7 +128,8 @@ public void run() {
 
                     } else {
                         try {
-                            XMPUtil.writeXMP(file, entry, panel.getDatabase());
+                            XMPUtil.writeXMP(file, entry, panel.getDatabase(),
+                                    XMPPreferences.fromPreferences(Globals.prefs));
                             if (files.size() == 1) {
                                 message = Localization.lang("Wrote XMP-metadata");
                             }

src/main/java/net/sf/jabref/gui/entryeditor/EntryEditor.java

@@ -440,7 +440,7 @@ private void setupToolBar() {
         leftPan.add(closeBut, BorderLayout.NORTH);
 
         // Create type-label
-        TypedBibEntry typedEntry = new TypedBibEntry(entry, Optional.empty(), panel.getBibDatabaseContext().getMode());
+        TypedBibEntry typedEntry = new TypedBibEntry(entry, panel.getBibDatabaseContext().getMode());
         leftPan.add(new TypeLabel(typedEntry.getTypeForDisplay()), BorderLayout.CENTER);
         TypeButton typeButton = new TypeButton();
 

src/main/java/net/sf/jabref/gui/maintable/MainTable.java

@@ -510,7 +510,7 @@ private boolean matches(int row, Matcher<BibEntry> m) {
     private boolean isComplete(int row) {
         try {
             BibEntry entry = getBibEntry(row);
-            TypedBibEntry typedEntry = new TypedBibEntry(entry, Optional.of(panel.getDatabase()), panel.getBibDatabaseContext().getMode());
+            TypedBibEntry typedEntry = new TypedBibEntry(entry, panel.getBibDatabaseContext());
             return typedEntry.hasAllRequiredFields();
         } catch (NullPointerException ex) {
             return true;

src/main/java/net/sf/jabref/gui/util/comparator/FirstColumnComparator.java

@@ -16,7 +16,6 @@
 package net.sf.jabref.gui.util.comparator;
 
 import java.util.Comparator;
-import java.util.Optional;
 
 import net.sf.jabref.BibDatabaseContext;
 import net.sf.jabref.logic.TypedBibEntry;
@@ -35,8 +34,8 @@ public int compare(BibEntry e1, BibEntry e2) {
         int score1 = 0;
         int score2 = 0;
 
-        TypedBibEntry typedEntry1 = new TypedBibEntry(e1, Optional.of(database.getDatabase()), database.getMode());
-        TypedBibEntry typedEntry2 = new TypedBibEntry(e2, Optional.of(database.getDatabase()), database.getMode());
+        TypedBibEntry typedEntry1 = new TypedBibEntry(e1, database);
+        TypedBibEntry typedEntry2 = new TypedBibEntry(e2, database);
         if (typedEntry1.hasAllRequiredFields()) {
             score1++;
         }

src/main/java/net/sf/jabref/importer/EntryFromPDFCreator.java

@@ -13,6 +13,7 @@
 import net.sf.jabref.external.ExternalFileType;
 import net.sf.jabref.external.ExternalFileTypes;
 import net.sf.jabref.gui.IconTheme;
+import net.sf.jabref.logic.xmp.XMPPreferences;
 import net.sf.jabref.logic.xmp.XMPUtil;
 import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.pdfimport.PdfImporter;
@@ -122,7 +123,8 @@ private void addEntryDataFromPDDocumentInformation(File pdfFile, BibEntry entry)
      */
     private void addEntryDataFromXMP(File aFile, BibEntry entry) {
         try {
-            List<BibEntry> entrys = XMPUtil.readXMP(aFile.getAbsoluteFile(), Globals.prefs);
+            List<BibEntry> entrys = XMPUtil.readXMP(aFile.getAbsoluteFile(),
+                    XMPPreferences.fromPreferences(Globals.prefs));
             addEntrysToEntry(entry, entrys);
         } catch (IOException e) {
             // no canceling here, just no data added.

src/main/java/net/sf/jabref/importer/fileformat/PdfXmpImporter.java

@@ -26,6 +26,7 @@
 import net.sf.jabref.Globals;
 import net.sf.jabref.importer.ParserResult;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.xmp.XMPPreferences;
 import net.sf.jabref.logic.xmp.XMPUtil;
 
 /**
@@ -55,7 +56,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
     public ParserResult importDatabase(Path filePath, Charset defaultEncoding) {
         Objects.requireNonNull(filePath);
         try {
-            return new ParserResult(XMPUtil.readXMP(filePath, Globals.prefs));
+            return new ParserResult(XMPUtil.readXMP(filePath, XMPPreferences.fromPreferences(Globals.prefs)));
         } catch (IOException exception) {
             return ParserResult.fromErrorMessage(exception.getLocalizedMessage());
         }
@@ -76,7 +77,7 @@ protected boolean isRecognizedFormat(BufferedReader reader) throws IOException {
     @Override
     public boolean isRecognizedFormat(Path filePath, Charset defaultEncoding) throws IOException {
         Objects.requireNonNull(filePath);
-        return XMPUtil.hasMetadata(filePath, Globals.prefs);
+        return XMPUtil.hasMetadata(filePath, XMPPreferences.fromPreferences(Globals.prefs));
     }
 
     @Override

src/main/java/net/sf/jabref/logic/TypedBibEntry.java

@@ -42,18 +42,14 @@ public TypedBibEntry(BibEntry entry, BibDatabaseMode mode) {
         this(entry, Optional.empty(), mode);
     }
 
-    public TypedBibEntry(BibEntry entry, Optional<BibDatabase> database, BibDatabaseMode mode) {
+    private TypedBibEntry(BibEntry entry, Optional<BibDatabase> database, BibDatabaseMode mode) {
         this.entry = Objects.requireNonNull(entry);
         this.database = Objects.requireNonNull(database);
         this.mode = mode;
     }
 
     public TypedBibEntry(BibEntry entry, BibDatabaseContext databaseContext) {
-        this(entry, databaseContext.getDatabase(), databaseContext.getMode());
-    }
-
-    public TypedBibEntry(BibEntry entry, BibDatabase database, BibDatabaseMode mode) {
-        this(entry, Optional.of(database), mode);
+        this(entry, Optional.of(databaseContext.getDatabase()), databaseContext.getMode());
     }
 
     /**

src/main/java/net/sf/jabref/logic/bibtex/BibEntryWriter.java

@@ -83,7 +83,7 @@ public void writeWithoutPrependedNewlines(BibEntry entry, Writer out, BibDatabas
     private void writeRequiredFieldsFirstRemainingFieldsSecond(BibEntry entry, Writer out,
                                                                BibDatabaseMode bibDatabaseMode) throws IOException {
         // Write header with type and bibtex-key.
-        TypedBibEntry typedEntry = new TypedBibEntry(entry, Optional.empty(), bibDatabaseMode);
+        TypedBibEntry typedEntry = new TypedBibEntry(entry, bibDatabaseMode);
         out.write('@' + typedEntry.getTypeForDisplay() + '{');
 
         writeKeyField(entry, out);

src/main/java/net/sf/jabref/logic/xmp/XMPPreferences.java

@@ -0,0 +1,37 @@
+package net.sf.jabref.logic.xmp;
+
+import java.util.List;
+
+import net.sf.jabref.preferences.JabRefPreferences;
+
+public class XMPPreferences {
+
+    private final boolean useXMPPrivacyFilter;
+    private final List<String> xmpPrivacyFilter;
+    private final String keywordSeparator;
+
+
+    public XMPPreferences(boolean useXMPPrivacyFilter, List<String> xmpPrivacyFilter, String keywordSeparator) {
+        this.useXMPPrivacyFilter = useXMPPrivacyFilter;
+        this.xmpPrivacyFilter = xmpPrivacyFilter;
+        this.keywordSeparator = keywordSeparator;
+    }
+
+    public static XMPPreferences fromPreferences(JabRefPreferences jabrefPreferences) {
+        return new XMPPreferences(jabrefPreferences.getBoolean(JabRefPreferences.USE_XMP_PRIVACY_FILTER),
+                jabrefPreferences.getStringList(JabRefPreferences.XMP_PRIVACY_FILTERS),
+                jabrefPreferences.get(JabRefPreferences.KEYWORD_SEPARATOR));
+    }
+
+    public boolean isUseXMPPrivacyFilter() {
+        return useXMPPrivacyFilter;
+    }
+
+    public List<String> getXmpPrivacyFilter() {
+        return xmpPrivacyFilter;
+    }
+
+    public String getKeywordSeparator() {
+        return keywordSeparator;
+    }
+}