Exemple #1
0
  @Override
  public String format(String field) {
    FileListTableModel tableModel = new FileListTableModel();
    if (field == null) {
      return "";
    }

    tableModel.setContent(field);
    String link = null;
    if (fileType == null) {
      // No file type specified. Simply take the first link.
      if (tableModel.getRowCount() > 0) {
        link = tableModel.getEntry(0).getLink();
      }
    } else {
      // A file type is specified:
      for (int i = 0; i < tableModel.getRowCount(); i++) {
        FileListEntry flEntry = tableModel.getEntry(i);
        if (flEntry.getType().getName().toLowerCase().equals(fileType)) {
          link = flEntry.getLink();
          break;
        }
      }
    }

    if (link == null) {
      return "";
    }

    String[] dirs;
    // We need to resolve the file directory from the database's metadata,
    // but that is not available from a formatter. Therefore, as an
    // ugly hack, the export routine has set a global variable before
    // starting the export, which contains the database's file directory:
    if (Globals.prefs.fileDirForDatabase != null) {
      dirs = Globals.prefs.fileDirForDatabase;
    } else {
      dirs = new String[] {Globals.prefs.get(Globals.FILE_FIELD + "Directory")};
    }

    File f = FileUtil.expandFilename(link, dirs);

    /*
     * Stumbled over this while investigating
     *
     * https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
     */
    if (f != null) {
      try {
        return f.getCanonicalPath(); // f.toURI().toString();
      } catch (IOException e) {
        e.printStackTrace();
        return f.getPath();
      }
    } else {
      return link;
    }
  }
Exemple #2
0
 private void doMakePathsRelative(BibtexEntry entry, NamedCompound ce) {
   String oldValue = entry.getField(Globals.FILE_FIELD);
   if (oldValue == null) {
     return;
   }
   FileListTableModel flModel = new FileListTableModel();
   flModel.setContent(oldValue);
   if (flModel.getRowCount() == 0) {
     return;
   }
   boolean changed = false;
   for (int i = 0; i < flModel.getRowCount(); i++) {
     FileListEntry flEntry = flModel.getEntry(i);
     String oldFileName = flEntry.getLink();
     String newFileName =
         FileUtil.shortenFileName(
                 new File(oldFileName), panel.metaData().getFileDirectory(Globals.FILE_FIELD))
             .toString();
     if (!oldFileName.equals(newFileName)) {
       flEntry.setLink(newFileName);
       changed = true;
     }
   }
   if (changed) {
     String newValue = flModel.getStringRepresentation();
     assert (!oldValue.equals(newValue));
     entry.setField(Globals.FILE_FIELD, newValue);
     ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
   }
 }
Exemple #3
0
 private static void fixWrongFileEntries(BibtexEntry entry, NamedCompound ce) {
   String oldValue = entry.getField(Globals.FILE_FIELD);
   if (oldValue == null) {
     return;
   }
   FileListTableModel flModel = new FileListTableModel();
   flModel.setContent(oldValue);
   if (flModel.getRowCount() == 0) {
     return;
   }
   boolean changed = false;
   for (int i = 0; i < flModel.getRowCount(); i++) {
     FileListEntry flEntry = flModel.getEntry(i);
     String link = flEntry.getLink();
     String description = flEntry.getDescription();
     if ("".equals(link) && (!"".equals(description))) {
       // link and description seem to be switched, quickly fix that
       flEntry.setLink(flEntry.getDescription());
       flEntry.setDescription("");
       changed = true;
     }
   }
   if (changed) {
     String newValue = flModel.getStringRepresentation();
     assert (!oldValue.equals(newValue));
     entry.setField(Globals.FILE_FIELD, newValue);
     ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
   }
 }
 public Object getColumnValue(BibtexEntry entry, int column) {
   if (column < PAD) {
     Object o;
     switch (column) {
       case FILE_COL:
         o = entry.getField(GUIGlobals.FILE_FIELD);
         if (o != null) {
           FileListTableModel model = new FileListTableModel();
           model.setContent((String) o);
           fileLabel.setToolTipText(model.getToolTipHTMLRepresentation());
           if (model.getRowCount() > 0) fileLabel.setIcon(model.getEntry(0).getType().getIcon());
           return fileLabel;
         } else return null;
       case URL_COL:
         o = entry.getField("url");
         if (o != null) {
           urlLabel.setToolTipText((String) o);
           return urlLabel;
         } else return null;
       default:
         return null;
     }
   } else {
     String field = fields[column - PAD];
     if (field.equals("author") || field.equals("editor")) {
       // For name fields, tap into a MainTableFormat instance and use
       // the same name formatting as is used in the entry table:
       if (frame.basePanel() != null)
         return frame.basePanel().tableFormat.formatName(entry.getField(field));
     }
     return entry.getField(field);
   }
 }
    /**
     * If the user has signalled the opening of a context menu, the event gets redirected to this
     * method. Here we open a file link menu if the user is pointing at a file link icon. Otherwise
     * a general context menu should be shown.
     *
     * @param e The triggering mouse event.
     */
    public void processPopupTrigger(MouseEvent e) {
      BibtexEntry entry = sortedEntries.get(entryTable.rowAtPoint(e.getPoint()));
      BasePanel p = entryHome.get(entry);
      int col = entryTable.columnAtPoint(e.getPoint());
      JPopupMenu menu = new JPopupMenu();
      int count = 0;

      if (col == FILE_COL) {
        // We use a FileListTableModel to parse the field content:
        Object o = entry.getField(GUIGlobals.FILE_FIELD);
        FileListTableModel fileList = new FileListTableModel();
        fileList.setContent((String) o);
        // If there are one or more links, open the first one:
        for (int i = 0; i < fileList.getRowCount(); i++) {
          FileListEntry flEntry = fileList.getEntry(i);
          String description = flEntry.getDescription();
          if ((description == null) || (description.trim().length() == 0))
            description = flEntry.getLink();
          menu.add(
              new ExternalFileMenuItem(
                  p.frame(),
                  entry,
                  description,
                  flEntry.getLink(),
                  flEntry.getType().getIcon(),
                  p.metaData(),
                  flEntry.getType()));
          count++;
        }
      }

      if (count > 0) menu.show(entryTable, e.getX(), e.getY());
    }
 public void mouseClicked(MouseEvent e) {
   if (e.isPopupTrigger()) {
     processPopupTrigger(e);
     return;
   }
   // if (e.)
   final int col = entryTable.columnAtPoint(e.getPoint()),
       row = entryTable.rowAtPoint(e.getPoint());
   if (col < PAD) {
     BibtexEntry entry = sortedEntries.get(row);
     BasePanel p = entryHome.get(entry);
     switch (col) {
       case FILE_COL:
         Object o = entry.getField(GUIGlobals.FILE_FIELD);
         if (o != null) {
           FileListTableModel tableModel = new FileListTableModel();
           tableModel.setContent((String) o);
           if (tableModel.getRowCount() == 0) return;
           FileListEntry fl = tableModel.getEntry(0);
           (new ExternalFileMenuItem(
                   frame, entry, "", fl.getLink(), null, p.metaData(), fl.getType()))
               .actionPerformed(null);
         }
         break;
       case URL_COL:
         Object link = entry.getField("url");
         try {
           if (link != null) Util.openExternalViewer(p.metaData(), (String) link, "url");
         } catch (IOException ex) {
           ex.printStackTrace();
         }
         break;
     }
   }
 }
  @Override
  public void actionPerformed(ActionEvent actionEvent) {
    setEnabled(false);
    panel.output(Localization.lang("Writing XMP-metadata..."));
    panel.frame().setProgressBarIndeterminate(true);
    panel.frame().setProgressBarVisible(true);
    BibEntry entry = editor.getEntry();

    // Make a list of all PDFs linked from this entry:
    List<File> files = new ArrayList<>();

    // First check the (legacy) "pdf" field:
    entry
        .getField(FieldName.PDF)
        .ifPresent(
            pdf ->
                FileUtil.expandFilename(
                        pdf,
                        panel
                            .getBibDatabaseContext()
                            .getFileDirectory(
                                FieldName.PDF, Globals.prefs.getFileDirectoryPreferences()))
                    .ifPresent(files::add));

    // Then check the "file" field:
    List<String> dirs =
        panel.getBibDatabaseContext().getFileDirectory(Globals.prefs.getFileDirectoryPreferences());
    if (entry.hasField(FieldName.FILE)) {
      FileListTableModel tm = new FileListTableModel();
      entry.getField(FieldName.FILE).ifPresent(tm::setContent);
      for (int j = 0; j < tm.getRowCount(); j++) {
        FileListEntry flEntry = tm.getEntry(j);
        if ((flEntry.type.isPresent()) && "pdf".equalsIgnoreCase(flEntry.type.get().getName())) {
          FileUtil.expandFilename(flEntry.link, dirs).ifPresent(files::add);
        }
      }
    }

    // We want to offload the actual work to a background thread, so we have a worker
    // thread:
    AbstractWorker worker = new WriteXMPWorker(files, entry);
    // Using Spin, we get a thread that gets synchronously offloaded to a new thread,
    // blocking the execution of this method:
    worker.getWorker().run();
    // After the worker thread finishes, we are unblocked and ready to print the
    // status message:
    panel.output(message);
    panel.frame().setProgressBarVisible(false);
    setEnabled(true);
  }
  public String format(String field) {
    StringBuilder sb = new StringBuilder();

    // Build the table model containing the links:
    FileListTableModel tableModel = new FileListTableModel();
    if (field == null) return "";
    tableModel.setContent(field);

    int piv = 1; // counter for relevant iterations
    for (int i = 0; i < tableModel.getRowCount(); i++) {
      FileListEntry flEntry = tableModel.getEntry(i);
      // Use this entry if we don't discriminate on types, or if the type fits:
      if ((fileType == null) || flEntry.getType().getName().toLowerCase().equals(fileType)) {

        for (FormatEntry entry : format) {
          switch (entry.getType()) {
            case STRING:
              sb.append(entry.getString());
              break;
            case ITERATION_COUNT:
              sb.append(String.valueOf(piv));
              break;
            case FILE_PATH:
              if (flEntry.getLink() == null) break;

              String dir;
              // We need to resolve the file directory from the database's metadata,
              // but that is not available from a formatter. Therefore, as an
              // ugly hack, the export routine has set a global variable before
              // starting the export, which contains the database's file directory:
              if (Globals.prefs.fileDirForDatabase != null) dir = Globals.prefs.fileDirForDatabase;
              else dir = Globals.prefs.get(GUIGlobals.FILE_FIELD + "Directory");

              File f = Util.expandFilename(flEntry.getLink(), new String[] {dir});
              /*
               * Stumbled over this while investigating
               *
               * https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
               */
              if (f != null) {
                try {
                  sb.append(replaceStrings(f.getCanonicalPath())); // f.toURI().toString();
                } catch (IOException ex) {
                  ex.printStackTrace();
                  sb.append(replaceStrings(f.getPath()));
                }
              } else {
                sb.append(replaceStrings(flEntry.getLink()));
              }

              break;
            case RELATIVE_FILE_PATH:
              if (flEntry.getLink() == null) break;

              /*
               * Stumbled over this while investigating
               *
               * https://sourceforge.net/tracker/index.php?func=detail&aid=1469903&group_id=92314&atid=600306
               */
              sb.append(replaceStrings(flEntry.getLink())); // f.toURI().toString();

              break;
            case FILE_EXTENSION:
              if (flEntry.getLink() == null) break;
              int index = flEntry.getLink().lastIndexOf('.');
              if ((index >= 0) && (index < flEntry.getLink().length() - 1))
                sb.append(replaceStrings(flEntry.getLink().substring(index + 1)));
              break;
            case FILE_TYPE:
              sb.append(replaceStrings(flEntry.getType().getName()));
              break;
            case FILE_DESCRIPTION:
              sb.append(replaceStrings(flEntry.getDescription()));
              break;
          }
        }

        piv++; // update counter
      }
    }

    return sb.toString();
  }
Exemple #9
0
  private void doRenamePDFs(BibtexEntry entry, NamedCompound ce) {
    // Extract the path
    String oldValue = entry.getField(Globals.FILE_FIELD);
    if (oldValue == null) {
      return;
    }
    FileListTableModel flModel = new FileListTableModel();
    flModel.setContent(oldValue);
    if (flModel.getRowCount() == 0) {
      return;
    }
    boolean changed = false;

    for (int i = 0; i < flModel.getRowCount(); i++) {
      String realOldFilename = flModel.getEntry(i).getLink();

      if (cleanUpRenamePDFonlyRelativePaths.isSelected()
          && (new File(realOldFilename).isAbsolute())) {
        continue;
      }

      String newFilename = Util.getLinkedFileName(panel.database(), entry);
      // String oldFilename = bes.getField(GUIGlobals.FILE_FIELD); // would have to be stored for
      // undoing purposes

      // Add extension to newFilename
      newFilename = newFilename + "." + flModel.getEntry(i).getType().getExtension();

      // get new Filename with path
      // Create new Path based on old Path and new filename
      File expandedOldFile =
          FileUtil.expandFilename(
              realOldFilename, panel.metaData().getFileDirectory(Globals.FILE_FIELD));
      if (expandedOldFile.getParent() == null) {
        // something went wrong. Just skip this entry
        continue;
      }
      String newPath =
          expandedOldFile
              .getParent()
              .concat(System.getProperty("file.separator"))
              .concat(newFilename);

      if (new File(newPath).exists()) {
        // we do not overwrite files
        // TODO: we could check here if the newPath file is linked with the current entry. And if
        // not, we could add a link
        continue;
      }

      // do rename
      boolean renameSuccessful = FileUtil.renameFile(expandedOldFile.toString(), newPath);

      if (renameSuccessful) {
        changed = true;

        // Change the path for this entry
        String description = flModel.getEntry(i).getDescription();
        ExternalFileType type = flModel.getEntry(i).getType();
        flModel.removeEntry(i);

        // we cannot use "newPath" to generate a FileListEntry as newPath is absolute, but we want
        // to keep relative paths whenever possible
        File parent = (new File(realOldFilename)).getParentFile();
        String newFileEntryFileName;
        if (parent == null) {
          newFileEntryFileName = newFilename;
        } else {
          newFileEntryFileName =
              parent.toString().concat(System.getProperty("file.separator")).concat(newFilename);
        }
        flModel.addEntry(i, new FileListEntry(description, newFileEntryFileName, type));
      } else {
        unsuccessfulRenames++;
      }
    }

    if (changed) {
      String newValue = flModel.getStringRepresentation();
      assert (!oldValue.equals(newValue));
      entry.setField(Globals.FILE_FIELD, newValue);
      // we put an undo of the field content here
      // the file is not being renamed back, which leads to inconsistencies
      // if we put a null undo object here, the change by "doMakePathsRelative" would overwrite the
      // field value nevertheless.
      ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
    }
  }
Exemple #10
0
  public void run() {

    if (!goOn) return;

    for (int i = 0; i < entries.length; i++) {

      BibtexEntry entry = entries[i];

      // Make a list of all PDFs linked from this entry:
      List<File> files = new ArrayList<File>();

      // First check the (legacy) "pdf" field:
      String pdf = entry.getField("pdf");
      String dir = panel.metaData().getFileDirectory("pdf");
      File f = Util.expandFilename(pdf, new String[] {dir, "."});
      if (f != null) files.add(f);

      // Then check the "file" field:
      dir = panel.metaData().getFileDirectory(GUIGlobals.FILE_FIELD);
      String field = entry.getField(GUIGlobals.FILE_FIELD);
      if (field != null) {
        FileListTableModel tm = new FileListTableModel();
        tm.setContent(field);
        for (int j = 0; j < tm.getRowCount(); j++) {
          FileListEntry flEntry = tm.getEntry(j);
          if ((flEntry.getType() != null)
              && (flEntry.getType().getName().toLowerCase().equals("pdf"))) {
            f = Util.expandFilename(flEntry.getLink(), new String[] {dir, "."});
            if (f != null) files.add(f);
          }
        }
      }

      optDiag.progressArea.append(entry.getCiteKey() + "\n");

      if (files.size() == 0) {
        skipped++;
        optDiag.progressArea.append("  " + Globals.lang("Skipped - No PDF linked") + ".\n");
      } else
        for (File file : files) {
          if (!file.exists()) {
            skipped++;
            optDiag.progressArea.append(
                "  " + Globals.lang("Skipped - PDF does not exist") + ":\n");
            optDiag.progressArea.append("    " + file.getPath() + "\n");

          } else {
            try {
              XMPUtil.writeXMP(file, entry, database);
              optDiag.progressArea.append("  " + Globals.lang("Ok") + ".\n");
              entriesChanged++;
            } catch (Exception e) {
              optDiag.progressArea.append(
                  "  " + Globals.lang("Error while writing") + " '" + file.getPath() + "':\n");
              optDiag.progressArea.append("    " + e.getLocalizedMessage() + "\n");
              errors++;
            }
          }
        }

      if (optDiag.canceled) {
        optDiag.progressArea.append("\n" + Globals.lang("Operation canceled.\n"));
        break;
      }
    }
    optDiag.progressArea.append(
        "\n"
            + Globals.lang(
                "Finished writing XMP for %0 file (%1 skipped, %2 errors).",
                String.valueOf(entriesChanged), String.valueOf(skipped), String.valueOf(errors)));
    optDiag.done();
  }
  @Override
  public void run() {
    if (!goOn) {
      panel.output(
          Localization.lang("This operation requires one or more entries to be selected."));
      return;
    }
    entriesChangedCount = 0;
    panel.frame().setProgressBarValue(0);
    panel.frame().setProgressBarVisible(true);
    int weightAutoSet = 10; // autoSet takes 10 (?) times longer than checkExisting
    int progressBarMax =
        (autoSet ? weightAutoSet * sel.size() : 0) + (checkExisting ? sel.size() : 0);
    panel.frame().setProgressBarMaximum(progressBarMax);
    int progress = 0;
    final NamedCompound ce = new NamedCompound(Localization.lang("Automatically set file links"));

    Set<BibEntry> changedEntries = new HashSet<>();

    // First we try to autoset fields
    if (autoSet) {
      Collection<BibEntry> entries = new ArrayList<>(sel);

      // Start the automatically setting process:
      Runnable r =
          AutoSetLinks.autoSetLinks(
              entries, ce, changedEntries, null, panel.getBibDatabaseContext(), null, null);
      JabRefExecutorService.INSTANCE.executeAndWait(r);
    }
    progress += sel.size() * weightAutoSet;
    panel.frame().setProgressBarValue(progress);
    // The following loop checks all external links that are already set.
    if (checkExisting) {
      boolean removeAllBroken = false;
      mainLoop:
      for (BibEntry aSel : sel) {
        panel.frame().setProgressBarValue(progress++);
        final String old = aSel.getField(Globals.FILE_FIELD);
        // Check if a extension is set:
        if ((old != null) && !(old.isEmpty())) {
          FileListTableModel tableModel = new FileListTableModel();
          tableModel.setContentDontGuessTypes(old);

          // We need to specify which directories to search in for Util.expandFilename:
          List<String> dirsS = panel.getBibDatabaseContext().getFileDirectory();
          List<File> dirs = new ArrayList<>();
          for (String dirs1 : dirsS) {
            dirs.add(new File(dirs1));
          }

          for (int j = 0; j < tableModel.getRowCount(); j++) {
            FileListEntry flEntry = tableModel.getEntry(j);
            // See if the link looks like an URL:
            boolean httpLink = flEntry.link.toLowerCase(Locale.ENGLISH).startsWith("http");
            if (httpLink) {
              continue; // Don't check the remote file.
              // TODO: should there be an option to check remote links?
            }

            // A variable to keep track of whether this link gets deleted:
            boolean deleted = false;

            // Get an absolute path representation:
            Optional<File> file = FileUtil.expandFilename(flEntry.link, dirsS);
            if ((!file.isPresent()) || !file.get().exists()) {
              int answer;
              if (removeAllBroken) {
                answer = 2; // We should delete this link.
              } else {
                answer =
                    JOptionPane.showOptionDialog(
                        panel.frame(),
                        Localization.lang(
                            "<HTML>Could not find file '%0'<BR>linked from entry '%1'</HTML>",
                            flEntry.link, aSel.getCiteKey()),
                        Localization.lang("Broken link"),
                        JOptionPane.YES_NO_CANCEL_OPTION,
                        JOptionPane.QUESTION_MESSAGE,
                        null,
                        brokenLinkOptions,
                        brokenLinkOptions[0]);
              }
              switch (answer) {
                case 1:
                  // Assign new file.
                  FileListEntryEditor flEditor =
                      new FileListEntryEditor(
                          panel.frame(), flEntry, false, true, panel.getBibDatabaseContext());
                  flEditor.setVisible(true, true);
                  break;
                case 2:
                  // Clear field:
                  tableModel.removeEntry(j);
                  deleted = true; // Make sure we don't investigate this link further.
                  j--; // Step back in the iteration, because we removed an entry.
                  break;
                case 3:
                  // Clear field:
                  tableModel.removeEntry(j);
                  deleted = true; // Make sure we don't investigate this link further.
                  j--; // Step back in the iteration, because we removed an entry.
                  removeAllBroken = true; // Notify for further cases.
                  break;
                default:
                  // Cancel
                  break mainLoop;
              }
            }

            // Unless we deleted this link, see if its file type is recognized:
            if (!deleted
                && flEntry.type.isPresent()
                && (flEntry.type.get() instanceof UnknownExternalFileType)) {
              String[] options =
                  new String[] {
                    Localization.lang("Define '%0'", flEntry.type.get().getName()),
                    Localization.lang("Change file type"),
                    Localization.lang("Cancel")
                  };
              String defOption = options[0];
              int answer =
                  JOptionPane.showOptionDialog(
                      panel.frame(),
                      Localization.lang(
                          "One or more file links are of the type '%0', which is undefined. What do you want to do?",
                          flEntry.type.get().getName()),
                      Localization.lang("Undefined file type"),
                      JOptionPane.YES_NO_CANCEL_OPTION,
                      JOptionPane.QUESTION_MESSAGE,
                      null,
                      options,
                      defOption);
              if (answer == JOptionPane.CANCEL_OPTION) {
                // User doesn't want to handle this unknown link type.
              } else if (answer == JOptionPane.YES_OPTION) {
                // User wants to define the new file type. Show the dialog:
                ExternalFileType newType =
                    new ExternalFileType(
                        flEntry.type.get().getName(),
                        "",
                        "",
                        "",
                        "new",
                        IconTheme.JabRefIcon.FILE.getSmallIcon());
                ExternalFileTypeEntryEditor editor =
                    new ExternalFileTypeEntryEditor(panel.frame(), newType);
                editor.setVisible(true);
                if (editor.okPressed()) {
                  // Get the old list of types, add this one, and update the list in prefs:
                  List<ExternalFileType> fileTypes =
                      new ArrayList<>(
                          ExternalFileTypes.getInstance().getExternalFileTypeSelection());
                  fileTypes.add(newType);
                  Collections.sort(fileTypes);
                  ExternalFileTypes.getInstance().setExternalFileTypes(fileTypes);
                  panel.getMainTable().repaint();
                }
              } else {
                // User wants to change the type of this link.
                // First get a model of all file links for this entry:
                FileListEntryEditor editor =
                    new FileListEntryEditor(
                        panel.frame(), flEntry, false, true, panel.getBibDatabaseContext());
                editor.setVisible(true, false);
              }
            }
          }

          if (!tableModel.getStringRepresentation().equals(old)) {
            // The table has been modified. Store the change:
            String toSet = tableModel.getStringRepresentation();
            if (toSet.isEmpty()) {
              ce.addEdit(new UndoableFieldChange(aSel, Globals.FILE_FIELD, old, null));
              aSel.clearField(Globals.FILE_FIELD);
            } else {
              ce.addEdit(new UndoableFieldChange(aSel, Globals.FILE_FIELD, old, toSet));
              aSel.setField(Globals.FILE_FIELD, toSet);
            }
            changedEntries.add(aSel);
          }
        }
      }
    }

    if (!changedEntries.isEmpty()) {
      // Add the undo edit:
      ce.end();
      panel.getUndoManager().addEdit(ce);
      panel.markBaseChanged();
      entriesChangedCount = changedEntries.size();
    }
  }