Switch to Apache POI for XLSX support. Fixes yarl#136

This has only received VERY LIMITED testing.

It now writes .xlsx files and reads either .xls or .xlsx

In addition to testing, packaging should also be reviewed. It may
be possible to remove some of the bundled JARs (or better yet,
switch to Maven for dependency management).

Author: tfmorris

lib/SparseBitSet-1.2.jar

@@ -30,7 +30,9 @@
 import com.drew.metadata.exif.ExifSubIFDDirectory;
 import java.awt.Desktop;
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.TimeZone;
@@ -40,13 +42,12 @@
 import javafx.scene.text.TextAlignment;
 import javafx.scene.text.TextFlow;
 import javafx.stage.Stage;
-import jxl.CellView;
-import jxl.Workbook;
-import jxl.read.biff.BiffException;
-import jxl.write.Label;
-import jxl.write.WritableSheet;
-import jxl.write.WritableWorkbook;
-import jxl.write.WriteException;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellType;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.xssf.streaming.SXSSFSheet;
+import org.apache.poi.xssf.streaming.SXSSFWorkbook;
 import pattypan.Session;
 import pattypan.Settings;
 import pattypan.Template;
@@ -103,7 +104,7 @@ private WikiPane setActions() {
         createSpreadsheet();
         showOpenFileButton();
         Settings.saveProperties();
-      } catch (IOException | BiffException | WriteException ex) {
+      } catch (IOException  ex) {
         addElement(new WikiLabel("create-file-error"));
         Session.LOGGER.log(Level.WARNING, 
             "Error occurred during creation of spreadsheet file: {0}",
@@ -135,43 +136,49 @@ private void showOpenFileButton() {
     nextButton.setVisible(true);
   }
 
-  private void autoSizeColumn(int column, WritableSheet sheet) {
-    CellView cell = sheet.getColumnView(column);
-    cell.setAutosize(true);
-    sheet.setColumnView(column, cell);
+  private void autoSizeColumn(int column, Sheet sheet) {
+    sheet.autoSizeColumn(column);
   }
 
-  private void createSpreadsheet() throws IOException, BiffException, WriteException {
-    File f = new File(Session.DIRECTORY, fileName.getText() + ".xls");
-    WritableWorkbook workbook = Workbook.createWorkbook(f);
+  private void createSpreadsheet() throws IOException {
+    File f = new File(Session.DIRECTORY, fileName.getText() + ".xlsx");
+    // Autosize appears to only be supported for OOXML workbooks, so making this specific instead of generic
+    //    boolean xml = true;
+    //    final Workbook workbook = xml ? new SXSSFWorkbook() : new HSSFWorkbook();
+    final SXSSFWorkbook workbook = new SXSSFWorkbook();
 
     createDataSheet(workbook);
     createTemplateSheet(workbook);
 
-    workbook.write();
+    try (OutputStream os = new FileOutputStream(f)){
+      workbook.write(os);
+      os.flush();
+    }
     workbook.close();
     Session.FILE = f;
   }
 
   /**
    *
    * @param workbook
-   * @throws WriteException
    */
-  private void createDataSheet(WritableWorkbook workbook) throws WriteException {
-    WritableSheet sheet = workbook.createSheet("Data", 0);
+  private void createDataSheet(SXSSFWorkbook workbook) {
+    SXSSFSheet sheet = workbook.createSheet("Data");
 
     // first row (header)
+    Row header = sheet.createRow(0);
     int column = 0;
     for (String variable : Session.VARIABLES) {
-      sheet.addCell(new Label(column++, 0, variable));
+      Cell c = header.createCell(column++);
+      c.setCellValue(variable);
     }
 
     // next rows with path and name
     int row = 1;
     for (File file : Session.FILES) {
-      sheet.addCell(new Label(0, row, file.getAbsolutePath()));
-      sheet.addCell(new Label(1, row++, Util.getNameFromFilename(file.getName())));
+      Row cells = sheet.createRow(row++);
+      cells.createCell(0, CellType.STRING).setCellValue(file.getAbsolutePath());
+      cells.createCell(1, CellType.STRING).setCellValue(Util.getNameFromFilename(file.getName()));
     }
 
     if (Session.METHOD.equals("template")) {
@@ -181,7 +188,8 @@ private void createDataSheet(WritableWorkbook workbook) throws WriteException {
           column = Session.VARIABLES.indexOf(tf.name);
           row = 1;
           for (File file : Session.FILES) {
-            sheet.addCell(new Label(column, row++, tf.value));
+            // TODO: We may not have the cells created yet here. Let's see what happens
+            sheet.getRow(row++).getCell(column).setCellValue(tf.value);
           }
         }
       }
@@ -191,32 +199,36 @@ private void createDataSheet(WritableWorkbook workbook) throws WriteException {
     if (column >= 0 && !Settings.getSetting("exifDate").isEmpty()) {
       row = 1;
       for (File file : Session.FILES) {
-        sheet.addCell(new Label(column, row++, getExifDate(file)));
+        // TODO: We may not have the cells created yet here. Let's see what happens
+        sheet.getRow(row++).getCell(column).setCellValue(getExifDate(file));
       }
     }
 
-    for (int num = 0; num < sheet.getColumns(); num++) {
+    sheet.trackAllColumnsForAutoSizing();
+    for (int num = 0; num < sheet.getRow(0).getLastCellNum(); num++) {
       autoSizeColumn(num, sheet);
     }
   }
 
   /**
    *
    * @param workbook
-   * @throws WriteException
    */
-  private void createTemplateSheet(WritableWorkbook workbook) throws WriteException {
-    WritableSheet templateSheet = workbook.createSheet("Template", 1);
-    templateSheet.addCell(new Label(0, 0, "'" + Session.WIKICODE));
-    //                                    ^^
+  private void createTemplateSheet(SXSSFWorkbook workbook)  {
+    SXSSFSheet templateSheet = workbook.createSheet("Template");
+    Row row = templateSheet.createRow(0);
+    Cell cell = row.createCell(0);
+    cell.setCellValue("'" + Session.WIKICODE);
+    //                 ^^
     // leading apostrophe prevents turning wikitext into formula in Excel
 
+    templateSheet.trackAllColumnsForAutoSizing();
     autoSizeColumn(0, templateSheet);
   }
 
   /**
    *
-   * @param filePath
+   * @param file
    * @return
    */
   private String getExifDate(File file) {

lib/commons-codec-1.15.jar

@@ -23,18 +23,22 @@
  */
 package pattypan.panes;
 
-import freemarker.core.InvalidReferenceException;
 import freemarker.template.Configuration;
 import freemarker.template.Template;
 import freemarker.template.TemplateException;
 import freemarker.template.TemplateExceptionHandler;
+import java.io.BufferedInputStream;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.TimeZone;
@@ -43,13 +47,17 @@
 import javafx.scene.layout.VBox;
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
-import jxl.Cell;
-import jxl.CellType;
-import jxl.DateCell;
-import jxl.Sheet;
-import jxl.Workbook;
-import jxl.WorkbookSettings;
-import jxl.read.biff.BiffException;
+import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.apache.poi.poifs.filesystem.FileMagic;
+import org.apache.poi.poifs.filesystem.POIFSFileSystem;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellType;
+import org.apache.poi.ss.usermodel.DateUtil;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+
 import pattypan.Session;
 import pattypan.Settings;
 import pattypan.UploadElement;
@@ -236,10 +244,9 @@ private void addInfo(String text, String cssClass) {
    * @throws Exception when essential headers are missing
    */
   private void readHeaders(Sheet sheet) throws Exception {
-    int columns = sheet.getColumns();
-    ArrayList<String> cols = new ArrayList<>();
-    for (int col = 0; col < columns; col++) {
-      cols.add(sheet.getCell(col, 0).getContents());
+    List<String> cols = new ArrayList<>();
+    for (Cell c : sheet.getRow(0)) {
+      cols.add(c.getStringCellValue());
     }
 
     if (cols.isEmpty()) {
@@ -264,18 +271,22 @@ private String getCellValue(Sheet sheet, int column, int row) {
     formatDate.setTimeZone(TimeZone.getTimeZone("UTC"));
     formatDateHour.setTimeZone(TimeZone.getTimeZone("UTC"));
 
-    Cell valueCell = sheet.getCell(column, row);
-    String value;
+    Cell valueCell = sheet.getRow(row).getCell(column);
+    String value = null;
 
-    if (valueCell.getType() == CellType.DATE) {
-      DateCell dateCell = (DateCell) valueCell;
+    if (valueCell != null) {
+      if (valueCell.getCellType() == CellType.NUMERIC && DateUtil.isCellDateFormatted(valueCell)) {
+      Date date = DateUtil.getJavaDate(valueCell.getNumericCellValue());
+      // FIXME: Restore more sophisticated date handling
+      value = formatDate.format(date);
       //@TODO: more elegant hour detection
-      value = dateCell.getContents().contains(":")
-              ? formatDateHour.format(dateCell.getDate())
-              : formatDate.format(dateCell.getDate());
-    } else {
-      value = sheet.getCell(column, row).getContents().trim();
-    }
+//      value = dateCell.getContents().contains(":")
+//              ? formatDateHour.format(dateCell.getDate())
+//              : formatDate.format(dateCell.getDate());
+        } else {
+          value = valueCell.getStringCellValue().trim();
+        }
+      }
     return value;
   }
 
@@ -294,9 +305,7 @@ private void loadSpreadsheet(File file) {
       readSpreadSheet();
     } catch (IOException ex) {
       addInfo("File error: there are problems opening file. It may be corrupted.");
-    } catch (BiffException ex) {
-      addInfo("File error: file needs to be saved in binnary format. Please save your file in \"Excel 97-2003 format\"");
-    } catch (InvalidReferenceException ex) {
+    } catch (TemplateException ex) {
       addInfo("File error: variables mismatch. Column headers variables must match wikitemplate variables.");
     } catch (Exception ex) {
       addInfo(ex.getMessage());
@@ -312,14 +321,27 @@ private void loadSpreadsheet(File file) {
    */
   private ArrayList<Map<String, String>> readDescriptions(Sheet sheet) {
     ArrayList<Map<String, String>> descriptions = new ArrayList<>();
-    int rows = sheet.getRows();
-    int columns = sheet.getColumns();
+    int rows = sheet.getLastRowNum();
+    int columns = sheet.getRow(0).getLastCellNum();
 
+    // Collect header labels
+    String[] labels = new String[columns];
+    Row cells = sheet.getRow(0);
+    for (int col = 0; col < columns; col++) {
+      Cell cell = cells.getCell(col);
+      if (cell != null) {
+        String value = cell.getStringCellValue();
+        labels[col] = value;
+      } else {
+        labels[col] = null;
+      }
+    }
     for (int row = 1; row < rows; row++) {
       Map<String, String> description = new HashMap();
+      cells  = sheet.getRow(row);
       for (int column = 0; column < columns; column++) {
-        String label = sheet.getCell(column, 0).getContents().trim();
-        if (label.isEmpty()) {
+        String label = labels[column];
+        if (label == null || label.isEmpty()) {
           continue;
         }
         String value = getCellValue(sheet, column, row);
@@ -333,17 +355,19 @@ private ArrayList<Map<String, String>> readDescriptions(Sheet sheet) {
   /**
    * Reads spreadsheet stored in Session.FILE.
    */
-  private void readSpreadSheet() throws BiffException, IOException, Exception {
+  private void readSpreadSheet() throws IOException, TemplateException, Exception {
     infoContainer.getChildren().clear();
     Session.SCENES.remove("CheckPane");
 
-    WorkbookSettings ws = new WorkbookSettings();
-    ws.setEncoding("Cp1252");
+    InputStream inputStream = new BufferedInputStream(new FileInputStream(Session.FILE));
+    Workbook wb = FileMagic.valueOf(inputStream) == FileMagic.OOXML ? new XSSFWorkbook(inputStream)
+            : new HSSFWorkbook(new POIFSFileSystem(inputStream));
+
+//    ws.setEncoding("Cp1252"); // FIXME
 
     try {
-      Workbook workbook = Workbook.getWorkbook(Session.FILE, ws);
-      Sheet dataSheet = workbook.getSheet(0);
-      Sheet templateSheet = workbook.getSheet(1);
+      Sheet dataSheet = wb.getSheetAt(0);
+      Sheet templateSheet = wb.getSheetAt(1);
       readHeaders(dataSheet);
       addFilesToUpload(readDescriptions(dataSheet), readTemplate(templateSheet));
     } catch (IndexOutOfBoundsException ex) {
@@ -362,7 +386,7 @@ private void readSpreadSheet() throws BiffException, IOException, Exception {
    */
   private Template readTemplate(Sheet sheet) throws Exception {
     try {
-      String text = sheet.getCell(0, 0).getContents();
+      String text = sheet.getRow(0).getCell(0).getStringCellValue();
       return new Template("wikitemplate", new StringReader(text), cfg);
     } catch (ArrayIndexOutOfBoundsException ex) {
       throw new Exception("Error: template in spreadsheet looks empty. Check if wikitemplate is present in second tab of your spreadsheet (first row and first column).");