Merge branch '26-upload-pause-resume' into 'master'

Resolve "Upload pause-resume"

Closes #26

See merge request !19

anno-gui/src/main/java/org/eclipse/wb/swt/SWTResourceManager.java

-/*******************************************************************************
- * Copyright (c) 2011 Google, Inc.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
- *
- * Contributors:
- *    Google, Inc. - initial API and implementation
- *******************************************************************************/
+/*******************************************************************************
+ * Copyright (c) 2011 Google, Inc.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *    Google, Inc. - initial API and implementation
+ *******************************************************************************/
 package org.eclipse.wb.swt;
 
 import java.io.FileInputStream;

anno-gui/src/main/java/org/genesys2/anno/gui/SwtLogAppender.java

@@ -15,16 +15,12 @@
  */
 package org.genesys2.anno.gui;
 
-import java.util.concurrent.atomic.AtomicBoolean;
-
 import org.apache.log4j.LogManager;
 import org.apache.log4j.PatternLayout;
 import org.apache.log4j.WriterAppender;
 import org.apache.log4j.spi.LoggingEvent;
 import org.eclipse.swt.events.DisposeEvent;
 import org.eclipse.swt.events.DisposeListener;
-import org.eclipse.swt.events.PaintEvent;
-import org.eclipse.swt.events.PaintListener;
 import org.eclipse.swt.widgets.Display;
 import org.eclipse.swt.widgets.Text;
 
@@ -33,9 +29,8 @@ public class SwtLogAppender extends WriterAppender {
 	private static final String DEFAULT_LAYOUT_PATTERN = "%d{yyyy-MM-dd HH:mm:ss} %t %-5p %c{1}:%L - %m%n";
 	private Text text;
 	private Display display;
-	private int maxBufferSize = 100000;
+	private int maxBufferSize = 1000000;
 	private StringBuffer logBuffer = new StringBuffer();
-	private AtomicBoolean resetText = new AtomicBoolean(true);
 
 	public SwtLogAppender(Text text2) {
 		this.text = text2;
@@ -45,15 +40,6 @@ public class SwtLogAppender extends WriterAppender {
 				close();
 			}
 		});
-		text.addPaintListener(new PaintListener() {
-			@Override
-			public void paintControl(PaintEvent e) {
-				if (resetText.getAndSet(false)) {
-					text.setText(logBuffer.toString());
-					text.setSelection(logBuffer.length());
-				}
-			}
-		});
 		display = text.getDisplay();
 		LogManager.getRootLogger().addAppender(this);
 		PatternLayout patternLayout = new org.apache.log4j.PatternLayout();
@@ -98,14 +84,15 @@ public class SwtLogAppender extends WriterAppender {
 				logBuffer.replace(0, pos + 1, "");
 			}
 		}
-		resetText.set(true);
 
 		// System.err.println(mes);
-		display.asyncExec(new Runnable() {
-			@Override
-			public void run() {
-				if (text != null) {
-					text.redraw();
+		display.asyncExec(() -> {
+			if (text != null) {
+				int scrollPos = text.getLineCount() - 1;
+				text.setText(logBuffer.toString());
+				int topIndex = text.getTopIndex();
+				if ((scrollPos <= 0 && topIndex == 0) || topIndex >= scrollPos - 3) {
+					text.setSelection(text.getText().length() * 2);
 				}
 			}
 		});

anno-gui/src/main/java/org/genesys2/anno/gui/LogViewer.java → anno-gui/src/main/java/org/genesys2/anno/gui/TimedList.java

-/**
- * Copyright 2014 Global Crop Diversity Trust
- * 
+/*
+ * Copyright 2019 Global Crop Diversity Trust
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *   http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- **/
-
+ */
 package org.genesys2.anno.gui;
 
-import org.eclipse.swt.SWT;
-import org.eclipse.swt.widgets.Composite;
-import org.eclipse.swt.widgets.Text;
-import org.eclipse.swt.widgets.ToolBar;
-import org.eclipse.swt.widgets.ToolItem;
-
-import swing2swt.layout.BorderLayout;
-
-public class LogViewer extends Composite {
-	private Text txtLogtext;
-
-	/**
-	 * Create the composite.
-	 * 
-	 * @param parent
-	 * @param style
-	 */
-	public LogViewer(Composite parent, int style) {
-		super(parent, style);
-		setLayout(new BorderLayout(0, 0));
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Date;
 
-		ToolBar toolBar = new ToolBar(this, SWT.FLAT | SWT.RIGHT);
-		toolBar.setLayoutData(BorderLayout.NORTH);
+/**
+ * The Class TimedList.
+ *
+ * @param <T> the generic type
+ */
+public class TimedList<T> extends ArrayList<T> {
+	private static final long serialVersionUID = 2721716147790325499L;
+	private Date created = null;
 
-		ToolItem tltmClear = new ToolItem(toolBar, SWT.NONE);
-		tltmClear.setText("Clear");
+	public TimedList() {
+	}
+	
+	@Override
+	public void clear() {
+		created = null;
+		super.clear();
+	}
 
-		ToolItem tltmSave = new ToolItem(toolBar, SWT.NONE);
-		tltmSave.setText("Save...");
+	@Override
+	public boolean add(T e) {
+		if (created == null) {
+			created = new Date();
+		}
+		return super.add(e);
+	}
 
-		txtLogtext = new Text(this, SWT.BORDER | SWT.READ_ONLY | SWT.V_SCROLL | SWT.MULTI);
-		txtLogtext.setLayoutData(BorderLayout.CENTER);
+	@Override
+	public boolean addAll(Collection<? extends T> c) {
+		if (created == null) {
+			created = new Date();
+		}
+		return super.addAll(c);
+	}
 
+	@Override
+	public void add(int index, T element) {
+		if (created == null) {
+			created = new Date();
+		}
+		super.add(index, element);
 	}
 
 	@Override
-	protected void checkSubclass() {
-		// Disable the check that prevents subclassing of SWT components
+	public boolean addAll(int index, Collection<? extends T> c) {
+		if (created == null) {
+			created = new Date();
+		}
+		return super.addAll(index, c);
+	}
+
+	public Date getCreated() {
+		return created;
 	}
 
+	public boolean isOlderThanSeconds(int seconds) {
+		if (created == null) {
+			return true;
+		}
+		return (new Date().getTime() - created.getTime()) / 1000 > seconds;
+	}
 }

anno-gui/src/main/java/org/genesys2/anno/parser/MsAccessRowReader.java

@@ -54,21 +54,22 @@ public class MsAccessRowReader implements RowReader {
 		this.db = DatabaseBuilder.open(sourceFile);
 		_log.debug("CHARSET: " + db.getCharset());
 		this.table = db.getTable(sheetName);
-		this.cursor = table.getDefaultCursor();
+		this.cursor = table.newCursor().setIndexByColumnNames("INSTCODE").toCursor();
 
 	}
 
 	/// This is called in case data starts beyond 1st row
 	@Override
 	public void setSkipRows(int skipRows) {
-		_log.info("Skipping rows {}", skipRows);
+		// The -1 is because CSV and Excel include the header row in the count
+		_log.info("Skipping rows {}", skipRows - 1);
 		cursor.reset();
 
-		// try {
-		// cursor.moveNextRows(skipRows);
-		// } catch (IOException e) {
-		// _log.error("Could not skip rows", e);
-		// }
+		try {
+			cursor.moveNextRows(skipRows - 1);
+		} catch (IOException e) {
+			_log.error("Could not skip rows", e);
+		}
 	}
 
 	@Override