Open Ms Access as a file source

anno-gui/pom.xml

@@ -164,7 +164,7 @@
 		<dependency>
 			<groupId>com.healthmarketscience.jackcess</groupId>
 			<artifactId>jackcess</artifactId>
-			<version>2.1.4</version>
+			<version>2.1.6</version>
 		</dependency>
 		<dependency>
 			<groupId>org.hsqldb</groupId>

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

@@ -316,13 +316,6 @@ public class AppWindow {
 		threadPool.shutdown();
 	}
 
-	public static boolean isMac() {
-		if (System.getProperty("os.name").equals("Mac OS X")) {
-			return true;
-		}
-		return false;
-	}
-
 	/**
 	 * Create contents of the window.
 	 */
@@ -833,8 +826,8 @@ public class AppWindow {
 
 	public void addSourceFile() {
 		FileDialog fd = new FileDialog(shlGenesysMagic, SWT.MULTI);
-		fd.setFilterNames(new String[] { "Supported source files", "Excel files", "CSV files" });
-		fd.setFilterExtensions(new String[] { "*.xlsx;*.xls;*.csv;*.tab", "*.xlsx;*.xls", "*.csv;*.tab" });
+		fd.setFilterNames(new String[] { "Supported source files", "Excel files", "CSV files", "MS Access" });
+		fd.setFilterExtensions(new String[] { "*.xlsx;*.xls;*.csv;*.tab;*.accdb", "*.xlsx;*.xls", "*.csv;*.tab", "*.accdb" });
 		String response = fd.open();
 
 		if (response != null) {

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

@@ -30,6 +30,7 @@ import org.genesys2.anno.model.JdbcDrivers;
 import org.genesys2.anno.model.OAuthSettings;
 import org.genesys2.anno.model.Settings;
 import org.genesys2.anno.parser.CsvDataSourceParser;
+import org.genesys2.anno.parser.MsAccessDataSourceParser;
 import org.genesys2.anno.parser.XlsxDataSourceParser;
 import org.genesys2.anno.reader.JDBCRowReader;
 import org.genesys2.anno.util.ConnectionUtils;
@@ -65,6 +66,7 @@ public class SpringConfig {
 		DataSourceLoaderImpl dataSourceLoader = new DataSourceLoaderImpl();
 		dataSourceLoader.registerParser(new XlsxDataSourceParser());
 		dataSourceLoader.registerParser(new CsvDataSourceParser());
+		dataSourceLoader.registerParser(new MsAccessDataSourceParser());
 		return dataSourceLoader;
 	}
 

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

+/*
+ * Copyright 2018 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.parser;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.genesys2.anno.gui.DataSourceSheet;
+import org.genesys2.anno.gui.IDataSourceSheet;
+import org.genesys2.anno.gui.UnsupportedDataFormatException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.healthmarketscience.jackcess.Cursor;
+import com.healthmarketscience.jackcess.Database;
+import com.healthmarketscience.jackcess.DatabaseBuilder;
+import com.healthmarketscience.jackcess.Row;
+import com.healthmarketscience.jackcess.Table;
+
+/**
+ * The MsAccess DataSourceParser.
+ * 
+ *  @author Matija Obreza
+ */
+public class MsAccessDataSourceParser extends BasicDataSourceParser {
+	private static final Logger _log = LoggerFactory.getLogger(MsAccessDataSourceParser.class);
+
+	private final String[] supportedExtensions = new String[] { ".accdb" };
+
+	@Override
+	public String[] getSupportedExtensions() {
+		return supportedExtensions;
+	}
+
+	@Override
+	public Collection<? extends DataSourceSheet> findSheets(File sourceFile) throws UnsupportedDataFormatException {
+		try {
+			try (Database db = DatabaseBuilder.open(sourceFile)) {
+				_log.debug("CHARSET: " + db.getCharset());
+				db.getTableNames().stream().forEach(tableName -> System.out.println("Table: " + tableName));
+				return db.getTableNames().stream().sorted().map(tableName -> {
+					DataSourceSheet sheetDataSource = new DataSourceSheet(sourceFile);
+					sheetDataSource.setSheetName(tableName);
+					_log.debug("Creating sheet for table {}", tableName);
+					return sheetDataSource;
+				}).collect(Collectors.toList());
+			}
+		} catch (Throwable e) {
+			throw new UnsupportedDataFormatException(e.getMessage(), e);
+		}
+	}
+
+	@Override
+	public List<Object[]> loadRows(IDataSourceSheet dataSourceSheet, int maxRows, int startAt) throws UnsupportedDataFormatException, FileNotFoundException, IOException {
+		File sourceFile = dataSourceSheet.getSourceFile();
+		String sheetName = dataSourceSheet.getSheetName();
+
+		_log.debug("Reading {} from {}", sheetName, sourceFile);
+
+		List<Object[]> rows = new ArrayList<Object[]>(maxRows);
+
+		try {
+			try (Database db = DatabaseBuilder.open(sourceFile)) {
+				_log.debug("CHARSET: " + db.getCharset());
+				Table table = db.getTable(sheetName);
+				rows.add(table.getColumns().stream().map(column -> column.getName()).toArray());
+
+				Cursor cursor = table.getDefaultCursor();
+				cursor.moveNextRows(startAt);
+				for (int pos = maxRows; pos > 0; pos--) {
+					Row r = cursor.getNextRow();
+					if (r != null) {
+						rows.add(r.values().toArray());
+					}
+				}
+			}
+			return rows;
+		} catch (Throwable e) {
+			throw new UnsupportedDataFormatException(e.getMessage(), e);
+		}
+	}
+
+	@Override
+	public RowReader createRowReader(IDataSourceSheet dataSourceSheet) throws UnsupportedDataFormatException, IOException {
+		File sourceFile = dataSourceSheet.getSourceFile();
+		String sheetName = dataSourceSheet.getSheetName();
+
+		return new MsAccessRowReader(sourceFile, sheetName);
+	}
+
+}

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

+/*
+ * Copyright 2018 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.parser;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.healthmarketscience.jackcess.Cursor;
+import com.healthmarketscience.jackcess.Database;
+import com.healthmarketscience.jackcess.DatabaseBuilder;
+import com.healthmarketscience.jackcess.Row;
+import com.healthmarketscience.jackcess.Table;
+
+/**
+ * The Ms Access RowReader.
+ * 
+ * @author Matija Obreza
+ */
+public class MsAccessRowReader implements RowReader {
+	private static final Logger _log = LoggerFactory.getLogger(MsAccessRowReader.class);
+	private Database db;
+	private Table table;
+	private Cursor cursor;
+
+	/**
+	 * Instantiates a new ms access row reader.
+	 *
+	 * @param sourceFile
+	 *            the source file
+	 * @param sheetName
+	 *            the sheet name
+	 * @throws IOException
+	 *             Signals that an I/O exception has occurred.
+	 */
+	public MsAccessRowReader(File sourceFile, String sheetName) throws IOException {
+		this.db = DatabaseBuilder.open(sourceFile);
+		_log.debug("CHARSET: " + db.getCharset());
+		this.table = db.getTable(sheetName);
+		this.cursor = table.getDefaultCursor();
+
+	}
+
+	/// This is called in case data starts beyond 1st row
+	@Override
+	public void setSkipRows(int skipRows) {
+		_log.info("Skipping rows {}", skipRows);
+		cursor.reset();
+
+		// try {
+		// cursor.moveNextRows(skipRows);
+		// } catch (IOException e) {
+		// _log.error("Could not skip rows", e);
+		// }
+	}
+
+	@Override
+	public int getRowCount() {
+		return table.getRowCount();
+	}
+
+	@Override
+	public void close() throws IOException {
+		db.close();
+	}
+
+	@Override
+	public List<Object[]> readRows(int rowsToRead) throws IOException {
+		List<Object[]> rows = new ArrayList<Object[]>(rowsToRead);
+		int rowCount = 0;
+		while ((rowCount < rowsToRead) && cursor.moveToNextRow()) {
+			rowCount++;
+			Row r = cursor.getCurrentRow();
+			if (r != null) {
+				rows.add(r.values().toArray());
+			}
+		}
+		return rows;
+	}
+}