Now can run WhiteRabbit from command prompt

README.md

@@ -10,6 +10,7 @@ Features
 - Can scan databases in SQL Server, Oracle, PostgreSQL, MySQL, MS Access, Amazon RedShift, and CSV files
 - The scan report contains information on tables, fields, and frequency distributions of values
 - Cutoff on the minimum frequency of values to protect patient privacy
+- WhiteRabbit can be run with a graphical user interface or from the command prompt
 - Interactive tool (Rabbit in a Hat) for designing the ETL using the scan report as basis
 - Rabbit in a Hat generates ETL specification document according to OMOP template
 
@@ -48,6 +49,7 @@ WhiteRabbit
 1. Under the [Releases](https://github.com/OHDSI/WhiteRabbit/releases) tab, download WhiteRabbit*.zip
 2. Unzip the download
 3. Double-click on WhiteRabbit.jar to start White Rabbit.
+(See the Wiki for details on how to run from the command prompt instead)
 
 Rabbit-In-A-Hat
 
@@ -66,5 +68,7 @@ WhiteRabbit is licensed under Apache License 2.0
 Development
 ===========
 White Rabbit and Rabbit in a Hat are being developed in Eclipse. Contributions are welcome.
+
 ###Development status
-Beta testing - We invite everyone to try the software, and report any issues they may find.
+
+Production. This program is being used by many people.

iniFileExamples/WhiteRabbit.ini

@@ -0,0 +1,12 @@
+WORKING_FOLDER = /users/joe          # Path to the folder where all output will be written 
+DATA_TYPE = PostgreSQL               # "Delimited text files", "MySQL", "Oracle", "SQL Server", "PostgreSQL", "MS Access", or "Redshift"
+SERVER_LOCATION = 127.0.0.1          # Name or address of the server. For Postgres, add the database name 
+USER_NAME = joe                      # User name for the database 
+PASSWORD = supersecret               # Password for the database 
+DATABASE_NAME = my_database          # Name of the data schema used 
+DELIMITER = ,                        # The delimiter that separates values
+TABLES_TO_SCAN = *                   # Comma-delimited list of table names to scan. Use "*" (asterix) to include all tables in the database
+SCAN_FIELD_VALUES = yes              # Include a frequency count of field values in the scan report? "yes" or "no"
+MIN_CELL_COUNT = 5                   # Minimum frequency for a field value to be included in the report 
+MAX_DISTINCT_VALUES = 1000           # Maximum number of distinct values per field to be reported
+ROWS_PER_TABLE = 100000              # Maximum number of rows per table to be scanned for field values

src/org/ohdsi/utilities/WhiteRabbitLauncher.java

@@ -12,7 +12,7 @@ public static void main(String[] args) throws Exception {
 
 		float heapSizeMegs = (Runtime.getRuntime().maxMemory() / 1024) / 1024;
 
-		if (heapSizeMegs > MIN_HEAP) {
+		if (heapSizeMegs > MIN_HEAP || args.length > 0) {
 			System.out.println("Launching with current VM");
 			WhiteRabbitMain.main(args);
 		} else {

src/org/ohdsi/utilities/files/IniFile.java

@@ -0,0 +1,46 @@
+/*******************************************************************************
+ * Copyright 2016 Observational Health Data Sciences and Informatics
+ * 
+ * This file is part of WhiteRabbit
+ * 
+ * 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.ohdsi.utilities.files;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class IniFile {
+	private Map<String, String> settings = new HashMap<String, String>();
+
+	public IniFile(String filename){
+		for (String line : new ReadTextFile(filename)){
+			int indexOfHash = line.lastIndexOf('#');
+			if (indexOfHash != -1)
+				line = line.substring(0,indexOfHash);
+
+			int	indexOfEqualsSigns = line.indexOf('=');
+
+			if (indexOfEqualsSigns != -1)
+				settings.put(line.substring(0,indexOfEqualsSigns).trim().toLowerCase(), line.substring(indexOfEqualsSigns+1).trim());	
+		}
+	}
+
+	public String get(String fieldName){
+		String value = settings.get(fieldName.toLowerCase());
+		if (value == null)
+			return "";
+		else
+			return value;
+	}
+}

src/org/ohdsi/whiteRabbit/WhiteRabbitMain.java

@@ -74,6 +74,7 @@
 import org.ohdsi.databases.RichConnection;
 import org.ohdsi.utilities.DirectoryUtilities;
 import org.ohdsi.utilities.StringUtilities;
+import org.ohdsi.utilities.files.IniFile;
 import org.ohdsi.whiteRabbit.fakeDataGenerator.FakeDataGenerator;
 import org.ohdsi.whiteRabbit.scan.SourceDataScan;
 
@@ -119,27 +120,86 @@ public static void main(String[] args) {
 	}
 
 	public WhiteRabbitMain(String[] args) {
-		frame = new JFrame("White Rabbit");
+		if (args.length == 2 && args[0].equalsIgnoreCase("-ini"))
+			launchCommandLine(args[1]);
+		else {
+			frame = new JFrame("White Rabbit");
+
+			frame.addWindowListener(new WindowAdapter() {
+				public void windowClosing(WindowEvent e) {
+					System.exit(0);
+				}
+			});
+			frame.setLayout(new BorderLayout());
+			frame.setJMenuBar(createMenuBar());
 
-		frame.addWindowListener(new WindowAdapter() {
-			public void windowClosing(WindowEvent e) {
-				System.exit(0);
-			}
-		});
-		frame.setLayout(new BorderLayout());
-		frame.setJMenuBar(createMenuBar());
+			JComponent tabsPanel = createTabsPanel();
+			JComponent consolePanel = createConsolePanel();
 
-		JComponent tabsPanel = createTabsPanel();
-		JComponent consolePanel = createConsolePanel();
+			frame.add(consolePanel, BorderLayout.CENTER);
+			frame.add(tabsPanel, BorderLayout.NORTH);
 
-		frame.add(consolePanel, BorderLayout.CENTER);
-		frame.add(tabsPanel, BorderLayout.NORTH);
+			loadIcons(frame);
+			frame.pack();
+			frame.setVisible(true);
+			ObjectExchange.frame = frame;
+		}
+	}
 
-		loadIcons(frame);
-		frame.pack();
-		frame.setVisible(true);
-		ObjectExchange.frame = frame;
-		executeParameters(args);
+	private void launchCommandLine(String iniFileName) {
+		IniFile iniFile = new IniFile(iniFileName);
+		DbSettings dbSettings = new DbSettings();
+		if (iniFile.get("DATA_TYPE").equalsIgnoreCase("Delimited text files")) {
+			dbSettings.dataType = DbSettings.CSVFILES;
+			if (iniFile.get("DELIMITER").equalsIgnoreCase("tab"))
+				dbSettings.delimiter = '\t';
+			else
+				dbSettings.delimiter = iniFile.get("DELIMITER").charAt(0);
+		} else {
+			dbSettings.dataType = DbSettings.DATABASE;
+			dbSettings.user = iniFile.get("USER_NAME");
+			dbSettings.password = iniFile.get("PASSWORD");
+			dbSettings.server = iniFile.get("SERVER_LOCATION");
+			dbSettings.database = iniFile.get("DATABASE_NAME");
+			if (iniFile.get("DATA_TYPE").equalsIgnoreCase("MySQL"))
+				dbSettings.dbType = DbType.MYSQL;
+			else if (iniFile.get("DATA_TYPE").equalsIgnoreCase("Oracle"))
+				dbSettings.dbType = DbType.ORACLE;
+			else if (iniFile.get("DATA_TYPE").equalsIgnoreCase("PostgreSQL"))
+				dbSettings.dbType = DbType.POSTGRESQL;
+			else if (iniFile.get("DATA_TYPE").equalsIgnoreCase("Redshift"))
+				dbSettings.dbType = DbType.REDSHIFT;
+			else if (iniFile.get("DATA_TYPE").equalsIgnoreCase("SQL Server")) {
+				dbSettings.dbType = DbType.MSSQL;
+				if (iniFile.get("USER_NAME").length() != 0) { // Not using windows authentication
+					String[] parts = iniFile.get("USER_NAME").split("/");
+					if (parts.length == 2) {
+						dbSettings.user = parts[1];
+						dbSettings.domain = parts[0];
+					}
+				}
+			} else if (iniFile.get("DATA_TYPE").equalsIgnoreCase("MS Access"))
+				dbSettings.dbType = DbType.MSACCESS;
+		}
+		if (iniFile.get("TABLES_TO_SCAN").equalsIgnoreCase("*")) {
+			RichConnection connection = new RichConnection(dbSettings.server, dbSettings.domain, dbSettings.user, dbSettings.password, dbSettings.dbType);
+			for (String table : connection.getTableNames(dbSettings.database))
+				dbSettings.tables.add(table);
+			connection.close();
+		} else {
+			for (String table : iniFile.get("TABLES_TO_SCAN").split(",")) {
+				if (dbSettings.dataType == DbSettings.CSVFILES)
+					table = iniFile.get("WORKING_FOLDER") + "/" + table;
+				dbSettings.tables.add(table);
+			}
+		}
+
+		SourceDataScan sourceDataScan = new SourceDataScan();
+		int maxRows = Integer.parseInt(iniFile.get("ROWS_PER_TABLE"));
+		boolean scanValues = iniFile.get("SCAN_FIELD_VALUES").equalsIgnoreCase("yes");
+		int minCellCount = Integer.parseInt(iniFile.get("MIN_CELL_COUNT"));
+		int maxValues = Integer.parseInt(iniFile.get("MAX_DISTINCT_VALUES"));
+		sourceDataScan.process(dbSettings, maxRows, scanValues, minCellCount, maxValues, iniFile.get("WORKING_FOLDER") + "/ScanReport.xlsx");
 	}
 
 	private JComponent createTabsPanel() {
@@ -567,39 +627,6 @@ private Image loadIcon(String name, JFrame f) {
 		return null;
 	}
 
-	private void executeParameters(String[] args) {
-		String mode = null;
-		for (String arg : args) {
-			if (arg.startsWith("-")) {
-				mode = arg.toLowerCase();
-			} else {
-				if (mode.equals("-folder"))
-					folderField.setText(arg);
-				if (mode.equals("-targetpassword"))
-					targetPasswordField.setText(arg);
-				if (mode.equals("-targetserver"))
-					targetServerField.setText(arg);
-				if (mode.equals("-targettype"))
-					targetType.setSelectedItem(arg);
-				if (mode.equals("-targetdatabase"))
-					targetDatabaseField.setText(arg);
-				if (mode.equals("-targetuser"))
-					targetUserField.setText(arg);
-				if (mode.equals("-sourceserver"))
-					sourceServerField.setText(arg);
-				if (mode.equals("-sourcetype"))
-					sourceType.setSelectedItem(arg);
-				if (mode.equals("-sourcedatabase"))
-					sourceDatabaseField.setText(arg);
-				if (mode.equals("-sourceuser"))
-					sourceUserField.setText(arg);
-				if (mode.equals("-sourcepassword"))
-					sourcePasswordField.setText(arg);
-				mode = null;
-			}
-		}
-	}
-
 	private void pickFolder() {
 		JFileChooser fileChooser = new JFileChooser(new File(folderField.getText()));
 		fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);