Merge pull request #263 from OHDSI/release-0.10.2

Release 0.10.2

.gitignore

@@ -6,10 +6,13 @@ dist/
 /.classpath
 *.iml
 .idea/
+target/
+*.class
 
 # Repo specific ignores
 /ScanReport.xlsx
 *swp
 tmp/*
 Try*
-/examples/
+/examples/
+.DS_Store

docs/WhiteRabbit.md

@@ -36,6 +36,13 @@ Once the scan report is created, this report can then be used in the Rabbit-In-A
 
 Note: on releases earlier than version 0.8.0, open the respective WhiteRabbit.jar or RabbitInAHat.jar files instead.
 
+### Memory
+WhiteRabbit possibly does not start when the memory allocated by the JVM is too big or too small. 
+By default this is set to 1200m.
+To increase the memory (in this example to 2400m), either set the environment variable `EXTRA_JVM_ARGUMENTS=-Xmx2400m` before starting or edit in `bin/WhiteRabbit.bat` the line `%JAVACMD% %JAVA_OPTS% -Xmx2400m...`.
+To lower the memory, set one of these variables to e.g. `-Xmx600m`.
+If you have a 32-bit Java VM installed and problems persist, consider installing 64-bit Java.  
+
 ## Support
 All source code, descriptions and input/output examples are available on GitHub: <https://github.com/OHDSI/WhiteRabbit>
 

pom.xml

@@ -6,7 +6,7 @@
     <groupId>org.ohdsi</groupId>
     <artifactId>leporidae</artifactId>
     <packaging>pom</packaging>
-    <version>0.10.1</version>
+    <version>0.10.2</version>
     <modules>
         <module>rabbitinahat</module>
         <module>whiterabbit</module>

rabbit-core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.10.1</version>
+        <version>0.10.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -30,7 +30,7 @@
         <dependency>
             <groupId>mysql</groupId>
             <artifactId>mysql-connector-java</artifactId>
-            <version>5.1.37</version>
+            <version>8.0.16</version>
         </dependency>
         <dependency>
             <groupId>dom4j</groupId>
@@ -40,17 +40,17 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>3.9</version>
+            <version>3.17</version>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>3.9</version>
+            <version>3.17</version>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-excelant</artifactId>
-            <version>3.9</version>
+            <version>3.17</version>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
@@ -70,7 +70,7 @@
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
-            <version>9.4-1204-jdbc41</version>
+            <version>42.2.5</version>
         </dependency>
         <dependency>
             <groupId>com.cedarsoftware</groupId>

rabbit-core/src/main/java/org/ohdsi/databases/RichConnection.java

@@ -146,15 +146,22 @@ public List<String> getTableNames(String database) {
 		if (dbType == DbType.MYSQL) {
 			query = "SHOW TABLES IN " + database;
 		} else if (dbType == DbType.MSSQL || dbType == DbType.PDW || dbType == DbType.AZURE) {
-			query = "SELECT CONCAT(schemas.name, '.', tables.name) FROM " + database + ".sys.tables INNER JOIN " + database + ".sys.schemas ON tables.schema_id = schemas.schema_id ORDER BY schemas.name, tables.name";
+			query = "SELECT CONCAT(schemas.name, '.', tables_views.name) FROM " +
+					"(SELECT schema_id, name FROM %1$s.sys.tables UNION ALL SELECT schema_id, name FROM %1$s.sys.views) tables_views " +
+					"INNER JOIN %1$s.sys.schemas ON tables_views.schema_id = schemas.schema_id " +
+					"ORDER BY schemas.name, tables_views.name";
+			query = String.format(query, database);
+			System.out.println(query);
 		} else if (dbType == DbType.ORACLE) {
-			query = "SELECT table_name FROM all_tables WHERE owner='" + database.toUpperCase() + "'";
+			query = "SELECT table_name FROM " +
+					"(SELECT table_name, owner FROM all_tables UNION ALL SELECT view_name, owner FROM all_views) tables_views " +
+					"WHERE owner='" + database.toUpperCase() + "'";
 		} else if (dbType == DbType.POSTGRESQL || dbType == DbType.REDSHIFT) {
 			query = "SELECT table_name FROM information_schema.tables WHERE table_schema = '" + database.toLowerCase() + "' ORDER BY table_name";
 		} else if (dbType == DbType.MSACCESS) {
-			query = "SELECT Name FROM sys.MSysObjects WHERE Type=1 AND Flags=0;";
+			query = "SELECT Name FROM sys.MSysObjects WHERE (Type=1 OR Type=5) AND Flags=0;";
 		} else if (dbType == DbType.TERADATA) {
-			query = "SELECT TableName from dbc.tables WHERE tablekind = 'T' and databasename='" + database + "'";
+			query = "SELECT TableName from dbc.tables WHERE tablekind IN ('T','V') and databasename='" + database + "'";
 		} else if (dbType == DbType.BIGQUERY) {
 			query = "SELECT table_name from " + database + ".INFORMATION_SCHEMA.TABLES ORDER BY table_name;";
 		}

rabbitinahat/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.10.1</version>
+        <version>0.10.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/ETLTestFrameWorkGenerator.java

@@ -31,6 +31,7 @@
 import org.ohdsi.rabbitInAHat.dataModel.*;
 import org.ohdsi.rabbitInAHat.dataModel.ETL.FileFormat;
 
+// TODO: use templating to generate the R code (e.g. Jinja/Apache FreeMarker/Mustache). At least put static R code in separate (.R) files.
 public class ETLTestFrameWorkGenerator {
 
 	private static int DEFAULT = 0;
@@ -260,7 +261,7 @@ private void createAddFunctions() {
 					writer.println("    frameworkContext$sourceFieldsTested <- c(frameworkContext$sourceFieldsTested, '" + convertFieldToFullName(field) + "')");
 					writer.println("  }");
 					writer.println("  fields <- c(fields, \"" + sqlFieldName + "\")");
-					writer.println("  values <- c(values, " + createSqlValueCode(rFieldName) + ")");
+					writer.println("  values <- c(values, " + createValueCode(rFieldName) + ")");
 					writer.println("");
 				}
 				writer.println("  inserts <- list(testId = frameworkContext$testId, testDescription = frameworkContext$testDescription, table = \"" + sqlTableName
@@ -335,7 +336,7 @@ private void createLookupFunctions() {
 					writer.println("    } else {");
 					writer.println("      statement <- paste0(statement, \" AND\")");
 					writer.println("    }");
-					writer.println("    statement <- paste0(statement, \" " + sqlFieldName + " = \", " + createSqlValueCode(rFieldName) + ")");
+					writer.println("    statement <- paste0(statement, \" " + sqlFieldName + "\"," + createSqlValueCode(rFieldName) + ")");
 					writer.println("  }");
 					writer.println("");
 				}
@@ -454,7 +455,7 @@ private void createGenerateTestSqlFunction() {
 		writer.println("                     \"' AS test, CASE WHEN (SELECT COUNT(*) FROM @cdm_database_schema.\",");
 		writer.println("                     expect$table,");
 		writer.println("                     \" WHERE \",");
-		writer.println("                     paste(paste(expect$fields, operators, expect$values), collapse = \" AND \"),");
+		writer.println("                     paste(paste(expect$fields, expect$values), collapse = \" AND \"),");
 		writer.println("                     \") \",");
 		writer.println("                     if (expect$type == " + DEFAULT + ") \"= 0\" else if (expect$type == " + NEGATE
 				+ ") \"!= 0\" else paste(\"!=\", expect$rowCount),");
@@ -581,7 +582,14 @@ private String convertToRName(String name) {
 		return name;
 	}
 
-	 private String createSqlValueCode(String rFieldName) {
+	private String createSqlValueCode(String rFieldName) {
+		return "if (is.null(" + rFieldName + ")) \" IS NULL\" " +
+				"else if (is(" + rFieldName + ", \"subQuery\")) " +
+				"paste0(\" = (\", as.character(" + rFieldName + "), \")\") " +
+				"else paste0(\" = '\", as.character(" + rFieldName + "), \"'\")";
+	}
+
+	 private String createValueCode(String rFieldName) {
          return "if (is.null(" + rFieldName + ")) \"NULL\" " +
                  "else if (is(" + rFieldName + ", \"subQuery\")) " +
                  "paste0(\"(\", as.character(" + rFieldName + "), \")\") " +

rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/FilterDialog.java

@@ -8,6 +8,8 @@
 import java.awt.event.FocusListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
 
 import org.ohdsi.rabbitInAHat.ResizeListener;
 
@@ -16,6 +18,7 @@
 import javax.swing.JLabel;
 import javax.swing.JTextField;
 import javax.swing.SpringLayout;
+import javax.swing.WindowConstants;
 
 public class FilterDialog extends JDialog implements ActionListener, ResizeListener {
 
@@ -24,6 +27,7 @@ public class FilterDialog extends JDialog implements ActionListener, ResizeListe
 	 * 
 	 */
 	private static final long serialVersionUID = 7009265246652874341L;
+	private static FilterDialog instance;
 
 
 	private JTextField		sourceSearchField; 
@@ -34,9 +38,11 @@ public class FilterDialog extends JDialog implements ActionListener, ResizeListe
 
 	Container contentPane = this.getContentPane();
 
-	public FilterDialog(Window parentWindow){
-
-		super(parentWindow,"Filter",ModalityType.MODELESS);		
+	public FilterDialog(Window parentWindow) throws ExceptionInInitializerError{
+		super(parentWindow,"Filter",ModalityType.MODELESS);
+		if (alreadyOpened()) {
+			throw new ExceptionInInitializerError("An instance of FilterDialog already exists");
+		}
 		this.setResizable(false);
 		this.setLocation(parentWindow.getX()+parentWindow.getWidth()/2, parentWindow.getY()+100);
 
@@ -96,7 +102,28 @@ public FilterDialog(Window parentWindow){
 		layout.putConstraint(SpringLayout.EAST, contentPane, 5, SpringLayout.EAST, targetClearBtn);
 
 		this.pack();
-	};
+
+		// Make sure the instance is reset to null when the search dialog window is closed
+		this.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+		this.addWindowListener(new WindowAdapter() {
+			@Override
+			public void windowClosing(WindowEvent arg0) {
+				instance = null;
+			}
+		});
+
+		instance = this;
+	}
+
+	public static boolean alreadyOpened(){
+		return (instance != null);
+	}
+
+	public static void bringToFront(){
+		if (alreadyOpened()) {
+			instance.toFront();
+		}
+	}
 
 	public void setFilterPanel(MappingPanel aFilterPanel){
 		if (filterPanel != null) {

rabbitinahat/src/main/java/org/ohdsi/rabbitInAHat/RabbitInAHatMain.java

@@ -489,12 +489,14 @@ private void doSetTargetCDM(CDMVersion cdmVersion) {
 	}
 
 	private void doOpenFilterDialog() {
-		FilterDialog filter;
-		filter = new FilterDialog(frame);
-
-		filter.setFilterPanel(tableMappingPanel);
-
-		filter.setVisible(true);
+		if (FilterDialog.alreadyOpened()){
+			FilterDialog.bringToFront();
+		}
+		else {
+			FilterDialog filter = new FilterDialog(frame);
+			filter.setFilterPanel(tableMappingPanel);
+			filter.setVisible(true);
+		}
 	}
 
 	private void doMakeMappings() {

whiterabbit/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>leporidae</artifactId>
         <groupId>org.ohdsi</groupId>
-        <version>0.10.1</version>
+        <version>0.10.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -24,8 +24,7 @@
                 <artifactId>appassembler-maven-plugin</artifactId>
                 <configuration>
                     <assembleDirectory>${project.parent.basedir}/dist</assembleDirectory>
-		    <!--                   <extraJvmArguments>-Xmx1200m</extraJvmArguments> -->
-                    <extraJvmArguments>-Xmx2400m</extraJvmArguments>
+                    <extraJvmArguments>-Xmx1200m</extraJvmArguments>
                     <programs>
                         <program>
                             <mainClass>org.ohdsi.whiteRabbit.WhiteRabbitMain</mainClass>