Import of original WhiteRabbit application, to be modified

.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="lib/jtds-1.3.0.jar"/>
+	<classpathentry kind="lib" path="lib/ojdbc5.jar"/>
+	<classpathentry kind="lib" path="lib/ojdbc6.jar"/>
+	<classpathentry kind="lib" path="lib/postgresql-9.3-1101.jdbc41.jar"/>
+	<classpathentry kind="lib" path="lib/sqljdbc4.jar"/>
+	<classpathentry kind="lib" path="lib/mysql-connector-java-5.1.30-bin.jar"/>
+	<classpathentry kind="lib" path="lib/dom4j-1.6.1.jar"/>
+	<classpathentry kind="lib" path="lib/poi-3.9-20121203.jar"/>
+	<classpathentry kind="lib" path="lib/poi-excelant-3.9-20121203.jar"/>
+	<classpathentry kind="lib" path="lib/poi-ooxml-3.9-20121203.jar"/>
+	<classpathentry kind="lib" path="lib/poi-ooxml-schemas-3.9-20121203.jar"/>
+	<classpathentry kind="lib" path="lib/stax-api-1.0.1.jar"/>
+	<classpathentry kind="lib" path="lib/xmlbeans-2.3.0.jar"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.gitignore

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+/bin

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>WhiteRabbit</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/com.wdev91.eclipse.copyright.xml

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+<?xml version="1.0" encoding="UTF-8" ?>
+<project>
+	<owner></owner>
+	<copyright><![CDATA[Copyright 2014 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.
+
+@author Observational Health Data Sciences and Informatics
+@author Martijn Schuemie]]></copyright>
+	<header contentId="org.eclipse.ant.core.antBuildFile" excluded="true" />
+	<header contentId="org.eclipse.jdt.core.JARManifest" excluded="true" />
+	<header contentId="org.eclipse.jdt.core.javaSource" postBlankLines="0" lineFormat="false" preserveFirstLine="false">
+		<beginLine><![CDATA[/*******************************************************************************]]></beginLine>
+		<linePrefix><![CDATA[ * ]]></linePrefix>
+		<endLine><![CDATA[ ******************************************************************************/]]></endLine>
+	</header>
+	<header contentId="org.eclipse.core.runtime.text" postBlankLines="0" lineFormat="true" preserveFirstLine="false">
+		<beginLine><![CDATA[#-------------------------------------------------------------------------------]]></beginLine>
+		<linePrefix><![CDATA[# ]]></linePrefix>
+		<endLine><![CDATA[#-------------------------------------------------------------------------------]]></endLine>
+	</header>
+	<header contentId="org.eclipse.ui.views.log.log" excluded="true" />
+	<header contentId="org.eclipse.core.runtime.xml" postBlankLines="0" lineFormat="false" preserveFirstLine="true">
+		<beginLine><![CDATA[<!--]]></beginLine>
+		<linePrefix><![CDATA[  ]]></linePrefix>
+		<endLine><![CDATA[-->]]></endLine>
+		<firstLinePattern><![CDATA[<\?xml version=.*\?>]]></firstLinePattern>
+	</header>
+</project>

jarDesc/WhiteRabbit.MF

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+Manifest-Version: 1.0
+Class-Path: . WhiteRabbit_lib/jtds-1.3.0.jar WhiteRabbit_lib/ojdbc5.ja
+ r WhiteRabbit_lib/ojdbc6.jar WhiteRabbit_lib/postgresql-9.3-1101.jdbc
+ 41.jar WhiteRabbit_lib/sqljdbc4.jar WhiteRabbit_lib/mysql-connector-j
+ ava-5.1.30-bin.jar WhiteRabbit_lib/dom4j-1.6.1.jar WhiteRabbit_lib/po
+ i-3.9-20121203.jar WhiteRabbit_lib/poi-excelant-3.9-20121203.jar Whit
+ eRabbit_lib/poi-ooxml-3.9-20121203.jar WhiteRabbit_lib/poi-ooxml-sche
+ mas-3.9-20121203.jar WhiteRabbit_lib/stax-api-1.0.1.jar WhiteRabbit_l
+ ib/xmlbeans-2.3.0.jar
+Main-Class: org.ohdsi.whiteRabbit.interactiveMapping.RabbitInAHat
+

jarDesc/WhiteRabbit.jardesc

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+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+    <jar path="C:/home/Software/WhiteRabbit/WhiteRabbit.jar"/>
+    <options buildIfNeeded="true" compress="true" descriptionLocation="/WhiteRabbit/jarDesc/WhiteRabbit.jardesc" exportErrors="true" exportWarnings="true" includeDirectoryEntries="true" overwrite="false" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+    <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+    <selectedProjects/>
+    <manifest generateManifest="false" mainClassHandleIdentifier="=WhiteRabbit/src&lt;org.ohdsi.whiteRabbit{WhiteRabbitMain.java[WhiteRabbitMain" manifestLocation="/WhiteRabbit/jarDesc/WhiteRabbit.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="true" usesManifest="true">
+        <sealing sealJar="false">
+            <packagesToSeal/>
+            <packagesToUnSeal/>
+        </sealing>
+    </manifest>
+    <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+        <file path="/WhiteRabbit/LICENSE"/>
+        <file path="/WhiteRabbit/.gitignore"/>
+        <file path="/WhiteRabbit/README.md"/>
+        <folder path="/WhiteRabbit/jarDesc"/>
+        <file path="/WhiteRabbit/.classpath"/>
+        <file path="/WhiteRabbit/.project"/>
+        <javaElement handleIdentifier="=WhiteRabbit/src"/>
+    </selectedElements>
+</jardesc>

src/org/ohdsi/databases/DbType.java

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+/*******************************************************************************
+ * Copyright 2014 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.
+ * 
+ * @author Observational Health Data Sciences and Informatics
+ * @author Martijn Schuemie
+ ******************************************************************************/
+package org.ohdsi.databases;
+
+public class DbType {
+	public static DbType	MYSQL		= new DbType("mysql");
+	public static DbType	MSSQL		= new DbType("mssql");
+	public static DbType	ORACLE		= new DbType("oracle");
+	public static DbType	POSTGRESQL	= new DbType("postgresql");
+
+	private enum Type {
+		MYSQL, MSSQL, ORACLE, POSTGRESQL
+	};
+
+	private Type	type;
+
+	public DbType(String type) {
+		this.type = Type.valueOf(type.toUpperCase());
+	}
+
+	public boolean equals(Object other) {
+		if (other instanceof DbType && ((DbType) other).type == type)
+			return true;
+		else
+			return false;
+	}
+}

src/org/ohdsi/databases/QueryDB.java

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+/*******************************************************************************
+ * Copyright 2014 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.
+ * 
+ * @author Observational Health Data Sciences and Informatics
+ * @author Martijn Schuemie
+ ******************************************************************************/
+package org.ohdsi.databases;
+
+import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.ResultSet;
+import java.sql.ResultSetMetaData;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.Iterator;
+import java.util.Map;
+
+import org.ohdsi.utilities.files.ReadTextFile;
+import org.ohdsi.utilities.files.Row;
+
+public class QueryDB implements Iterable<Row>{
+	private String sql;
+	private Connection connection;
+
+	public QueryDB(InputStream sqlStream, Connection connection){
+		this(sqlStream,null,connection);
+	}
+
+	public QueryDB(InputStream sqlStream, Map<String, String> parameterToValue, Connection connection){
+		this.connection = connection;
+		sql = loadSQL(sqlStream);
+		if (parameterToValue != null)
+			for (String parameter : parameterToValue.keySet())
+				sql = sql.replaceAll(parameter, parameterToValue.get(parameter));
+		trimSQL();
+	}
+
+	public QueryDB(String sql, Connection connection){
+		this.connection = connection;
+		this.sql = sql;
+		trimSQL();
+	}
+
+	private void trimSQL() {
+		sql = sql.trim();
+		if (sql.endsWith(";"))
+			sql = sql.substring(0,sql.length()-1);
+	}
+
+	private String loadSQL(InputStream sqlStream) {
+		StringBuilder sql = new StringBuilder();
+		for (String line : new ReadTextFile(sqlStream)){
+			sql.append(line.trim());
+			sql.append('\n');
+		}
+		return sql.substring(0, sql.lastIndexOf(";"));
+	}
+
+	public boolean execute(){
+		boolean result = false;
+		for (String subQuery : sql.split(";"))
+			try {
+				Statement statement = connection.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
+				result = statement.execute(subQuery.toString());
+			} catch (SQLException e) {
+				if (e.getMessage().contains("ORA-00942") && sql.toUpperCase().startsWith("DROP"))
+					System.out.println("Tried dropping non-existing table");
+				else {	
+					System.err.println("SQL: " + subQuery);
+					e.printStackTrace();
+				}
+			}
+		try {
+			connection.close();
+		} catch (SQLException e) {
+			e.printStackTrace();
+		}
+		return result;
+	}
+
+	@Override
+	public Iterator<Row> iterator() {
+		return new DBRowIterator(sql);
+	}
+	public class DBRowIterator implements Iterator<Row>{
+
+		private ResultSet resultSet;
+
+		private boolean hasNext;
+
+		public DBRowIterator(String sql) {
+			try {
+				Statement statement = connection.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
+				resultSet = statement.executeQuery(sql.toString());
+				hasNext = resultSet.next();
+				if (!hasNext)
+					connection.close();
+			} catch (SQLException e){
+				System.err.println(sql.toString());
+				System.err.println(e.getMessage());
+				throw new RuntimeException(e);
+			}
+		}
+
+		@Override
+		public boolean hasNext() {
+			return hasNext;
+		}
+
+		@Override
+		public Row next() {
+			try {
+				Row row = new Row();
+				ResultSetMetaData metaData;
+				metaData = resultSet.getMetaData();
+				for (int i = 1; i < metaData.getColumnCount()+1; i++) {
+					String columnName = metaData.getColumnName(i);
+					String value = resultSet.getString(i);
+					if (value == null)
+						value = "";
+					row.add(columnName, value.replace(" 00:00:00", ""));
+				}
+				hasNext = resultSet.next();
+				if (!hasNext)
+					connection.close();
+				return row;
+			} catch (SQLException e) {
+				e.printStackTrace();
+				throw new RuntimeException(e);
+			}
+		}
+
+		@Override
+		public void remove() {
+		}
+	}
+}

src/org/ohdsi/databases/QueryParameters.java

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+/*******************************************************************************
+ * Copyright 2014 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.
+ * 
+ * @author Observational Health Data Sciences and Informatics
+ * @author Martijn Schuemie
+ ******************************************************************************/
+package org.ohdsi.databases;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class QueryParameters {
+	private Map<String, String> key2Value = new HashMap<String, String>();
+	public void set(String key, String value){
+		key2Value.put(key, value);
+	}
+
+	public void set(String key, int value){
+		key2Value.put(key, Integer.toString(value));
+	}
+
+	protected Map<String, String> getMap() {
+		return key2Value;
+	}
+
+}