Di 968 db liquibase for schema change

IRCT-API/pom.xml

@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.bd2k.irct</groupId>
@@ -7,6 +8,13 @@
 	</parent>
 	<artifactId>IRCT-API</artifactId>
 	<name>INTER-RESOURCE COMMUNICATION TOOL : API</name>
+
+	<properties>
+		<liquibase.version>3.5.3</liquibase.version>
+		<maven.compiler.version>1.7</maven.compiler.version>
+		<mysql-version>5.1.45</mysql-version>
+	</properties>
+
 	<description></description>
 	<dependencies>
 		<!-- APACHE HTTP CLIENT -->
@@ -63,59 +71,87 @@
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
         </dependency>
-
-
     </dependencies>
 	<build>
 		<sourceDirectory>src/main/java</sourceDirectory>
 		<resources>
-        <resource>
-            <directory>src/main/resources</directory>
-            <filtering>true</filtering>
-        </resource>
-    </resources>
+			<resource>
+				<directory>src/main/resources</directory>
+				<filtering>true</filtering>
+			</resource>
+		</resources>
 		<finalName>IRCT-API</finalName>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-eclipse-plugin</artifactId>
-				<configuration>
-					<downloadSources>true</downloadSources>
-					<downloadJavadocs>true</downloadJavadocs>
-				</configuration>
-			</plugin>
-
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-jar-plugin</artifactId>
-			</plugin>
-
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<configuration>
-					<source>1.7</source>
-					<target>1.7</target>
-				</configuration>
-			</plugin>
-
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-dependency-plugin</artifactId>
-				<executions>
-					<execution>
-						<id>copy-dependencies</id>
-						<phase>package</phase>
-						<goals>
-							<goal>copy-dependencies</goal>
-						</goals>
-						<configuration>
-							<includeScope>runtime</includeScope>
-							<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
-		</plugins>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-eclipse-plugin</artifactId>
+					<configuration>
+						<downloadSources>true</downloadSources>
+						<downloadJavadocs>true</downloadJavadocs>
+					</configuration>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-jar-plugin</artifactId>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-compiler-plugin</artifactId>
+					<configuration>
+						<source>${maven.compiler.version}</source>
+						<target>${maven.compiler.version}</target>
+					</configuration>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-dependency-plugin</artifactId>
+					<executions>
+						<execution>
+							<id>copy-dependencies</id>
+							<phase>package</phase>
+							<goals>
+								<goal>copy-dependencies</goal>
+							</goals>
+							<configuration>
+								<includeScope>runtime</includeScope>
+								<outputDirectory>${project.build.directory}/dependency-jars/</outputDirectory>
+							</configuration>
+						</execution>
+					</executions>
+				</plugin>
+				<plugin>
+				   <groupId>org.liquibase</groupId>
+				   <artifactId>liquibase-maven-plugin</artifactId>
+				   <version>${liquibase.version}</version>
+				   <configuration>                  
+				      <propertyFileWillOverride>true</propertyFileWillOverride>
+					  <propertyFile>edu/harvard/hms/dbmi/bd2k/irct/db/liquibase.properties</propertyFile>
+					  <changeLogFile>edu/harvard/hms/dbmi/bd2k/irct/db/changelog-master.xml</changeLogFile>
+				      <promptOnNonLocalDatabase>false</promptOnNonLocalDatabase>
+				   </configuration>                
+				   <executions>
+					 <execution>
+					   <phase>process-resources</phase>                                                                  
+					   <goals>
+						 <goal>update</goal>
+					   </goals>
+					 </execution>
+				   </executions>
+
+				   <!--  specify your own driver  -->
+				   <dependencies>
+				   		<dependency>
+				            <groupId>mysql</groupId>
+				            <artifactId>mysql-connector-java</artifactId>
+				            <version>${mysql-version}</version>
+				        </dependency>
+				   </dependencies>
+				</plugin> 
+			</plugins>
+		</pluginManagement>
 	</build>
 </project>

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/event/EventConverterImplementation.java

@@ -13,6 +13,7 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.MapKeyColumn;
@@ -31,7 +32,7 @@ public class EventConverterImplementation implements Serializable {
 	private static final long serialVersionUID = -8700481468758389000L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/join/IRCTJoin.java

@@ -14,10 +14,10 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.OneToMany;
 
-import edu.harvard.hms.dbmi.bd2k.irct.model.join.JoinImplementation;
 import edu.harvard.hms.dbmi.bd2k.irct.model.resource.Field;
 import edu.harvard.hms.dbmi.bd2k.irct.util.converter.JoinImplementationConverter;
 
@@ -34,7 +34,7 @@ public class IRCTJoin implements Serializable {
 	private static final long serialVersionUID = 5173414123049320818L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/join/Join.java

@@ -7,34 +7,25 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.MapKeyColumn;
 import javax.persistence.Transient;
 
-@Entity
+//@Entity
 public class Join implements Serializable {
 
 	private static final long serialVersionUID = 4869490865776072674L;
 
-	@Id
-	@GeneratedValue
+//	@Id
+//	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;
 
 	private JoinImplementation joinImplementation;
 
 	private IRCTJoin joinType;
 
-	@ElementCollection(fetch = FetchType.EAGER)
-	@MapKeyColumn(name = "name")
-	@Column(name = "value")
-	@CollectionTable(name = "where_values", joinColumns = @JoinColumn(name = "where_id"))
+//	@ElementCollection(fetch = FetchType.EAGER)
+//	@MapKeyColumn(name = "name")
+//	@Column(name = "value")
+//	@CollectionTable(name = "where_values", joinColumns = @JoinColumn(name = "where_id"))
 	private Map<String, String> stringValues;
 
 	@Transient

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/ontology/Entity.java

@@ -12,6 +12,7 @@
 import javax.json.JsonObjectBuilder;
 import javax.persistence.Convert;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.Transient;
 import java.util.ArrayList;
@@ -31,7 +32,7 @@ public class Entity {
 
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;
 
 	private String pui;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/process/IRCTProcess.java

@@ -14,6 +14,7 @@
 import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
@@ -35,7 +36,7 @@ public class IRCTProcess implements Serializable {
 	private static final long serialVersionUID = -1805899138692864630L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;
 
 	@ManyToOne

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/ClauseAbstract.java

@@ -8,6 +8,7 @@
 import javax.json.JsonObjectBuilder;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 
 /**
@@ -21,7 +22,7 @@
 public abstract class ClauseAbstract {
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;
 
 	/**

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/JoinType.java

@@ -15,6 +15,7 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.OneToMany;
 
@@ -30,7 +31,7 @@ public class JoinType implements Serializable {
 	private static final long serialVersionUID = 7650772906469344618L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/PredicateType.java

@@ -14,6 +14,7 @@
 import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.OneToMany;
 
@@ -36,7 +37,7 @@ public class PredicateType implements Serializable {
 	private static final long serialVersionUID = -8767223525164395205L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/Query.java

@@ -9,6 +9,7 @@
 import javax.json.Json;
 import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
+
 import javax.persistence.*;
 import java.io.Serializable;
 import java.util.*;
@@ -22,12 +23,12 @@
  *
  */
 @Entity
-@Inheritance(strategy = InheritanceType.TABLE_PER_CLASS)
+@Inheritance(strategy = InheritanceType.JOINED)
 public class Query implements Serializable {
 	private static final long serialVersionUID = -407606258205399129L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Long id;
 	private String name;
 
@@ -133,6 +134,7 @@ public String toString() {
 				+ where;
 	}
 
+	@SuppressWarnings("unchecked")
 	public <T extends ClauseAbstract> List<T> getClausesOfType(
 			Class<T> clauseType) {
 		List<T> returns = new ArrayList<T>();
@@ -218,7 +220,7 @@ public final SubQuery getSubQuery(String id) {
 	 *            SubQuery ID
 	 */
 	public final void removeSubQuery(Long id) {
-		this.subQueries.remove(id);
+		this.subQueries.remove(Long.toString(id));
 	}
 
 	/**

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/SelectOperationType.java

@@ -14,6 +14,7 @@
 import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.OneToMany;
 
@@ -36,7 +37,7 @@ public class SelectOperationType implements Serializable {
 	private static final long serialVersionUID = -2715703805087374126L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;

IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/SortOperationType.java

@@ -16,6 +16,7 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.OneToMany;
 
@@ -38,7 +39,7 @@ public class SortOperationType implements Serializable {
 	private static final long serialVersionUID = -2715703805087374126L;
 
 	@Id
-	@GeneratedValue
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private long id;
 
 	private String name;