Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Di 968 db liquibase for schema change #16

Open
wants to merge 8 commits into
base: master
Choose a base branch
from
Open

Di 968 db liquibase for schema change #16

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
edf8067
DI-968 database schema changes
YuAvillachLab Dec 7, 2017
7792858
DI-968 made changes to the persistence.xml ddl auto field to validate
YuAvillachLab Dec 7, 2017
1b84faf
DI-968 more changes on changelog-0.1.0.xml
YuAvillachLab Dec 8, 2017
052e91b
Merge branch 'master' into DI-968_DB_LiquibaseForSchemaChange
YuAvillachLab Feb 22, 2018
f685e3f
DI-968 fixed merge mess
YuAvillachLab Feb 22, 2018
eba26e4
DI-968 resolved running liquibase on non-local database problem by ad…
YuAvillachLab Mar 2, 2018
a77704c
DI-968 take out resource_IRCTJoin in changelog which causing problems
YuAvillachLab Mar 2, 2018
fee4cb8
DI-968 revert it back first
YuAvillachLab Mar 2, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
136 changes: 86 additions & 50 deletions IRCT-API/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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>
Expand All @@ -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 -->
Expand Down Expand Up @@ -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>
3 changes: 2 additions & 1 deletion ...-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/event/EventConverterImplementation.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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;
Expand Down
4 changes: 2 additions & 2 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/join/IRCTJoin.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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;
Expand Down
23 changes: 7 additions & 16 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/join/Join.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/ontology/Entity.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -31,7 +32,7 @@ public class Entity {


@Id
@GeneratedValue
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;

private String pui;
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/process/IRCTProcess.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/ClauseAbstract.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import javax.json.JsonObjectBuilder;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;

/**
Expand All @@ -21,7 +22,7 @@
public abstract class ClauseAbstract {

@Id
@GeneratedValue
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;

/**
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/JoinType.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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;
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/PredicateType.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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;
Expand Down
8 changes: 5 additions & 3 deletions IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/Query.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.*;
Expand All @@ -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;

Expand Down Expand Up @@ -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>();
Expand Down Expand Up @@ -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));
}

/**
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/SelectOperationType.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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;
Expand Down
3 changes: 2 additions & 1 deletion IRCT-API/src/main/java/edu/harvard/hms/dbmi/bd2k/irct/model/query/SortOperationType.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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;
Expand Down
Loading