From 052e566119392b236f87e4b5c4bfe1558c9046d7 Mon Sep 17 00:00:00 2001
From: Hongxin Zhang <jackson.zhang.828@gmail.com>
Date: Fri, 17 Mar 2017 14:35:20 -0400
Subject: [PATCH 1/3] Publish CancerHotspot in GitHub as maven repository

---
 model/pom.xml | 88 ++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 83 insertions(+), 5 deletions(-)

diff --git a/model/pom.xml b/model/pom.xml
index a7a6272..1d04877 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -2,15 +2,93 @@
 <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">
-    <parent>
-        <artifactId>master</artifactId>
-        <groupId>org.cmo.cancerhotspots</groupId>
-        <version>0.1.0</version>
-    </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>Cancer Hotspots Model</name>
     <description>Cancer Hotspots Model Module</description>
+
+    <groupId>org.cmo.cancerhotspots</groupId>
     <artifactId>model</artifactId>
+    <packaging>jar</packaging>
+    <version>0.1.0</version>
+
+    <url>https://github.com/cBioPortal/cancerhotspots/tree/master</url>
+
+    <properties>
+        <java.version>1.7</java.version>
+        <github.global.server>github</github.global.server>
+    </properties>
+
+    <build>
+        <finalName>model</finalName>
+
+        <plugins>
+            <plugin>
+                <groupId>com.github.github</groupId>
+                <artifactId>site-maven-plugin</artifactId>
+                <version>0.12</version>
+                <configuration>
+                    <message>Creating site for ${project.version}</message>
+                    <repositoryName>cancerhotspots</repositoryName>
+                    <repositoryOwner>cBioPortal</repositoryOwner>
+                    <noJekyll>true</noJekyll>
+                    <includes><include>**/*</include></includes>
+                    <merge>true</merge>
+                    <branch>refs/heads/mvn-repo</branch>
+                    <outputDirectory>${project.build.directory}/mvn-repo</outputDirectory>
+                    <server>github</server>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>site</goal>
+                        </goals>
+                        <phase>deploy</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <artifactId>maven-deploy-plugin</artifactId>
+                <version>2.8.1</version>
+                <configuration>
+                    <altDeploymentRepository>internal.repo::default::file://${project.build.directory}/mvn-repo</altDeploymentRepository>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <distributionManagement>
+        <repository>
+            <id>internal.repo</id>
+            <name>Temporary Staging Repository</name>
+            <url>file://${project.build.directory}/mvn-repo</url>
+        </repository>
+    </distributionManagement>
 
     <dependencies>
         <dependency>

From 49e662d3932fd28cf1753a0aebbd19203c9cc1dd Mon Sep 17 00:00:00 2001
From: Hongxin Zhang <jackson.zhang.828@gmail.com>
Date: Wed, 29 Mar 2017 16:44:59 -0400
Subject: [PATCH 2/3] Publish utils to github

---
 util/pom.xml | 90 ++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 87 insertions(+), 3 deletions(-)

diff --git a/util/pom.xml b/util/pom.xml
index ef4583a..c042c96 100644
--- a/util/pom.xml
+++ b/util/pom.xml
@@ -3,14 +3,98 @@
          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">
     <parent>
-        <artifactId>master</artifactId>
-        <groupId>org.cmo.cancerhotspots</groupId>
-        <version>0.1.0</version>
+        <groupId>org.springframework.boot</groupId>
+        <artifactId>spring-boot-starter-parent</artifactId>
+        <version>1.3.3.RELEASE</version>
     </parent>
+
     <modelVersion>4.0.0</modelVersion>
     <name>Cancer Hotspots Util</name>
     <description>Cancer Hotspots Utility Module</description>
+
+    <groupId>org.cmo.cancerhotspots</groupId>
     <artifactId>util</artifactId>
+    <packaging>jar</packaging>
+    <version>0.1.0</version>
+
+    <url>https://github.com/cBioPortal/cancerhotspots/tree/master</url>
+
+    <properties>
+        <java.version>1.7</java.version>
+        <github.global.server>github</github.global.server>
+    </properties>
+
+    <build>
+        <finalName>util</finalName>
+
+        <plugins>
+            <plugin>
+                <groupId>com.github.github</groupId>
+                <artifactId>site-maven-plugin</artifactId>
+                <version>0.12</version>
+                <configuration>
+                    <message>Creating site for ${project.version}</message>
+                    <repositoryName>cancerhotspots</repositoryName>
+                    <repositoryOwner>cBioPortal</repositoryOwner>
+                    <noJekyll>true</noJekyll>
+                    <includes><include>**/*</include></includes>
+                    <merge>true</merge>
+                    <branch>refs/heads/mvn-repo</branch>
+                    <outputDirectory>${project.build.directory}/mvn-repo</outputDirectory>
+                    <server>github</server>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>site</goal>
+                        </goals>
+                        <phase>deploy</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <artifactId>maven-deploy-plugin</artifactId>
+                <version>2.8.1</version>
+                <configuration>
+                    <altDeploymentRepository>internal.repo::default::file://${project.build.directory}/mvn-repo</altDeploymentRepository>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <distributionManagement>
+        <repository>
+            <id>internal.repo</id>
+            <name>Temporary Staging Repository</name>
+            <url>file://${project.build.directory}/mvn-repo</url>
+        </repository>
+    </distributionManagement>
 
     <dependencies>
         <dependency>

From 06274b878c67f5c3337b009b4ce38e8d9c343073 Mon Sep 17 00:00:00 2001
From: Hongxin Zhang <jackson.zhang.828@gmail.com>
Date: Wed, 29 Mar 2017 16:49:20 -0400
Subject: [PATCH 3/3] Upgrade version to 0.1.2

---
 model/pom.xml       | 4 ++--
 persistence/pom.xml | 6 +++---
 pipeline/pom.xml    | 6 +++---
 pom.xml             | 2 +-
 service/pom.xml     | 8 ++++----
 util/pom.xml        | 2 +-
 webapp/pom.xml      | 8 ++++----
 7 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/model/pom.xml b/model/pom.xml
index 1d04877..5658ee2 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -9,7 +9,7 @@
     <groupId>org.cmo.cancerhotspots</groupId>
     <artifactId>model</artifactId>
     <packaging>jar</packaging>
-    <version>0.1.0</version>
+    <version>0.1.2</version>
 
     <url>https://github.com/cBioPortal/cancerhotspots/tree/master</url>
 
@@ -94,7 +94,7 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>util</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>com.univocity</groupId>
diff --git a/persistence/pom.xml b/persistence/pom.xml
index 3e73883..024051e 100644
--- a/persistence/pom.xml
+++ b/persistence/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>master</artifactId>
         <groupId>org.cmo.cancerhotspots</groupId>
-        <version>0.1.0</version>
+        <version>0.1.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>Cancer Hotspots Persistence</name>
@@ -16,7 +16,7 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>model</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>com.univocity</groupId>
@@ -26,7 +26,7 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>util</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
diff --git a/pipeline/pom.xml b/pipeline/pom.xml
index eda82fb..1069be4 100644
--- a/pipeline/pom.xml
+++ b/pipeline/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>master</artifactId>
         <groupId>org.cmo.cancerhotspots</groupId>
-        <version>0.1.0</version>
+        <version>0.1.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>Cancer Hotspots Pipeline</name>
@@ -40,12 +40,12 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>model</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>service</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
diff --git a/pom.xml b/pom.xml
index 6a72edc..f8874ee 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
     <artifactId>master</artifactId>
     <packaging>pom</packaging>
     <name>Cancer Hotspots</name>
-    <version>0.1.0</version>
+    <version>0.1.2</version>
     <description>master maven module</description>
     <url>https://github.com/cBioPortal/cancerhotspots/</url>
 
diff --git a/service/pom.xml b/service/pom.xml
index c026c58..881cc88 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>master</artifactId>
         <groupId>org.cmo.cancerhotspots</groupId>
-        <version>0.1.0</version>
+        <version>0.1.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <name>Cancer Hotspots Service</name>
@@ -16,17 +16,17 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>model</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>util</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>persistence</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
diff --git a/util/pom.xml b/util/pom.xml
index c042c96..7df7d30 100644
--- a/util/pom.xml
+++ b/util/pom.xml
@@ -15,7 +15,7 @@
     <groupId>org.cmo.cancerhotspots</groupId>
     <artifactId>util</artifactId>
     <packaging>jar</packaging>
-    <version>0.1.0</version>
+    <version>0.1.2</version>
 
     <url>https://github.com/cBioPortal/cancerhotspots/tree/master</url>
 
diff --git a/webapp/pom.xml b/webapp/pom.xml
index 9af53bb..0456341 100644
--- a/webapp/pom.xml
+++ b/webapp/pom.xml
@@ -4,14 +4,14 @@
     <name>Cancer Hotspots Web</name>
     <description>Cancer Hotspots Web Module</description>
     <artifactId>webapp</artifactId>
-    <version>0.1.0</version>
+    <version>0.1.2</version>
     <!--<packaging>jar</packaging>-->
     <packaging>${packaging.type}</packaging>
 
     <parent>
         <groupId>org.cmo.cancerhotspots</groupId>
         <artifactId>master</artifactId>
-        <version>0.1.0</version>
+        <version>0.1.2</version>
     </parent>
 
     <properties>
@@ -179,12 +179,12 @@
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>model</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.cmo.cancerhotspots</groupId>
             <artifactId>service</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.2</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>