From 4c9875fce902bd8d03767688fa4fdbaaf6645737 Mon Sep 17 00:00:00 2001
From: Myung Choi <myungchoi@gmail.com>
Date: Fri, 12 Jul 2019 10:08:23 -0400
Subject: [PATCH] Rewriting omoponfhir main build

---
 .gitmodules                    | 12 +++++
 Dockerfile                     |  9 +---
 Jenkinsfile                    |  2 +-
 omoponfhir-omopv5-jpabase      |  1 +
 omoponfhir-omopv5-stu3-mapping |  1 +
 omoponfhir-stu3-server         |  1 +
 pom-docker-test.xml            | 74 -------------------------------
 pom-docker.xml                 | 80 ----------------------------------
 8 files changed, 17 insertions(+), 163 deletions(-)
 create mode 100644 .gitmodules
 create mode 160000 omoponfhir-omopv5-jpabase
 create mode 160000 omoponfhir-omopv5-stu3-mapping
 create mode 160000 omoponfhir-stu3-server
 delete mode 100644 pom-docker-test.xml
 delete mode 100644 pom-docker.xml

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..294356a
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,12 @@
+[submodule "omoponfhir-omopv5-jpabase"]
+	path = omoponfhir-omopv5-jpabase
+	url = https://github.com/omoponfhir/omoponfhir-omopv5-jpabase.git
+	branch = master
+[submodule "omoponfhir-omopv5-stu3-mapping"]
+	path = omoponfhir-omopv5-stu3-mapping
+	url = https://github.com/omoponfhir/omoponfhir-omopv5-stu3-mapping.git
+	branch = master
+[submodule "omoponfhir-stu3-server"]
+	path = omoponfhir-stu3-server
+	url = https://github.com/omoponfhir/omoponfhir-stu3-server.git
+	branch = master
diff --git a/Dockerfile b/Dockerfile
index 4a965c7..f7c735c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,14 +2,7 @@
 FROM maven:3.6.1-alpine as builder
 COPY . /usr/src/app
 WORKDIR /usr/src/app
-RUN apk update && apk upgrade && \
-    apk add --no-cache bash git openssh
-
-RUN git clone https://github.com/omoponfhir/omoponfhir-omopv5-jpabase.git
-RUN git clone https://github.com/omoponfhir/omoponfhir-omopv5-stu3-mapping.git
-RUN git clone https://github.com/omoponfhir/omoponfhir-stu3-server.git
-
-RUN mvn -f pom-docker.xml clean install
+RUN mvn clean install
 
 #Build the Tomcat container
 FROM tomcat:alpine
diff --git a/Jenkinsfile b/Jenkinsfile
index 4f5df6d..875d412 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -18,7 +18,7 @@ pipeline{
             //line between the ''' characters will be treated as separate lines of a shell script.
             
             steps{
-                sh '''mvn -f pom-docker-test.xml test'''
+                sh '''mvn test'''
             }
         }
 
diff --git a/omoponfhir-omopv5-jpabase b/omoponfhir-omopv5-jpabase
new file mode 160000
index 0000000..c805bbe
--- /dev/null
+++ b/omoponfhir-omopv5-jpabase
@@ -0,0 +1 @@
+Subproject commit c805bbecb84d572dd42058891879fd8ea92a6c88
diff --git a/omoponfhir-omopv5-stu3-mapping b/omoponfhir-omopv5-stu3-mapping
new file mode 160000
index 0000000..125f872
--- /dev/null
+++ b/omoponfhir-omopv5-stu3-mapping
@@ -0,0 +1 @@
+Subproject commit 125f8721f32fb95ce704d066016ae1f91e4122a2
diff --git a/omoponfhir-stu3-server b/omoponfhir-stu3-server
new file mode 160000
index 0000000..300f959
--- /dev/null
+++ b/omoponfhir-stu3-server
@@ -0,0 +1 @@
+Subproject commit 300f959d75b985faf31bcd464678f7dfb7ece160
diff --git a/pom-docker-test.xml b/pom-docker-test.xml
deleted file mode 100644
index 80069ac..0000000
--- a/pom-docker-test.xml
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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/maven-v4_0_0.xsd">
-
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>edu.gatech.chai</groupId>
-	<artifactId>omoponfhir</artifactId>
-	<packaging>pom</packaging>
-	<version>1.0.1</version>
-	<name>OMOPonFHIR</name>
-	<url>http://omoponfhir.org</url>
-
-	<organization>
-		<name>Georgia Tech Research Institute - CHAI</name>
-		<url>http://chai.gatech.edu</url>
-	</organization>
-
-	<description>OMOPonFHIR STU3 Server Build Test</description>
-
-	<prerequisites>
-		<maven>3.2</maven>
-	</prerequisites>
-
-	<licenses>
-		<license>
-			<name>Apache Software License 2.0</name>
-			<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
-		</license>
-	</licenses>
-
-	<properties>
-		<hapi_stable_version>3.8.0</hapi_stable_version>
-		<hapi_current_version>3.8.0-SNAPSHOT</hapi_current_version>
-		<omoponfhir_module_version>1.0.1</omoponfhir_module_version>
-		<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->
-		<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
-
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-	</properties>
-
-	<build>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<version>2.12.4</version>
-					<configuration>
-						<skipTests>true</skipTests>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.0</version>
-					<configuration>
-						<source>1.8</source>
-						<target>1.8</target>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-	</build>
-
-	<dependencies>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>3.8.1</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-</project>
\ No newline at end of file
diff --git a/pom-docker.xml b/pom-docker.xml
deleted file mode 100644
index 57da72b..0000000
--- a/pom-docker.xml
+++ /dev/null
@@ -1,80 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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/maven-v4_0_0.xsd">
-
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>edu.gatech.chai</groupId>
-	<artifactId>omoponfhir</artifactId>
-	<packaging>pom</packaging>
-	<version>1.0.1</version>
-	<name>OMOPonFHIR</name>
-	<url>http://omoponfhir.org</url>
-
-	<organization>
-		<name>Georgia Tech Research Institute - CHAI</name>
-		<url>http://chai.gatech.edu</url>
-	</organization>
-
-	<description>OMOPonFHIR STU3 Server Build</description>
-
-	<modules>
-		<module>omoponfhir-omopv5-jpabase</module>
-		<module>omoponfhir-omopv5-stu3-mapping</module>
-		<module>omoponfhir-stu3-server</module>
-	</modules>
-
-	<prerequisites>
-		<maven>3.2</maven>
-	</prerequisites>
-
-	<licenses>
-		<license>
-			<name>Apache Software License 2.0</name>
-			<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
-		</license>
-	</licenses>
-
-	<properties>
-		<hapi_stable_version>3.8.0</hapi_stable_version>
-		<hapi_current_version>3.8.0-SNAPSHOT</hapi_current_version>
-		<omoponfhir_module_version>1.0.1</omoponfhir_module_version>
-		<!-- configure timestamp in MANIFEST.MF for maven-war-provider -->
-		<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
-
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-	</properties>
-
-	<build>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<version>2.12.4</version>
-					<configuration>
-						<skipTests>true</skipTests>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.0</version>
-					<configuration>
-						<source>1.8</source>
-						<target>1.8</target>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-	</build>
-
-	<dependencies>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>3.8.1</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-</project>
\ No newline at end of file