Merge pull request #16 from rajaram5/develop

To test hub.docker trigger
FAIRDataTeam · Dec 20, 2017 · 538ff87 · 538ff87
2 parents 1026186 + 2ec528f
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diff --git a/.travis.yml b/.travis.yml
@@ -2,9 +2,9 @@ language: java
 jdk:
   - oraclejdk8
 before_install:
-  - git clone https://github.com/DTL-FAIRData/fairmetadata4j ~/fairmetadata4j
+  - git clone -b develop https://github.com/DTL-FAIRData/fairmetadata4j ~/fairmetadata4j
   - cd ~/fairmetadata4j
-  - git checkout 0.1-beta 	
+#  - git checkout 0.1-beta
   - mvn install
   - cd $TRAVIS_BUILD_DIR
 after_success:

diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,8 @@
+FROM tomcat:8.0-jre8-alpine
+
+MAINTAINER Rajaram Kaliyaperumal <rr.kaliyaperumal@gmail.com>
+
+# Copy setup file
+COPY dockerSetup.sh /
+# RUN setup file
+RUN sh /dockerSetup.sh
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
-[![Build Status](https://travis-ci.org/DTL-FAIRData/FAIRDataPoint.svg?branch=master)](https://travis-ci.org/DTL-FAIRData/FAIRDataPoint)
+[![Build Status](https://travis-ci.org/DTL-FAIRData/FAIRDataPoint.svg?branch=develop)](https://travis-ci.org/DTL-FAIRData/FAIRDataPoint)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/61f029299b814ca8be2b8edbaab6ce50)](https://www.codacy.com/app/rajaram5/FAIRDataPoint?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=DTL-FAIRData/FAIRDataPoint&amp;utm_campaign=Badge_Grade)
 [![Dependency Status](https://www.versioneye.com/user/projects/589dd946940b230031fbadd6/badge.svg?style=flat-square)](https://www.versioneye.com/user/projects/589dd946940b230031fbadd6)
-[![Coverage Status](https://coveralls.io/repos/github/DTL-FAIRData/FAIRDataPoint/badge.svg?branch=master)](https://coveralls.io/github/DTL-FAIRData/FAIRDataPoint?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/DTL-FAIRData/FAIRDataPoint/badge.svg?branch=develop)](https://coveralls.io/github/DTL-FAIRData/FAIRDataPoint?branch=develop)
 
 ### Summary 
 `FAIRDataPoint` is a REST api for creating, storing and servering `FAIR metadata`. The metadata contents are in this api are generated `semi-automatically` according to the [FAIR Data Point software specification](https://dtl-fair.atlassian.net/wiki/display/FDP/FAIR+Data+Point+software+specification) document. In the current version of api we support `GET, POST and PATCH` requests.

diff --git a/dockerSetup.sh b/dockerSetup.sh
@@ -0,0 +1,37 @@
+#!/bin/sh
+
+# Install nano, git and maven openjdk-8-jdk
+apk update
+apk upgrade
+apk add --no-cache bash nano git maven
+apk add --no-cache openjdk8
+
+# clone fairmetadata4j repository
+git clone --depth 1 -b develop https://github.com/DTL-FAIRData/fairmetadata4j /fairmetadata4j
+
+# Install fairmetadata4j
+cd  /fairmetadata4j
+mvn --quiet --fail-fast install
+
+# Clone FAIRDataPoint repository
+cd /
+git clone --depth 1 -b develop https://github.com/DTL-FAIRData/FAIRDataPoint /FAIRDataPoint
+
+# Build FAIRDataPoint
+cd /FAIRDataPoint
+mvn --quiet --fail-fast verify
+
+# Remove ROOT dir
+rm -rf /usr/local/tomcat/webapps/ROOT/*
+
+# Add FDP folder to tomcat webapps
+cp -rf /FAIRDataPoint/target/fdp/* /usr/local/tomcat/webapps/ROOT
+
+# Remove unused DIR
+cd /
+rm -rf /FAIRDataPoint
+rm -rf /fairmetadata4j
+rm -rf /root/.m2/repository/*
+
+# Remove unused apps
+apk del git maven openjdk8
diff --git a/hs_err_pid891.log b/hs_err_pid891.log
diff --git a/nb-configuration.xml b/nb-configuration.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-shared-configuration>
+    <!--
+This file contains additional configuration written by modules in the NetBeans IDE.
+The configuration is intended to be shared among all the users of project and
+therefore it is assumed to be part of version control checkout.
+Without this configuration present, some functionality in the IDE may be limited or fail altogether.
+-->
+    <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
+        <!--
+Properties that influence various parts of the IDE, especially code formatting and the like. 
+You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
+That way multiple projects can share the same settings (useful for formatting rules for example).
+Any value defined here will override the pom.xml file value but is only applicable to the current project.
+-->
+        <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>Tomcat</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>
+    </properties>
+</project-shared-configuration>
diff --git a/pom.xml b/pom.xml
@@ -1,26 +1,22 @@
 <?xml version="1.0"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
-         xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<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>
 
     <groupId>nl.dtls</groupId>
     <artifactId>fairdatapoint</artifactId>
-    <packaging>war</packaging>
     <version>0.1-beta</version>
-
+    <packaging>war</packaging>
+
     <name>FairDataPoint</name>
+    <description>A reference implementation of FAIRDataPoint api</description>
     <inceptionYear>2017</inceptionYear>
-    <description>
-        A reference implementation of FAIRDataPoint api
-    </description>
-
     <licenses>
         <license>
             <name>The MIT License</name>
             <url>https://opensource.org/licenses/MIT</url>
         </license>
     </licenses>
-    
+
     <developers>
         <developer>
             <name>Rajaram Kaliyaperumal</name>
@@ -39,61 +35,54 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>        
-        <springframework.version>4.3.5.RELEASE</springframework.version>
-        <springdata.version>2.5.6.RELEASE</springdata.version>        
+        <maven.compiler.target>1.8</maven.compiler.target>
+
+        <springframework.version>5.0.0.RELEASE</springframework.version>
+        <springdata.version>3.0.0.RELEASE</springdata.version>        
         <springfox-swagger.version>2.6.1</springfox-swagger.version>        
-        <springsecurity.version>4.2.1.RELEASE</springsecurity.version>
-        <javaxservlet.version>3.1.0</javaxservlet.version>
-        <jackson.version>2.8.6</jackson.version>
-        <rdf4j.version>2.1.4</rdf4j.version>
-        <log4j.version>2.7</log4j.version>
+        <springsecurity.version>4.2.3.RELEASE</springsecurity.version>
+        <javaxservlet.version>4.0.0</javaxservlet.version>
+        <jackson.version>2.9.2</jackson.version>
+        <rdf4j.version>2.2.2</rdf4j.version>
+        <log4j.version>2.9.1</log4j.version>
         <handlebars.version>4.0.6</handlebars.version>
         <fairmetadata.version>0.1-beta</fairmetadata.version>
         <velocity.version>1.7</velocity.version>
+        <snakeyaml.version>1.19</snakeyaml.version>        
+        <unirest.version>1.4.9</unirest.version>
         <junit.version>4.12</junit.version>
-        <mockito.version>2.6.2</mockito.version>
-        <plugin.mavenwar.version>3.0.0</plugin.mavenwar.version>
+        <mockito.version>2.11.0</mockito.version>
+
+        <plugin.mavenwar.version>3.2.0</plugin.mavenwar.version>
         <plugin.mavenlic.version>3.0</plugin.mavenlic.version>
         <plugin.coveralls.version>4.3.0</plugin.coveralls.version>
         <plugin.cobertura.version>2.7</plugin.cobertura.version>
     </properties>
 
+    <repositories>
+        <repository>
+            <id>jcenter-snapshots</id>
+            <name>jcenter</name>
+            <url>https://jcenter.bintray.com/</url>
+        </repository>
+    </repositories>
+
     <dependencies>
+        <!-- compile -->
         <dependency>
             <groupId>org.springframework</groupId>
-            <artifactId>spring-core</artifactId>
-            <version>${springframework.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework</groupId>
-            <artifactId>spring-beans</artifactId>
-            <version>${springframework.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework</groupId>
-            <artifactId>spring-web</artifactId>
+            <artifactId>spring-webmvc</artifactId>
             <version>${springframework.version}</version>
         </dependency>
         <dependency>
             <groupId>org.springframework.data</groupId>
             <artifactId>spring-data-rest-webmvc</artifactId>
             <version>${springdata.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.springframework</groupId>
-            <artifactId>spring-webmvc</artifactId>
-            <version>${springframework.version}</version>
-        </dependency>
         <dependency>
             <groupId>io.springfox</groupId>
             <artifactId>springfox-swagger2</artifactId>
             <version>${springfox-swagger.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>io.springfox</groupId>
-            <artifactId>springfox-swagger-ui</artifactId>
-            <version>${springfox-swagger.version}</version>
         </dependency>           
         <dependency>
             <groupId>org.springframework.security</groupId>
@@ -104,12 +93,11 @@
             <groupId>org.springframework.security</groupId>
             <artifactId>spring-security-config</artifactId>
             <version>${springsecurity.version}</version>
-        </dependency>     
+        </dependency>
         <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>javax.servlet-api</artifactId>
-            <version>${javaxservlet.version}</version>
-            <scope>provided</scope>
+            <groupId>nl.dtl</groupId>
+            <artifactId>fairmetadata4j</artifactId>
+            <version>${fairmetadata.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
@@ -120,17 +108,13 @@
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>
             <version>${log4j.version}</version>
-        </dependency>        
+        </dependency>    
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
             <version>${log4j.version}</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.velocity</groupId>
-            <artifactId>velocity</artifactId>
-            <version>${velocity.version}</version>
-        </dependency>        
+
         <dependency>
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-runtime</artifactId>
@@ -140,7 +124,12 @@
             <groupId>org.eclipse.rdf4j</groupId>
             <artifactId>rdf4j-rio-api</artifactId>
             <version>${rdf4j.version}</version>
-        </dependency>
+        </dependency>    
+        <dependency>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-sail-nativerdf</artifactId>
+            <version>${rdf4j.version}</version>
+        </dependency> 
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-annotations</artifactId>
@@ -151,16 +140,26 @@
             <artifactId>jackson-databind</artifactId>
             <version>${jackson.version}</version>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-            <version>${jackson.version}</version>
-        </dependency>
         <dependency>
             <groupId>com.github.jknack</groupId>
             <artifactId>handlebars-springmvc</artifactId>
             <version>${handlebars.version}</version>
+        </dependency>        
+        <dependency>
+            <groupId>com.mashape.unirest</groupId>
+            <artifactId>unirest-java</artifactId>
+            <version>${unirest.version}</version>
         </dependency>
+
+        <!-- provided -->     
+        <dependency>
+            <groupId>javax.servlet</groupId>
+            <artifactId>javax.servlet-api</artifactId>
+            <version>${javaxservlet.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <!-- test -->
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
@@ -179,19 +178,22 @@
             <version>${springframework.version}</version>
             <scope>test</scope>
         </dependency>
+
+        <!-- runtime -->
         <dependency>
-            <groupId>nl.dtl</groupId>
-            <artifactId>fairmetadata4j</artifactId>
-            <version>${fairmetadata.version}</version>
+            <groupId>io.springfox</groupId>
+            <artifactId>springfox-swagger-ui</artifactId>
+            <version>${springfox-swagger.version}</version>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.yaml</groupId>
+            <artifactId>snakeyaml</artifactId>
+            <version>${snakeyaml.version}</version>
+            <scope>runtime</scope>
         </dependency>
     </dependencies>
-    <repositories>
-        <repository>
-            <id>jcenter-snapshots</id>
-            <name>jcenter</name>
-            <url>https://jcenter.bintray.com/</url>
-        </repository>
-    </repositories>
+
     <build>
         <finalName>fdp</finalName>
         <pluginManagement>
@@ -221,6 +223,7 @@
                     <excludes>
                         <exclude>pom.xml</exclude>
                         <exclude>**/*.ttl</exclude>
+                        <exclude>**/*.yml</exclude>
                         <exclude>**/*.sparql</exclude>
                         <exclude>**/*.properties</exclude>
                         <exclude>**/log4j2.xml</exclude>
@@ -242,6 +245,7 @@
             </plugin>
         </plugins>
     </build>
+
     <reporting>
         <plugins>
             <plugin>
@@ -251,4 +255,4 @@
             </plugin>
         </plugins>
     </reporting>
-</project>
+</project>
diff --git a/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationFilter.java b/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationFilter.java
@@ -61,7 +61,7 @@ public void doFilterInternal(final HttpServletRequest request,
                 HttpHeaders.CONTENT_TYPE);
         response.setHeader(HttpHeaders.ALLOW, allowedMtds);
         response.setHeader(HttpHeaders.ACCESS_CONTROL_ALLOW_METHODS,
-                (HttpHeaders.ACCEPT));
+                allowedMtds);
         ThreadContext.put("ipAddress", request.getRemoteAddr());
         ThreadContext.put("responseStatus", String.valueOf(
                 response.getStatus()));

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationInitializer.java b/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationInitializer.java
@@ -37,12 +37,12 @@ public class ApplicationInitializer extends
         AbstractAnnotationConfigDispatcherServletInitializer {
     @Override
     protected Class<?>[] getRootConfigClasses() {
-        return new Class[]{};
+        return new Class[]{ RootConfig.class, RestApiContext.class };
     }
 
     @Override
     protected Class<?>[] getServletConfigClasses() {
-        return new Class[]{RestApiContext.class};
+        return new Class[]{};
     }
 
     @Override

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationSwaggerConfig.java b/src/main/java/nl/dtls/fairdatapoint/api/config/ApplicationSwaggerConfig.java
@@ -65,9 +65,8 @@ private ApiInfo apiInfo() {
                     + "<li><a target='_blank' href = 'https://dtl-fair."
                     + "atlassian.net/wiki/display/FDP/FAIR+Data+Point+"
                     + "Software+Specification'>API specs</li>"
-                    + "<li><a target='_blank' href = 'https://github.com/"
-                    + "DTL-FAIRData/ODEX-FAIRDataPoint/tree/master/fdp-api"
-                    + "/java'>Source code</a> </li></p>",
+                    + "<li><a target='_blank' href = 'https://github.com/DTL-FAIRData/"
+                    + "FAIRDataPoint'>Source code</a> </li></p>",
             "0.1-beta",
             "ATO",
             "rr.kaliyaperumal@gmail.com",