Merge pull request #333 from Rothamsted/master

aws EB #367

.travis.yml

@@ -7,7 +7,12 @@ addons:
   apt:
     packages:
       - libxml2-utils
-
+
+cache:
+  directories:
+    - $HOME/.m2
+    - $HOME/.npm
+
 install:
   - npm config set unsafe-perm true
   - npm install bower gulp -g

common/aratiny/aratiny-ws/pom.xml

@@ -274,17 +274,18 @@
 
 		<!-- 
 			This is used to run the build in 'console' mode, ie, start Neo4j (if the corresponding profile is enabled)
-			and jetty and keep them on until the maven user presses Enter.
+			and Jetty and then keep them on until the user presses Enter.
 
-			There is a (pseudo) test in ApiIT to deal with that, which starts the server and then waits for a user key-press, 
-			if this profile is enabled (and the the maven.profileId is set to 'console'). The build finishes after that step 
-			with the usual server shutdowns.
+			There is a (pseudo) test in ApiIT to deal with that, which is invoked aftet the server start and then the 
+			(pseudo)test checks if this profile is enabled and, if yes, waits for a user key-press. 
+			The build finishes after that step with the usual server shutdowns.
 
 			It's all a dirty trick, but we didn't find another way to do it: jetty:run is not enough, we need a whole build
 		-->
 		<profile>
 			<id>console</id>
 			<properties>
+			  <!-- The pseudo-test mentioned above checks if this profile is active via System.getProperty() -->
 				<maven.profileId>console</maven.profileId>
 			</properties>
 		</profile>

common/quickstart/aws/.ebextensions/00_instance.config

@@ -0,0 +1,4 @@
+option_settings:
+  aws:autoscaling:launchconfiguration:
+    InstanceType: <INSTANCE-TYPE>
+    EC2KeyName: <SSH-KEY-NAME>

common/quickstart/aws/.ebextensions/01_s3.config

@@ -0,0 +1,3 @@
+commands:
+  01_get_s3_bucket:
+    command: aws s3 cp s3://nfventures-testing.knetminer/arabidopsis_MD/ /home/ec2-user/knetminer-dataset --recursive

common/quickstart/aws/.gitignore

@@ -0,0 +1,5 @@
+
+# Elastic Beanstalk Files
+.elasticbeanstalk/*
+!.elasticbeanstalk/*.cfg.yml
+!.elasticbeanstalk/*.global.yml

common/quickstart/aws/Dockerfile

@@ -0,0 +1,5 @@
+FROM knetminer/knetminer:latest
+
+EXPOSE 8080
+
+WORKDIR /root/knetminer-build/knetminer/common/quickstart 

common/quickstart/aws/Dockerrun.aws.json

@@ -0,0 +1,15 @@
+{
+  "AWSEBDockerrunVersion": "1",
+  "Ports": [
+    {
+      "ContainerPort": "8080"
+    }
+  ],
+  "Volumes": [
+    {
+      "HostDirectory": "/home/ec2-user/knetminer-dataset",
+      "ContainerDirectory": "/root/knetminer-dataset"
+    }
+  ],
+  "Entrypoint": "./runtime-helper.sh"
+}

common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexLocalDataSource.java

@@ -67,6 +67,7 @@ private void init () {
 		init ( null, null, null );
 	}
 
+	@SuppressWarnings ( { "rawtypes", "unchecked" } )
 	private void init ( String dsName, String configXmlPath, String semanticMotifsPath )
 	{
 		// Config.xml location can be specified in different ways, see the constructors
@@ -116,9 +117,11 @@ private void init ( String dsName, String configXmlPath, String semanticMotifsPa
 		this.ondexServiceProvider.setExportVisible(Boolean.parseBoolean(this.getProperty("export_visible_network")));
 		log.info("Datasource "+dsName+" export visible: "+this.ondexServiceProvider.getExportVisible());
 		try {
-			this.ondexServiceProvider.createGraph(this.getProperty("DataPath"), this.getProperty("DataFile"),
-					semanticMotifsPath);
-		} catch (Exception e) {
+			this.ondexServiceProvider.createGraph (
+				this.getProperty("DataPath"), this.getProperty("DataFile"), semanticMotifsPath
+			);
+		} 
+		catch (Exception e) {
 			log.error("Failed to create Ondex graph", e);
 			throw new Error(e);
 		}