Updated to Xenon 2.1.0

xenon-middleware · Nov 2, 2017 · 422b132 · 422b132
1 parent 541b903
commit 422b132
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Showing 7 changed files with 48 additions and 59 deletions.
diff --git a/build.gradle b/build.gradle
@@ -8,6 +8,10 @@ plugins {
     id 'org.springframework.boot' version '1.5.6.RELEASE'
 }
 
+springBoot {
+  mainClass = 'nl.esciencecenter.computeservice.rest.Swagger2SpringBoot'
+}
+
 bootRepackage {
     mainClass = 'nl.esciencecenter.computeservice.rest.Swagger2SpringBoot'
 }
@@ -24,8 +28,7 @@ repositories {
 // In this section you declare the dependencies for your production and test code
 dependencies {
     // Xenon
-    compile "com.github.NLeSC:Xenon:master-SNAPSHOT"
-    //compile group: 'nl.esciencecenter.xenon', name: 'xenon', version: '2.0.0'
+    compile group: 'nl.esciencecenter.xenon', name: 'xenon', version: '2.1.0'
 
     //Spring(boot)
     compile group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '1.5.6.RELEASE'

diff --git a/src/main/java/nl/esciencecenter/computeservice/config/ComputeResource.java b/src/main/java/nl/esciencecenter/computeservice/config/ComputeResource.java
@@ -22,7 +22,7 @@
 public class ComputeResource {
 	@JsonProperty("scheduler")
 	private AdaptorConfig schedulerConfig;
-	@JsonProperty("filesystem")
+	@JsonProperty(value="filesystem", required=false)
 	private AdaptorConfig filesystemConfig;
 
 	@JsonProperty(value="cwlCommand", required=false)

diff --git a/src/main/java/nl/esciencecenter/computeservice/rest/Swagger2SpringBoot.java b/src/main/java/nl/esciencecenter/computeservice/rest/Swagger2SpringBoot.java
@@ -1,11 +1,5 @@
 package nl.esciencecenter.computeservice.rest;
 
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.catalina.servlets.WebdavServlet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
@@ -15,18 +9,13 @@
 import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.boot.context.embedded.EmbeddedServletContainerInitializedEvent;
-import org.springframework.boot.web.servlet.FilterRegistrationBean;
-import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.context.ApplicationListener;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
-import org.springframework.web.cors.CorsConfiguration;
-import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
-import org.springframework.web.filter.CorsFilter;
 
 import springfox.documentation.swagger2.annotations.EnableSwagger2;
 
@@ -40,27 +29,6 @@
 		"nl.esciencecenter.computeservice.cwl.*" })
 public class Swagger2SpringBoot implements CommandLineRunner, ApplicationListener<EmbeddedServletContainerInitializedEvent> {
 	private static final Logger logger = LoggerFactory.getLogger(Swagger2SpringBoot.class);
-
-// I can't get the CORS for the embedded webdav to work, so it's not much sense
-// to include it.
-//	@Bean
-//	public static ServletRegistrationBean servletRegistrationBean() {
-//
-//		final ServletRegistrationBean registration = new ServletRegistrationBean(new WebdavServlet());
-//
-//		final Map<String, String> params = new HashMap<String, String>();
-//		params.put("debug", "1");
-//		params.put("listings", "true");
-//		params.put("readonly", "false");
-//		
-//		params.put("cors.allowed.origins", "*");
-//
-//		registration.setInitParameters(params);
-//		registration.addUrlMappings("/webdav/*");		
-//		registration.setLoadOnStartup(1);
-//		
-//		return registration;
-//	}
 
 	@Value("${server.address}")
 	String bindAdress;

diff --git a/src/main/java/nl/esciencecenter/computeservice/rest/service/JobService.java b/src/main/java/nl/esciencecenter/computeservice/rest/service/JobService.java
@@ -14,7 +14,6 @@
 import nl.esciencecenter.computeservice.rest.model.JobState;
 import nl.esciencecenter.computeservice.rest.model.StatePreconditionException;
 import nl.esciencecenter.computeservice.rest.model.WorkflowBinding;
-import nl.esciencecenter.xenon.XenonException;
 import nl.esciencecenter.xenon.filesystems.Path;
 
 @Service

diff --git a/src/main/java/nl/esciencecenter/computeservice/rest/service/XenonService.java b/src/main/java/nl/esciencecenter/computeservice/rest/service/XenonService.java
@@ -101,7 +101,6 @@ private void initialize() throws XenonException, IOException {
 		// TODO: Is assertions the nicest way?
 		assert(resource != null);
 		assert(resource.getSchedulerConfig() != null);
-		assert(resource.getFilesystemConfig() != null);
 
 
 		// Start up submitted jobs
@@ -170,18 +169,51 @@ public JobService getJobService() {
 	public void setJobService(JobService jobService) {
 		this.jobService = jobService;
 	}
-
-	public Scheduler getScheduler() throws XenonException {
-		if (scheduler == null) {
-			// Initialize xenon scheduler
-			ComputeResource resource = getConfig().defaultComputeResource();
-			AdaptorConfig schedulerConfig = resource.getSchedulerConfig();
-
+
+	private void checkSchedulerStates() throws XenonException {
+		ComputeResource resource = getConfig().defaultComputeResource();
+		AdaptorConfig schedulerConfig = resource.getSchedulerConfig();
+		AdaptorConfig fileSystemConfig = resource.getFilesystemConfig();
+
+		boolean useSchedulerFilesystem = fileSystemConfig == null;
+		boolean recreateScheduler = false;
+		boolean recreateFileSystem = false;
+		if(useSchedulerFilesystem) {
+			if (scheduler == null || !scheduler.isOpen() || remoteFileSystem == null || !remoteFileSystem.isOpen()) {
+				recreateScheduler = true;
+				recreateFileSystem = true;
+			}
+
+		} else {
+			if (scheduler == null || !scheduler.isOpen()) {
+				recreateScheduler = true;
+			}
+			if (remoteFileSystem == null || !remoteFileSystem.isOpen()) {
+				recreateFileSystem = true;
+			}
+		}
+		if (recreateScheduler) {
 			logger.debug("Creating a scheduler to run jobs...");
 			scheduler = Scheduler.create(schedulerConfig.getAdaptor(), schedulerConfig.getLocation(),
-					schedulerConfig.getCredential(), schedulerConfig.getProperties());
+										 schedulerConfig.getCredential(), schedulerConfig.getProperties());
+		}
+		if (recreateFileSystem) {
+			if (useSchedulerFilesystem && Scheduler.getAdaptorDescription(scheduler.getAdaptorName()).usesFileSystem()) {
+				logger.debug("Using scheduler filesystem as a remote filesystem...");
+				remoteFileSystem = scheduler.getFileSystem();
+			} else {
+				// Initialize remote filesystem
+				logger.debug("Creating remote filesystem...");
+				remoteFileSystem = FileSystem.create(fileSystemConfig.getAdaptor(), fileSystemConfig.getLocation(),
+													 fileSystemConfig.getCredential(), fileSystemConfig.getProperties());
+
+				logger.debug("Remote working directory: " + remoteFileSystem.getWorkingDirectory());
+			}
 		}
+	}
 
+	public Scheduler getScheduler() throws XenonException {
+		checkSchedulerStates();
 		return scheduler;
 	}
 
@@ -197,16 +229,7 @@ public void setScheduler(Scheduler scheduler) {
 	}
 
 	public FileSystem getRemoteFileSystem() throws XenonException {
-		if (remoteFileSystem == null || !remoteFileSystem.isOpen()) {
-			// Initialize remote filesystem
-			logger.debug("Creating remote filesystem...");
-			ComputeResource resource = getConfig().defaultComputeResource();
-			AdaptorConfig fileSystemConfig = resource.getFilesystemConfig();
-			remoteFileSystem = FileSystem.create(fileSystemConfig.getAdaptor(), fileSystemConfig.getLocation(),
-					fileSystemConfig.getCredential(), fileSystemConfig.getProperties());
-
-			logger.debug("Remote working directory: " + remoteFileSystem.getWorkingDirectory());
-		}
+		checkSchedulerStates();
 		return remoteFileSystem;
 	}
 

diff --git a/src/main/java/nl/esciencecenter/computeservice/rest/service/tasks/CwlStageInTask.java b/src/main/java/nl/esciencecenter/computeservice/rest/service/tasks/CwlStageInTask.java
@@ -25,7 +25,6 @@
 import nl.esciencecenter.computeservice.rest.service.staging.StringToFileStagingObject;
 import nl.esciencecenter.computeservice.rest.service.staging.XenonStager;
 import nl.esciencecenter.xenon.XenonException;
-import nl.esciencecenter.xenon.filesystems.FileSystem;
 import nl.esciencecenter.xenon.filesystems.Path;
 
 

diff --git a/src/main/java/nl/esciencecenter/computeservice/rest/service/tasks/DeleteJobTask.java b/src/main/java/nl/esciencecenter/computeservice/rest/service/tasks/DeleteJobTask.java
@@ -5,7 +5,6 @@
 
 import nl.esciencecenter.computeservice.rest.model.Job;
 import nl.esciencecenter.computeservice.rest.model.JobRepository;
-import nl.esciencecenter.computeservice.rest.service.JobService;
 import nl.esciencecenter.computeservice.rest.service.XenonService;
 import nl.esciencecenter.xenon.XenonException;
 import nl.esciencecenter.xenon.filesystems.FileSystem;
@@ -17,13 +16,11 @@ public class DeleteJobTask implements Runnable {
 	private String jobId;
 	private XenonService service;
 	private JobRepository repository;
-	private JobService jobService;
 
 	public DeleteJobTask(String jobId, XenonService service) throws XenonException {
 		this.jobId = jobId;
 		this.service = service;
 		this.repository = service.getRepository();
-		this.jobService = service.getJobService();
 	}
 
 	@Override