ref 8819: Extend The Algorithms Importer to Manage Many Processes as Black Boxes

https://support.d4science.org/issues/8819

Updated the support for Processes as Black Boxes

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@150373 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -468,7 +468,6 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-assembly-plugin</artifactId>
-				<version>2.2</version>
 				<configuration>
 					<descriptors>
 						<descriptor>${distroDirectory}/descriptor.xml</descriptor>

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/blackbox/MainGenerator.java

@@ -105,7 +105,7 @@ public class MainGenerator {
 						serviceCredentials.getUserName(),
 						Files.newInputStream(producedScript, StandardOpenOption.READ),
 						
-						producedScript.getFileName().toString(), R_DESCRIPTION+project.getProjectConfig().getLanguage(),
+						"Main.R", R_DESCRIPTION+project.getProjectConfig().getLanguage(),
 						R_MIMETYPE, project.getProjectFolder().getFolder().getId());
 			} catch (IOException e) {
 				logger.error(e.getLocalizedMessage());

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/generator/ProjectBuilder.java

@@ -122,6 +122,7 @@ public class ProjectBuilder {
 	public Project buildRepackage() throws StatAlgoImporterServiceException {
 		checkInfoForRepackage();
 		createBackupOfPackageProject();
+		createMainCodeIfRequest();
 		repackageProjectPackage();
 		return project;
 	}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/is/AvailableProjectConfigJAXB.java

@@ -39,7 +39,9 @@ public class AvailableProjectConfigJAXB {
 
 	@Override
 	public String toString() {
-		return "ProjectConfigJAXB [language=" + language + ", support=" + support + "]";
+		return "AvailableProjectConfigJAXB [language=" + language + ", support=" + support + "]";
 	}
 
+	
+
 }

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/is/BuildSAIDescriptor.java

@@ -27,11 +27,11 @@ public class BuildSAIDescriptor {
 			ArrayList<ProjectSetup> availableProjectConfigurations = new ArrayList<>();
 			ProjectSetup r = new ProjectSetup("R", ProjectSupportType.REdit);
 			availableProjectConfigurations.add(r);
-			ProjectSetup rBlackBox = new ProjectSetup("R-black box", ProjectSupportType.BlackBox);
+			ProjectSetup rBlackBox = new ProjectSetup("R-blackbox", ProjectSupportType.BlackBox);
 			availableProjectConfigurations.add(rBlackBox);
 			ProjectSetup java = new ProjectSetup("Java", ProjectSupportType.BlackBox);
 			availableProjectConfigurations.add(java);
-			ProjectSetup knimeWorkflow = new ProjectSetup("Knime Workflow", ProjectSupportType.BlackBox);
+			ProjectSetup knimeWorkflow = new ProjectSetup("Knime-Workflow", ProjectSupportType.BlackBox);
 			availableProjectConfigurations.add(knimeWorkflow);
 			ProjectSetup linuxCompiled = new ProjectSetup("Linux-compiled", ProjectSupportType.BlackBox);
 			availableProjectConfigurations.add(linuxCompiled);
@@ -54,13 +54,13 @@ public class BuildSAIDescriptor {
 			ArrayList<ProjectSetup> availableProjectConfigurations = new ArrayList<>();
 
 			logger.debug("SAIDescriptorJAXB: " + saiDescriptorJAXB);
-			if (saiDescriptorJAXB != null && saiDescriptorJAXB.getAvailableprojectconfigurations() != null
+			if (saiDescriptorJAXB != null && saiDescriptorJAXB.getAvailableprojectconfiguration() != null
-					&& !saiDescriptorJAXB.getAvailableprojectconfigurations().isEmpty()) {
+					&& !saiDescriptorJAXB.getAvailableprojectconfiguration().isEmpty()) {
 
 				ProjectSupportType type;
 
 				for (AvailableProjectConfigJAXB availableProjectConfigJAXB : saiDescriptorJAXB
-						.getAvailableprojectconfigurations()) {
+						.getAvailableprojectconfiguration()) {
 					type = ProjectSupportType.valueOf(availableProjectConfigJAXB.getSupport());
 					if (type != null) {
 						availableProjectConfigurations
@@ -73,11 +73,11 @@ public class BuildSAIDescriptor {
 
 				ProjectSetup r = new ProjectSetup("R", ProjectSupportType.REdit);
 				availableProjectConfigurations.add(r);
-				ProjectSetup rBlackBox = new ProjectSetup("R-black box", ProjectSupportType.BlackBox);
+				ProjectSetup rBlackBox = new ProjectSetup("R-blackbox", ProjectSupportType.BlackBox);
 				availableProjectConfigurations.add(rBlackBox);
 				ProjectSetup java = new ProjectSetup("Java", ProjectSupportType.BlackBox);
 				availableProjectConfigurations.add(java);
-				ProjectSetup knimeWorkflow = new ProjectSetup("Knime Workflow", ProjectSupportType.BlackBox);
+				ProjectSetup knimeWorkflow = new ProjectSetup("Knime-Workflow", ProjectSupportType.BlackBox);
 				availableProjectConfigurations.add(knimeWorkflow);
 				ProjectSetup linuxCompiled = new ProjectSetup("Linux-compiled", ProjectSupportType.BlackBox);
 				availableProjectConfigurations.add(linuxCompiled);

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/is/InformationSystemUtils.java

@@ -43,7 +43,7 @@ public class InformationSystemUtils {
 			List<GenericResource> accountingResources = client.submit(query);
 			logger.debug("Resources: " + accountingResources);
 
-			SAIDescriptorJAXB enableTabs = null;
+			SAIDescriptorJAXB saiDescriptorJaxB = null;
 
 			for (GenericResource genericResource : accountingResources) {
 				if (genericResource.scopes() != null) {
@@ -62,8 +62,8 @@ public class InformationSystemUtils {
 							JAXBParser<SAIDescriptorJAXB> parser = new JAXBParser<SAIDescriptorJAXB>(
 									SAIDescriptorJAXB.class);
 							logger.debug("Body: " + genericResource.profile().bodyAsString());
-							enableTabs = (SAIDescriptorJAXB) parser.parse(genericResource.profile().bodyAsString());
+							saiDescriptorJaxB = (SAIDescriptorJAXB) parser.parse(genericResource.profile().bodyAsString());
-							logger.debug("Enable: " + enableTabs);
+							logger.debug("Enable: " + saiDescriptorJaxB);
 						} catch (Throwable e) {
 							String error = "Error in discovery SAI profile generic resource on IS in scope " + scope + ". "
 									+ "Resource parsing failed!";
@@ -80,7 +80,7 @@ public class InformationSystemUtils {
 				}
 			}
 
-			return enableTabs;
+			return saiDescriptorJaxB;
 
 		} catch (StatAlgoImporterServiceException e) {
 			throw e;

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/is/SAIDescriptorJAXB.java

@@ -1,5 +1,6 @@
 package org.gcube.portlets.user.statisticalalgorithmsimporter.server.is;
 
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -18,20 +19,20 @@ import javax.xml.bind.annotation.XmlRootElement;
 @XmlAccessorType(XmlAccessType.FIELD)
 public class SAIDescriptorJAXB {
 
-	@XmlElement(name = "availableprojectconfigurations")
+	@XmlElement(name = "availableprojectconfiguration")
-	private List<AvailableProjectConfigJAXB> availableprojectconfigurations = null;
+	private List<AvailableProjectConfigJAXB> availableprojectconfiguration = new ArrayList<>();
 
-	public List<AvailableProjectConfigJAXB> getAvailableprojectconfigurations() {
+	public List<AvailableProjectConfigJAXB> getAvailableprojectconfiguration() {
-		return availableprojectconfigurations;
+		return availableprojectconfiguration;
 	}
 
-	public void setAvailableprojectconfigurations(List<AvailableProjectConfigJAXB> availableprojectconfigurations) {
+	public void setAvailableprojectconfiguration(List<AvailableProjectConfigJAXB> availableprojectconfiguration) {
-		this.availableprojectconfigurations = availableprojectconfigurations;
+		this.availableprojectconfiguration = availableprojectconfiguration;
 	}
 
 	@Override
 	public String toString() {
-		return "SAIDescriptorJAXB [availableprojectconfigurations=" + availableprojectconfigurations + "]";
+		return "SAIDescriptorJAXB [availableprojectconfiguration=" + availableprojectconfiguration + "]";
 	}
 
 }

src/test/java/org/gcube/portlets/user/statisticalalgorithmsimporter/ISResourceTest.java

@@ -0,0 +1,66 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter;
+
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.JAXBContext;
+
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.AvailableProjectConfigJAXB;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.SAIDescriptorJAXB;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.Constants;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import junit.framework.TestCase;
+
+/**
+ * 
+ * @author Giancarlo Panichi
+ *
+ *
+ */
+public class ISResourceTest extends TestCase {
+	private static Logger logger = LoggerFactory.getLogger(ISResourceTest.class);
+
+	public void test() {
+		if (Constants.TEST_ENABLE) {
+
+			try {
+				JAXBContext jaxbContext = JAXBContext.newInstance(SAIDescriptorJAXB.class);
+				StringWriter sw = new StringWriter();
+
+				SAIDescriptorJAXB saiDescriptor = new SAIDescriptorJAXB();
+				List<AvailableProjectConfigJAXB> list = new ArrayList<>();
+				AvailableProjectConfigJAXB a1 = new AvailableProjectConfigJAXB();
+				a1.setLanguage("R");
+				a1.setSupport("REditor");
+				list.add(a1);
+				a1 = new AvailableProjectConfigJAXB();
+				a1.setLanguage("Linux");
+				a1.setSupport("BlackBox");
+				list.add(a1);
+				a1 = new AvailableProjectConfigJAXB();
+				a1.setLanguage("Octave");
+				a1.setSupport("BlackBox");
+				list.add(a1);
+				saiDescriptor.setAvailableprojectconfiguration(list);
+				jaxbContext.createMarshaller().marshal(saiDescriptor, sw);
+				logger.debug(sw.toString());
+				SAIDescriptorJAXB descr = (SAIDescriptorJAXB) jaxbContext.createUnmarshaller()
+						.unmarshal(new StringReader(sw.toString()));
+				logger.debug("SAIDescriptor: " + descr);
+				assertTrue("Success", true);
+			} catch (Throwable e) {
+				logger.error(e.getLocalizedMessage(), e);
+				fail("Error:" + e.getLocalizedMessage());
+
+			}
+
+		} else {
+			assertTrue("Success", true);
+		}
+	}
+
+}

src/test/java/org/gcube/portlets/user/statisticalalgorithmsimporter/StatAlgoImporterTest.java

@@ -11,13 +11,8 @@ package org.gcube.portlets.user.statisticalalgorithmsimporter;
  * 
  *
  */
-public class TestStatAlgoImporter {
+public class StatAlgoImporterTest {
 
-	/**
+	
-	 * @param args
-	 */
-	public static void main(String[] args) {
-		
-	}
 
 }

src/test/resources/log4j.properties

@@ -0,0 +1,20 @@
+# A default log4j configuration for log4j users.
+#
+# To use this configuration, deploy it into your application's WEB-INF/classes
+# directory.  You are also encouraged to edit it as you like.
+
+log4j.rootLogger=DEBUG, stdout, rollingFile
+
+# Redirect log messages to console
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Target=System.out
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
+
+
+log4j.appender.rollingFile=org.apache.log4j.RollingFileAppender
+log4j.appender.rollingFile.File=test.log
+log4j.appender.rollingFile.MaxFileSize=20MB
+log4j.appender.rollingFile.MaxBackupIndex=2
+log4j.appender.rollingFile.layout = org.apache.log4j.PatternLayout
+log4j.appender.rollingFile.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n

test.log

@@ -0,0 +1,33 @@
+2017-06-14 14:35:14 DEBUG ISResourceTest:50 - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><saidescriptor><availableprojectconfigurations><language>R</language><support>REditor</support></availableprojectconfigurations><availableprojectconfigurations><language>Linux</language><support>BlackBox</support></availableprojectconfigurations><availableprojectconfigurations><language>Octave</language><support>BlackBox</support></availableprojectconfigurations></saidescriptor>
+2017-06-14 14:36:11 DEBUG ISResourceTest:49 - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><saidescriptor><availableprojectconfigurations><language>R</language><support>REditor</support></availableprojectconfigurations><availableprojectconfigurations><language>Linux</language><support>BlackBox</support></availableprojectconfigurations><availableprojectconfigurations><language>Octave</language><support>BlackBox</support></availableprojectconfigurations></saidescriptor>
+2017-06-14 14:36:11 ERROR ISResourceTest:55 - org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.SAIDescriptorJAXB cannot be cast to org.gcube.portlets.user.statisticalalgorithmsimporter.shared.descriptor.SAIDescriptor
+java.lang.ClassCastException: org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.SAIDescriptorJAXB cannot be cast to org.gcube.portlets.user.statisticalalgorithmsimporter.shared.descriptor.SAIDescriptor
+	at org.gcube.portlets.user.statisticalalgorithmsimporter.ISResourceTest.test(ISResourceTest.java:50)
+	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+	at java.lang.reflect.Method.invoke(Method.java:498)
+	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
+	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
+	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
+	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
+	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
+	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
+	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
+	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
+	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
+	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
+	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
+	at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
+	at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
+	at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
+	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:459)
+	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:678)
+	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:382)
+	at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:192)
+2017-06-14 14:36:58 DEBUG ISResourceTest:49 - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><saidescriptor><availableprojectconfigurations><language>R</language><support>REditor</support></availableprojectconfigurations><availableprojectconfigurations><language>Linux</language><support>BlackBox</support></availableprojectconfigurations><availableprojectconfigurations><language>Octave</language><support>BlackBox</support></availableprojectconfigurations></saidescriptor>
+2017-06-14 14:36:58 DEBUG ISResourceTest:52 - SAIDescriptor: SAIDescriptorJAXB [availableprojectconfigurations=[AvailableProjectConfigJAXB [language=R, support=REditor], AvailableProjectConfigJAXB [language=Linux, support=BlackBox], AvailableProjectConfigJAXB [language=Octave, support=BlackBox]]]
+2017-06-14 14:42:05 DEBUG ISResourceTest:48 - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><saidescriptor><availableprojectconfiguration><language>R</language><support>REditor</support></availableprojectconfiguration><availableprojectconfiguration><language>Linux</language><support>BlackBox</support></availableprojectconfiguration><availableprojectconfiguration><language>Octave</language><support>BlackBox</support></availableprojectconfiguration></saidescriptor>
+2017-06-14 14:42:05 DEBUG ISResourceTest:51 - SAIDescriptor: SAIDescriptorJAXB [availableprojectconfiguration=[AvailableProjectConfigJAXB [language=R, support=REditor], AvailableProjectConfigJAXB [language=Linux, support=BlackBox], AvailableProjectConfigJAXB [language=Octave, support=BlackBox]]]
+2017-06-14 14:47:07 DEBUG ISResourceTest:48 - <?xml version="1.0" encoding="UTF-8" standalone="yes"?><saidescriptor><availableprojectconfiguration><language>R</language><support>REditor</support></availableprojectconfiguration><availableprojectconfiguration><language>Linux</language><support>BlackBox</support></availableprojectconfiguration><availableprojectconfiguration><language>Octave</language><support>BlackBox</support></availableprojectconfiguration></saidescriptor>
+2017-06-14 14:47:07 DEBUG ISResourceTest:51 - SAIDescriptor: SAIDescriptorJAXB [availableprojectconfiguration=[AvailableProjectConfigJAXB [language=R, support=REditor], AvailableProjectConfigJAXB [language=Linux, support=BlackBox], AvailableProjectConfigJAXB [language=Octave, support=BlackBox]]]