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
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7d94425542
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09758721d6
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pom.xml
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pom.xml
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@ -468,7 +468,6 @@
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>2.2</version>
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<configuration>
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<descriptors>
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<descriptor>${distroDirectory}/descriptor.xml</descriptor>
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@ -105,7 +105,7 @@ public class MainGenerator {
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serviceCredentials.getUserName(),
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Files.newInputStream(producedScript, StandardOpenOption.READ),
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producedScript.getFileName().toString(), R_DESCRIPTION+project.getProjectConfig().getLanguage(),
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"Main.R", R_DESCRIPTION+project.getProjectConfig().getLanguage(),
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R_MIMETYPE, project.getProjectFolder().getFolder().getId());
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} catch (IOException e) {
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logger.error(e.getLocalizedMessage());
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@ -122,6 +122,7 @@ public class ProjectBuilder {
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public Project buildRepackage() throws StatAlgoImporterServiceException {
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checkInfoForRepackage();
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createBackupOfPackageProject();
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createMainCodeIfRequest();
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repackageProjectPackage();
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return project;
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}
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@ -39,7 +39,9 @@ public class AvailableProjectConfigJAXB {
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@Override
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public String toString() {
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return "ProjectConfigJAXB [language=" + language + ", support=" + support + "]";
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return "AvailableProjectConfigJAXB [language=" + language + ", support=" + support + "]";
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}
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}
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@ -27,11 +27,11 @@ public class BuildSAIDescriptor {
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ArrayList<ProjectSetup> availableProjectConfigurations = new ArrayList<>();
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ProjectSetup r = new ProjectSetup("R", ProjectSupportType.REdit);
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availableProjectConfigurations.add(r);
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ProjectSetup rBlackBox = new ProjectSetup("R-black box", ProjectSupportType.BlackBox);
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ProjectSetup rBlackBox = new ProjectSetup("R-blackbox", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(rBlackBox);
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ProjectSetup java = new ProjectSetup("Java", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(java);
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ProjectSetup knimeWorkflow = new ProjectSetup("Knime Workflow", ProjectSupportType.BlackBox);
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ProjectSetup knimeWorkflow = new ProjectSetup("Knime-Workflow", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(knimeWorkflow);
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ProjectSetup linuxCompiled = new ProjectSetup("Linux-compiled", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(linuxCompiled);
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@ -54,13 +54,13 @@ public class BuildSAIDescriptor {
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ArrayList<ProjectSetup> availableProjectConfigurations = new ArrayList<>();
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logger.debug("SAIDescriptorJAXB: " + saiDescriptorJAXB);
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if (saiDescriptorJAXB != null && saiDescriptorJAXB.getAvailableprojectconfigurations() != null
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&& !saiDescriptorJAXB.getAvailableprojectconfigurations().isEmpty()) {
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if (saiDescriptorJAXB != null && saiDescriptorJAXB.getAvailableprojectconfiguration() != null
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&& !saiDescriptorJAXB.getAvailableprojectconfiguration().isEmpty()) {
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ProjectSupportType type;
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for (AvailableProjectConfigJAXB availableProjectConfigJAXB : saiDescriptorJAXB
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.getAvailableprojectconfigurations()) {
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.getAvailableprojectconfiguration()) {
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type = ProjectSupportType.valueOf(availableProjectConfigJAXB.getSupport());
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if (type != null) {
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availableProjectConfigurations
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@ -73,11 +73,11 @@ public class BuildSAIDescriptor {
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ProjectSetup r = new ProjectSetup("R", ProjectSupportType.REdit);
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availableProjectConfigurations.add(r);
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ProjectSetup rBlackBox = new ProjectSetup("R-black box", ProjectSupportType.BlackBox);
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ProjectSetup rBlackBox = new ProjectSetup("R-blackbox", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(rBlackBox);
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ProjectSetup java = new ProjectSetup("Java", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(java);
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ProjectSetup knimeWorkflow = new ProjectSetup("Knime Workflow", ProjectSupportType.BlackBox);
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ProjectSetup knimeWorkflow = new ProjectSetup("Knime-Workflow", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(knimeWorkflow);
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ProjectSetup linuxCompiled = new ProjectSetup("Linux-compiled", ProjectSupportType.BlackBox);
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availableProjectConfigurations.add(linuxCompiled);
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@ -43,7 +43,7 @@ public class InformationSystemUtils {
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List<GenericResource> accountingResources = client.submit(query);
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logger.debug("Resources: " + accountingResources);
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SAIDescriptorJAXB enableTabs = null;
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SAIDescriptorJAXB saiDescriptorJaxB = null;
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for (GenericResource genericResource : accountingResources) {
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if (genericResource.scopes() != null) {
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@ -62,8 +62,8 @@ public class InformationSystemUtils {
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JAXBParser<SAIDescriptorJAXB> parser = new JAXBParser<SAIDescriptorJAXB>(
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SAIDescriptorJAXB.class);
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logger.debug("Body: " + genericResource.profile().bodyAsString());
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enableTabs = (SAIDescriptorJAXB) parser.parse(genericResource.profile().bodyAsString());
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logger.debug("Enable: " + enableTabs);
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saiDescriptorJaxB = (SAIDescriptorJAXB) parser.parse(genericResource.profile().bodyAsString());
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logger.debug("Enable: " + saiDescriptorJaxB);
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} catch (Throwable e) {
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String error = "Error in discovery SAI profile generic resource on IS in scope " + scope + ". "
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+ "Resource parsing failed!";
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@ -80,7 +80,7 @@ public class InformationSystemUtils {
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}
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}
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return enableTabs;
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return saiDescriptorJaxB;
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} catch (StatAlgoImporterServiceException e) {
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throw e;
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@ -1,5 +1,6 @@
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package org.gcube.portlets.user.statisticalalgorithmsimporter.server.is;
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import java.util.ArrayList;
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import java.util.List;
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import javax.xml.bind.annotation.XmlAccessType;
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@ -18,20 +19,20 @@ import javax.xml.bind.annotation.XmlRootElement;
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@XmlAccessorType(XmlAccessType.FIELD)
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public class SAIDescriptorJAXB {
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@XmlElement(name = "availableprojectconfigurations")
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private List<AvailableProjectConfigJAXB> availableprojectconfigurations = null;
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@XmlElement(name = "availableprojectconfiguration")
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private List<AvailableProjectConfigJAXB> availableprojectconfiguration = new ArrayList<>();
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public List<AvailableProjectConfigJAXB> getAvailableprojectconfigurations() {
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return availableprojectconfigurations;
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public List<AvailableProjectConfigJAXB> getAvailableprojectconfiguration() {
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return availableprojectconfiguration;
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}
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public void setAvailableprojectconfigurations(List<AvailableProjectConfigJAXB> availableprojectconfigurations) {
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this.availableprojectconfigurations = availableprojectconfigurations;
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public void setAvailableprojectconfiguration(List<AvailableProjectConfigJAXB> availableprojectconfiguration) {
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this.availableprojectconfiguration = availableprojectconfiguration;
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}
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@Override
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public String toString() {
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return "SAIDescriptorJAXB [availableprojectconfigurations=" + availableprojectconfigurations + "]";
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return "SAIDescriptorJAXB [availableprojectconfiguration=" + availableprojectconfiguration + "]";
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}
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}
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@ -0,0 +1,66 @@
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package org.gcube.portlets.user.statisticalalgorithmsimporter;
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import java.io.StringReader;
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import java.io.StringWriter;
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import java.util.ArrayList;
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import java.util.List;
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import javax.xml.bind.JAXBContext;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.AvailableProjectConfigJAXB;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.SAIDescriptorJAXB;
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import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.Constants;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import junit.framework.TestCase;
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/**
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*
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* @author Giancarlo Panichi
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*
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*
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*/
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public class ISResourceTest extends TestCase {
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private static Logger logger = LoggerFactory.getLogger(ISResourceTest.class);
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public void test() {
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if (Constants.TEST_ENABLE) {
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try {
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JAXBContext jaxbContext = JAXBContext.newInstance(SAIDescriptorJAXB.class);
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StringWriter sw = new StringWriter();
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SAIDescriptorJAXB saiDescriptor = new SAIDescriptorJAXB();
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List<AvailableProjectConfigJAXB> list = new ArrayList<>();
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AvailableProjectConfigJAXB a1 = new AvailableProjectConfigJAXB();
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a1.setLanguage("R");
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a1.setSupport("REditor");
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list.add(a1);
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a1 = new AvailableProjectConfigJAXB();
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a1.setLanguage("Linux");
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a1.setSupport("BlackBox");
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list.add(a1);
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a1 = new AvailableProjectConfigJAXB();
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a1.setLanguage("Octave");
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a1.setSupport("BlackBox");
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list.add(a1);
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saiDescriptor.setAvailableprojectconfiguration(list);
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jaxbContext.createMarshaller().marshal(saiDescriptor, sw);
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logger.debug(sw.toString());
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SAIDescriptorJAXB descr = (SAIDescriptorJAXB) jaxbContext.createUnmarshaller()
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.unmarshal(new StringReader(sw.toString()));
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logger.debug("SAIDescriptor: " + descr);
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assertTrue("Success", true);
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} catch (Throwable e) {
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logger.error(e.getLocalizedMessage(), e);
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fail("Error:" + e.getLocalizedMessage());
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}
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} else {
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assertTrue("Success", true);
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}
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}
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}
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@ -11,13 +11,8 @@ package org.gcube.portlets.user.statisticalalgorithmsimporter;
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*
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*
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*/
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public class TestStatAlgoImporter {
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public class StatAlgoImporterTest {
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/**
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* @param args
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*/
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public static void main(String[] args) {
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}
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}
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@ -0,0 +1,20 @@
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# A default log4j configuration for log4j users.
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#
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# To use this configuration, deploy it into your application's WEB-INF/classes
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# directory. You are also encouraged to edit it as you like.
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log4j.rootLogger=DEBUG, stdout, rollingFile
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# Redirect log messages to console
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log4j.appender.stdout=org.apache.log4j.ConsoleAppender
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log4j.appender.stdout.Target=System.out
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log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
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log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
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log4j.appender.rollingFile=org.apache.log4j.RollingFileAppender
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log4j.appender.rollingFile.File=test.log
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log4j.appender.rollingFile.MaxFileSize=20MB
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log4j.appender.rollingFile.MaxBackupIndex=2
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log4j.appender.rollingFile.layout = org.apache.log4j.PatternLayout
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log4j.appender.rollingFile.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
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@ -0,0 +1,33 @@
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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>
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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>
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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
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java.lang.ClassCastException: org.gcube.portlets.user.statisticalalgorithmsimporter.server.is.SAIDescriptorJAXB cannot be cast to org.gcube.portlets.user.statisticalalgorithmsimporter.shared.descriptor.SAIDescriptor
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at org.gcube.portlets.user.statisticalalgorithmsimporter.ISResourceTest.test(ISResourceTest.java:50)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
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at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
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at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
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at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
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at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
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at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
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at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
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at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
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at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
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at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
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at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
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at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
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at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
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at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
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at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:459)
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at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:678)
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at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:382)
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at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:192)
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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>
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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]]]
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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>
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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]]]
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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>
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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]]]
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