1452: Implement a GUI for StatMan Algorithms Importer

Task-Url: https://support.d4science.org/issues/1452

Added Annotation Parser

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122702 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -302,6 +302,25 @@
 			<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
 		</dependency>
 
+		<!-- 52n-wps-client -->
+		<dependency>
+			<groupId>org.n52.wps</groupId>
+			<artifactId>52n-wps-client-lib</artifactId>
+			<version>3.2.0</version>
+			<exclusions>
+				<exclusion>
+					<artifactId>gt-opengis</artifactId>
+					<groupId>org.geotools</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.n52.wps</groupId>
+			<artifactId>52n-wps-r</artifactId>
+			<version>(0.0.1,5.0.0)</version>
+		</dependency>
+
+
 
 		<!-- LOGGING -->
 		<dependency>
@@ -515,7 +534,21 @@
 		</plugins>
 
 	</build>
+	<repositories>
+		<repository>
+			<id>n52-releases</id>
+			<name>52n Releases</name>
+			<url>http://52north.org/maven/repo/releases/</url>
+			<releases>
+				<enabled>true</enabled>
+			</releases>
+			<snapshots>
+				<enabled>true</enabled>
+			</snapshots>
+		</repository>
+	</repositories>
 
+	
 	<dependencyManagement>
 		<dependencies>
 			<dependency>

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/project/ProjectManager.java

@@ -14,7 +14,6 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.client.type.Session
 import org.gcube.portlets.user.statisticalalgorithmsimporter.client.utils.UtilsGXT3;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterSessionExpiredException;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.InputData;
-import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.MainCode;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.ProjectFolder;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.ItemDescription;
@@ -403,7 +402,7 @@ public class ProjectManager {
 
 		Log.debug("Set Main Code: " + itemDescription);
 		StatAlgoImporterServiceAsync.INSTANCE.setMainCode(itemDescription,
-				new AsyncCallback<Void>() {
+				new AsyncCallback<Project>() {
 
 					@Override
 					public void onFailure(Throwable caught) {
@@ -421,8 +420,8 @@ public class ProjectManager {
 					}
 
 					@Override
-					public void onSuccess(Void result) {
-						project.setMainCode(new MainCode(itemDescription));
+					public void onSuccess(Project result) {
+						project=result;
 						fireProjectStatusMainCodeSetEvent();
 					}
 				});
@@ -433,7 +432,7 @@ public class ProjectManager {
 			final StatAlgoImporterMonitor monitor) {
 		StatAlgoImporterServiceAsync.INSTANCE.setNewMainCode(
 				newMainCodeEvent.getFile(), newMainCodeEvent.getCode(),
-				new AsyncCallback<ItemDescription>() {
+				new AsyncCallback<Project>() {
 
 					@Override
 					public void onFailure(Throwable caught) {
@@ -452,8 +451,8 @@ public class ProjectManager {
 					}
 
 					@Override
-					public void onSuccess(ItemDescription itemDescription) {
-						project.setMainCode(new MainCode(itemDescription));
+					public void onSuccess(Project result) {
+						project=result;
 						fireProjectStatusMainCodeSetEvent();
 						monitor.hide();
 					}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/rpc/StatAlgoImporterService.java

@@ -47,7 +47,7 @@ public interface StatAlgoImporterService extends RemoteService {
 			throws StatAlgoImporterServiceException;
 
 	//
-	public void setMainCode(ItemDescription itemDescription)
+	public Project setMainCode(ItemDescription itemDescription)
 			throws StatAlgoImporterServiceException;
 
 	public void addResourceToProject(ItemDescription itemDescription)
@@ -73,7 +73,7 @@ public interface StatAlgoImporterService extends RemoteService {
 	public Project restoreUISession(String value)
 			throws StatAlgoImporterServiceException;
 
-	public ItemDescription setNewMainCode(ItemDescription itemDescription,
+	public Project setNewMainCode(ItemDescription itemDescription,
 			String code) throws StatAlgoImporterServiceException;
 
 	public void publishSoftware() throws StatAlgoImporterServiceException;

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/rpc/StatAlgoImporterServiceAsync.java

@@ -39,7 +39,8 @@ public interface StatAlgoImporterServiceAsync {
 	void createProjectOnWorkspace(ItemDescription itemDescription,
 			AsyncCallback<Void> callback);
 	
-	void setMainCode(ItemDescription itemDescription, AsyncCallback<Void> callback);
+	void setMainCode(ItemDescription itemDescription,
+			AsyncCallback<Project> callback);
 
 	void addResourceToProject(ItemDescription itemDescription,
 			AsyncCallback<Void> asyncCallback);
@@ -55,7 +56,8 @@ public interface StatAlgoImporterServiceAsync {
 
 	void saveCode(String code, AsyncCallback<Void> asyncCallback);
 	
-	void setNewMainCode(ItemDescription itemDescription, String code, AsyncCallback<ItemDescription> asyncCallback);
+	void setNewMainCode(ItemDescription itemDescription, String code,
+			AsyncCallback<Project> asyncCallback);
 
 	void createSoftware(InputData inputData, AsyncCallback<Void> callback);
 

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/GlobalVariablesPanel.java

@@ -429,7 +429,7 @@ public class GlobalVariablesPanel extends ContentPanel {
 		return listGlobalVarialbles;
 	}
 
-	public void setMainCode(Project project) {
+	public void clearVariables(Project project) {
 		storeGlobalVariable.clear();
 		storeGlobalVariable.commitChanges();
 		seq = 0;

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/InputOutputVariablesPanel.java

@@ -485,7 +485,7 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		return listInputOutputVarialbles;
 	}
 
-	public void setMainCode(Project project) {
+	public void clearVariables(Project project) {
 		storeInputOutputVariables.clear();
 		storeInputOutputVariables.commitChanges();
 		seq = 0;

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/InputVariableTabPanel.java

@@ -77,9 +77,10 @@ public class InputVariableTabPanel extends TabPanel {
 	//
 	public void setMainCode(Project project) {
 		try {
-			globalVariablesPanel.setMainCode(project);
-			inputOutputVariablesPanel.setMainCode(project);
-
+			globalVariablesPanel.update(project);
+			inputOutputVariablesPanel.update(project);
+			projectInfoPanel.update(project);
+			interpreterInfoPanel.update(project);
 			forceLayout();
 		} catch (Throwable e) {
 			Log.error("Error in InputVariableTabPanel: "

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/tools/input/InterpreterInfoPanel.java

@@ -391,10 +391,14 @@ public class InterpreterInfoPanel extends ContentPanel {
 				seq = project.getInputData().getInterpreterInfo()
 						.getInterpreterPackagesInfo().size();
 			} else {
+				storeInterpreterPackageInfo.clear();
+				storeInterpreterPackageInfo.commitChanges();
 				seq = 0;
 			}
 		} else {
 			interpreterVersion.clear();
+			storeInterpreterPackageInfo.clear();
+			storeInterpreterPackageInfo.commitChanges();
 			seq = 0;
 		}
 

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/StatAlgoImporterServiceImpl.java

@@ -11,6 +11,7 @@ import javax.servlet.http.HttpSession;
 import org.apache.commons.io.IOUtils;
 import org.gcube.application.framework.core.session.ASLSession;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.client.rpc.StatAlgoImporterService;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation.WPS4RParser;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.file.CodeReader;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.generator.ProjectBuilder;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.server.social.AlgorithmNotification;
@@ -260,21 +261,25 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 	}
 
 	@Override
-	public void setMainCode(ItemDescription itemDescription)
+	public Project setMainCode(ItemDescription itemDescription)
 			throws StatAlgoImporterServiceException {
 		try {
 			HttpSession session = this.getThreadLocalRequest().getSession();
-			SessionUtil.getAslSession(session);
+			ASLSession aslSession=SessionUtil.getAslSession(session);
 			logger.debug("SetMainCode()");
 			Project project = SessionUtil.getProjectSession(session);
 			if (project != null) {
 				project.setMainCode(new MainCode(itemDescription));
+				project.setInputData(null);
+				project.setProjectTarget(null);
+				WPS4RParser wps4Parser=new WPS4RParser(project, aslSession);
+				project=wps4Parser.parse();
 				SessionUtil.setProjectSession(session, project);
 			} else {
 				throw new StatAlgoImporterServiceException("No project open!");
 			}
 
-			return;
+			return project;
 		} catch (StatAlgoImporterServiceException e) {
 			e.printStackTrace();
 			throw e;
@@ -498,7 +503,7 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 	}
 
 	@Override
-	public ItemDescription setNewMainCode(ItemDescription fileDescription,
+	public Project setNewMainCode(ItemDescription fileDescription,
 			String code) throws StatAlgoImporterServiceException {
 		try {
 			HttpSession session = this.getThreadLocalRequest().getSession();
@@ -513,8 +518,12 @@ public class StatAlgoImporterServiceImpl extends RemoteServiceServlet implements
 						aslSession, fileDescription, code, project);
 				MainCode mainCode = new MainCode(mainCodeItemDescription);
 				project.setMainCode(mainCode);
+				project.setInputData(null);
+				project.setProjectTarget(null);
+				WPS4RParser wps4Parser=new WPS4RParser(project, aslSession);
+				project=wps4Parser.parse();
 				SessionUtil.setProjectSession(session, project);
-				return mainCodeItemDescription;
+				return project;
 			} else {
 				throw new StatAlgoImporterServiceException("No project open!");
 			}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/annotation/WPS4RParser.java

@@ -0,0 +1,174 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.gcube.application.framework.core.session.ASLSession;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.server.storage.FilesStorage;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.DataType;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.IOType;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.InputOutputVariables;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.ProjectInfo;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.InputData;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.ItemDescription;
+import org.n52.wps.server.r.R_Config;
+import org.n52.wps.server.r.metadata.RAnnotationParser;
+import org.n52.wps.server.r.syntax.RAnnotation;
+import org.n52.wps.server.r.syntax.RAnnotationType;
+import org.n52.wps.server.r.syntax.RAttribute;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * 
+ * @author Giancarlo Panichi email: <a
+ *         href="mailto:g.panichi@isti.cnr.it">g.panichi@isti.cnr.it</a>
+ *
+ */
+public class WPS4RParser {
+	
+	public static final Logger logger = LoggerFactory
+			.getLogger(WPS4RParser.class);
+
+	
+	private Project project;
+	private ASLSession aslSession;
+
+	public WPS4RParser(Project project, ASLSession aslSession) {
+		this.project = project;
+		this.aslSession = aslSession;
+	}
+
+	public Project parse() throws StatAlgoImporterServiceException {
+		ItemDescription mainCode = project.getMainCode().getItemDescription();
+		FilesStorage fileStorage = new FilesStorage();
+		InputStream is = fileStorage.retrieveItemOnWorkspace(
+				aslSession.getUsername(), mainCode.getId());
+
+		R_Config config = R_Config.getInstance();
+
+		List<RAnnotation> annotations;
+		try {
+			RAnnotationParser parser = new RAnnotationParser(config);
+			annotations = parser.parseAnnotationsfromScript(is);
+		} catch (Throwable e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+		} finally {
+			try {
+				is.close();
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
+
+		WPSAlgorithmInfo wpsAlgorithmInfo = mapAnnotations(annotations);
+		logger.debug("wpsAlgorithmInfo: "+wpsAlgorithmInfo);
+		if (wpsAlgorithmInfo.getAlgorithmName() == null)
+			return project;
+		else
+			return mapToProject(wpsAlgorithmInfo);
+
+	}
+
+	private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo) throws StatAlgoImporterServiceException {
+		if(project==null){
+			throw new StatAlgoImporterServiceException("Open project before!");
+		}
+		
+		if(project.getInputData()==null){
+			ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
+			InputData inputData=new InputData(projectInfo, null, null, wpsAlgorithmInfo.getInputOutputVariables());
+			project.setInputData(inputData);
+		} else {
+			InputData inputData=project.getInputData();
+			ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
+			inputData.setProjectInfo(projectInfo);
+			inputData.setListInputOutputVariables(wpsAlgorithmInfo.getInputOutputVariables());	
+			inputData.setListGlobalVariables(null);
+		}
+		return project;
+		
+	}
+
+	private WPSAlgorithmInfo mapAnnotations(List<RAnnotation> annotations)
+			throws StatAlgoImporterServiceException {
+		try {
+
+			WPSAlgorithmInfo wpsAlgorithmInfo = new WPSAlgorithmInfo();
+			ArrayList<InputOutputVariables> inputOutputVariables = new ArrayList<>();
+			int index=1;
+			for (RAnnotation rAnnotation : annotations) {
+				if (rAnnotation.getType().equals(RAnnotationType.DESCRIPTION)) {
+					wpsAlgorithmInfo.setVersion(rAnnotation
+							.getStringValue(RAttribute.VERSION));
+					wpsAlgorithmInfo.setDescription(rAnnotation
+							.getStringValue(RAttribute.ABSTRACT));
+					wpsAlgorithmInfo.setAlgorithmName(rAnnotation
+							.getStringValue(RAttribute.TITLE));
+					wpsAlgorithmInfo.setVersion(rAnnotation
+							.getStringValue(RAttribute.VERSION));
+				} else if (rAnnotation.getType().equals(RAnnotationType.OUTPUT)
+						|| rAnnotation.getType().equals(RAnnotationType.INPUT)) {
+					// output, text, Random number list,
+
+					String type = rAnnotation.getStringValue(RAttribute.TYPE);
+					String name = rAnnotation
+							.getStringValue(RAttribute.IDENTIFIER);
+					String description = rAnnotation
+							.getStringValue(RAttribute.TITLE);
+					String defaultValue = rAnnotation
+							.getStringValue(RAttribute.DEFAULT_VALUE);
+					if (type == null)
+						type = "string";
+					if (name == null)
+						name = "";
+					if (description == null)
+						description = "";
+					if (defaultValue == null)
+						defaultValue = "";
+
+					IOType ioType = IOType.INPUT;
+
+					if (rAnnotation.getType().equals(RAnnotationType.OUTPUT))
+						ioType = IOType.OUTPUT;
+
+					DataType dataType = WPStype2DataType(type);
+					if (defaultValue != null && defaultValue.contains("|")
+							&& dataType == DataType.STRING)
+						dataType = DataType.ENUMERATED;
+
+					InputOutputVariables ioVariable = new InputOutputVariables(
+							index, name, description, defaultValue, dataType, ioType,
+							"");
+					inputOutputVariables.add(ioVariable);
+					index++;
+				}
+			}
+			wpsAlgorithmInfo.setInputOutputVariables(inputOutputVariables);
+			return wpsAlgorithmInfo;
+
+		} catch (Throwable e) {
+			e.printStackTrace();
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+		}
+	}
+
+	private static DataType WPStype2DataType(String type) {
+		if (type.equalsIgnoreCase("double"))
+			return DataType.DOUBLE;
+		else if (type.equalsIgnoreCase("integer"))
+			return DataType.INTEGER;
+		else if (type.equalsIgnoreCase("string"))
+			return DataType.STRING;
+		else if (type.equalsIgnoreCase("boolean"))
+			return DataType.BOOLEAN;
+		else
+			return DataType.FILE;
+	}
+}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/annotation/WPSAlgorithmInfo.java

@@ -0,0 +1,77 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.InputOutputVariables;
+
+/**
+ * 
+ * @author Giancarlo Panichi email: <a
+ *         href="mailto:g.panichi@isti.cnr.it">g.panichi@isti.cnr.it</a>
+ *
+ */
+public class WPSAlgorithmInfo implements Serializable {
+
+	private static final long serialVersionUID = 6333710590825979561L;
+	private String description;
+	private String algorithmName;
+	private String version;
+	private ArrayList<InputOutputVariables> inputOutputVariables;
+
+	public WPSAlgorithmInfo() {
+		super();
+	}
+
+	public WPSAlgorithmInfo(String description, String algorithmName,
+			String version, ArrayList<InputOutputVariables> inputOutputVariables) {
+		super();
+		this.description = description;
+		this.algorithmName = algorithmName;
+		this.version = version;
+		this.inputOutputVariables = inputOutputVariables;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public String getAlgorithmName() {
+		return algorithmName;
+	}
+
+	public void setAlgorithmName(String algorithmName) {
+		this.algorithmName = algorithmName;
+	}
+
+	public String getVersion() {
+		return version;
+	}
+
+	public void setVersion(String version) {
+		this.version = version;
+	}
+
+	public ArrayList<InputOutputVariables> getInputOutputVariables() {
+		return inputOutputVariables;
+	}
+
+	public void setInputOutputVariables(
+			ArrayList<InputOutputVariables> inputOutputVariables) {
+		this.inputOutputVariables = inputOutputVariables;
+	}
+
+	@Override
+	public String toString() {
+		return "WPSAlgorithmInfo [description=" + description
+				+ ", algorithmName=" + algorithmName + ", version=" + version
+				+ ", inputOutputVariables=" + inputOutputVariables + "]";
+	}
+
+	
+
+}