1452: Implement a GUI for StatMan Algorithms Importer

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

Updated Code Generator

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122182 82a268e6-3cf1-43bd-a215-b396298e98cf

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

@@ -1,16 +1,20 @@
 package org.gcube.portlets.user.statisticalalgorithmsimporter.server.generator;
 
-import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
 import java.util.Arrays;
 import java.util.List;
 
-import org.apache.commons.io.IOUtils;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.exception.StatAlgoImporterServiceException;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.EnvironmentVariables;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.IOType;
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.input.SelectedRowsVariables;
 import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Project;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * 
@@ -21,6 +25,9 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project.Proj
 public class AlgorithmGenerator {
 
 	private static final String EXTENTION_JAVA = ".java";
+	public static final Logger logger = LoggerFactory
+			.getLogger(AlgorithmGenerator.class);
+
 	private Project project;
 
 	public AlgorithmGenerator(Project project) {
@@ -33,23 +40,240 @@ public class AlgorithmGenerator {
 		return "AlgorithmGenerator [project=" + project + "]";
 	}
 
-	public File createAlgorithm() throws StatAlgoImporterServiceException {
+	public Path createAlgorithm() throws StatAlgoImporterServiceException,
+			IOException {
+
 		try {
-			File fileTmp = File.createTempFile(project.getClassName(),
+			Path tempFile = Files.createTempFile(project.getClassName(),
 					EXTENTION_JAVA);
-			fileTmp.deleteOnExit();
+
-			/*
+			List<String> lines = createJavaCode();
-			List<String> lines = Arrays.asList("The first line", "The second line");
+			Files.write(tempFile, lines, Charset.defaultCharset(),
-			Path file = Paths.g;
+					StandardOpenOption.WRITE);
-			Files.write(file, lines, Charset.forName("UTF-8"));
+			logger.debug(tempFile.toString());
-			 */
+			return tempFile;
-			return fileTmp;
 
 		} catch (IOException e) {
+			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();
-			throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
+			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
+					e);
 		}
 
 	}
 
+	private List<String> createJavaCode() {
+		String mainScriptRelativePath = retrieveMainScriptRelativePath();
+		String packageUrl = retrievePackageUrl();
+
+		List<String> code = Arrays
+				.asList("package org.gcube.dataanalysis.executor.rscripts;",
+						"",
+						"import java.io.File;",
+						"import java.util.ArrayList;",
+						"import java.util.LinkedHashMap;",
+						"import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;",
+						"import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;",
+						"import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;",
+						"import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;",
+						"", "public class " + project.getClassName()
+								+ " extends GenericRScript {", "",
+
+						"	public static enum operators {",
+						"		EQUAL, NOT_EQUAL, CONTAINS, BEGINS_WITH, ENDS_WITH",
+						"	};",
+
+						"	@Override", "	public String getDescription() {",
+						"		return \"" + project.getDescription() + "\";", "	}",
+						"", "	protected void initVariables(){",
+						"		mainScriptName=\"" + mainScriptRelativePath + "\";",
+						"		packageURL=\"" + packageUrl + "\";",
+						"   	environmentalvariables = new ArrayList<String>();");
+
+		for (EnvironmentVariables envVariable : project.getInputData()
+				.getListEnvironmentVariables()) {
+			code.add("		environmentalvariables.add(\"" + envVariable.getName()
+					+ "\")");
+		}
+
+		for (SelectedRowsVariables selVariable : project.getInputData()
+				.getListSelectedRows()) {
+			switch (selVariable.getIoType()) {
+			case INPUT:
+				code.add("		inputvariables.add(\"" + selVariable.getName()
+						+ "\")");
+				break;
+			case OUTPUT:
+				code.add("		outputvariables.add(\"" + selVariable.getName()
+						+ "\")");
+				break;
+			default:
+				break;
+
+			}
+		}
+
+		code.add("	}");
+		code.add("	@Override");
+		code.add("	protected void setInputParameters() {");
+		createInputParameters(code);
+
+		code.add("	}");
+		code.add("	@Override");
+		code.add("	public StatisticalType getOutput() {");
+		createOutputParameters(code);
+		code.add("		PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, \"Output\", \"\");");
+		code.add("		return o;");
+		code.add("	}");
+		code.add("}");
+		return code;
+	}
+
+	private void createInputParameters(List<String> code) {
+
+		for (SelectedRowsVariables selVariable : project.getInputData()
+				.getListSelectedRows()) {
+			if (selVariable.getIoType().compareTo(IOType.INPUT) == 0) {
+				switch (selVariable.getDataType()) {
+				case BOOLEAN:
+					code.add("		inputs.add(new PrimitiveType(Boolean.class.getName(), null,PrimitiveTypes.BOOLEAN, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+					break;
+				case DOUBLE:
+					code.add("		inputs.add(new PrimitiveType(Double.class.getName(), null,PrimitiveTypes.NUMBER, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+					break;
+				case ENUMERATED:
+					code.add("		inputs.add(new PrimitiveType(Enum.class.getName(), operators.values(),PrimitiveTypes.ENUMERATED, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+					break;
+				case FILE:
+					code.add("		inputs.add(new PrimitiveType(File.class.getName(), null,PrimitiveTypes.FILE, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+
+					break;
+				case INTEGER:
+					code.add("		inputs.add(new PrimitiveType(Integer.class.getName(), null,PrimitiveTypes.NUMBER, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+					break;
+				case STRING:
+					code.add("		inputs.add(new PrimitiveType(String.class.getName(), null,PrimitiveTypes.STRING, \""
+							+ selVariable.getName()
+							+ "\", \""
+							+ selVariable.getDescription()
+							+ "\", \""
+							+ selVariable.getDefaultValue() + "\"));");
+
+					break;
+				default:
+					break;
+
+				}
+
+			}
+		}
+
+	}
+
+	/*
+	 * PrimitiveTypes
+	 * 
+	 * STRING, NUMBER, ENUMERATED, CONSTANT, RANDOM, FILE, MAP, BOOLEAN, IMAGES
+	 */
+
+	private void createOutputParameters(List<String> code) {
+		for (SelectedRowsVariables selVariable : project.getInputData()
+				.getListSelectedRows()) {
+			if (selVariable.getIoType().compareTo(IOType.OUTPUT) == 0) {
+				switch (selVariable.getDataType()) {
+				case BOOLEAN:
+					code.add("		output.put(\""
+							+ selVariable.getName()
+							+ "\",new PrimitiveType(Boolean.class.getName(), new File(outputValues.get(\""
+							+ selVariable.getName()
+							+ "\")), PrimitiveTypes.BOOLEAN, \""
+							+ selVariable.getName() + "\", \""
+							+ selVariable.getName() + "\"));");
+					break;
+				case DOUBLE:
+					code.add("		output.put(\""
+							+ selVariable.getName()
+							+ "\",new PrimitiveType(Double.class.getName(), new File(outputValues.get(\""
+							+ selVariable.getName()
+							+ "\")), PrimitiveTypes.NUMBER, \""
+							+ selVariable.getName() + "\", \""
+							+ selVariable.getName() + "\"));");
+					break;
+				case ENUMERATED:
+					break;
+				case FILE:
+					code.add("		output.put(\""
+							+ selVariable.getName()
+							+ "\",new PrimitiveType(File.class.getName(), new File(outputValues.get(\""
+							+ selVariable.getName()
+							+ "\")), PrimitiveTypes.FILE, \""
+							+ selVariable.getName() + "\", \""
+							+ selVariable.getName() + "\"));");
+
+					break;
+				case INTEGER:
+					code.add("		output.put(\""
+							+ selVariable.getName()
+							+ "\",new PrimitiveType(Integer.class.getName(), new File(outputValues.get(\""
+							+ selVariable.getName()
+							+ "\")), PrimitiveTypes.NUMBER, \""
+							+ selVariable.getName() + "\", \""
+							+ selVariable.getName() + "\"));");
+					break;
+				case STRING:
+					code.add("		output.put(\""
+							+ selVariable.getName()
+							+ "\",new PrimitiveType(String.class.getName(), new File(outputValues.get(\""
+							+ selVariable.getName()
+							+ "\")), PrimitiveTypes.STRING, \""
+							+ selVariable.getName() + "\", \""
+							+ selVariable.getName() + "\"));");
+
+					break;
+				default:
+					break;
+
+				}
+
+			}
+		}
+	}
+
+	private String retrieveMainScriptRelativePath() {
+		String projectPath = project.getProjectFolder().getItemDescription()
+				.getPath();
+		String mainCodePath = project.getMainCode().getItemDescription()
+				.getPath();
+		return mainCodePath.substring(projectPath.length());
+	}
+
+	private String retrievePackageUrl() {
+		return project.getProjectTarget().getPackageUrl().getPublicLink();
+	}
+
 }

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/shared/project/Project.java

@@ -9,8 +9,7 @@ import java.io.Serializable;
  *
  */
 public class Project implements Serializable {
-
+	
-
 	private static final long serialVersionUID = -7906477664944910362L;
 
 	private String name;
@@ -19,6 +18,7 @@ public class Project implements Serializable {
 	private ProjectFolder projectFolder;
 	private MainCode mainCode;
 	private InputData inputData;
+	private ProjectTarget projectTarget;
 
 	public Project() {
 		super();
@@ -78,13 +78,25 @@ public class Project implements Serializable {
 		this.inputData = inputData;
 	}
 
+	public ProjectTarget getProjectTarget() {
+		return projectTarget;
+	}
+
+	public void setProjectTarget(ProjectTarget projectTarget) {
+		this.projectTarget = projectTarget;
+	}
+
 	@Override
 	public String toString() {
 		return "Project [name=" + name + ", description=" + description
 				+ ", className=" + className + ", projectFolder="
 				+ projectFolder + ", mainCode=" + mainCode + ", inputData="
-				+ inputData + "]";
+				+ inputData + ", projectTarget=" + projectTarget + "]";
 	}
 
+	
+	
+
+	
 
 }

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/shared/project/ProjectTarget.java

@@ -0,0 +1,54 @@
+package org.gcube.portlets.user.statisticalalgorithmsimporter.shared.project;
+
+import java.io.Serializable;
+
+import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.ItemDescription;
+
+/**
+ * 
+ * @author Giancarlo Panichi email: <a
+ *         href="mailto:g.panichi@isti.cnr.it">g.panichi@isti.cnr.it</a>
+ *
+ */
+public class ProjectTarget implements Serializable {
+
+	private static final long serialVersionUID = 480665662744105383L;
+	private ItemDescription packageUrl;
+	private ItemDescription codeSource;
+	private ItemDescription codeJar;
+
+	public ProjectTarget() {
+		super();
+	}
+
+	public ItemDescription getPackageUrl() {
+		return packageUrl;
+	}
+
+	public void setPackageUrl(ItemDescription packageUrl) {
+		this.packageUrl = packageUrl;
+	}
+
+	public ItemDescription getCodeSource() {
+		return codeSource;
+	}
+
+	public void setCodeSource(ItemDescription codeSource) {
+		this.codeSource = codeSource;
+	}
+
+	public ItemDescription getCodeJar() {
+		return codeJar;
+	}
+
+	public void setCodeJar(ItemDescription codeJar) {
+		this.codeJar = codeJar;
+	}
+
+	@Override
+	public String toString() {
+		return "ProjectTarget [packageUrl=" + packageUrl + ", codeSource="
+				+ codeSource + ", codeJar=" + codeJar + "]";
+	}
+
+}

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/shared/workspace/ItemDescription.java

@@ -17,6 +17,7 @@ public class ItemDescription implements Serializable {
 	private String owner;
 	private String path;
 	private String type;
+	private String publicLink;
 	
 	public ItemDescription(){
 		super();
@@ -71,13 +72,26 @@ public class ItemDescription implements Serializable {
 	public void setType(String type) {
 		this.type = type;
 	}
+	
+	public String getPublicLink() {
+		return publicLink;
+	}
+
+	public void setPublicLink(String publicLink) {
+		this.publicLink = publicLink;
+	}
 
 	@Override
 	public String toString() {
 		return "ItemDescription [id=" + id + ", name=" + name + ", owner="
-				+ owner + ", path=" + path + ", type=" + type + "]";
+				+ owner + ", path=" + path + ", type=" + type + ", publicLink="
+				+ publicLink + "]";
 	}
+	
+	
+	
 
 	
 	
+	
 }

src/test/resources/org/gcube/portlets/user/statisticalalgorithmsimporter/example/FileTemplate.java

@@ -3,7 +3,7 @@ package org.gcube.dataanalysis.executor.rscripts;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
- 
+
 import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
 import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
 import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
@@ -11,6 +11,11 @@ import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;
  
 public class KnitrCompiler extends GenericRScript {
  
+	public static enum operators {
+		EQUAL, NOT_EQUAL, CONTAINS, BEGINS_WITH, ENDS_WITH
+	};
+	
+	
 	@Override
 	public String getDescription() {
 		return "An algorithm to compile Knitr documents. Developed by IRD (reference Julien Bard, julien.barde@ird.fr)";
@@ -28,6 +33,8 @@ public class KnitrCompiler extends GenericRScript {
  
 	@Override
 	protected void setInputParameters() {
+		
+		inputs.add(new PrimitiveType(Enum.class.getName(), operators.values(), PrimitiveTypes.ENUMERATED, name, description, defaultvalue));
 		inputs.add(new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "zipfile", "The file containing R and the markdown (Rnw) files to compile","knitr_wfs.zip"));
 		inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "file.inout", "The name of the R file in the zip package", "main.r"));
 	}