1452: Implement a GUI for StatMan Algorithms Importer

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

Fixed parser on input files

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122461 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/client/codeparser/CodeParser.java

@@ -16,7 +16,7 @@ import com.google.gwt.regexp.shared.RegExp;
 public class CodeParser {
 
 	private static final String IMAGE_PATTERN = "([^\\s]+(\\.(jpg|png|gif|bmp)\"))";
-	private static final String FILE_PATTERN = "([^\\s]+(\\.(txt|csv|pdf|doc)\"))";
+	private static final String FILE_PATTERN = "([^\\s]+(\\.(txt|csv|pdf|doc|zip|bin|dat|mat|java|m|exe|sh|tar|gz|r)\"))";
 	private static final String ENUM1_PATTERN = "(c\\([^\\)]*\\))";
 	private static final String ENUM2_PATTERN = "(\\{[^\\}]*\\})";
 
@@ -33,7 +33,7 @@ public class CodeParser {
 
 		if (parameter.contains("<-")) {
 			String[] varDescription = parameter.split("<-");
-			String checkDataTypeValue=varDescription[1].trim();
+			String checkDataTypeValue = varDescription[1].trim();
 			if (checkDataTypeValue.endsWith(";"))
 				checkDataTypeValue = checkDataTypeValue.substring(0,
 						checkDataTypeValue.length() - 1);
@@ -49,12 +49,12 @@ public class CodeParser {
 
 			selectedRowsVariables = new InputOutputVariables(
 					varDescription[0].trim(), varDescription[0].trim(),
-					defaultValue, checkDataType(checkDataTypeValue),
+					defaultValue, checkDataType(checkDataTypeValue), ioType,
-					ioType, parameter);
+					parameter);
 		} else {
 			if (parameter.contains("=")) {
 				String[] varDescription = parameter.split("=");
-				String checkDataTypeValue=varDescription[1].trim();
+				String checkDataTypeValue = varDescription[1].trim();
 				if (checkDataTypeValue.endsWith(";"))
 					checkDataTypeValue = checkDataTypeValue.substring(0,
 							checkDataTypeValue.length() - 1);

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

@@ -42,6 +42,7 @@ import com.sencha.gxt.widget.core.client.event.SelectEvent;
 import com.sencha.gxt.widget.core.client.event.SelectEvent.SelectHandler;
 import com.sencha.gxt.widget.core.client.form.ComboBox;
 import com.sencha.gxt.widget.core.client.form.TextField;
+import com.sencha.gxt.widget.core.client.form.validator.RegExValidator;
 import com.sencha.gxt.widget.core.client.grid.ColumnConfig;
 import com.sencha.gxt.widget.core.client.grid.ColumnModel;
 import com.sencha.gxt.widget.core.client.grid.Grid;
@@ -191,15 +192,26 @@ public class GlobalVariablesPanel extends ContentPanel {
 		comboInputType.setTriggerAction(TriggerAction.ALL);
 		addHandlersForComboInputType(inputTypePropertiesCombo.label());
 		
+		//
+		TextField nameColumnEditing = new TextField();
+		nameColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField descriptionColumnEditing = new TextField();
+		descriptionColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField defaultValueColumnEditing = new TextField();
+		defaultValueColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		
 		gridGlobalVariableEditing = new GridRowEditing<GlobalVariables>(
 				gridGlobalVariable);
-		gridGlobalVariableEditing.addEditor(nameColumn, new TextField());
+		gridGlobalVariableEditing.addEditor(nameColumn, nameColumnEditing);
 		gridGlobalVariableEditing.addEditor(descriptionColumn,
-				new TextField());
+				descriptionColumnEditing);
 		gridGlobalVariableEditing.addEditor(inputTypeColumn,
 				comboInputType);
 		gridGlobalVariableEditing.addEditor(defaultValueColumn,
-				new TextField());
+				defaultValueColumnEditing);
 
 		btnAdd = new TextButton("Add");
 		btnAdd.setIcon(StatAlgoImporterResources.INSTANCE.add16());

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

@@ -41,6 +41,7 @@ import com.sencha.gxt.widget.core.client.event.SelectEvent;
 import com.sencha.gxt.widget.core.client.event.SelectEvent.SelectHandler;
 import com.sencha.gxt.widget.core.client.form.ComboBox;
 import com.sencha.gxt.widget.core.client.form.TextField;
+import com.sencha.gxt.widget.core.client.form.validator.RegExValidator;
 import com.sencha.gxt.widget.core.client.grid.ColumnConfig;
 import com.sencha.gxt.widget.core.client.grid.ColumnModel;
 import com.sencha.gxt.widget.core.client.grid.Grid;
@@ -163,12 +164,14 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		ColumnModel<InputOutputVariables> columns = new ColumnModel<InputOutputVariables>(
 				l);
 
-		storeInputOutputVariables = new ListStore<InputOutputVariables>(props.id());
+		storeInputOutputVariables = new ListStore<InputOutputVariables>(
+				props.id());
 
 		/*
-		 * ArrayList<InputOutputVariablesVariables> list = new ArrayList<>(); for (int i
+		 * ArrayList<InputOutputVariablesVariables> list = new ArrayList<>();
-		 * = 0; i < 10; i++) { list.add(new InputOutputVariablesVariables(i, "Test" + i,
+		 * for (int i = 0; i < 10; i++) { list.add(new
-		 * "Desc", "defaultValue", InputType.STRING)); }
+		 * InputOutputVariablesVariables(i, "Test" + i, "Desc", "defaultValue",
+		 * InputType.STRING)); }
 		 * 
 		 * storeEnvironmentVariable.addAll(list);
 		 */
@@ -182,8 +185,8 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		final GridSelectionModel<InputOutputVariables> sm = new GridSelectionModel<InputOutputVariables>();
 		sm.setSelectionMode(SelectionMode.SINGLE);
 
-		gridInputOutputVariables = new Grid<InputOutputVariables>(storeInputOutputVariables,
+		gridInputOutputVariables = new Grid<InputOutputVariables>(
-				columns);
+				storeInputOutputVariables, columns);
 		gridInputOutputVariables.setSelectionModel(sm);
 		gridInputOutputVariables.getView().setStripeRows(true);
 		gridInputOutputVariables.getView().setColumnLines(true);
@@ -194,18 +197,21 @@ public class InputOutputVariablesPanel extends ContentPanel {
 
 		/*
 		 * GridDragSource<InputOutputVariablesVariables> ds = new
-		 * GridDragSource<InputOutputVariablesVariables>( gridEnvironmentVariable);
+		 * GridDragSource<InputOutputVariablesVariables>(
-		 * ds.addDragStartHandler(new DndDragStartHandler() {
+		 * gridEnvironmentVariable); ds.addDragStartHandler(new
+		 * DndDragStartHandler() {
 		 * 
 		 * @Override public void onDragStart(DndDragStartEvent event) {
 		 * 
-		 * @SuppressWarnings("unchecked") ArrayList<InputOutputVariablesVariables>
+		 * @SuppressWarnings("unchecked")
-		 * draggingSelection = (ArrayList<InputOutputVariablesVariables>) event
+		 * ArrayList<InputOutputVariablesVariables> draggingSelection =
-		 * .getData(); Log.debug("Start Drag: " + draggingSelection);
+		 * (ArrayList<InputOutputVariablesVariables>) event .getData();
+		 * Log.debug("Start Drag: " + draggingSelection);
 		 * 
 		 * } }); GridDropTarget<InputOutputVariablesVariables> dt = new
-		 * GridDropTarget<InputOutputVariablesVariables>( gridEnvironmentVariable);
+		 * GridDropTarget<InputOutputVariablesVariables>(
-		 * dt.setFeedback(Feedback.BOTH); dt.setAllowSelfAsSource(true);
+		 * gridEnvironmentVariable); dt.setFeedback(Feedback.BOTH);
+		 * dt.setAllowSelfAsSource(true);
 		 */
 
 		// EDITING //
@@ -248,14 +254,26 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		storeComboIOType.commitChanges();
 
 		//
+		TextField nameColumnEditing = new TextField();
+		nameColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField descriptionColumnEditing = new TextField();
+		descriptionColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField defaultValueColumnEditing = new TextField();
+		defaultValueColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
 
 		gridInputOutputVariablesEditing = new GridRowEditing<InputOutputVariables>(
 				gridInputOutputVariables);
-		gridInputOutputVariablesEditing.addEditor(nameColumn, new TextField());
+		gridInputOutputVariablesEditing
-		gridInputOutputVariablesEditing.addEditor(descriptionColumn, new TextField());
+				.addEditor(nameColumn, nameColumnEditing);
-		gridInputOutputVariablesEditing.addEditor(dataTypeColumn, comboDataType);
+		gridInputOutputVariablesEditing.addEditor(descriptionColumn,
-		gridInputOutputVariablesEditing.addEditor(defaultValueColumn, new TextField());
+				descriptionColumnEditing);
-
+		gridInputOutputVariablesEditing
+				.addEditor(dataTypeColumn, comboDataType);
+		gridInputOutputVariablesEditing.addEditor(defaultValueColumn,
+				defaultValueColumnEditing);
 		gridInputOutputVariablesEditing.addEditor(ioTypeColumn, comboIOType);
 
 		btnAdd = new TextButton();
@@ -282,16 +300,18 @@ public class InputOutputVariablesPanel extends ContentPanel {
 				storeInputOutputVariables.remove(rowIndex);
 				storeInputOutputVariables.commitChanges();
 
-				gridInputOutputVariablesEditing.getCancelButton().setVisible(true);
+				gridInputOutputVariablesEditing.getCancelButton().setVisible(
+						true);
 				btnAdd.setEnabled(true);
 				if (addStatus) {
 					addStatus = false;
 				}
 
-				List<InputOutputVariables> listIOVariables=storeInputOutputVariables.getAll();
+				List<InputOutputVariables> listIOVariables = storeInputOutputVariables
-				List<InputOutputVariables> listNewIOVariables= new ArrayList<InputOutputVariables>();
+						.getAll();
-				for(int i=0; i<listIOVariables.size(); i++){
+				List<InputOutputVariables> listNewIOVariables = new ArrayList<InputOutputVariables>();
-					InputOutputVariables var=listIOVariables.get(i);
+				for (int i = 0; i < listIOVariables.size(); i++) {
+					InputOutputVariables var = listIOVariables.get(i);
 					var.setId(i);
 					listNewIOVariables.add(var);
 				}
@@ -300,8 +320,8 @@ public class InputOutputVariablesPanel extends ContentPanel {
 				storeInputOutputVariables.addAll(listNewIOVariables);
 				storeInputOutputVariables.commitChanges();
 
-				seq=listNewIOVariables.size();
+				seq = listNewIOVariables.size();
-				Log.debug("Current Seq: "+seq);
+				Log.debug("Current Seq: " + seq);
 
 			}
 		});
@@ -349,8 +369,7 @@ public class InputOutputVariablesPanel extends ContentPanel {
 							btnAdd.setEnabled(true);
 
 						} catch (Throwable e) {
-							Log.error("Error: "
+							Log.error("Error: " + e.getLocalizedMessage());
-									+ e.getLocalizedMessage());
 							e.printStackTrace();
 						}
 					}
@@ -364,7 +383,8 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		vlc.setScrollMode(ScrollMode.NONE);
 
 		// vlc.add(toolBar, new VerticalLayoutData(1, -1, new Margins(0)));
-		vlc.add(gridInputOutputVariables, new VerticalLayoutData(1, 1, new Margins(0)));
+		vlc.add(gridInputOutputVariables, new VerticalLayoutData(1, 1,
+				new Margins(0)));
 
 		add(vlc, new MarginData(new Margins(0)));
 
@@ -393,6 +413,7 @@ public class InputOutputVariablesPanel extends ContentPanel {
 			seq++;
 			inputOutputVariable.setId(seq);
 			Log.debug("New Input/Output Variable: " + inputOutputVariable);
+
 			storeInputOutputVariables.add(inputOutputVariable);
 			storeInputOutputVariables.commitChanges();
 
@@ -412,12 +433,14 @@ public class InputOutputVariablesPanel extends ContentPanel {
 			seq++;
 			InputOutputVariables newInputOutputVariablesVariable = new InputOutputVariables(
 					seq, "", "", "", DataType.STRING, IOType.INPUT, "");
-			Log.debug("New Input/Output Variable: " + newInputOutputVariablesVariable);
+			Log.debug("New Input/Output Variable: "
+					+ newInputOutputVariablesVariable);
 			gridInputOutputVariablesEditing.cancelEditing();
 			addStatus = true;
 			gridInputOutputVariablesEditing.getCancelButton().setVisible(false);
 			storeInputOutputVariables.add(newInputOutputVariablesVariable);
-			int row = storeInputOutputVariables.indexOf(newInputOutputVariablesVariable);
+			int row = storeInputOutputVariables
+					.indexOf(newInputOutputVariablesVariable);
 
 			storeComboDataType.clear();
 			storeComboDataType.addAll(DataType.asList());
@@ -446,7 +469,7 @@ public class InputOutputVariablesPanel extends ContentPanel {
 		} else {
 			storeInputOutputVariables.clear();
 			storeInputOutputVariables.commitChanges();
-			seq=0;
+			seq = 0;
 		}
 
 	}

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

@@ -33,6 +33,7 @@ import com.sencha.gxt.widget.core.client.event.SelectEvent;
 import com.sencha.gxt.widget.core.client.event.SelectEvent.SelectHandler;
 import com.sencha.gxt.widget.core.client.form.FieldLabel;
 import com.sencha.gxt.widget.core.client.form.TextField;
+import com.sencha.gxt.widget.core.client.form.validator.RegExValidator;
 import com.sencha.gxt.widget.core.client.grid.ColumnConfig;
 import com.sencha.gxt.widget.core.client.grid.ColumnModel;
 import com.sencha.gxt.widget.core.client.grid.Grid;
@@ -140,12 +141,19 @@ public class InterpreterInfoPanel extends ContentPanel {
 		gridInterpreterPackageInfo.setColumnReordering(false);
 
 		// EDITING //
+		TextField nameColumnEditing=new TextField();
+		nameColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField versionColumnEditing=new TextField();
+		versionColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		
 		gridInterpreterPackageInfoEditing = new GridRowEditing<InterpreterPackageInfo>(
 				gridInterpreterPackageInfo);
 		gridInterpreterPackageInfoEditing
-				.addEditor(nameColumn, new TextField());
+				.addEditor(nameColumn, nameColumnEditing);
 		gridInterpreterPackageInfoEditing.addEditor(versionColumn,
-				new TextField());
+				versionColumnEditing);
 
 		btnAdd = new TextButton("Add");
 		btnAdd.setIcon(StatAlgoImporterResources.INSTANCE.add16());
@@ -250,6 +258,8 @@ public class InterpreterInfoPanel extends ContentPanel {
 		interpreterVersion = new TextField();
 		interpreterVersion.setAllowBlank(false);
 		interpreterVersion.setEmptyText("Enter version...");
+		interpreterVersion.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
 		FieldLabel interpreterVersionLabel = new FieldLabel(interpreterVersion,
 				"Version");
 

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

@@ -110,6 +110,8 @@ public class ProjectInfoPanel extends ContentPanel {
 		algorithmDescription = new TextField();
 		algorithmDescription.setAllowBlank(false);
 		algorithmDescription.setEmptyText("Enter description...");
+		algorithmDescription.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
 		FieldLabel descriptionLabel = new FieldLabel(
 				algorithmDescription, "Description");
 		descriptionLabel.setLabelWidth(LABAEL_WIDTH);
@@ -122,6 +124,7 @@ public class ProjectInfoPanel extends ContentPanel {
 				props.name(), 100, "Name");
 		// nameColumn.setMenuDisabled(true);
 	
+
 		ColumnConfig<RequestedVRE, String> descriptionColumn = new ColumnConfig<RequestedVRE, String>(
 				props.description(), 100, "Description");
 		// descriptionColumn.setMenuDisabled(true);
@@ -169,10 +172,18 @@ public class ProjectInfoPanel extends ContentPanel {
 		gridRequestedVRE.setColumnReordering(false);
 
 		// EDITING //
+		TextField nameColumnEditing=new TextField();
+		nameColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		TextField descriptionColumnEditing=new TextField();
+		descriptionColumnEditing.addValidator(new RegExValidator("^[^\"]*$",
+				"Attention character \" is not allowed"));
+		
+		
 		gridRequestedVREEditing = new GridRowEditing<RequestedVRE>(
 				gridRequestedVRE);
-		gridRequestedVREEditing.addEditor(nameColumn, new TextField());
+		gridRequestedVREEditing.addEditor(nameColumn, nameColumnEditing);
-		gridRequestedVREEditing.addEditor(descriptionColumn, new TextField());
+		gridRequestedVREEditing.addEditor(descriptionColumn, descriptionColumnEditing);
 
 		btnAdd = new TextButton("Add");
 		btnAdd.setIcon(StatAlgoImporterResources.INSTANCE.add16());

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

@@ -4,6 +4,7 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.ProcessBuilder.Redirect;
+import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -383,6 +384,7 @@ public class ProjectBuilder {
 			throw new StatAlgoImporterServiceException(e.getLocalizedMessage(),
 					e);
 		}
+
 		return;
 
 	}
@@ -457,6 +459,21 @@ public class ProjectBuilder {
 			int exitValue = process.waitFor();
 			logger.debug("Create Algo Class: Exit Value is " + exitValue);
 
+			DirectoryStream<Path> packageHomeStream = Files
+					.newDirectoryStream(packageHome);
+			boolean createdFilesClass = false;
+			for (Path path : packageHomeStream) {
+				if (path.toString().endsWith(".class")) {
+					createdFilesClass = true;
+					break;
+				}
+			}
+
+			if (!createdFilesClass) {
+				throw new StatAlgoImporterServiceException(
+						"Error in the creation of the class files!");
+			}
+
 		} catch (IOException | InterruptedException e) {
 			logger.error(e.getLocalizedMessage());
 			e.printStackTrace();