Generate gene reaction rules

.classpath

@@ -28,5 +28,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="lib" path="C:/Users/Asus/Downloads/Java_Binding_1_1/WolframAlphaJavaLibrary/WolframAlpha-1.1.jar"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

pom.xml

@@ -120,6 +120,11 @@
             <artifactId>json-simple</artifactId>
             <version>1.1.1</version>
         </dependency>
+        <dependency>
+    		<groupId>com.bpodgursky</groupId>
+    		<artifactId>jbool_expressions</artifactId>
+    		<version>1.23</version>
+		</dependency>
         <!-- </dependency> <groupId>org.sing_group</groupId> <artifactId>gc4s</artifactId> 
             <version>1.2.2</version> </dependency> -->
     </dependencies>

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/BiggMain.java

@@ -19,7 +19,7 @@ public class BiggMain {
 
 	public static void main(String[] args) throws Exception {
 
-		String workFolderID = "/workdir/"; //Docker (/workdir/)
+		String workFolderID = "C:/Users/Asus/Desktop/"; //Docker (/workdir/)
 		String paramsPath = workFolderID.concat("workerSubmissions/params.txt");
 		FileUtils.extractZipFile(workFolderID+"Bigg_Files/Results.tgz", workFolderID+"Bigg_Files/");
 		

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/blast/Properties.java

@@ -26,7 +26,7 @@ public class Properties {
 	private static final Logger logger = LoggerFactory.getLogger(Properties.class);
 
 	public Properties() {
-		String propertiesFilePath = "/workdir/" + "configurations.txt";
+		String propertiesFilePath = "C:/Users/Asus/Desktop/" + "configurations.txt";
 		allProperties = FileUtils.readPropertiesFile(false,propertiesFilePath);
 		
 		boolean go = assignVariables();

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/data/BiggDataCenter.java

@@ -8,6 +8,7 @@ import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.math.MathContext;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.NoSuchFileException;
 import java.util.ArrayList;
@@ -16,17 +17,28 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import com.bpodgursky.jbool_expressions.*;
+import com.bpodgursky.jbool_expressions.parsers.ExprParser;
+import com.bpodgursky.jbool_expressions.rules.Rule;
+import com.bpodgursky.jbool_expressions.rules.RuleSet;
+import com.wolfram.*;
+import com.wolfram.alpha.WAEngine;
+import com.wolfram.alpha.WAQuery;
+import com.wolfram.alpha.WAQueryResult;
+import com.wolfram.alpha.net.*;
+import com.wolfram.alpha.visitor.*;
 
 import pt.uminho.ceb.biosystems.merlin.bigg.blast.Properties;
 import pt.uminho.ceb.biosystems.merlin.bigg.data.BiggUtils;
 
 import org.apache.commons.io.IOUtils;
+import org.hibernate.criterion.LogicalExpression;
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
 
 public class BiggDataCenter {
-
+	
 	private static List<String> metaboliteBiggIds = new ArrayList<String>();
 	private static List<String> reactionBiggIds = new ArrayList<String>();
 	private static List<String> modelBiggIds = new ArrayList<String>();
@@ -1046,7 +1058,7 @@ public class BiggDataCenter {
 	public static Map<String,String> genesReactionsRuleFile(String path) throws Exception {
 		
 		Map<String,String> geneReactionRuleMap = new HashMap<String, String>();
-		Map<String,List<String>> geneReactionRuleMapList = new HashMap<String,List<String>>();
+		Map<String,List<String>> geneReactionRuleMapList = new HashMap<String,List<String>>();		
 		
 		try {
 			List<String> modelFiles = new ArrayList<String>();

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/operation/CreateModelfromBigg.java

+package  pt.uminho.ceb.biosystems.merlin.bigg.operation;
+
+import es.uvigo.ei.aibench.core.operation.annotation.Direction;
+import es.uvigo.ei.aibench.core.operation.annotation.Operation;
+import es.uvigo.ei.aibench.core.operation.annotation.Port;
+import es.uvigo.ei.aibench.workbench.Workbench;
+import pt.uminho.ceb.biosystems.merlin.aibench.datatypes.WorkspaceAIB;
+
+@Operation(name="CreateModelfromBigg", description="Create model from BiGG data.")
+public class CreateModelfromBigg {
+	private String databaseName;
+	private String biggAllinfo;
+	private String biggSpecificModelsinfo;
+	private String biggSpecificOrganisms;
+	private String biggRandomModelsinfo;
+
+
+	/**
+	 * @param project
+	 */
+	@Port(direction=Direction.INPUT, name="Select Workspace", validateMethod = "checkProject", order=1)
+	public void setProject(WorkspaceAIB project) {
+
+	}
+
+	public void checkProject(WorkspaceAIB project) {
+
+		if(project==null) {
+
+			throw new IllegalArgumentException("Please select a workspace.");
+		}
+		else {
+			this.databaseName = project.getName();
+
+		} 
+	}
+
+
+	/**
+	 * @param biggAllinfo 
+	 */
+	@Port(direction=Direction.INPUT, name="Use all BiGG data", order=1)
+	public void setOption1(String biggAllinfo) {
+
+		this.biggAllinfo = biggAllinfo;
+
+	}
+	
+	
+	/**
+	 * @param biggSpecificModelsinfo 
+	 */
+	@Port(direction=Direction.INPUT, name="Use specific BiGG models data", order=1)
+	public void setOption2(String biggSpecificModelsinfo) {
+
+		this.biggSpecificModelsinfo = biggSpecificModelsinfo;
+
+	}
+	
+	
+	/**
+	 * @param biggSpecificOrganisms 
+	 */
+	@Port(direction=Direction.INPUT, name="Use specific BiGG organisms data", order=1)
+	public void setOption3(String biggSpecificOrganisms) {
+
+		this.biggSpecificOrganisms = biggSpecificOrganisms;
+
+	}
+	
+	
+	/**
+	 * @param biggSpecificOrganisms 
+	 */
+	@Port(direction=Direction.INPUT, name="Use random BiGG models data", order=1)
+	public void setOption4(String biggRandomModelsinfo) {
+
+		this.biggRandomModelsinfo = biggRandomModelsinfo;
+
+	}
+
+
+	
+	
+	
+	
+	
+	
+	
+	
+	
+	public void onValidationError(Throwable arg0) {
+
+		Workbench.getInstance().error(arg0);
+	}
+
+}

src/main/java/pt/uminho/ceb/biosystems/merlin/bigg/operation/CreateModelfromBiggGUI.java

+//package pt.uminho.ceb.biosystems.merlin.bigg.operation;
+//
+//import java.awt.Component;
+//import java.awt.FlowLayout;
+//import java.awt.event.ActionEvent;
+//import java.awt.event.ActionListener;
+//import java.io.File;
+//import java.io.FileNotFoundException;
+//import java.util.ArrayList;
+//import java.util.Scanner;
+//
+//import javax.swing.ImageIcon;
+//import javax.swing.InputMap;
+//import javax.swing.JButton;
+//import javax.swing.JFrame;
+//import javax.swing.JPanel;
+//import javax.swing.JPasswordField;
+//import javax.swing.JTextField;
+//import javax.swing.KeyStroke;
+//
+//import org.sing_group.gc4s.dialog.AbstractInputJDialog;
+//import org.sing_group.gc4s.input.InputParameter;
+//import org.sing_group.gc4s.input.InputParametersPanel;
+//import org.sing_group.gc4s.input.combobox.ExtendedJComboBox;
+//
+//import es.uvigo.ei.aibench.core.ParamSpec;
+//import es.uvigo.ei.aibench.core.operation.OperationDefinition;
+//import es.uvigo.ei.aibench.workbench.InputGUI;
+//import es.uvigo.ei.aibench.workbench.ParamsReceiver;
+//import es.uvigo.ei.aibench.workbench.Workbench;
+//import pt.uminho.ceb.biosystems.merlin.aibench.utilities.CreateImageIcon;
+//import pt.uminho.ceb.biosystems.merlin.utilities.io.FileUtils;
+//
+//
+//public class CreateModelfromBiggGUI extends AbstractInputJDialog implements InputGUI{
+//	private static final long serialVersionUID = 1L;
+//
+//	public static String[] options = {
+//			"Use all BiGG informations",
+//			"Use specific BiGG models information", 
+//			"Use specific BiGG organisms information",
+//			"Use random BiGG models information"
+//	};
+//	
+//	public static ExtendedJComboBox<String> choosenOption = new ExtendedJComboBox<String>(options);
+//	public static JTextField choosenModels = new JTextField();
+//	public static JTextField choosenOrganism = new JPasswordField();
+//	public static  JTextField evalue = new JTextField();
+//	public static  JTextField querycoverage = new JTextField();
+//	public static  JTextField bitscore = new JTextField();
+//	
+//	private ParamsReceiver rec;
+//
+//	public CreateModelfromBiggGUI() {
+//		super(new JFrame());
+//		fill();
+//	}
+//
+//	public String getDialogTitle() {
+//		return "create model from BiGG";
+//	}
+//
+//	public String getDescription() {
+//		return "use BiGG information to create a model.";
+//	}
+//
+//	public JPanel getInputComponentsPane() {
+//		return new InputParametersPanel(getInputParameters());
+//	}
+//
+//	@Override
+//	protected Component getButtonsPane() {
+//		final JPanel buttonsPanel = new JPanel(new FlowLayout());
+//
+//		okButton = new JButton("save");
+//		okButton.setEnabled(true);
+//		okButton.setToolTipText("save");
+//		okButton.setIcon(new CreateImageIcon(new ImageIcon(getClass().getClassLoader().getResource("icons/Save.png")),0.1).resizeImageIcon());
+//		ActionListener listener= new ActionListener() {
+//
+//			@Override
+//			public void actionPerformed(ActionEvent arg0) {
+//
+//				String passText = new String(password.getPassword());
+//
+//				rec.paramsIntroduced(
+//						new ParamSpec[]{
+//								new ParamSpec("Host",String.class,host.getText(),null),
+//								new ParamSpec("Port",String.class,port.getText(),null),
+//								new ParamSpec("User",String.class,username.getText(),null),
+//								new ParamSpec("Password",String.class,passText,null),
+//								new ParamSpec("Database Type",String.class,dbType.getSelectedItem().toString(),null),
+//						}
+//						);
+//				if(dbType.getSelectedItem().toString().equals("H2")) {
+//					if(!username.getText().equals("")&& !String.valueOf(password.getPassword()).equals("")) {
+//
+//						dispose();
+//
+//					}
+//				}
+//				if(dbType.getSelectedItem().toString().equals("MySQL")) {
+//					if(!username.getText().equals("")&& !String.valueOf(password.getPassword()).equals("")&&!port.getText().equals("")&&!host.getText().equals("")) {
+//						if (port.getText().matches("[0-9]+")) {
+//							dispose();
+//						}
+//					}
+//				}
+//
+//			}
+//		};
+//		okButton.addActionListener(listener);
+//
+//		cancelButton = new JButton("cancel");
+//		cancelButton.setToolTipText("cancel");
+//		cancelButton.setIcon(new CreateImageIcon(new ImageIcon(getClass().getClassLoader().getResource("icons/Cancel.png")),0.1).resizeImageIcon());
+//		cancelButton.addActionListener(event -> {
+//
+////			String[] options = new String[2];
+////			options[0] = "yes";
+////			options[1] = "no";
+////
+////			int result = CustomGUI.stopQuestion("cancel confirmation", "are you sure you want to cancel the operation?", options);
+//
+//			//if(result == 0) {
+//				canceled = true;
+//				dispose();
+//
+//			//}
+//
+//		});
+//
+//
+//		buttonsPanel.add(okButton);
+//		buttonsPanel.add(cancelButton);
+//
+//		getRootPane().setDefaultButton(okButton);
+//		InputMap im = okButton.getInputMap();
+//		im.put(KeyStroke.getKeyStroke("ENTER"), "pressed");
+//		im.put(KeyStroke.getKeyStroke("released ENTER"), "released");
+//
+//		ActionListener updateDbType = new ActionListener() {
+//
+//			@Override
+//			public void actionPerformed(ActionEvent arg0) {
+//				if(dbType.getSelectedItem().toString().equals("MySQL")) {
+//					fillWithoutDbMySQL();
+//				}else {
+//					fillWithoutDbH2();
+//				}
+//
+//
+//			}
+//		};
+//
+//		dbType.addActionListener(updateDbType);
+//
+//
+//		return buttonsPanel;
+//
+//
+//	}
+//	private InputParameter[] getInputParameters() {
+//		InputParameter[] parameters = new InputParameter[5];
+//		parameters[0] = 
+//				new InputParameter(
+//						"database type", 
+//						dbType, 
+//						"select database type"
+//						);
+//
+//		parameters[1] = 
+//				new InputParameter(
+//						"username", 
+//						username, 
+//						"set username"
+//						);
+//		parameters[2] = 
+//				new InputParameter(
+//						"password", 
+//						password, 
+//						"set password"
+//						);
+//		parameters[3] = 
+//				new InputParameter(
+//						"host", 
+//						host, 
+//						"set host"
+//						);
+//		parameters[4] = 
+//				new InputParameter(
+//						"port", 
+//						port, 
+//						"set port"
+//						);
+//
+//
+//		return parameters;
+//	}
+//
+//	public void fill () {
+//
+//		ArrayList<String> listLines= new ArrayList<>();
+//		String confPath = FileUtils.getConfFolderPath().concat("database_settings.conf");
+//		File configfile= new File(confPath);
+//		try {
+//			Scanner file= new Scanner(configfile);
+//			while(file.hasNextLine()==true) {
+//				listLines.add(file.nextLine());
+//			}
+//			file.close();
+//		} catch (FileNotFoundException e) {
+//			e.printStackTrace();
+//		}
+//
+//		for (String item : listLines) {
+//
+//			if(item.startsWith("dbtype")) {
+//				String[]parts=item.split(":");
+//
+//
+//				if(parts[1].trim().equals("h2")) {
+//					for (String dbOption : items) {
+//						if(dbOption.equals("H2")) {
+//							dbType.setSelectedItem(dbOption);
+//							fillWithoutDbH2();
+//							continue;
+//						}
+//					}
+//
+//				}
+//
+//				if(parts[1].trim().equals("mysql")) {
+//					for (String dbOption : items) {
+//						if(dbOption.equals("MySQL")) {
+//							dbType.setSelectedItem(dbOption);
+//							fillWithoutDbMySQL();
+//							continue;
+//						}
+//					}
+//				}
+//			}
+//		}
+//	}
+//	public void fillWithoutDbMySQL() {
+//		ArrayList<String> listLines= new ArrayList<>();
+//		String confPath = FileUtils.getConfFolderPath().concat("database_settings.conf");
+//		File configfile= new File(confPath);
+//		try {
+//			Scanner file= new Scanner(configfile);
+//			while(file.hasNextLine()==true) {
+//				listLines.add(file.nextLine());
+//			}
+//			file.close();
+//		} catch (FileNotFoundException e) {
+//			e.printStackTrace();
+//		}
+//
+//		for (String item : listLines) {
+//
+//			if(item.startsWith("username")) {
+//
+//				String[]parts=item.split(":");
+//				username.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//			if(item.startsWith("password")) {
+//				String[]parts=item.split(":");
+//				password.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//			if(item.startsWith("host")) {
+//				String[]parts=item.split(":");
+//				host.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//			if(item.startsWith("port")) {
+//				String[]parts=item.split(":");
+//				port.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//		}
+//		port.setEditable(true);
+//		host.setEditable(true);
+//	}
+//	public void fillWithoutDbH2() {
+//		ArrayList<String> listLines= new ArrayList<>();
+//		String confPath = FileUtils.getConfFolderPath().concat("database_settings.conf");
+//		File configfile= new File(confPath);
+//		try {
+//			Scanner file= new Scanner(configfile);
+//			while(file.hasNextLine()==true) {
+//				listLines.add(file.nextLine());
+//			}
+//			file.close();
+//		} catch (FileNotFoundException e) {
+//			e.printStackTrace();
+//		}
+//
+//		for (String item : listLines) {
+//
+//			if(item.startsWith("h2_username")) {
+//				String[]parts=item.split(":");
+//				username.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//			if(item.startsWith("h2_password")) {
+//				String[]parts=item.split(":");
+//				password.setText(parts[1].trim());
+//				continue;
+//
+//			}
+//			host.setText("");
+//			port.setText("");
+//		}
+//		port.setEditable(false);
+//		host.setEditable(false);
+//	}
+//
+//	@Override
+//	public void setVisible(boolean b) {
+//		this.pack();
+//		super.setVisible(b);
+//	}
+//
+//	@Override
+//	public void init(ParamsReceiver arg0, OperationDefinition<?> arg1) {
+//		this.rec = arg0;
+//		this.setTitle(arg1.getName());
+//		this.setVisible(true);		
+//	}
+//
+//	/* (non-Javadoc)
+//	 * @see es.uvigo.ei.aibench.workbench.InputGUI#onValidationError(java.lang.Throwable)
+//	 */
+//	public void onValidationError(Throwable arg0) {
+//
+//		Workbench.getInstance().error(arg0);
+//	}
+//
+//	@Override
+//	public void finish() {
+//
+//	}
+//}