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Commit caf12fff authored by Piotr Gawron's avatar Piotr Gawron
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remove of old sbgnml command line util - the functionality is available via API

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1 merge request!782Resolve "Replace deprecated APIs"
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annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
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......@@ -60,7 +60,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
}
String query = "https://identifiers.org/rest/identifiers/validate/" + id;
logger.debug(query);
try {
String page = getWebPageContent(query);
Gson gson = new Gson();
......
converter-SBGNML/pom.xml
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......@@ -109,13 +109,6 @@
<version>${log4j-jcl-version}</version>
</dependency>
<!-- Commons CLI by Apache -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons-cli.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
......
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlConsoleConverter.java deleted 100644 → 0
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package lcsb.mapviewer.converter.model.sbgnml.console;
import java.io.FileNotFoundException;
import lcsb.mapviewer.converter.ConverterException;
import org.apache.logging.log4j.*;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.model.sbgnml.console.gui.GraphicalInterface;
import lcsb.mapviewer.model.map.model.Model;
/**
* This class is entry point for console tool to convert data from CellDesigner
* file to SBGN-ML format and back.
*
* @author Michał Kuźma
*
*/
public class SbgnmlConsoleConverter {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(SbgnmlConsoleConverter.class.getName());
/**
* Options from the input.
*/
private SbgnmlRunOptions inputOptions;
/**
* Default constructor.
*
* @param args
* parameters with which the program was run
*/
public SbgnmlConsoleConverter(String[] args) {
inputOptions = new SbgnmlRunOptions(args);
}
/**
* Main entry point to the program.
*
* @param args
* parameters with which the program was run
*/
public static void main(String[] args) {
SbgnmlConsoleConverter main = new SbgnmlConsoleConverter(args);
try {
main.run();
} catch (Exception e) {
main.logger.error(e, e);
}
}
/**
* Method used to convert data from one file format to another.
*
* @param inputFilename
* path to the input file
* @param outputFilename
* path to the output file
* @param reversed
* true if conversion should be done from CellDesigner to SBGN-ML
* file
* @throws InvalidInputDataExecption
* thrown when there is a problem with conversion
*/
public static void convert(String inputFilename, String outputFilename, boolean reversed)
throws InvalidInputDataExecption, ConverterException {
Converter parser;
Converter exporter;
if (reversed) {
parser = new CellDesignerXmlParser();
exporter = new SbgnmlXmlConverter();
} else {
parser = new SbgnmlXmlConverter();
exporter = new CellDesignerXmlParser();
}
Model model;
try {
model = parser.createModel(new ConverterParams().filename(inputFilename));
} catch (FileNotFoundException e) {
throw new InvalidInputDataExecption("Problem with input file: " + inputFilename, e);
}
try {
exporter.model2File(model, outputFilename);
} catch (Exception e) {
throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
}
}
/**
* This method transform {@link #inputOptions input data}.
*
* @throws InvalidInputDataExecption
* thrown when the input data are invalid
*/
private void run() throws InvalidInputDataExecption, ConverterException {
if (inputOptions.noOptionsGiven()) {
GraphicalInterface gui = new GraphicalInterface();
gui.execute();
} else {
if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
if (!inputOptions.isValidInput()) {
logger.warn("Invalid input data");
}
inputOptions.printHelp();
} else {
logger.debug("Running...");
convert(inputOptions.getInputFilename(), inputOptions.getOutputFilename(), inputOptions.isReversedOption());
}
}
}
}
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlRunOptions.java deleted 100644 → 0
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package lcsb.mapviewer.converter.model.sbgnml.console;
import org.apache.commons.cli.BasicParser;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.logging.log4j.*;
/**
* This class is used to parse and store input data for {@link SbgnmlConsoleConverter}
* .
*
* @author Michał Kuźma
*
*/
public class SbgnmlRunOptions {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(SbgnmlRunOptions.class.getName());
/**
* What is the abbreviation of help option.
*/
private static final String HELP_OPTION = "h";
/**
* What is the abbreviation of output file option.
*/
private static final String OUTPUT_OPTION = "o";
/**
* What is the abbreviation of input file option.
*/
private static final String INPUT_OPTION = "i";
/**
* What is the abbreviation of reversed converter mode option (CellDesigner to SBGN-ML).
*/
private static final String REVERSED_OPTION = "r";
/**
* Object with available input options.
*/
private Options options;
/**
* What should be the command line to run the program.
*/
private String commandLineRun = null;
/**
* Was the input valid?
*/
private boolean validInput = false;
/**
* Data parsed from input.
*/
private CommandLine commandLine;
/**
* Default constructor that parses data.
*
* @param args
* parameters used to run the program
*/
public SbgnmlRunOptions(String[] args) {
options = new Options();
options.addOption(createOption("input", INPUT_OPTION, true, "input-file", "input file"));
options.addOption(createOption("output", OUTPUT_OPTION, true, "output-file", "converted output file"));
OptionBuilder.isRequired(false);
options.addOption(REVERSED_OPTION, false, "convert from CellDesigner to SBGN-ML");
options.addOption(HELP_OPTION, false, "print this help menu");
commandLineRun = "java -jar " + new java.io.File(SbgnmlConsoleConverter.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getName()
+ " [options]";
CommandLineParser parser = new BasicParser();
try {
validInput = true;
commandLine = parser.parse(options, args);
if (getInputFilename() == null || getOutputFilename() == null
|| (isReversedOption() && (!getInputFilename().endsWith(".xml") || !getOutputFilename().endsWith(".sbgn")))
|| (!isReversedOption() && (!getInputFilename().endsWith(".sbgn") || !getOutputFilename().endsWith(".xml")))) {
validInput = false;
}
} catch (ParseException e) {
validInput = false;
logger.info(e.getMessage());
}
}
/**
* Creates new {@link Option} object.
*
* @param optionName
* full name of the option
* @param optionAbbreviation
* abbreviation of the option
* @param hasArgument
* has the option argument
* @param argumentName
* name of the argument
* @param description
* description of the option
* @return {@link Option} created from input values
*/
private Option createOption(String optionName, String optionAbbreviation, boolean hasArgument, String argumentName, String description) {
OptionBuilder.hasArg(hasArgument);
if (hasArgument) {
OptionBuilder.withArgName(argumentName);
}
OptionBuilder.withDescription(description);
OptionBuilder.withLongOpt(optionName);
return OptionBuilder.create(optionAbbreviation);
}
/**
* @return the options
* @see #options
*/
public Options getOptions() {
return options;
}
/**
* @param options
* the options to set
* @see #options
*/
public void setOptions(Options options) {
this.options = options;
}
/**
* @return the commandLineRun
* @see #commandLineRun
*/
public String getCommandLineRun() {
return commandLineRun;
}
/**
* @param commandLineRun
* the commandLineRun to set
* @see #commandLineRun
*/
public void setCommandLineRun(String commandLineRun) {
this.commandLineRun = commandLineRun;
}
/**
* @return the validInput
* @see #validInput
*/
public boolean isValidInput() {
return validInput;
}
/**
* @param validInput
* the validInput to set
* @see #validInput
*/
public void setValidInput(boolean validInput) {
this.validInput = validInput;
}
/**
* @return the commandLine
* @see #commandLine
*/
public CommandLine getCommandLine() {
return commandLine;
}
/**
* @param commandLine
* the commandLine to set
* @see #commandLine
*/
public void setCommandLine(CommandLine commandLine) {
this.commandLine = commandLine;
}
/**
* Prints help to the console how to used the program (what parameters to put
* and what are they used for).
*/
public void printHelp() {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(commandLineRun, options);
}
/**
* Checks if {@link #HELP_OPTION} was selected in the input.
*
* @return <code>true</code> if {@link #HELP_OPTION} was selected,
* <code>false</code> otherwise
*/
public boolean isHelpOption() {
return commandLine.hasOption(HELP_OPTION);
}
/**
* Checks if {@link #REVERSED} was selected in the input.
*
* @return <code>true</code> if {@link #REVERSED_OPTION} was selected,
* <code>false</code> otherwise
*/
public boolean isReversedOption() {
return commandLine.hasOption(REVERSED_OPTION);
}
/**
* Returns name of the input file.
*
* @return name of the input file
*/
public String getInputFilename() {
return commandLine.getOptionValue(INPUT_OPTION);
}
/**
* Returns name of the output file.
*
* @return name of the output file
*/
public String getOutputFilename() {
return commandLine.getOptionValue(OUTPUT_OPTION);
}
/**
* Returns true if no options were given when executing application.
* @return true if no options were given when executing application
*/
public boolean noOptionsGiven() {
return commandLine.getOptions().length == 0;
}
}
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/GraphicalInterface.java deleted 100644 → 0
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− 320
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package lcsb.mapviewer.converter.model.sbgnml.console.gui;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.ByteArrayOutputStream;
import java.io.FileDescriptor;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.io.PrintWriter;
import javax.swing.JButton;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.filechooser.FileNameExtensionFilter;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.sbgnml.console.SbgnmlConsoleConverter;
/**
* Graphical User Interface for SBGN-ML, CellDesigner converter.
**/
public class GraphicalInterface {
/**
* Path of the input file.
*/
private String szInputFilePath = null;
/**
* Path of the output file.
*/
private String szOutputFilePath = null;
/**
* Path of the log file.
*/
private String szLogsFilePath = null;
/**
* Should the conversion go from CellDesigner to SBGN-ML file.
*/
private boolean cellDesigner2Sbgnml = false;
/**
* Input text with path to input file.
*/
private JTextField jtfOpenFilePath;
/**
* Input text with path to output file.
*/
private JTextField jtfSaveFilePath;
/**
* Input text with path to log file.
*/
private JTextField jtfLogFilePath;
/**
* Button used for opening files.
*/
private JButton btnOpenInput;
/**
* Button used for saving converted files.
*/
private JButton btnSaveOutput;
/**
* Button used for saving log file.
*/
private JButton btnLogsFile;
/**
* Button for staring conversion.
*/
private JButton btnParse;
/**
* Button for closing application.
*/
private JButton btnClose;
/**
* Label with copyrights.
*/
private JLabel fundingLabel;
/**
* Launch the application.
*
*/
public void execute() {
try {
final JFrame frame = new JFrame("SBGN-ML to SBML Converter");
JPanel panel = new JPanel();
panel.setLayout(null);
// CHECKSTYLE:OFF
jtfOpenFilePath = new JTextField(70);
jtfSaveFilePath = new JTextField(70);
jtfLogFilePath = new JTextField(70);
jtfOpenFilePath.setBounds(265, 5, 600, 28);
jtfSaveFilePath.setBounds(265, 55, 600, 28);
jtfLogFilePath.setBounds(265, 105, 600, 28);
jtfLogFilePath.setEditable(false);
jtfOpenFilePath.setEditable(false);
jtfSaveFilePath.setEditable(false);
btnOpenInput = new JButton();
btnOpenInput.setBounds(10, 5, 218, 28);
btnOpenInput.setText("Open Input File");
btnOpenInput.addActionListener(createOpenButtonListener());
btnSaveOutput = new JButton();
btnSaveOutput.setBounds(10, 55, 218, 28);
btnSaveOutput.setText("Save output file");
btnSaveOutput.addActionListener(createSaveButtonListener());
btnLogsFile = new JButton();
btnLogsFile.setBounds(10, 105, 218, 28);
btnLogsFile.setText("Save Model consistency logs");
btnLogsFile.addActionListener(createSaveLogsListener());
btnParse = new JButton();
btnParse.setBounds(10, 205, 218, 28);
btnParse.setText("Convert");
btnParse.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (null == szInputFilePath) {
JOptionPane.showMessageDialog(
frame, "Error: No path for the input file! Press " + btnOpenInput.getText() + " button to load input file!", "No input file!",
JOptionPane.ERROR_MESSAGE);
}
else if (null == szOutputFilePath) {
JOptionPane.showMessageDialog(
frame, "Error: No path for the output file! Press " + btnSaveOutput.getText() + " button to save output file!", "No output file path!",
JOptionPane.ERROR_MESSAGE);
}
else {
if (null == szLogsFilePath) {
int reply = JOptionPane.showConfirmDialog(
frame, "Warning: No path for the model consistency check logs file! Do you want to add it now?", "No model consistency check file path!",
JOptionPane.YES_NO_OPTION);
if (reply == JOptionPane.YES_OPTION) {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle("Specify a file to save Logs");
int userSelection = fileChooser.showSaveDialog(null);
if (userSelection == JFileChooser.APPROVE_OPTION) {
szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
int iPathSize = szLogsFilePath.length();
String strExtension = szLogsFilePath.substring(iPathSize - 4, iPathSize);
if (!strExtension.toLowerCase().equals(".txt")) {
szLogsFilePath = szLogsFilePath.concat(".txt");
}
jtfLogFilePath.setText(szLogsFilePath);
}
}
}
ByteArrayOutputStream baos = new ByteArrayOutputStream();
System.setOut(new PrintStream(baos));
try {
SbgnmlConsoleConverter.convert(szInputFilePath, szOutputFilePath, cellDesigner2Sbgnml);
} catch (InvalidInputDataExecption | ConverterException e1) {
JOptionPane.showMessageDialog(frame, "Problems, when converting the file:\n" + e1.getMessage(), "Converter problem!", JOptionPane.ERROR_MESSAGE);
return;
}
System.setOut(new PrintStream(new FileOutputStream(FileDescriptor.out)));
if (null != szLogsFilePath) {
PrintWriter logsFile = null;
try {
logsFile = new PrintWriter(szLogsFilePath);
} catch (FileNotFoundException ex) {
JOptionPane.showMessageDialog(frame, "Error: Couldn't open the logs file ", "Problems with opening logs file!", JOptionPane.ERROR_MESSAGE);
}
logsFile.println(baos.toString());
logsFile.close();
JOptionPane.showMessageDialog(
frame, "Parsing finished: output file available at: " + szOutputFilePath
+ "\nIf anything went wrong, logs with all warnings can be found at: " + szLogsFilePath);
} else {
JOptionPane.showMessageDialog(frame, "Parsing finished: output file available at: " + szOutputFilePath);
}
}
}
});
btnClose = new JButton();
btnClose.setBounds(520, 205, 147, 28);
btnClose.setText("Close");
btnClose.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
frame.dispose();
}
});
fundingLabel = new JLabel("@Copyright: EISBM - eTRIKS");
fundingLabel.setBounds(700, 205, 300, 28);
panel.add(btnOpenInput);
panel.add(btnSaveOutput);
panel.add(btnLogsFile);
panel.add(btnParse);
panel.add(btnClose);
panel.add(jtfOpenFilePath);
panel.add(jtfSaveFilePath);
panel.add(jtfLogFilePath);
frame.add(panel);
frame.setSize(900, 280);
frame.setLocationRelativeTo(null);
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.setVisible(true);
// CHECKSTYLE:ON
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Creates listener to open dialog for saving logs.
*
* @return listener resposinble to open dialog for saving log file
*/
public ActionListener createSaveLogsListener() {
return new ActionListener() {
public void actionPerformed(ActionEvent e) {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle("Specify a file to save Logs");
int userSelection = fileChooser.showSaveDialog(null);
if (userSelection == JFileChooser.APPROVE_OPTION) {
szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
if (!szLogsFilePath.toLowerCase().endsWith(".txt")) {
szLogsFilePath = szLogsFilePath.concat(".txt");
}
jtfLogFilePath.setText(szLogsFilePath);
}
}
};
}
/**
* Creates listener to open dialog for saving output.
*
* @return listener resposinble to open dialog for saving output
*/
public ActionListener createSaveButtonListener() {
return new ActionListener() {
public void actionPerformed(ActionEvent e) {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle("Specify a file to save");
fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
int userSelection = fileChooser.showSaveDialog(null);
if (userSelection == JFileChooser.APPROVE_OPTION) {
szOutputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
jtfSaveFilePath.setText(szOutputFilePath);
}
}
};
}
/**
* Creates listener to open dialog for opening input file.
*
* @return listener resposinble to open dialog for input file
*/
public ActionListener createOpenButtonListener() {
return new ActionListener() {
public void actionPerformed(ActionEvent e) {
JFileChooser fileChooser = new JFileChooser();
fileChooser.setDialogTitle("Open a file to parse");
fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
int userSelection = fileChooser.showOpenDialog(null);
if (userSelection == JFileChooser.APPROVE_OPTION) {
szInputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
cellDesigner2Sbgnml = szInputFilePath.endsWith(".xml");
jtfOpenFilePath.setText(szInputFilePath);
szOutputFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.'));
if (cellDesigner2Sbgnml) {
szOutputFilePath = szOutputFilePath.concat("_converted.sbgn");
} else {
szOutputFilePath = szOutputFilePath.concat("_converted.xml");
}
jtfSaveFilePath.setText(szOutputFilePath);
szLogsFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.')).concat("_logs.txt");
jtfLogFilePath.setText(szLogsFilePath);
}
}
};
}
}
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/package-info.java deleted 100644 → 0
+ 0
− 8
View file @ 320fc51c
/**
*
*/
/**
* @author Michał Kuźma
*
*/
package lcsb.mapviewer.converter.model.sbgnml.console.gui;
\ No newline at end of file
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/package-info.java deleted 100644 → 0
+ 0
− 5
View file @ 320fc51c
/**
* Package where console application interface for CellDesigner-SBGNML
* transformation is implemented.
*/
package lcsb.mapviewer.converter.model.sbgnml.console;
\ No newline at end of file
pom.xml
+ 0
− 2
View file @ caf12fff
......@@ -48,8 +48,6 @@
<apache.commons-text.version>1.6</apache.commons-text.version>
<commons-cli.version>1.4</commons-cli.version>
<batik.version>1.10</batik.version>
<xml-apis.version>1.4.01</xml-apis.version>
......
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