MGG ( Microbetag Gui )
MGG Progress Documentation
WEEK 1 & WEEK 2
- ImportFileTask
- ImportFileTaskFactory
These classes enable users to import and process CSV/TSV files.
ImportFileTask
/**
* This class represents a task for importing a CSV file and processing it into a JSON array.
*
* The CSV file is read and parsed into a list of string arrays, where each array represents a row in the CSV file.
* The task then creates a JSON array where each JSON object corresponds to a row in the CSV file.
* The JSON array is then set in the MGGManager
*
* The task also provides options to display the JSON data in a panel and to write the JSON data to a file.
*
*/
public class ImportFileTask extends AbstractTask {
final CySwingApplication swingApplication;
final CyApplicationManager cyApplicationManager;
private final MGGManager mggManager;
private String filePath;
private JSONObject jsonObject;
@Tunable(description = "Display Data", groups = { "Display Settings" },
tooltip="If checked, the Data will be displayed in a panel")
public boolean showJSONInPanel = true;
@Tunable(description="Write JSON to file",groups = { "Create File Settings" },tooltip="If checked,
a new JSON file will be created in the same path as the original file",exampleStringValue="true")
public boolean writeToFile = true;
@Tunable(description="Choose input type", groups={"Input Settings"}, gravity=1.0, required=true)
public ListSingleSelection<String> input = new ListSingleSelection<>("abundance_table", "network");
@Tunable(description="Choose taxonomy Database", groups={"Input Settings"}, gravity=2.0, required=true)
public ListSingleSelection<String>taxonomy = new ListSingleSelection<>("gtdb", "dada2", "qiime2");
@Tunable(description="PhenDB", longDescription="Choose whether to use PhenDB.", groups={"Input Settings"},
gravity=3.0, exampleStringValue="True, False", required=true)
public boolean phenDB;
@Tunable(description="FAPROTAX", longDescription="Choose whether to use FAPROTAX.",
groups={"Input Settings"}, gravity=4.0, exampleStringValue="True, False", required=true)
public boolean faproTax;
@Tunable(description="NetCooperate", longDescription="Choose whether to use NetCooperate.",
groups={"Input Settings"}, gravity=5.0, exampleStringValue="True, False", required=true)
public boolean netCooperate;
@Tunable(description="NetCmpt", longDescription="Choose whether to use NetCmpt.",
groups={"Input Settings"}, gravity=6.0, exampleStringValue="True, False", required=true)
public boolean netCmpt;
@Tunable(description="Pathway Complementarity", longDescription="Choose whether to use pathway complementarity.", groups={"Input Settings"},
gravity=7.0, exampleStringValue="True, False", required=true)
public boolean pathwayComplementarity;
/**
* Constructor for the ImportFileTask class.
*
* @param cytoscapeDesktopService The CySwingApplication service, which provides access to Cytoscape desktop components.
* @param cyApplicationManager2 The CyApplicationManager service, which provides access to the current network and view.
* @param filePath The path of the CSV file to import.
*
*/
public ImportFileTask(String filePath,MGGManager mggManager) {
this.swingApplication = mggManager.getService(CySwingApplication.class);
this.cyApplicationManager = mggManager.getService(CyApplicationManager.class);
this.filePath = filePath;
this.mggManager = mggManager;
}
@Override
public void run(TaskMonitor taskMonitor) {
taskMonitor.setTitle("Importing File");
taskMonitor.setStatusMessage("Reading file");
try {
// Call CSVReader from Utils to parse the TSV/CSV file with tab delimiter
List<String[]> csvData = CSVReader.readCSV(taskMonitor, filePath);
// Find the headers(the first row that has more than 1 columns)
String[] headers = null;
for (int i = 0; i < csvData.size(); i++) {
String[] row = csvData.get(i);
if (row.length > 1) {
headers = row;
csvData.remove(i); // remove the header row
break;
}
}
taskMonitor.setStatusMessage("Processing data");
// Create JSONArray to hold the JSONObjects
JSONArray jsonArray = new JSONArray();
JSONArray header = new JSONArray();
for (String hdr:headers) {
header.add(hdr);
}
jsonArray.add(header);
// Iterate each row of CSV
for (String[] values : csvData) {
// Skip rows with only one column
if (values.length <= 1) {
continue;
}
JSONArray row=new JSONArray();
for (String value:values) {
row.add(value);
}
jsonArray.add(row);
}
// Create a new JSONObject
JSONObject jsonObject = new JSONObject();
// Add the jsonArray to the jsonObject
jsonObject.put("data", jsonArray);
// Create a new JSONArray for the input parameters
JSONArray inputParameters = new JSONArray();
inputParameters.add(input.getSelectedValue());
inputParameters.add(taxonomy.getSelectedValue());
inputParameters.add(phenDB);
inputParameters.add(faproTax);
inputParameters.add(netCooperate);
inputParameters.add(netCmpt);
inputParameters.add(pathwayComplementarity);
// Add the input parameters to the jsonObject
jsonObject.put("inputParameters", inputParameters);
// Set the JSON array in the MGGManager
mggManager.setJsonObject(jsonObject);
taskMonitor.setStatusMessage("Displaying data in panel");
if (writeToFile) {
try {
String jsonFilePath = filePath + ".json";
FileWriter writer = new FileWriter(jsonFilePath);
writer.write(jsonArray.toJSONString());
writer.close();
} catch (IOException e) {
taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Error while writing the file: " + e.getMessage());
e.printStackTrace();
}
}
// Show the JSON data in a panel if showJSONInPanel
if (showJSONInPanel) {
SwingUtilities.invokeLater(() -> showDataInPanel(jsonObject));
}
taskMonitor.setProgress(1.0);
taskMonitor.setStatusMessage("Finished processing file.");
} catch (IOException e) {
taskMonitor.showMessage(TaskMonitor.Level.ERROR, " Error while processing the file: " + e.getMessage());
e.printStackTrace();
}}
private void showDataInPanel(JSONObject jsonObject) {
//JSONDisplayPanel panel = new JSONDisplayPanel(mggManager, jsonObject);
JsonResultPanel panel = new JsonResultPanel(mggManager, jsonObject);
mggManager.registerService(panel, CytoPanelComponent.class, new Properties());
/*
* JFrame frame = new JFrame("OTU/ASV Data");
* frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
* frame.getContentPane().add(panel); frame.pack(); frame.setVisible(true);
*/
}
ImportFileTaskFactory
public class ImportFileTaskFactory implements TaskFactory {
private final MGGManager mggManager;
public ImportFileTaskFactory(MGGManager mggManager) {
this.mggManager=mggManager;
}
@Override
public TaskIterator createTaskIterator() {
// Use a JFileChooser to get the file path
JFileChooser fileChooser = new JFileChooser();
int option = fileChooser.showOpenDialog(null);
if (option == JFileChooser.APPROVE_OPTION) {
File selectedFile = fileChooser.getSelectedFile();
String filePath = selectedFile.getAbsolutePath();
return new TaskIterator(new ImportFileTask(filePath, mggManager));
} else if (option == JFileChooser.CANCEL_OPTION) {
// User cancelled the file selection, return an empty TaskIterator
return new TaskIterator();
} else {
// An error occurred or no file was selected
String errorMessage = "Error selecting file";
// You can display an error message or handle the error in any other way appropriate for your application
JOptionPane.showMessageDialog(null, errorMessage, "Error", JOptionPane.ERROR_MESSAGE);
// Return an empty TaskIterator or any other appropriate error handling
return new TaskIterator();
}
}
@Override
public boolean isReady() {
return true;
}
}