Skip to content

Commit

Permalink
Bug fixes and New features added
Browse files Browse the repository at this point in the history 
 1) Experiment module:
         * Added import function to import design result
 2) Harvesting module:
        * do not allow to import stocks that already exist in database
        * fixed pedigree generation for PP mating type
        * when create entries for stock_composition table, bulk composition should be synced lastly.
    3) Inventory Module: Allow copy-paste the error message for failed imported stocks
  • Loading branch information
@Felicity117
Felicity117 committed Jun 4, 2018
1 parent 6ca83b0 commit b7ea2fa
Show file tree
Hide file tree
Showing 18 changed files with 369 additions and 144 deletions.
4 changes: 0 additions & 4 deletions AccreteGB-src/src/main/java/org/accretegb/modules/config/AccreteGBConfiguration.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,10 +39,6 @@ public class AccreteGBConfiguration {

private String rPath;

private AccreteGBConfiguration() {
loadConfigs();
}

public static synchronized AccreteGBConfiguration getConfiguration() {
if (accreteGBConfiguration == null) {
accreteGBConfiguration = new AccreteGBConfiguration();
Expand Down
3 changes: 3 additions & 0 deletions ...src/src/main/java/org/accretegb/modules/customswingcomponent/BoundsPopupMenuListener.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,7 @@ public void setScrollBarRequired(boolean scrollBarRequired)
/**
* Alter the bounds of the popup just before it is made visible.
*/
@Override
public void popupMenuWillBecomeVisible(PopupMenuEvent e)
{
JComboBox comboBox = (JComboBox)e.getSource();
Expand Down Expand Up @@ -336,8 +337,10 @@ protected boolean horizontalScrollBarWillBeVisible(BasicComboPopup popup, JScrol
return popupWidth > scrollPane.getPreferredSize().width;
}

@Override
public void popupMenuCanceled(PopupMenuEvent e) {}

@Override
public void popupMenuWillBecomeInvisible(PopupMenuEvent e)
{
// In its normal state the scrollpane does not have a scrollbar
Expand Down
195 changes: 194 additions & 1 deletion ...ain/java/org/accretegb/modules/germplasm/experimentaldesign/ExperimentSelectionPanel.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,18 @@
import org.accretegb.modules.customswingcomponent.Utils;
import org.accretegb.modules.germplasm.stocksinfo.CreateStocksInfoPanel;
import org.accretegb.modules.germplasm.stocksinfo.StocksInfoPanel;
import org.accretegb.modules.hibernate.Classification;
import org.accretegb.modules.hibernate.ExperimentFactor;
import org.accretegb.modules.hibernate.ExperimentFactorValue;
import org.accretegb.modules.hibernate.HibernateSessionFactory;
import org.accretegb.modules.hibernate.MeasurementUnit;
import org.accretegb.modules.hibernate.Passport;
import org.accretegb.modules.hibernate.Stock;
import org.accretegb.modules.hibernate.dao.ExperimentDAO;
import org.accretegb.modules.hibernate.dao.ExperimentFactorDAO;
import org.accretegb.modules.hibernate.dao.ExperimentFactorValueDAO;
import org.accretegb.modules.hibernate.dao.MeasurementUnitDAO;
import org.accretegb.modules.hibernate.dao.StockDAO;
import org.accretegb.modules.tab.TabComponentPanel;
import org.accretegbR.experimental.AlphaDesign;
import org.accretegbR.experimental.CompleteRandomizedDesign;
Expand All @@ -32,6 +36,7 @@
import javax.swing.*;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
import javax.swing.filechooser.FileNameExtensionFilter;
import javax.swing.table.DefaultTableModel;
import javax.swing.text.JTextComponent;

Expand All @@ -51,6 +56,12 @@
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -460,11 +471,193 @@ public void actionPerformed(ActionEvent e) {
}
});
randomizeButton.setName("Button");
designSelectionPanel.add(randomizeButton, "tag submit, sizegroup bttn, alignx right");
JPanel subPanel = new JPanel();
subPanel.add(randomizeButton, "pushx, align right");
setRandomizeButton(randomizeButton);
JButton importButton = new JButton("Import");
importButton.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
importDesignButtonActionPerformed();
}
});
subPanel.add(importButton,"pushx, align right");
designSelectionPanel.add(subPanel, "w 100%, spanx");
return designSelectionPanel;
}

/**
* import design
*/
public void importDesignButtonActionPerformed(){
int option = JOptionPane.showOptionDialog(null,
"Choose an option to proceed",
"",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.INFORMATION_MESSAGE,
null,
new String[]{"Import a file","Download a template","Cancel"},
"default");
String selectedExperiment = (String) experimentSelectionBox.getSelectedItem();
if(option ==JOptionPane.OK_OPTION )
{
//import a file
if (selectedExperiment.equalsIgnoreCase(ExperimentConstants.SPLIT_DESIGN)){
if(!isSplitDesignInputValid()){
return;
}
}
if(isStockNameEmpty()){
try {
final JFileChooser fc = new JFileChooser();
fc.setFileFilter(new FileNameExtensionFilter("Comma separated files(.csv)", "csv"));
int status = fc.showOpenDialog(this);
if (fc.getSelectedFile() == null)
{
return;
}
String filename = fc.getSelectedFile().toString();
if (status == JFileChooser.APPROVE_OPTION) {
if (!(filename.trim().endsWith(".csv"))) {
JLabel errorFields = new JLabel("<HTML><FONT COLOR = Blue>"
+ "File should have a .csv extension only"
+ ".</FONT></HTML>");
JOptionPane.showMessageDialog(null,errorFields);
} else {
DefaultTableModel model = (DefaultTableModel) getExperimentalOutputPanel().getTable().getModel();
Utils.removeAllRowsFromTable(model);
BufferedReader br = new BufferedReader(new FileReader(new File(filename)));
// skip first line
String first = br.readLine();
String line = br.readLine().trim();
HashMap<String, Stock> stockNames = new HashMap<String, Stock>();
if (!selectedExperiment.equalsIgnoreCase(ExperimentConstants.SPLIT_DESIGN)){
while (line != null) {
System.out.println(line);
line = line.trim();
String[] row = line.split(",");
if(row.length != 3 ){
line = br.readLine();
continue;
}
Object[] newRow = new Object[model.getColumnCount()];
newRow[0] = new Boolean(false);
newRow[1] = row[0]; //plot
newRow[2] = row[1]; //replication
newRow[3] = null; //Exp_id
newRow[4] = null; //Exp_factor_value_id
String stockName = row[2];
if(stockNames.containsKey(stockName)){
newRow[5] = stockNames.get(stockName).getStockId(); //stock_id
}else{
System.out.println("\nlooking for "+stockName);
List<Stock> stocks = StockDAO.getInstance().findStockByName(stockName);
if(stocks.size() == 0){
continue;
}
newRow[5] = stocks.get(0).getStockId(); //stock_id
stockNames.put(stockName, stocks.get(0));
}
newRow[6] = stockName; //stockName
Stock s = stockNames.get(stockName);
Passport p = s.getPassport();
if (p != null ){
newRow[7] = p.getAccession_name(); //Accession_name
newRow[8] = p.getPedigree(); //pedigree
newRow[11] = p.getClassification() == null ? "NULL" : p.getClassification().getClassificationCode(); //ClassificationCode
newRow[12] = p.getTaxonomy() == null ? "NULL" : p.getTaxonomy().getPopulation();// Population
}
newRow[9] = s.getStockGeneration() == null ? "NULL" : s.getStockGeneration().getGeneration(); //generation
newRow[10] = s.getStockGeneration() == null ? "NULL" : s.getStockGeneration().getCycle(); //cycle
model.addRow(newRow);
line = br.readLine();
}
}else{
while (line != null) {
System.out.println(line);
line = line.trim();
String[] row = line.split(",");
if(row.length != 6 ){
line = br.readLine();
continue;
}
Object[] newRow = new Object[model.getColumnCount()];
newRow[0] = new Boolean(false);
newRow[1] = row[0]; //plot
newRow[2] = row[1]; //splot
newRow[3] = row[2]; //replication
newRow[4] = row[3]; //tr1
newRow[5] = row[4]; //tr2
newRow[6] = null; //Exp_id
newRow[7] = null; //Exp_factor_value_id
String stockName = row[5];
if(stockNames.containsKey(stockName)){
newRow[8] = stockNames.get(stockName).getStockId(); //stock_id
}else{
System.out.println("\nlooking for "+stockName);
List<Stock> stocks = StockDAO.getInstance().findStockByName(stockName);
if(stocks.size() == 0){
continue;
}
newRow[8] = stocks.get(0).getStockId(); //stock_id
stockNames.put(stockName, stocks.get(0));
}
newRow[9] = stockName; //stockName
Stock s = stockNames.get(stockName);
Passport p = s.getPassport();
if (p != null ){
newRow[10] = p.getAccession_name(); //Accession_name
newRow[11] = p.getPedigree(); //pedigree
newRow[14] = p.getClassification() == null ? "NULL" : p.getClassification().getClassificationCode(); //ClassificationCode
newRow[15] = p.getTaxonomy() == null ? "NULL" : p.getTaxonomy().getPopulation();// Population
}
newRow[12] = s.getStockGeneration() == null ? "NULL" : s.getStockGeneration().getGeneration(); //generation
newRow[13] = s.getStockGeneration() == null ? "NULL" : s.getStockGeneration().getCycle(); //cycle
model.addRow(newRow);
line = br.readLine();
}
}
getExperimentalOutputPanel().getTable().setModel(model);
br.close();
setNumberOfItems();
}
}

}catch (Exception E) {
System.out.println(E.toString());
E.printStackTrace();
}
}

}else if(option == JOptionPane.NO_OPTION){
//download a template
JFileChooser fileChooser = new JFileChooser();
File file = new File(System.getProperty("java.io.tmpdir") + "/" + selectedExperiment.replace("\\s+", "_")+".csv");
fileChooser.setSelectedFile(file);
int approve = fileChooser.showSaveDialog(this);
if (approve != JFileChooser.APPROVE_OPTION) {
return;
}
file = fileChooser.getSelectedFile();
BufferedWriter writer;
try {
writer = new BufferedWriter(new FileWriter(file));
if (!selectedExperiment.equalsIgnoreCase(ExperimentConstants.SPLIT_DESIGN)){
writer.write("Plot,Replication,Stock Name");
}else{
writer.write("Plot,Splot,Replication,tr1,tr2,Stock Name");
}
writer.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return ;
}else{
return;
}

}

/**
* Generate ScrollPane for inputing treatment info
*/
Expand Down
26 changes: 4 additions & 22 deletions AccreteGB-src/src/main/java/org/accretegb/modules/germplasm/harvesting/Bulk.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,10 @@ private void addListeners() {

final CheckBoxIndexColumnTable table = getBulkTablePanel().getTable();
Utils.removeAllRowsFromTable((DefaultTableModel)table.getModel());
table.getModel().addTableModelListener(new TableModelListener() {
public void tableChanged(TableModelEvent e) {
getBulkTablePanel().getNumberOfRows().setText(String.valueOf(getBulkTablePanel().getTable().getRowCount()));
}});
importStocks.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
showPopup();
Expand Down Expand Up @@ -329,27 +333,6 @@ public void actionPerformed(ActionEvent e) {
}
}
});
table.getModel().addTableModelListener(new TableModelListener() {
public void tableChanged(TableModelEvent e) {
bulkTablePanel.getNumberOfRows().setText(String.valueOf(bulkTablePanel.getTable().getRowCount()));
int quantityColumn = table.getIndexOf(ColumnConstants.QUANTITY);
if(e.getColumn() != quantityColumn)
return;
int unitIdColumn = table.getIndexOf(ColumnConstants.UNIT_ID);
int unitColumn = table.getIndexOf(ColumnConstants.UNIT);
MeasurementUnit count = unitsList.get(1);
for(MeasurementUnit unit : unitsList) {
if(unit.getUnitType().equals("count"))
count = unit;
}
for(int row : table.getSelectedRows()) {
if(table.getValueAt(row, unitColumn) == null && Utils.isInteger(String.valueOf(table.getValueAt(row, quantityColumn)))) {
table.setValueAt(count.getMeasurementUnitId(), row, unitIdColumn);
table.setValueAt(count.getUnitType(), row, unitColumn);
}// if not null
}//for
}
});

getBulkTablePanel().getTable().addMouseListener(new MouseAdapter() {
@Override
Expand Down Expand Up @@ -558,7 +541,6 @@ private JPanel getButtonsPanel() {
buttonsPanel.add(multiply);
buttonsPanel.add(mixButton);
buttonsPanel.add(unmixButton, "wrap");

return buttonsPanel;
}

Expand Down
Loading

0 comments on commit b7ea2fa

Please sign in to comment.