diff --git a/Map.csv b/Map.csv index 46d7a06..69ab3fb 100644 --- a/Map.csv +++ b/Map.csv @@ -8,19 +8,22 @@ sampleCollection.id=PROJECT_ID sampleCollection.acronym=TITLE sampleCollection.name=name sampleCollection.description=DESCRIPTION -sampleCollection.collectionType=GROUP_NAME sampleCollection.contactInformation=CONTACT_ID study.id=STUDY_CODE study.name=NAME -study.description=KI_STUDY_NAME +study.description=DESCRIPTION study.contactInformation=CONTACT_ID +study.studyDesign=KI_STUDY_TYPE list.sex.Male=Sexvalue2 -list.sex.Female=Sexvalue1 -list.sex.Unknown=Sexvalue3 +list.sex.Female=Sexvalue3 +list.sex.Undifferentiated=Sexvalue1 +list.materialType.Blood=Material Typevalue1 list.materialType.Immortalized\ Cell\ Lines=Material Typevalue2 -list.materialType.Isolated\ Pathogen=Material Typevalue5 -list.materialType.Plasma=Material Typevalue4 -list.materialType.Tissue\ (FFPE)=Material Typevalue7 -list.dataCategories.Physiological/Biochemical\ measurements=DCvalue1 -list.collectionType.Twin-study=CTvalue1 -list.collectionType.Quality\ control=CTvalue2 +list.materialType.Isolated\ Pathogen=Material Typevalue4 +list.materialType.Tissue\ (Frozen)=Material Typevalue7 +list.dataCategories.Biological\ samples=DCvalue3 +list.dataCategories.Physiological/Biochemical\ measurements=DCvalue2 +list.dataCategories.Other=DCvalue1 +list.collectionType.Twin-study=CTvalue2 +list.collectionType.Population-based=CTvalue3 +list.collectionType.Disease\ specific=CTvalue4 diff --git a/build/built-jar.properties b/build/built-jar.properties index 4d2f031..1caa836 100644 --- a/build/built-jar.properties +++ b/build/built-jar.properties @@ -1,4 +1,4 @@ -#Thu, 03 Mar 2016 15:10:23 +0100 - - -C\:\\Users\\suyama\\Documents\\NetBeansProjects\\Mapper= +#Mon, 07 Mar 2016 14:21:51 +0100 + + +C\:\\Users\\suyama\\Documents\\NetBeansProjects\\Mapper= diff --git a/build/classes/.netbeans_automatic_build b/build/classes/.netbeans_automatic_build deleted file mode 100644 index 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- diff --git a/dist/Mapper.jar b/dist/Mapper.jar index 6702101..a659c13 100644 Binary files a/dist/Mapper.jar and b/dist/Mapper.jar differ diff --git a/dist/README.TXT b/dist/README.TXT index e6392f4..7d7bae8 100644 --- a/dist/README.TXT +++ b/dist/README.TXT @@ -29,4 +29,4 @@ the projects runtime path. * To set a main class in a standard Java project, right-click the project node in the Projects window and choose Properties. Then click Run and enter the class name in the Main Class field. Alternatively, you can manually type the -class name in the manifest Main-Class element. +class name in the manifest Main-Class element. diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml index 7c28631..1beac2b 100644 --- a/nbproject/private/private.xml +++ b/nbproject/private/private.xml @@ -1,12 +1,10 @@ - - - - - - file:/C:/Users/suyama/Documents/NetBeansProjects/MapperMe/src/my/mapper/MapperMeUI.java - file:/C:/Users/suyama/Documents/NetBeansProjects/MapperMe/Map.csv - file:/C:/Users/suyama/Documents/NetBeansProjects/MapperMe/Standard.csv - file:/C:/Users/suyama/Documents/NetBeansProjects/MapperMe/Standard_List_Values.csv - - - + + + + + + file:/C:/Users/suyama/Documents/NetBeansProjects/Mapper/Map.csv + file:/C:/Users/suyama/Documents/NetBeansProjects/Mapper/src/my/mapper/MapperUI.java + + + diff --git a/src/my/mapper/MapperUI.java b/src/my/mapper/MapperUI.java index 6ee1569..5772254 100644 --- a/src/my/mapper/MapperUI.java +++ b/src/my/mapper/MapperUI.java @@ -13,15 +13,14 @@ import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; -import java.util.HashMap; import java.util.Iterator; import java.util.List; -import java.util.Map; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JLabel; +import javax.swing.JOptionPane; import javax.swing.JTable; import javax.swing.table.DefaultTableModel; @@ -35,8 +34,6 @@ public class MapperUI extends javax.swing.JFrame { * Creates new form MapperUI */ private String refAttr = ""; - private String refEntity = ""; - String tabName=""; private static final String STANDARD_FILE_NAME = "Standard.csv"; private static final String STANDARD_LIST_VALUES_FILE_NAME = "Standard_List_Values.csv"; @@ -52,85 +49,61 @@ public MapperUI() { @SuppressWarnings("unchecked") public void readEntityFileInTable(JTable TheTable, JLabel TheLabel, JComboBox TheComboBox){ - - JFileChooser fileChooser = new JFileChooser(); fileChooser.setCurrentDirectory(new File(System.getProperty("user.home"))); int result = fileChooser.showOpenDialog(this); if (result == JFileChooser.APPROVE_OPTION) { File selectedFile = fileChooser.getSelectedFile(); TheLabel.setText(selectedFile.getAbsolutePath()); - System.out.println("File chosen"); - } - else if(result == JFileChooser.CANCEL_OPTION){ - System.out.println("File not chosen"); - } - // parse file and fill table - String csvFile = TheLabel.getText(); - BufferedReader br = null; - String line = ""; - String separator = (String) TheComboBox.getSelectedItem(); - if(("Tab".equals(separator))){ - separator="\t"; - } - - String[] term = null; - int row = 0; + + String csvFile = TheLabel.getText(); + BufferedReader br = null; + String line = ""; + String separator = (String) TheComboBox.getSelectedItem(); - DefaultTableModel myModel = (DefaultTableModel)TheTable.getModel(); - //Reset the table - while(myModel.getRowCount()>0) - { - myModel.removeRow(0); - } + if(("Tab".equals(separator))){ + separator="\t"; + } - // read file + String[] term = null; - try { - - Map maps = new HashMap(); - - br = new BufferedReader(new FileReader(csvFile)); - //while ((line = br.readLine()) != null) { - line = br.readLine(); - // use comma as separator - term = line.split(separator); - - //maps.put(term[0], term[1]); - - //} + DefaultTableModel myModel = (DefaultTableModel)TheTable.getModel(); - //loop map - int size = term.length; + while(myModel.getRowCount()>0){ + myModel.removeRow(0); + } + + try { + br = new BufferedReader(new FileReader(csvFile)); + line = br.readLine(); + term = line.split(separator); int columnNumber = 1; - for (String str : term) { - //fill jTable3 - mapper talbe - //System.out.println(str); - //row = myModel.getRowCount()+1; + + for (String str : term) { Object[] RowData = {columnNumber,str}; - + myModel.addRow(RowData); columnNumber++; - } - - } - catch (FileNotFoundException e) { - e.printStackTrace(); - } - catch (IOException e) { - e.printStackTrace(); - } - finally { - if (br != null) { - try { - br.close(); - } - catch (IOException e) { - e.printStackTrace(); - } - } - } - + } + + } + catch (FileNotFoundException e) { + e.printStackTrace(); + } + catch (IOException e) { + e.printStackTrace(); + } + finally { + if (br != null) { + try { + br.close(); + } + catch (IOException e) { + e.printStackTrace(); + } + } + } + } } @@ -152,50 +125,24 @@ public void readListValuesFileInTable(JTable TheTable, JLabel TheLabel, JComboBo } String[] term = null; - int row = 0; DefaultTableModel myModel = (DefaultTableModel)TheTable.getModel(); - //Reset the table myModel.setRowCount(0); - /* - while(myModel.getRowCount()>0) - { - myModel.removeRow(0); - } - */ - // read file - - try - { + try{ String line = ""; - //Create the file reader + br = new BufferedReader(new FileReader(csvFile)); - - - - - br.readLine(); // Read and skip the first line. - //Read the file line by line - - while ((line = br.readLine()) != null) - { - + br.readLine(); + while ((line = br.readLine()) != null){ term = line.split(separator); Object[] RowData = {term[0],term[1]}; - myModel.addRow(RowData); - - } - - - } catch (Exception e) { e.printStackTrace(); } - finally - { + finally{ try { br.close(); } catch (IOException e) { @@ -203,64 +150,33 @@ public void readListValuesFileInTable(JTable TheTable, JLabel TheLabel, JComboBo } } } - else if(result == JFileChooser.CANCEL_OPTION){ - } - - - - - - - - - } - private void getStandardEntityAttribute(String entity, JTable standardTable ){ - + private void getStandardEntityAttribute(JTable standardTable ){ int selRow = standardTable.getSelectedRow(); refAttr = (String) standardTable.getValueAt(selRow, 1); - refEntity = entity; - } - private void getStandardListValues(String entity, JTable standardTable) { + private void getStandardListValues(JTable standardTable) { int selRow = standardTable.getSelectedRow(); refAttr = (String) standardTable.getValueAt(selRow, 1); - refEntity = entity; } private void setStandardEntityAttribute(JTable localTable) { - // TODO add your handling code here: - /* - if (refEntity != ""){ - int selRow = localTable.getSelectedRow(); - localTable.setValueAt(refEntity, selRow, 2); - } - */ if (refAttr != ""){ int selRow = localTable.getSelectedRow(); localTable.setValueAt(refAttr, selRow, 2); } - refEntity=""; refAttr=""; } private void setStandardListValues(JTable localTable) { - // TODO add your handling code here: - /* - if (refEntity != ""){ - int selRow = localTable.getSelectedRow(); - localTable.setValueAt(refEntity, selRow, 2); - } - */ if (refAttr != ""){ int selRow = localTable.getSelectedRow(); localTable.setValueAt(refAttr, selRow, 2); } - refEntity=""; refAttr=""; } @@ -972,19 +888,15 @@ private List initEntity(String pathToFile){ DefaultTableModel tableModelEntityMap = (DefaultTableModel)TableEntityMap.getModel(); List entityNameList = new ArrayList(); String[] term = null; - try - { + try{ String line = ""; - //Create the file reader + fileReader = new BufferedReader(new FileReader(pathToFile)); String entity = ""; + fileReader.readLine(); - - fileReader.readLine(); // Read and skip the first line. - //Read the file line by line - while ((line = fileReader.readLine()) != null) - { + while ((line = fileReader.readLine()) != null){ term = line.split(DELIMITER); Object[] RowData = {term[0],term[1],term[2]}; @@ -1003,15 +915,11 @@ private List initEntity(String pathToFile){ tableModelEntityMap.addRow(RowDataMap); } - - - } catch (Exception e) { e.printStackTrace(); } - finally - { + finally{ try { fileReader.close(); } catch (IOException e) { @@ -1031,20 +939,15 @@ private List initList(String pathToFile){ DefaultTableModel tableModelListValuesMap = (DefaultTableModel)TableListMap.getModel(); List listValuesNameList = new ArrayList(); String[] term = null; - try - { + try{ String line = ""; - //Create the file reader + fileReader = new BufferedReader(new FileReader(pathToFile)); String entity = ""; + fileReader.readLine(); - - fileReader.readLine(); // Read and skip the first line. - //Read the file line by line - - while ((line = fileReader.readLine()) != null) - { + while ((line = fileReader.readLine()) != null){ term = line.split(DELIMITER); Object[] RowData = {term[0],term[1]}; @@ -1059,18 +962,12 @@ private List initList(String pathToFile){ } tableModelListValuesMap.addRow(RowData); - - } - - - } catch (Exception e) { e.printStackTrace(); } - finally - { + finally{ try { fileReader.close(); } catch (IOException e) { @@ -1093,38 +990,23 @@ private void populateEntityTableFromStandardFile(String entity){ tableModelEntity.setRowCount(0); String[] term = null; - try - { + try{ String line = ""; - //Create the file reader - fileReader = new BufferedReader(new FileReader(pathToFile)); - - - - fileReader.readLine(); // Read and skip the first line. - //Read the file line by line - while ((line = fileReader.readLine()) != null) - { - + fileReader = new BufferedReader(new FileReader(pathToFile)); + fileReader.readLine(); + while ((line = fileReader.readLine()) != null){ term = line.split(DELIMITER); Object[] RowData = {term[0],term[1],term[2]}; if (entity.equals(term[0])){ tableModelEntity.addRow(RowData); } - - - } - - - } catch (Exception e) { e.printStackTrace(); } - finally - { + finally{ try { fileReader.close(); } catch (IOException e) { @@ -1147,38 +1029,23 @@ private void populateListValuesTableFromStandardFile(String listValue){ tableModelListValues.setRowCount(0); String[] term = null; - try - { + try{ String line = ""; - //Create the file reader - fileReader = new BufferedReader(new FileReader(pathToFile)); - - - - fileReader.readLine(); // Read and skip the first line. - //Read the file line by line - while ((line = fileReader.readLine()) != null) - { - + fileReader = new BufferedReader(new FileReader(pathToFile)); + fileReader.readLine(); + while ((line = fileReader.readLine()) != null){ term = line.split(DELIMITER); Object[] RowData = {term[0],term[1]}; if (listValue.equals(term[0])){ tableModelListValues.addRow(RowData); } - - - } - - - } catch (Exception e) { e.printStackTrace(); } - finally - { + finally{ try { fileReader.close(); } catch (IOException e) { @@ -1188,7 +1055,7 @@ private void populateListValuesTableFromStandardFile(String listValue){ } private void mapEntityAttributeResult(JTable TableLocalAttr, JComboBox ComboEntity){ - System.out.println("mapEntityAttributeResult method called"); + DefaultTableModel tableModelLocalAttr = (DefaultTableModel)TableLocalAttr.getModel(); DefaultTableModel tableModelEntityMap = (DefaultTableModel)TableEntityMap.getModel(); String entity = ComboEntity.getSelectedItem().toString(); @@ -1208,16 +1075,15 @@ private void mapEntityAttributeResult(JTable TableLocalAttr, JComboBox ComboEnt } } } - - } + JOptionPane.showMessageDialog(null, ComboEntity.getSelectedItem().toString()+" Entity has been mapped!"); + } private void mapListValuesResult(JTable TableLocalValue, JComboBox ComboList){ - System.out.println("mapListValuesResult method called"); DefaultTableModel tableModelLocalValue = (DefaultTableModel)TableLocalValue.getModel(); DefaultTableModel tableModelListMap = (DefaultTableModel)TableListMap.getModel(); String attribute = ComboList.getSelectedItem().toString(); @@ -1237,17 +1103,16 @@ private void mapListValuesResult(JTable TableLocalValue, JComboBox ComboList){ } } } - - } + JOptionPane.showMessageDialog(null, ComboList.getSelectedItem().toString()+" Attribute has been mapped!"); + } private void formWindowOpened(java.awt.event.WindowEvent evt) {//GEN-FIRST:event_formWindowOpened - //Select Entity tab jTabbedPaneMain.setSelectedIndex(0); String pathToFile; @@ -1259,27 +1124,21 @@ private void formWindowOpened(java.awt.event.WindowEvent evt) {//GEN-FIRST:event pathToFile = current+"\\"+STANDARD_LIST_VALUES_FILE_NAME; ComboList.setModel(new javax.swing.DefaultComboBoxModel(initList(pathToFile).toArray())); - }//GEN-LAST:event_formWindowOpened private void jButtonSaveEntityActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonSaveEntityActionPerformed - // TODO add your handling code here: - mapEntityAttributeResult(TableLocalAttr, ComboEntity); }//GEN-LAST:event_jButtonSaveEntityActionPerformed private void setStandardEntityAttribute(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_setStandardEntityAttribute - // TODO add your handling code here: setStandardEntityAttribute(TableLocalAttr); }//GEN-LAST:event_setStandardEntityAttribute private void getStandardEntityAttribute(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_getStandardEntityAttribute - // TODO add your handling code here: - getStandardEntityAttribute(ComboEntity.getSelectedItem().toString(), TableStandardAttr); + getStandardEntityAttribute(TableStandardAttr); }//GEN-LAST:event_getStandardEntityAttribute private void jButtonBrowseEntityActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonBrowseEntityActionPerformed - // TODO add your handling code here: readEntityFileInTable(TableLocalAttr, LabelEntityFile, ComboSeparatorEntity); }//GEN-LAST:event_jButtonBrowseEntityActionPerformed @@ -1288,7 +1147,6 @@ private void ComboSeparatorEntityActionPerformed(java.awt.event.ActionEvent evt) }//GEN-LAST:event_ComboSeparatorEntityActionPerformed private void ComboEntityActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_ComboEntityActionPerformed - // TODO add your handling code here: populateEntityTableFromStandardFile(ComboEntity.getSelectedItem().toString()); }//GEN-LAST:event_ComboEntityActionPerformed @@ -1297,27 +1155,22 @@ private void ComboSeparatorListActionPerformed(java.awt.event.ActionEvent evt) { }//GEN-LAST:event_ComboSeparatorListActionPerformed private void jButtonBrowseListValuesActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonBrowseListValuesActionPerformed - // TODO add your handling code here: readListValuesFileInTable(TableLocalValue, LabelListFile, ComboSeparatorList); }//GEN-LAST:event_jButtonBrowseListValuesActionPerformed private void ComboListActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_ComboListActionPerformed - // TODO add your handling code here: populateListValuesTableFromStandardFile(ComboList.getSelectedItem().toString()); }//GEN-LAST:event_ComboListActionPerformed private void getStandardListValues(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_getStandardListValues - // TODO add your handling code here: - getStandardListValues(ComboList.getSelectedItem().toString(), TableStandardValue); + getStandardListValues(TableStandardValue); }//GEN-LAST:event_getStandardListValues private void setStandardListValues(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_setStandardListValues - // TODO add your handling code here: setStandardListValues(TableLocalValue); }//GEN-LAST:event_setStandardListValues private void jButtonSaveListValuesActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonSaveListValuesActionPerformed - // TODO add your handling code here: mapListValuesResult(TableLocalValue, ComboList); }//GEN-LAST:event_jButtonSaveListValuesActionPerformed @@ -1330,18 +1183,15 @@ private void TableListMapsetSCMIABIS(java.awt.event.MouseEvent evt) {//GEN-FIRST }//GEN-LAST:event_TableListMapsetSCMIABIS private void jButtonSaveMapActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButtonSaveMapActionPerformed - // TODO add your handling code here: saveMapToFile(); }//GEN-LAST:event_jButtonSaveMapActionPerformed private void ComboEntityItemStateChanged(java.awt.event.ItemEvent evt) {//GEN-FIRST:event_ComboEntityItemStateChanged - // TODO add your handling code here: DefaultTableModel tableModelLocalAttr = (DefaultTableModel)TableLocalAttr.getModel(); tableModelLocalAttr.setRowCount(0); }//GEN-LAST:event_ComboEntityItemStateChanged private void ComboListItemStateChanged(java.awt.event.ItemEvent evt) {//GEN-FIRST:event_ComboListItemStateChanged - // TODO add your handling code here: //DefaultTableModel tableModelLocalValue = (DefaultTableModel)TableLocalValue.getModel(); //tableModelLocalValue.setRowCount(0); }//GEN-LAST:event_ComboListItemStateChanged @@ -1355,18 +1205,20 @@ private void saveMapToFile(){ FileWriter fw = null; try { mappingFile.createNewFile(); + LabelMapFile.setText(mappingFile.getAbsolutePath()); fw = new FileWriter(mappingFile); writeEntityMapToFile(TableEntityMap, fw); writeListValuesMapToFile(TableListMap, fw); + JOptionPane.showMessageDialog(null, "The map file has been saved to the location "+mappingFile.getAbsolutePath()); } catch (IOException ex) { Logger.getLogger(MapperUI.class.getName()).log(Level.SEVERE, null, ex); } finally { if(fw != null) try { - fw.close(); + fw.close(); } catch (IOException ex) { - Logger.getLogger(MapperUI.class.getName()).log(Level.SEVERE, null, ex); + Logger.getLogger(MapperUI.class.getName()).log(Level.SEVERE, null, ex); } } } @@ -1559,6 +1411,4 @@ public void run() { private javax.swing.JScrollPane jScrollPane6; private javax.swing.JTabbedPane jTabbedPaneMain; // End of variables declaration//GEN-END:variables - - }