change mapper output to generate the file according to the latest parser

requirement.
MIABIS · Oct 19, 2015 · afa72e5 · afa72e5
1 parent 7a6df05
commit afa72e5
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Showing 2 changed files with 70 additions and 43 deletions.
diff --git a/Map.csv b/Map.csv
@@ -1,23 +1,29 @@
-1,PROJECT_ID,Sample Collection,ID
-2,name,Sample Collection,Name
-3,TITLE,Sample Collection,Acronym
-4,DESCRIPTION,Sample Collection,Description
-9,CONTACT_ID,Sample Collection,Contact Information ID
-1,STUDY_CODE,Study,ID
-2,NAME,Study,Name
-4,DESCRIPTION,Study,Description
-5,KI_STUDY_TYPE,Study,Study Design
-9,CONTACT_ID,Study,Contact Information ID
-1,provid,Sample,Sample ID
-3,SAMPLE_TYPE,Sample,Material Type
-7,T_GENDER,Sample,Sex
-13,PROJECT_ID,Sample,Sample Collection ID
-14,STUDY_CODE,Sample,Study ID
-2,FIRST_NAME,Contact Information,First Name
-3,LAST_NAME,Contact Information,Last Name
-4,PHONE_NO,Contact Information,Phone
-5,EMAIL_ADDRESS,Contact Information,Email
-6,ADDRESS,Contact Information,Address
-7,ZIPCODE,Contact Information,ZIP
-8,CITY,Contact Information,City
-9,COUNTRY,Contact Information,Country
+#Sample Collection
+sampleCollection.ID=PROJECT_ID
+sampleCollection.Name=name
+sampleCollection.Acronym=TITLE
+sampleCollection.Description=DESCRIPTION
+sampleCollection.Contact Information ID=CONTACT_ID
+#Study
+study.ID=STUDY_CODE
+study.Name=NAME
+study.Description=DESCRIPTION
+study.Study Design=KI_STUDY_TYPE
+study.Principal Investigator=GROUP_NAME
+study.Contact Information ID=CONTACT_ID
+#Sample
+sample.Sample ID=provid
+sample.Material Type=SAMPLE_TYPE
+sample.Sex=T_GENDER
+sample.Sample Collection ID=PROJECT_ID
+sample.Study ID=STUDY_CODE
+#Contact Information
+
+contactInformation.First Name=FIRST_NAME
+contactInformation.Last Name=LAST_NAME
+contactInformation.Phone=PHONE_NO
+contactInformation.Email=EMAIL_ADDRESS
+contactInformation.Address=ADDRESS
+contactInformation.ZIP=ZIPCODE
+contactInformation.City=CITY
+contactInformation.Country=COUNTRY
diff --git a/src/my/mapper/MapperUI.java b/src/my/mapper/MapperUI.java
@@ -3,7 +3,7 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package src.my.mapper;
+package my.mapper;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -1151,10 +1151,10 @@ private void saveMapToFile(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_sav
         try {
             mappingFile.createNewFile();
             fw = new FileWriter(mappingFile);
-            writeMapToFile(TableSCBiobank, fw);
-            writeMapToFile(TableSTBiobank, fw);
-            writeMapToFile(TableSABiobank, fw);
-            writeMapToFile(TableCIBiobank, fw);
+            writeMapToFile(TableSCBiobank, fw, "Sample Collection");
+            writeMapToFile(TableSTBiobank, fw, "Study");
+            writeMapToFile(TableSABiobank, fw, "Sample");
+            writeMapToFile(TableCIBiobank, fw, "Contact Information");
         } catch (IOException ex) {
             Logger.getLogger(MapperUI.class.getName()).log(Level.SEVERE, null, ex);
         }
@@ -1169,30 +1169,51 @@ private void saveMapToFile(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_sav
 
     }//GEN-LAST:event_saveMapToFile
 
-    private void writeMapToFile(JTable jTable, FileWriter fw) throws IOException{
+    private void writeMapToFile(JTable jTable, FileWriter fw, String entityName) throws IOException{
         DefaultTableModel dtm = (DefaultTableModel) jTable.getModel();
 
         int nRow = dtm.getRowCount(), nCol = dtm.getColumnCount();
         System.out.println(" row "+nRow+" cols "+nCol);
         System.out.println(" dtm.getValueAt(0,0) "+dtm.getValueAt(0,0));
         System.out.println(" dtm.getValueAt(0,3) "+dtm.getValueAt(0,3));
         int prevRow = 0;
+        fw.write("#"+entityName);
+        fw.write(System.lineSeparator());
+        StringBuffer miabisEntityName = new StringBuffer();
+        String[] strArr = entityName.split("\\s");
+        int count = 0;
+        for (String str : strArr) {
+            char[] stringArray = str.trim().toCharArray();
+            if(count == 0){
+            	stringArray[0] = Character.toLowerCase(stringArray[0]);
+            }
+            else{
+            	stringArray[0] = Character.toUpperCase(stringArray[0]);
+            }
+            str = new String(stringArray);
+            miabisEntityName.append(str);
+            count++;
+        }
         for (int i = 0 ; i < nRow ; i++){
-            for (int j = 0 ; j < nCol ; j++){
-            //if(j != 1){
-                    if(dtm.getValueAt(i,2) != null && dtm.getValueAt(i,3) != null){
-                            if(i > prevRow){
-                                    fw.write(System.lineSeparator());
-                            }
-                            fw.write(dtm.getValueAt(i,j).toString());
-                            if(j == 0 || j==1 || j==2){
-                                    fw.write(",");
-                            }
-                            prevRow = i;
-                    }
-
+            //for (int j = 0 ; j < nCol ; j++){
+	            //if(j != 1){
+	                    if(dtm.getValueAt(i,2) != null && dtm.getValueAt(i,3) != null){
+	                            if(i > prevRow){
+	                                    fw.write(System.lineSeparator());
+	                            }
+	                            fw.write(miabisEntityName.toString());
+	                            fw.write(".");
+	                            fw.write(dtm.getValueAt(i,3).toString());
+	                            fw.write("=");
+	                            fw.write(dtm.getValueAt(i,1).toString());
+	                            /*if(j == 0 || j==1 || j==2){
+	                                    fw.write(",");
+	                            }*/
+	                            prevRow = i;
+	                    }
+
+	            //}
             //}
-            }
 
         }
 	fw.write(System.lineSeparator());