Fixed xlsx read errors

src/main/Main.java

@@ -225,6 +225,13 @@ public class Main {
 			 obj.put("Subject age", currentRow[1]);
 			 obj.put("Subject sex", SFB_JSON_Util.getGenderFromStringStart(currentRow[2]).toString());
 			
+			 if (currentRow[3].equals("patient")) {
+				 currentRow[3] = "Patient";
+			 }
+			 if (currentRow[3].toLowerCase().equals("healthy control subject")) {
+				 currentRow[3] = "Healthy control subject";
+			 }
+			 
 			 if (!currentRow[3].equals("Healthy test subject") && !currentRow[3].equals("Patient") && !currentRow[3].equals("Healthy control subject"))
 				 currentRow[3] = "Healthy test subject";
 			 

src/utils/CSV_Reader.java

@@ -5,15 +5,11 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Calendar;
-import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.Scanner;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
-
-import java.io.InputStream;
-
 public class CSV_Reader {
 	
 	private String[] headers;
@@ -198,14 +194,18 @@ public class CSV_Reader {
 			
 			LinkedList<CellData> cellDatas = null;
 			String[] sharedStrings = null;
+			LinkedList<Integer> dateStyles = null;
 			
 			while(ze != null) {
 				String fileName = ze.getName();
 				
-				if ((sheet == null && fileName.contains("worksheets")) || (sheet != null && fileName.endsWith(sheet + ".xml"))) {
+				int workSheetsIndx = fileName.indexOf("/worksheets/");
+				if ((sheet == null && workSheetsIndx != -1 && fileName.lastIndexOf("/") == workSheetsIndx + 11 && fileName.endsWith(".xml")) || (sheet != null && fileName.endsWith(sheet + ".xml"))) {
 					cellDatas = cellDataFromXLSXextractedXML(readZipEntryToString(zis));
 				} else if (fileName.endsWith("sharedStrings.xml")) {
 					sharedStrings = sharedStringsFromXML(readZipEntryToString(zis));
+				} else if (fileName.endsWith("styles.xml")) {
+					dateStyles = dateStylesFromXML(readZipEntryToString(zis));
 				}
 				
 				
@@ -241,7 +241,14 @@ public class CSV_Reader {
             			continue;
             		}
             		c.value = sharedStrings[val];
-            		
+            	}
+            	//Handle Styled Entries
+            	if(c.type == CellData.Type.STYLED) {
+            		if (dateStyles.contains(c.style)) {
+            			c.switchType(CellData.Type.DATE);
+            		} else {
+            			c.switchType(CellData.Type.NUMBER);
+            		}
             	}
             }
             int w = maxX - minX + 1;
@@ -282,6 +289,34 @@ public class CSV_Reader {
         return xml.toString();
 	}
 	
+	private static LinkedList<Integer> dateStylesFromXML(String xml) {
+		int cellStylesIndx = xml.indexOf("<cellXfs");
+		LinkedList<Integer> dateStyles = new LinkedList<>();
+		if (cellStylesIndx == -1)
+			return dateStyles;
+		
+		xml = xml.substring(cellStylesIndx, xml.indexOf("</cellXfs>", cellStylesIndx));
+		int index = 0;
+		int elementIndex = -1;
+		while((index = xml.indexOf("<xf", index)) != -1) {
+			elementIndex++;
+			int endOfTag = xml.indexOf('>', index);
+			
+			int numFormatIdIndx = xml.indexOf("numFmtId=\"", index);
+			if (numFormatIdIndx > endOfTag) {
+				index = endOfTag;
+				continue;
+			}
+			numFormatIdIndx += 10;
+			int formatId = Integer.parseInt(xml.substring(numFormatIdIndx, xml.indexOf('\"', numFormatIdIndx)));
+			
+			if (formatId == 14 || formatId == 15 || formatId == 16 || formatId == 17 || formatId == 22)
+				dateStyles.add(elementIndex);
+			index = endOfTag;
+		}
+		return dateStyles;
+	}
+	
 	private static String[] sharedStringsFromXML(String xml) {
 		LinkedList<String> res = new LinkedList<>();
 		
@@ -308,16 +343,19 @@ public class CSV_Reader {
 			CellData.Type type = CellData.Type.NUMBER;
 			int typeString = sheetData.indexOf("t=\"s\"", index);
 			boolean isStr = typeString != -1 && typeString < endOfTag;
+			int style = 0;
 			
 			if (isStr) {
 				type = CellData.Type.STRING;
-			}
-			
-			int typeDate = sheetData.indexOf("s=\"1\"", index);
-			boolean isDate = typeDate != -1 && typeDate < endOfTag;
+			} else {
 			
-			if (isDate) {
-				type = CellData.Type.DATE;
+				int typeStyled = sheetData.indexOf("s=\"", index);
+				boolean isStyled = typeStyled != -1 && typeStyled < endOfTag;
+				
+				if (isStyled) {
+					type = CellData.Type.STYLED;
+					style = Integer.parseInt(sheetData.substring (typeStyled + 3, sheetData.indexOf('\"', typeStyled + 3)));
+				}
 			}
 			
 			int valOpen = sheetData.indexOf("<v>", endOfTag);
@@ -329,7 +367,7 @@ public class CSV_Reader {
 			}
 			String value = sheetData.substring(valOpen + 3, valClose);
 			
-			cellData.add(new CellData(cellID, value, type));
+			cellData.add(new CellData(cellID, value, type, style));
 			index = endOfTag;
 		}
 		
@@ -338,18 +376,24 @@ public class CSV_Reader {
 	
 	private static class CellData {
 		private static final Calendar CALENDAR = Calendar.getInstance();
-		public static enum Type {NUMBER, STRING, DATE}
+		public static enum Type {NUMBER, STRING, DATE, STYLED}
 		
 		public String cellID;
 		public String value;
 		public Type type;
+		public int style;
 		
-		public CellData(String cellID, String value, Type type) {
+		public CellData(String cellID, String value, Type type, int style) {
 			this.cellID = cellID;
 			this.value = value;
 			this.type = type;
-			
-			if (type == Type.DATE) {
+			this.style = style;
+		
+		}
+		
+		public void switchType(Type newType) {
+			type = newType;
+			if (newType == Type.DATE) {
 				if (this.value.contains(".")) {
 					this.value = this.value.substring(0, value.indexOf("."));
 				}