Fixing GATKReport exception handling when loading a report

* allowing tables with no description to go through
   * GATKReportTable should be more lenient with the format requirements (added to-dos for roger)

public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java

@@ -28,10 +28,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.io.BufferedReader;
+import java.io.*;
-import java.io.File;
-import java.io.FileReader;
-import java.io.PrintStream;
 import java.util.Collection;
 import java.util.TreeMap;
 
@@ -85,10 +82,17 @@ public class GATKReport {
      * @param file the file to load
      */
     private void loadReport(File file) {
+        BufferedReader reader;
+        String reportHeader;
         try {
-            BufferedReader reader = new BufferedReader(new FileReader(file));
+            reader = new BufferedReader(new FileReader(file));
+            reportHeader = reader.readLine();
+        } catch (FileNotFoundException e) {
+            throw new ReviewedStingException("Could not open file : " + file);
+        } catch (IOException e) { 
+            throw new ReviewedStingException("Could not read file : " + file);                            
+        }   
 
-            String reportHeader = reader.readLine();
 
         // Read the first line for the version and number of tables.
         version = GATKReportVersion.fromHeader(reportHeader);
@@ -101,20 +105,9 @@ public class GATKReport {
         // Read each tables according ot the number of tables
         for (int i = 0; i < nTables; i++) {
             addTable(new GATKReportTable(reader, version));
-
-                /*
-                if ( !blankLine.equals("") ) {
-                    throw new StingException("The GATK Report File is corrupted or not formatted correctly");
-                }
-                */
         }
 
 
-        } catch (Exception e) {
-            // todo - improve exception handling
-            //throw new StingException("Cannot read GATKReport: " + e);
-            e.printStackTrace();
-        }
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.io.BufferedReader;
+import java.io.IOException;
 import java.io.PrintStream;
 import java.util.*;
 import java.util.regex.Matcher;
@@ -54,9 +55,13 @@ public class GATKReportTable {
 
     private GATKReportColumns columns;
 
-    public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
+    private static final String COULD_NOT_READ_HEADER = "Could not read the header of this file -- ";
-        try {
+    private static final String COULD_NOT_READ_COLUMN_NAMES = "Could not read the column names of this file -- ";
+    private static final String COULD_NOT_READ_DATA_LINE = "Could not read a data line of this table -- ";
+    private static final String COULD_NOT_READ_EMPTY_LINE = "Could not read the last empty line of this table -- ";
+    private static final String OLD_GATK_TABLE_VERSION = "We no longer support older versions of the GATK Tables";
 
+    public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
         int counter = 0;
 
         switch (version) {
@@ -66,14 +71,18 @@ public class GATKReportTable {
     
                 // Read in the headers
                 for (int i = 0; i < nHeaders; i++) {
+                    try {
                         tableHeaders[i] = reader.readLine();
+                    } catch (IOException e) {
+                        throw new ReviewedStingException(COULD_NOT_READ_HEADER + e.getMessage());
+                    }
                 }
                 String[] tableData = tableHeaders[0].split(":");
                 String[] userData = tableHeaders[1].split(":");
     
                 // Fill in the fields
                 tableName = userData[2];
-                    tableDescription = userData[3];
+                tableDescription = (userData.length <= 3) ? "" : userData[3];                                           // table may have no description! (and that's okay)
                 primaryKeyDisplay = Boolean.parseBoolean(tableData[2]);
                 columns = new GATKReportColumns();
     
@@ -82,7 +91,12 @@ public class GATKReportTable {
     
     
                 // Read column names
-                    String columnLine = reader.readLine();
+                String columnLine;
+                try {
+                columnLine = reader.readLine();
+                } catch (IOException e) {
+                    throw new ReviewedStingException(COULD_NOT_READ_COLUMN_NAMES);
+                }
     
                 List<Integer> columnStarts = TextFormattingUtils.getWordStarts(columnLine);
                 String[] columnNames = TextFormattingUtils.splitFixedWidth(columnLine, columnStarts);
@@ -106,7 +120,13 @@ public class GATKReportTable {
     
                 for (int i = 0; i < nRows; i++) {
                     // read line
-                        List<String> lineSplits = Arrays.asList(TextFormattingUtils.splitFixedWidth(reader.readLine(), columnStarts));
+                    String dataLine;
+                    try {
+                        dataLine = reader.readLine(); 
+                    } catch (IOException e) {
+                        throw new ReviewedStingException(COULD_NOT_READ_DATA_LINE + e.getMessage());
+                    }
+                    List<String> lineSplits = Arrays.asList(TextFormattingUtils.splitFixedWidth(dataLine, columnStarts));
     
                     for (int columnIndex = 0; columnIndex < nColumns; columnIndex++) {
     
@@ -127,12 +147,15 @@ public class GATKReportTable {
                 }
     
     
+                try {
                     reader.readLine();
-                    // When you see empty line or null, quit out
+                } catch (IOException e) {
+                    throw new ReviewedStingException(COULD_NOT_READ_EMPTY_LINE + e.getMessage());
                 }  
-        } catch (Exception e) {
+            break;
-            //throw new StingException("Cannot read GATKReport: " + e);
+            
-            e.printStackTrace();
+            default: 
+                throw new ReviewedStingException(OLD_GATK_TABLE_VERSION);
         }
     }
 
@@ -418,12 +441,11 @@ public class GATKReportTable {
         if (newValue != null)
             value = newValue;
 
-        if (column.getDataType().equals(GATKReportDataType.fromObject(value)) ||
+        // todo -- Types have to be more flexible. For example, %d should accept Integers, Shorts and Bytes.
-                column.getDataType().equals(GATKReportDataType.Unknown) )
+        if (column.getDataType().equals(GATKReportDataType.fromObject(value)) || column.getDataType().equals(GATKReportDataType.Unknown) )
             columns.get(columnName).put(primaryKey, value);
         else
-            throw new ReviewedStingException(String.format("Tried to add an object of type: %s to a column of type: %s",
+            throw new ReviewedStingException(String.format("Tried to add an object of type: %s to a column of type: %s", GATKReportDataType.fromObject(value).name(), column.getDataType().name()));
-                    GATKReportDataType.fromObject(value).name(), column.getDataType().name()));
     }
 
     /**