webservices/compbio/stat/collector/InputFilter.java

   1 package compbio.stat.collector;\r
   2 \r
   3 import java.io.BufferedReader;\r
   4 import java.io.File;\r
   5 import java.io.FileReader;\r
   6 import java.io.IOException;\r
   7 \r
   8 import org.apache.log4j.Logger;\r
   9 \r
  10 import compbio.util.FileUtil;\r
  11 import compbio.util.Util;\r
  12 import compbio.ws.client.WSTester;\r
  13 \r
  14 public class InputFilter {\r
  15 \r
  16         private static final Logger log = Logger.getLogger(InputFilter.class);\r
  17 \r
  18         /**\r
  19          * Accepts input as valid unless it is a test input\r
  20          * \r
  21          * @param input\r
  22          * @return\r
  23          */\r
  24         static boolean accept(File input) {\r
  25                 if (input == null)\r
  26                         return true;\r
  27                 assert input.isFile() : "Input file is not a file! " + input;\r
  28                 String[] fastainput = WSTester.fastaInput2records.split("\n");\r
  29                 assert fastainput.length == 4;\r
  30                 String[] aligninput = WSTester.fastaAlignment.split("\n");\r
  31                 assert aligninput.length == 4;\r
  32                 String[] rnaaligninput = WSTester.clustalRNAAlignment.split("\n");\r
  33                 assert aligninput.length == 5;\r
  34                 // We do now know the type of the input here so must compare with both\r
  35                 // references\r
  36                 boolean isReference = compareLines(input, fastainput);\r
  37                 if (!isReference) {\r
  38                         isReference = compareLines(input, aligninput);\r
  39                 }\r
  40                 if (!isReference) {\r
  41                         isReference = compareClustalLines(input, rnaaligninput);\r
  42                 }\r
  43                 // only accept genuine input\r
  44                 return !isReference;\r
  45         }\r
  46 \r
  47         private static boolean compareLines(File input, String[] reference) {\r
  48                 BufferedReader reader = null;\r
  49                 boolean status = true;\r
  50                 try {\r
  51                         reader = new BufferedReader(new FileReader(input));\r
  52                         // only compare first four lines of the file with reference\r
  53                         // because the reference length is only 4 lines\r
  54                         for (int i = 0; i < reference.length; i++) {\r
  55                                 String line = reader.readLine();\r
  56                                 if (Util.isEmpty(line)) {\r
  57                                         status = false;\r
  58                                         break;\r
  59                                 }\r
  60                                 line = line.trim();\r
  61                                 if (!line.equals(reference[i].trim())) {\r
  62                                         status = false;\r
  63                                         break;\r
  64                                 }\r
  65                         }\r
  66                         reader.close();\r
  67                 } catch (IOException ioe) {\r
  68                         log.warn(ioe, ioe.getCause());\r
  69                 } finally {\r
  70                         FileUtil.closeSilently(reader);\r
  71                 }\r
  72                 return status;\r
  73         }\r
  74 \r
  75         private static boolean compareClustalLines(File input, String[] reference) {\r
  76                 BufferedReader reader = null;\r
  77                 boolean status = true;\r
  78                 try {\r
  79                         reader = new BufferedReader(new FileReader(input));\r
  80                         // only compare first four lines of the file with reference\r
  81                         // because the reference length is only 4 lines\r
  82                         int i = 0;\r
  83                         String line;\r
  84                         while (null != (line = reader.readLine())) {\r
  85                                 if (!Util.isEmpty(line)) {\r
  86                                         line = line.trim();\r
  87                                         if (!line.equals(reference[i].trim())) {\r
  88                                                 status = false;\r
  89                                                 break;\r
  90                                         }\r
  91                                         ++i;\r
  92                                 }\r
  93                         }\r
  94                         reader.close();\r
  95                 } catch (IOException ioe) {\r
  96                         log.warn(ioe, ioe.getCause());\r
  97                 } finally {\r
  98                         FileUtil.closeSilently(reader);\r
  99                 }\r
 100                 return status;\r
 101         }\r
 102 }\r