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          * Accepts input as valid unless it is a test input\r
  19          * \r
  20          * @param input\r
  21          * @return\r
  22          */\r
  23         static boolean accept(File input) {\r
  24                 if (input == null)\r
  25                         return true;\r
  26                 assert input.isFile() : "Input file is not a file! " + input;\r
  27                 String[] fastainput = WSTester.fastaInput2records.split("\n");\r
  28                 assert fastainput.length == 4;\r
  29                 String[] aligninput = WSTester.fastaAlignment.split("\n");\r
  30                 assert aligninput.length == 4;\r
  31                 // We do now know the type of the input here so must compare with both\r
  32                 // references\r
  33                 boolean isReference = compareLines(input, fastainput);\r
  34                 if (!isReference) {\r
  35                         isReference = compareLines(input, aligninput);\r
  36                 }\r
  37                 // only accept genuine input\r
  38                 return !isReference;\r
  39         }\r
  40 \r
  41         private static boolean compareLines(File input, String[] reference) {\r
  42                 BufferedReader reader = null;\r
  43                 boolean status = true;\r
  44                 try {\r
  45                         reader = new BufferedReader(new FileReader(input));\r
  46                         // only compare first four lines of the file with reference\r
  47                         // because the reference length is only 4 lines\r
  48                         for (int i = 0; i < 4; i++) {\r
  49                                 String line = reader.readLine();\r
  50                                 if (Util.isEmpty(line)) {\r
  51                                         status = false;\r
  52                                         break;\r
  53                                 }\r
  54                                 line = line.trim();\r
  55                                 if (!line.equals(reference[i].trim())) {\r
  56                                         status = false;\r
  57                                         break;\r
  58                                 }\r
  59                         }\r
  60                         reader.close();\r
  61                 } catch (IOException ioe) {\r
  62                         log.warn(ioe, ioe.getCause());\r
  63                 } finally {\r
  64                         FileUtil.closeSilently(reader);\r
  65                 }\r
  66                 return status;\r
  67         }\r
  68 }\r