runner/compbio/runner/Util.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.runner;\r
  20 \r
  21 import java.io.File;\r
  22 import java.io.FileInputStream;\r
  23 import java.io.FileNotFoundException;\r
  24 import java.io.FileOutputStream;\r
  25 import java.io.IOException;\r
  26 import java.util.List;\r
  27 import java.util.Map;\r
  28 \r
  29 import org.apache.log4j.Logger;\r
  30 \r
  31 import compbio.data.sequence.Alignment;\r
  32 import compbio.data.sequence.ClustalAlignmentUtil;\r
  33 import compbio.data.sequence.FastaSequence;\r
  34 import compbio.data.sequence.RNAstruct;\r
  35 import compbio.data.sequence.Score;\r
  36 import compbio.data.sequence.SequenceUtil;\r
  37 import compbio.data.sequence.UnknownFileFormatException;\r
  38 import compbio.engine.client.ConfExecutable;\r
  39 import compbio.engine.client.ConfiguredExecutable;\r
  40 import compbio.engine.client.Executable;\r
  41 import compbio.engine.conf.PropertyHelperManager;\r
  42 import compbio.metadata.JobSubmissionException;\r
  43 import compbio.metadata.PresetManager;\r
  44 import compbio.metadata.RunnerConfig;\r
  45 import compbio.util.PropertyHelper;\r
  46 \r
  47 public final class Util {\r
  48 \r
  49         public static Logger log = Logger.getLogger(Util.class);\r
  50 \r
  51         private static final PropertyHelper ph = PropertyHelperManager\r
  52                         .getPropertyHelper();\r
  53 \r
  54         public static final String SPACE = " ";\r
  55 \r
  56         public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
  57                         Class<? extends Executable<T>> clazz) {\r
  58                 try {\r
  59                         return ConfExecutable.getRunnerOptions(clazz);\r
  60                 } catch (FileNotFoundException e) {\r
  61                         log.error(\r
  62                                         "Could not load " + clazz + " Parameters !"\r
  63                                                         + e.getMessage(), e.getCause());\r
  64                 } catch (IOException e) {\r
  65                         log.error("IO exception while reading " + clazz + " Parameters !"\r
  66                                         + e.getMessage(), e.getCause());\r
  67                 }\r
  68                 return null;\r
  69         }\r
  70 \r
  71         public static <T> PresetManager<T> getPresets(\r
  72                         Class<? extends Executable<T>> clazz) {\r
  73                 try {\r
  74                         return ConfExecutable.getRunnerPresets(clazz);\r
  75                 } catch (FileNotFoundException e) {\r
  76                         log.warn(\r
  77                                         "No presets are found for " + clazz + " executable! "\r
  78                                                         + e.getLocalizedMessage(), e.getCause());\r
  79                 } catch (IOException e) {\r
  80                         log.warn("IO exception while reading presents! for " + clazz\r
  81                                         + " executable! " + e.getLocalizedMessage(), e.getCause());\r
  82                 }\r
  83                 return null;\r
  84         }\r
  85 \r
  86         public static final Alignment readClustalFile(String workDirectory,\r
  87                         String clustFile) throws UnknownFileFormatException, IOException,\r
  88                         FileNotFoundException, NullPointerException {\r
  89                 assert !compbio.util.Util.isEmpty(workDirectory);\r
  90                 assert !compbio.util.Util.isEmpty(clustFile);\r
  91                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
  92                                 workDirectory, clustFile));\r
  93                 log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
  94                 if (!(cfile.exists() && cfile.length() > 0)) {\r
  95                         throw new FileNotFoundException("Result for the jobId "\r
  96                                         + workDirectory + " with file name " + clustFile\r
  97                                         + " is not found!");\r
  98                 }\r
  99                 return ClustalAlignmentUtil.readClustalFile(cfile);\r
 100         }\r
 101 \r
 102         public static final Map<String, Score> readJronnFile(String workDirectory,\r
 103                         String clustFile) throws UnknownFileFormatException, IOException,\r
 104                         FileNotFoundException, NullPointerException {\r
 105                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 106                 assert !compbio.util.Util.isEmpty(clustFile);\r
 107                 File cfile = new File(compbio.engine.client.Util.getFullPath(\r
 108                                 workDirectory, clustFile));\r
 109                 log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
 110                 if (!(cfile.exists() && cfile.length() > 0)) {\r
 111                         throw new FileNotFoundException("Result for the jobId "\r
 112                                         + workDirectory + " with file name " + clustFile\r
 113                                         + " is not found!");\r
 114                 }\r
 115                 return SequenceUtil.readJRonn(cfile);\r
 116         }\r
 117 \r
 118         public static void writeInput(List<FastaSequence> sequences,\r
 119                         ConfiguredExecutable<?> exec) throws JobSubmissionException {\r
 120 \r
 121                 try {\r
 122                         File filein = new File(exec.getInput());\r
 123                         FileOutputStream fout = new FileOutputStream(filein);\r
 124                         log.debug("File path: " + filein.getAbsolutePath());\r
 125                         SequenceUtil.writeFasta(fout, sequences);\r
 126                         fout.close();\r
 127                 } catch (IOException e) {\r
 128                         log.error("IOException while writing input file into the disk: "\r
 129                                         + e.getLocalizedMessage(), e);\r
 130                         throw new JobSubmissionException(\r
 131                                         "We are sorry by JABAWS server seems to have a problem! "\r
 132                                                         + e.getLocalizedMessage(), e);\r
 133                 }\r
 134         }\r
 135         \r
 136         public static void writeClustalInput(List<FastaSequence> sequences,\r
 137                         ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {\r
 138                 \r
 139                 try {\r
 140                         File filein = new File(exec.getInput());\r
 141                         FileOutputStream fout = new FileOutputStream(filein);\r
 142                         log.debug("File path: " + filein.getAbsolutePath());\r
 143                         SequenceUtil.writeClustal(fout, sequences, gapChar);\r
 144                         fout.close();\r
 145                 } catch (IOException e) {\r
 146                         log.error("IOException while writing input file into the disk: "\r
 147                                         + e.getLocalizedMessage(), e);\r
 148                         throw new JobSubmissionException(\r
 149                                         "We are sorry but JABAWS server seems to have a problem! "\r
 150                                                 + e.getLocalizedMessage(), e);\r
 151                 }\r
 152         }\r
 153         \r
 154         public static final RNAstruct readRNAStructFile(String workDirectory,\r
 155                         String structFile) throws IOException, FileNotFoundException {\r
 156                 assert !compbio.util.Util.isEmpty(workDirectory);\r
 157                 assert !compbio.util.Util.isEmpty(structFile);\r
 158                 File sfile = new File(compbio.engine.client.Util.getFullPath(\r
 159                                 workDirectory, structFile));\r
 160                 log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());\r
 161                 if(!(sfile.exists() && sfile.length() > 0)) {\r
 162                         throw new FileNotFoundException("Result for the jobId "\r
 163                                         + workDirectory + "with file name " + structFile\r
 164                                         + " is not found!");\r
 165                 }\r
 166                 return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(\r
 167                                 new FileInputStream(sfile));\r
 168         }\r
 169         \r
 170         \r
 171 \r
 172 }\r