-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.util.List;\r
+import java.util.Map;\r
\r
import org.apache.log4j.Logger;\r
\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.ClustalAlignmentUtil;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.engine.client.ConfExecutable;\r
import compbio.engine.client.ConfiguredExecutable;\r
import compbio.engine.client.Executable;\r
import compbio.engine.conf.PropertyHelperManager;\r
-import compbio.metadata.LimitsManager;\r
+import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.PresetManager;\r
import compbio.metadata.RunnerConfig;\r
import compbio.util.PropertyHelper;\r
\r
public final class Util {\r
\r
- private static Logger log = Logger.getLogger(Util.class);\r
-\r
- private static final PropertyHelper ph = PropertyHelperManager\r
- .getPropertyHelper();\r
-\r
- public static final String SPACE = " ";\r
-\r
- /**\r
- * For now just assume that all parameters which came in needs setting it\r
- * will be a client responsibility to prepare RunnerConfig object then\r
- * \r
- * @param rconfig\r
- * @return\r
- * \r
- * public static List<String> toOptionString(RunnerConfig<?>\r
- * rconfig) { String option = ""; List<String> options = new\r
- * ArrayList<String>(); for (Parameter<?> par :\r
- * rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())\r
- * { option = par.getOptionName(); } else { option =\r
- * par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
- * separate options options.add(option); } return options; }\r
- */\r
-\r
- public static <T> LimitsManager<T> getLimits(\r
- Class<? extends Executable<T>> clazz) {\r
- LimitsManager<T> limits = null;\r
- try {\r
- limits = ConfExecutable.getRunnerLimits(clazz);\r
- if (limits == null) {\r
+ public static Logger log = Logger.getLogger(Util.class);\r
+\r
+ private static final PropertyHelper ph = PropertyHelperManager\r
+ .getPropertyHelper();\r
+\r
+ public static final String SPACE = " ";\r
+\r
+ public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
+ Class<? extends Executable<T>> clazz) {\r
+ try {\r
+ return ConfExecutable.getRunnerOptions(clazz);\r
+ } catch (FileNotFoundException e) {\r
+ log.error(\r
+ "Could not load " + clazz + " Parameters !"\r
+ + e.getMessage(), e.getCause());\r
+ } catch (IOException e) {\r
+ log.error("IO exception while reading " + clazz + " Parameters !"\r
+ + e.getMessage(), e.getCause());\r
+ }\r
return null;\r
- }\r
- } catch (FileNotFoundException e) {\r
- log.warn("No limits are found for " + clazz + " executable! "\r
- + e.getLocalizedMessage(), e.getCause());\r
- return null;\r
- } catch (IOException e) {\r
- log.warn("IO exception while attempting to read limits for "\r
- + clazz + " executable! " + e.getLocalizedMessage(), e\r
- .getCause());\r
- return null;\r
}\r
- return limits;\r
- }\r
\r
- public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
- Class<? extends Executable<T>> clazz) {\r
- try {\r
- return ConfExecutable.getRunnerOptions(clazz);\r
- } catch (FileNotFoundException e) {\r
- log.error("Could not load " + clazz + " Parameters !"\r
- + e.getMessage(), e.getCause());\r
- } catch (IOException e) {\r
- log.error("IO exception while reading " + clazz + " Parameters !"\r
- + e.getMessage(), e.getCause());\r
+ public static <T> PresetManager<T> getPresets(\r
+ Class<? extends Executable<T>> clazz) {\r
+ try {\r
+ return ConfExecutable.getRunnerPresets(clazz);\r
+ } catch (FileNotFoundException e) {\r
+ log.warn(\r
+ "No presets are found for " + clazz + " executable! "\r
+ + e.getLocalizedMessage(), e.getCause());\r
+ } catch (IOException e) {\r
+ log.warn("IO exception while reading presents! for " + clazz\r
+ + " executable! " + e.getLocalizedMessage(), e.getCause());\r
+ }\r
+ return null;\r
}\r
- return null;\r
- }\r
\r
- public static <T> PresetManager<T> getPresets(\r
- Class<? extends Executable<T>> clazz) {\r
- try {\r
- return ConfExecutable.getRunnerPresets(clazz);\r
- } catch (FileNotFoundException e) {\r
- log.warn("No presets are found for " + clazz + " executable! "\r
- + e.getLocalizedMessage(), e.getCause());\r
- } catch (IOException e) {\r
- log.warn("IO exception while reading presents! for " + clazz\r
- + " executable! " + e.getLocalizedMessage(), e.getCause());\r
+ public static final Alignment readClustalFile(String workDirectory,\r
+ String clustFile) throws UnknownFileFormatException, IOException,\r
+ FileNotFoundException, NullPointerException {\r
+ assert !compbio.util.Util.isEmpty(workDirectory);\r
+ assert !compbio.util.Util.isEmpty(clustFile);\r
+ File cfile = new File(compbio.engine.client.Util.getFullPath(\r
+ workDirectory, clustFile));\r
+ log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
+ if (!(cfile.exists() && cfile.length() > 0)) {\r
+ throw new FileNotFoundException("Result for the jobId "\r
+ + workDirectory + " with file name " + clustFile\r
+ + " is not found!");\r
+ }\r
+ return ClustalAlignmentUtil.readClustalFile(cfile);\r
}\r
- return null;\r
- }\r
\r
- public static final Alignment readClustalFile(String workDirectory,\r
- String clustFile) throws UnknownFileFormatException, IOException,\r
- FileNotFoundException, NullPointerException {\r
- assert !compbio.util.Util.isEmpty(workDirectory);\r
- assert !compbio.util.Util.isEmpty(clustFile);\r
- File cfile = new File(compbio.engine.client.Util.getFullPath(\r
- workDirectory, clustFile));\r
- log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
- if (!(cfile.exists() && cfile.length() > 0)) {\r
- throw new FileNotFoundException("Result for the jobId "\r
- + workDirectory + " with file name " + clustFile\r
- + " is not found!");\r
+ public static final Map<String, Score> readJronnFile(String workDirectory,\r
+ String clustFile) throws UnknownFileFormatException, IOException,\r
+ FileNotFoundException, NullPointerException {\r
+ assert !compbio.util.Util.isEmpty(workDirectory);\r
+ assert !compbio.util.Util.isEmpty(clustFile);\r
+ File cfile = new File(compbio.engine.client.Util.getFullPath(\r
+ workDirectory, clustFile));\r
+ log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
+ if (!(cfile.exists() && cfile.length() > 0)) {\r
+ throw new FileNotFoundException("Result for the jobId "\r
+ + workDirectory + " with file name " + clustFile\r
+ + " is not found!");\r
+ }\r
+ return SequenceUtil.readJRonn(cfile);\r
}\r
- return ClustalAlignmentUtil.readClustalFile(cfile);\r
- }\r
-\r
- public static void writeInput(List<FastaSequence> sequences,\r
- ConfiguredExecutable<?> exec) {\r
\r
- File filein = new File(exec.getInput());\r
- try {\r
- FileOutputStream fout = new FileOutputStream(filein);\r
- log.debug("File path: " + filein.getAbsolutePath());\r
- SequenceUtil.writeFasta(fout, sequences);\r
- fout.close();\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
+ public static void writeInput(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<?> exec) throws JobSubmissionException {\r
+\r
+ try {\r
+ File filein = new File(exec.getInput());\r
+ FileOutputStream fout = new FileOutputStream(filein);\r
+ log.debug("File path: " + filein.getAbsolutePath());\r
+ SequenceUtil.writeFasta(fout, sequences);\r
+ fout.close();\r
+ } catch (IOException e) {\r
+ log.error("IOException while writing input file into the disk: "\r
+ + e.getLocalizedMessage(), e);\r
+ throw new JobSubmissionException(\r
+ "We are sorry by JABAWS server seems to have a problem! "\r
+ + e.getLocalizedMessage(), e);\r
+ }\r
}\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff