-/* 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
package compbio.runner;\r
\r
import java.io.File;\r
+import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.ClustalAlignmentUtil;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
import compbio.data.sequence.Score;\r
+import compbio.data.sequence.RNAStructReader;\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
- return null;\r
- }\r
- } catch (FileNotFoundException e) {\r
- log.warn(\r
- "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(),\r
- e.getCause());\r
- return null;\r
- }\r
- return limits;\r
- }\r
+ public static Logger log = Logger.getLogger(Util.class);\r
\r
public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
Class<? extends Executable<T>> clazz) {\r
}\r
\r
public static void writeInput(List<FastaSequence> sequences,\r
- ConfiguredExecutable<?> exec) {\r
-\r
- File filein = new File(exec.getInput());\r
+ ConfiguredExecutable<?> exec) throws JobSubmissionException {\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 (FileNotFoundException e) {\r
- e.printStackTrace();\r
} catch (IOException e) {\r
- e.printStackTrace();\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
+ public static void writeClustalInput(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<?> exec, char gapChar) 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.writeClustal(fout, sequences, gapChar);\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 but JABAWS server seems to have a problem! "\r
+ + e.getLocalizedMessage(), e);\r
+ }\r
+ }\r
+\r
+ public static RNAStructScoreManager readRNAStruct(String workDirectory,\r
+ String structFile) throws IOException, FileNotFoundException {\r
+ \r
+ assert !compbio.util.Util.isEmpty(workDirectory);\r
+ assert !compbio.util.Util.isEmpty(structFile);\r
+ // The stdout from RNAalifold\r
+ File sFile = new File(compbio.engine.client.Util.getFullPath(\r
+ workDirectory, structFile));\r
+ // Base pair probability matrix (-p option)\r
+ File aliFile = new File(compbio.engine.client.Util.getFullPath(\r
+ workDirectory, "alifold.out"));\r
+ // Check that stdout file exists\r
+ if(!(sFile.exists() && sFile.length() > 0)) {\r
+ throw new FileNotFoundException("Result for the jobId "\r
+ + workDirectory + "with file name " + structFile\r
+ + " is not found!");\r
+ }\r
+ // Check that base pair probability file exists\r
+ if(!aliFile.exists()) {\r
+ log.warn("The file alifold.out is not found for the jobId "\r
+ + workDirectory + "Is the -p or --MEA option not specified?");\r
+ return RNAStructReader.readRNAStructStream(new FileInputStream(sFile));\r
+ \r
+ } else {\r
+ return RNAStructReader.readRNAStructStream(new FileInputStream(sFile), \r
+ new FileInputStream(aliFile));\r
}\r
}\r
\r
}\r
+\r
+\r
git://source.jalview.org / jabaws.git / blobdiff