X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2FUtil.java;h=f033bf01d616434001a3225f990d5d25ac478627;hb=a966c1a63f4365f34a0567514dee6d1bc4d3af91;hp=2f040aa80f363b41e439f32fa060b0798e256924;hpb=8033a51860de2200a54e64add0809d6780f5b092;p=jabaws.git

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index 2f040aa..f033bf0 100644
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -19,6 +19,7 @@
 package compbio.runner;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -30,6 +31,7 @@ import org.apache.log4j.Logger;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAstruct;
 import compbio.data.sequence.Score;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
@@ -37,58 +39,20 @@ import compbio.engine.client.ConfExecutable;
 import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.Executable;
 import compbio.engine.conf.PropertyHelperManager;
-import compbio.metadata.LimitsManager;
+import compbio.metadata.JobSubmissionException;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 import compbio.util.PropertyHelper;
 
 public final class Util {
 
-	private static Logger log = Logger.getLogger(Util.class);
+	public static Logger log = Logger.getLogger(Util.class);
 
 	private static final PropertyHelper ph = PropertyHelperManager
 			.getPropertyHelper();
 
 	public static final String SPACE = " ";
 
-	/**
-	 * For now just assume that all parameters which came in needs setting it
-	 * will be a client responsibility to prepare RunnerConfig object then
-	 * 
-	 * @param rconfig
-	 * @return
-	 * 
-	 *         public static List<String> toOptionString(RunnerConfig<?>
-	 *         rconfig) { String option = ""; List<String> options = new
-	 *         ArrayList<String>(); for (Parameter<?> par :
-	 *         rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
-	 *         { option = par.getOptionName(); } else { option =
-	 *         par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
-	 *         separate options options.add(option); } return options; }
-	 */
-
-	public static <T> LimitsManager<T> getLimits(
-			Class<? extends Executable<T>> clazz) {
-		LimitsManager<T> limits = null;
-		try {
-			limits = ConfExecutable.getRunnerLimits(clazz);
-			if (limits == null) {
-				return null;
-			}
-		} catch (FileNotFoundException e) {
-			log.warn(
-					"No limits are found for " + clazz + " executable! "
-							+ e.getLocalizedMessage(), e.getCause());
-			return null;
-		} catch (IOException e) {
-			log.warn("IO exception while attempting to read limits for "
-					+ clazz + " executable! " + e.getLocalizedMessage(),
-					e.getCause());
-			return null;
-		}
-		return limits;
-	}
-
 	public static synchronized <T> RunnerConfig<T> getSupportedOptions(
 			Class<? extends Executable<T>> clazz) {
 		try {
@@ -152,19 +116,57 @@ public final class Util {
 	}
 
 	public static void writeInput(List<FastaSequence> sequences,
-			ConfiguredExecutable<?> exec) {
+			ConfiguredExecutable<?> exec) throws JobSubmissionException {
 
-		File filein = new File(exec.getInput());
 		try {
+			File filein = new File(exec.getInput());
 			FileOutputStream fout = new FileOutputStream(filein);
 			log.debug("File path: " + filein.getAbsolutePath());
 			SequenceUtil.writeFasta(fout, sequences);
 			fout.close();
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
 		} catch (IOException e) {
-			e.printStackTrace();
+			log.error("IOException while writing input file into the disk: "
+					+ e.getLocalizedMessage(), e);
+			throw new JobSubmissionException(
+					"We are sorry by JABAWS server seems to have a problem! "
+							+ e.getLocalizedMessage(), e);
+		}
+	}
+	
+	public static void writeClustalInput(List<FastaSequence> sequences,
+			ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {
+		
+		try {
+			File filein = new File(exec.getInput());
+			FileOutputStream fout = new FileOutputStream(filein);
+			log.debug("File path: " + filein.getAbsolutePath());
+			SequenceUtil.writeClustal(fout, sequences, gapChar);
+			fout.close();
+		} catch (IOException e) {
+			log.error("IOException while writing input file into the disk: "
+					+ e.getLocalizedMessage(), e);
+			throw new JobSubmissionException(
+					"We are sorry but JABAWS server seems to have a problem! "
+						+ e.getLocalizedMessage(), e);
+		}
+	}
+	
+	public static final RNAstruct readRNAStructFile(String workDirectory,
+			String structFile) throws IOException, FileNotFoundException {
+		assert !compbio.util.Util.isEmpty(workDirectory);
+		assert !compbio.util.Util.isEmpty(structFile);
+		File sfile = new File(compbio.engine.client.Util.getFullPath(
+				workDirectory, structFile));
+		log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
+		if(!(sfile.exists() && sfile.length() > 0)) {
+			throw new FileNotFoundException("Result for the jobId "
+					+ workDirectory + "with file name " + structFile
+					+ " is not found!");
 		}
+		return compbio.data.sequence.SequenceUtil.readRNAalifoldResults(
+				new FileInputStream(sfile));
 	}
+	
+	
 
 }