JWS-114 Bumping varied config files and jetbrains xmls. Also adding some java classes...

[jabaws.git] / runner / compbio / runner / Util.java

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
new file mode 100644 (file)
index 0000000..7734c86
--- /dev/null
+++ b/runner/compbio/runner/Util.java
@@ -0,0 +1,134 @@
+/* Copyright (c) 2011 Peter Troshin
+ *  
+ *  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
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
+
+package compbio.runner;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.ClustalAlignmentUtil;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.SequenceUtil;
+import compbio.data.sequence.UnknownFileFormatException;
+import compbio.engine.client.ConfExecutable;
+import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.Executable;
+import compbio.engine.conf.PropertyHelperManager;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.PresetManager;
+import compbio.metadata.RunnerConfig;
+import compbio.util.PropertyHelper;
+
+public final class Util {
+
+       public static Logger log = Logger.getLogger(Util.class);
+
+       private static final PropertyHelper ph = PropertyHelperManager
+                       .getPropertyHelper();
+
+       public static final String SPACE = " ";
+
+       public static synchronized <T> RunnerConfig<T> getSupportedOptions(
+                       Class<? extends Executable<T>> clazz) {
+               try {
+                       return ConfExecutable.getRunnerOptions(clazz);
+               } catch (FileNotFoundException e) {
+                       log.error(
+                                       "Could not load " + clazz + " Parameters !"
+                                                       + e.getMessage(), e.getCause());
+               } catch (IOException e) {
+                       log.error("IO exception while reading " + clazz + " Parameters !"
+                                       + e.getMessage(), e.getCause());
+               }
+               return null;
+       }
+
+       public static <T> PresetManager<T> getPresets(
+                       Class<? extends Executable<T>> clazz) {
+               try {
+                       return ConfExecutable.getRunnerPresets(clazz);
+               } catch (FileNotFoundException e) {
+                       log.warn(
+                                       "No presets are found for " + clazz + " executable! "
+                                                       + e.getLocalizedMessage(), e.getCause());
+               } catch (IOException e) {
+                       log.warn("IO exception while reading presents! for " + clazz
+                                       + " executable! " + e.getLocalizedMessage(), e.getCause());
+               }
+               return null;
+       }
+
+       public static final Alignment readClustalFile(String workDirectory,
+                       String clustFile) throws UnknownFileFormatException, IOException,
+                       FileNotFoundException, NullPointerException {
+               assert !compbio.util.Util.isEmpty(workDirectory);
+               assert !compbio.util.Util.isEmpty(clustFile);
+               File cfile = new File(compbio.engine.client.Util.getFullPath(
+                               workDirectory, clustFile));
+               log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());
+               if (!(cfile.exists() && cfile.length() > 0)) {
+                       throw new FileNotFoundException("Result for the jobId "
+                                       + workDirectory + " with file name " + clustFile
+                                       + " is not found!");
+               }
+               return ClustalAlignmentUtil.readClustalFile(cfile);
+       }
+
+       public static final Map<String, Score> readJronnFile(String workDirectory,
+                       String clustFile) throws UnknownFileFormatException, IOException,
+                       FileNotFoundException, NullPointerException {
+               assert !compbio.util.Util.isEmpty(workDirectory);
+               assert !compbio.util.Util.isEmpty(clustFile);
+               File cfile = new File(compbio.engine.client.Util.getFullPath(
+                               workDirectory, clustFile));
+               log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());
+               if (!(cfile.exists() && cfile.length() > 0)) {
+                       throw new FileNotFoundException("Result for the jobId "
+                                       + workDirectory + " with file name " + clustFile
+                                       + " is not found!");
+               }
+               return SequenceUtil.readJRonn(cfile);
+       }
+
+       public static void writeInput(List<FastaSequence> sequences,
+                       ConfiguredExecutable<?> exec) throws JobSubmissionException {
+
+               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 (IOException e) {
+                       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);
+               }
+       }
+
+}