\r
Think hard on what to do with large output files? \r
e.g. serve the hits table in full, but retrieve alignments on demand.\r
-What actually neeeds to be sent? \r
+What actually needs to be sent? \r
\r
Add facility to distribute other results of the calculations like the trees and \r
annotation file for probcons. \r
+++ /dev/null
-package compbio.data.sequence;\r
-\r
-import java.util.Arrays;\r
-\r
-public class AnnotatedSequence extends FastaSequence {\r
-\r
- private float[] annotation;\r
-\r
- private AnnotatedSequence() {\r
- super();\r
- // JAXB default constructor\r
- }\r
-\r
- public AnnotatedSequence(String id, String sequence, float[] annotation) {\r
- super(id, sequence);\r
- this.annotation = annotation;\r
- if (annotation == null || annotation.length != sequence.length()) {\r
- throw new IllegalArgumentException("The length of the annotation ("\r
- + ((annotation != null) ? annotation.length : "0")\r
- + ") does not match the length of the sequence ("\r
- + sequence.length() + ")!");\r
- }\r
- }\r
-\r
- public AnnotatedSequence(FastaSequence fsequence, float[] annotation) {\r
- this(fsequence.getId(), fsequence.getSequence(), annotation);\r
- }\r
-\r
- public float[] getAnnotation() {\r
- return annotation;\r
- }\r
-\r
- @Override\r
- public int hashCode() {\r
- final int prime = 7;\r
- int result = super.hashCode();\r
- result = prime * result + Arrays.hashCode(annotation);\r
- return result;\r
- }\r
-\r
- @Override\r
- public boolean equals(Object obj) {\r
- if (this == obj)\r
- return true;\r
- if (!super.equals(obj))\r
- return false;\r
- if (getClass() != obj.getClass())\r
- return false;\r
- AnnotatedSequence other = (AnnotatedSequence) obj;\r
- if (!Arrays.equals(annotation, other.annotation))\r
- return false;\r
- return true;\r
- }\r
-\r
- @Override\r
- public String toString() {\r
- return super.toString() + "Annotation:\n "\r
- + Arrays.toString(annotation) + "\n";\r
- }\r
-\r
-}\r
--- /dev/null
+package compbio.data.sequence;\r
+\r
+public enum DisorderMethod {\r
+\r
+ JRonn, Disembl\r
+}\r
+++ /dev/null
-package compbio.data.sequence;\r
-\r
-import java.util.ArrayList;\r
-import java.util.EnumMap;\r
-import java.util.List;\r
-import java.util.Map;\r
-\r
-import compbio.util.annotation.NotThreadSafe;\r
-\r
-/**\r
- * TODO complete\r
- * \r
- * @author pvtroshin\r
- * \r
- * @param <T>\r
- * enum type\r
- */\r
-@NotThreadSafe\r
-// @XmlAccessorType(XmlAccessType.FIELD)\r
-public class MultiAnnotatedSequence<T extends Enum<T>> {\r
-\r
- private EnumMap<T, ArrayList<Float>> annotations;\r
-\r
- MultiAnnotatedSequence() {\r
- // default constructor for JAXB\r
- }\r
-\r
- public MultiAnnotatedSequence(Class<T> enumeration) {\r
- this.annotations = new EnumMap<T, ArrayList<Float>>(enumeration);\r
- }\r
-\r
- public void addAnnotation(T type, ArrayList<Float> annotation) {\r
- assert type != null : "Type is expected";\r
- assert annotation != null : "Not empty value is expected!";\r
- if (!annotations.isEmpty()) {\r
- assert annotations.values().iterator().next().size() == annotation\r
- .size() : "Annotations must contain the same number of elements!";\r
- }\r
- this.annotations.put(type, annotation);\r
- }\r
-\r
- public Map<T, List<Float>> getAnnotations() {\r
- return new EnumMap<T, List<Float>>(this.annotations);\r
- }\r
-\r
- @Override\r
- public int hashCode() {\r
- final int prime = 31;\r
- int result = 1;\r
- result = prime * result\r
- + ((annotations == null) ? 0 : annotations.hashCode());\r
- return result;\r
- }\r
-\r
- @Override\r
- public boolean equals(Object obj) {\r
- if (this == obj)\r
- return true;\r
- if (obj == null)\r
- return false;\r
- if (getClass() != obj.getClass())\r
- return false;\r
- MultiAnnotatedSequence other = (MultiAnnotatedSequence) obj;\r
- if (annotations == null) {\r
- if (other.annotations != null)\r
- return false;\r
- } else if (!annotations.equals(other.annotations))\r
- return false;\r
- return true;\r
- }\r
-\r
- @Override\r
- public String toString() {\r
- String value = "";\r
- for (Map.Entry<T, ArrayList<Float>> annt : annotations.entrySet()) {\r
- value += annt.getKey() + " ";\r
- value += annt.getValue() + "\n";\r
- }\r
- return value;\r
- }\r
-\r
-}\r
NUMBER_FORMAT.setMaximumFractionDigits(3);\r
}\r
\r
- private ConservationMethod method;\r
+ private Enum<?> method;\r
\r
private List<Float> scores;\r
\r
* the actual conservation values for each column of the\r
* alignment\r
*/\r
- public Score(ConservationMethod method, List<Float> scores) {\r
+ public Score(Enum<?> method, List<Float> scores) {\r
this.method = method;\r
this.scores = new ArrayList<Float>(scores);\r
}\r
\r
+ public Score(Enum<?> method, float[] scores) {\r
+ this.method = method;\r
+ this.scores = toList(scores);\r
+ }\r
+\r
+ private List<Float> toList(float[] values) {\r
+ List<Float> vlist = new ArrayList<Float>();\r
+ for (float v : values) {\r
+ vlist.add(new Float(v));\r
+ }\r
+ return vlist;\r
+ }\r
/**\r
* Returns the ConservationMethod\r
* \r
* @return the ConservationMethod\r
*/\r
- public ConservationMethod getMethod() {\r
+ public Enum<?> getMethod() {\r
return method;\r
}\r
\r
import java.io.OutputStream;\r
import java.io.OutputStreamWriter;\r
import java.util.ArrayList;\r
+import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
+import java.util.Map;\r
import java.util.Scanner;\r
+import java.util.Set;\r
import java.util.logging.Level;\r
import java.util.regex.Matcher;\r
import java.util.regex.Pattern;\r
outWriter.close();\r
}\r
\r
- public static List<AnnotatedSequence> readJRonn(final File result)\r
+ public static Map<String, Score> readJRonn(final File result)\r
throws IOException, UnknownFileFormatException {\r
InputStream input = new FileInputStream(result);\r
- List<AnnotatedSequence> sequences = readJRonn(input);\r
+ Map<String, Score> sequences = readJRonn(input);\r
input.close();\r
return sequences;\r
}\r
* is thrown if the inStream represents an unknown source of\r
* data, i.e. not a JRonn output\r
*/\r
- public static List<AnnotatedSequence> readJRonn(final InputStream inStream)\r
+ public static Map<String, Score> readJRonn(final InputStream inStream)\r
throws IOException, UnknownFileFormatException {\r
- final List<AnnotatedSequence> seqs = new ArrayList<AnnotatedSequence>();\r
+ final Map<String, Score> seqs = new HashMap<String, Score>();\r
\r
final BufferedReader infasta = new BufferedReader(\r
new InputStreamReader(inStream, "UTF8"), 16000);\r
"File does not look like Jronn horizontally formatted output file!\n"\r
+ JRONN_WRONG_FORMAT_MESSAGE);\r
}\r
- seqs.add(new AnnotatedSequence(sname, sequence, annotation));\r
+ seqs.put(sname, new Score(DisorderMethod.JRonn, annotation));\r
}\r
} while (line != null);\r
\r
infasta.close();\r
return seqs;\r
}\r
-\r
private static float[] convertToNumber(String[] annotValues)\r
throws UnknownFileFormatException {\r
float[] annotation = new float[annotValues.length];\r
* \r
* TODO complete!\r
* \r
- * # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983\r
- * 0.85864 0.44331 .... # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512\r
- * 0.37094\r
+ * RESIDUE COILS REM465 HOTLOOPS\r
+ * \r
+ * M 0.86010 0.88512 0.37094\r
+ * \r
+ * T 0.79983 0.85864 0.44331 ....\r
+ * \r
+ * RESIDUE COILS REM465 HOTLOOPS\r
+ * \r
+ * M 0.86010 0.88512 0.37094\r
+ * \r
* \r
* @param input\r
* @return\r
* @throws IOException\r
* @throws UnknownFileFormatException\r
*/\r
- static List<MultiAnnotatedSequence<DisemblResultAnnot>> readDisembl(\r
- final InputStream input) throws IOException,\r
- UnknownFileFormatException {\r
+ static Map<FastaSequence, Set<Score>> readDisembl(final InputStream input)\r
+ throws IOException, UnknownFileFormatException {\r
Scanner scan = new Scanner(input);\r
scan.useDelimiter("# RESIDUE COILS REM465 HOTLOOPS\n");\r
if (!scan.hasNext()) {\r
+ " No such line was found!");\r
}\r
\r
- List<MultiAnnotatedSequence<DisemblResultAnnot>> results = new ArrayList<MultiAnnotatedSequence<DisemblResultAnnot>>();\r
+ Map<FastaSequence, Set<Score>> results = new HashMap<FastaSequence, Set<Score>>();\r
int seqCounter = 0;\r
while (scan.hasNext()) {\r
seqCounter++;\r
ArrayList<Float> coils = new ArrayList<Float>();\r
ArrayList<Float> rem = new ArrayList<Float>();\r
ArrayList<Float> hotloops = new ArrayList<Float>();\r
-\r
- MultiAnnotatedSequence<DisemblResultAnnot> disemblRes = new MultiAnnotatedSequence<DisemblResultAnnot>(\r
- DisemblResultAnnot.class);\r
-\r
+ FastaSequence fs = new FastaSequence(Integer.toString(seqCounter),\r
+ singleSeq);\r
while (scansingle.hasNextLine()) {\r
String valueLine = scansingle.nextLine();\r
Scanner values = new Scanner(valueLine);\r
hotloops.add(values.nextFloat());\r
values.close();\r
}\r
- disemblRes.addAnnotation(DisemblResultAnnot.COILS, coils);\r
- disemblRes.addAnnotation(DisemblResultAnnot.REM465, rem);\r
- disemblRes.addAnnotation(DisemblResultAnnot.HOTLOOPS, hotloops);\r
- // TODO\r
- // disemblRes.sequence = seqbuffer.toString();\r
+ Set<Score> scores = new HashSet<Score>();\r
+ scores.add(new Score(DisemblResultAnnot.COILS, coils));\r
+ scores.add(new Score(DisemblResultAnnot.HOTLOOPS, hotloops));\r
+ scores.add(new Score(DisemblResultAnnot.REM465, rem));\r
+ results.put(fs, scores);\r
+\r
scansingle.close();\r
- results.add(disemblRes);\r
}\r
\r
input.close();\r
return results;\r
}\r
-\r
/**\r
* Read AACon result with no alignment files. This method leaves incoming\r
* the InputStream results open!\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.AnnotatedSequence;\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
\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("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
+ 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
- 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
+\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
- 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
+\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 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
+ 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 ClustalAlignmentUtil.readClustalFile(cfile);\r
- }\r
-\r
- public static final List<AnnotatedSequence> readJronnFile(\r
- String workDirectory, String clustFile)\r
- 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
+ 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 SequenceUtil.readJRonn(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
+\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
+ }\r
}\r
- }\r
\r
}\r
\r
package compbio.runner.disorder;\r
\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
import java.util.Arrays;\r
+import java.util.Map;\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.Alignment;\r
-import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.data.sequence.Score;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
* print 'Mode: "default"(nothing) or "scores" which will give scores per\r
* residue in TAB separated format'\r
*/\r
-public class Disembl extends SkeletalExecutable<Disembl> implements\r
- PipedExecutable<Disembl> {\r
+public class Disembl extends SkeletalExecutable<Disembl>\r
+ implements\r
+ PipedExecutable<Disembl> {\r
\r
private static Logger log = Logger.getLogger(Disembl.class);\r
\r
}\r
\r
@SuppressWarnings("unchecked")\r
- public Alignment getResults(String workDirectory)\r
+ public Map<String, Score> getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
- try {\r
- return Util.readClustalFile(workDirectory, getOutput());\r
- } catch (FileNotFoundException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (IOException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (UnknownFileFormatException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (NullPointerException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- }\r
+\r
+ return null;\r
}\r
\r
@Override\r
import java.io.InputStream;\r
import java.util.Arrays;\r
import java.util.List;\r
+import java.util.Map;\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.AnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.engine.client.CommandBuilder;\r
*/\r
public class Jronn extends SkeletalExecutable<Jronn> {\r
\r
- private static Logger log = Logger.getLogger(Jronn.class);\r
-\r
- /**\r
- * Number of cores to use, defaults to 1 for local execution or the value of\r
- * "jronn.cluster.cpunum" property for cluster execution\r
- */\r
- private int ncoreNumber = 0;\r
-\r
- private final String ncorePrm = "-n=";\r
-\r
- // Cache for Limits information\r
- private static LimitsManager<Jronn> limits;\r
-\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
- public static final String STAT_FILE = "stat.txt";\r
-\r
- public Jronn() {\r
- addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE,\r
- "-f=H"));\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public List<AnnotatedSequence> getResults(String workDirectory)\r
- throws ResultNotAvailableException {\r
- List<AnnotatedSequence> sequences = null;\r
- try {\r
- InputStream inStream = new FileInputStream(new File(workDirectory,\r
- getOutput()));\r
- sequences = SequenceUtil.readJRonn(inStream);\r
- inStream.close();\r
- } catch (FileNotFoundException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (IOException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (UnknownFileFormatException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (NullPointerException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
+ private static Logger log = Logger.getLogger(Jronn.class);\r
+\r
+ /**\r
+ * Number of cores to use, defaults to 1 for local execution or the value of\r
+ * "jronn.cluster.cpunum" property for cluster execution\r
+ */\r
+ private int ncoreNumber = 0;\r
+\r
+ private final String ncorePrm = "-n=";\r
+\r
+ // Cache for Limits information\r
+ private static LimitsManager<Jronn> limits;\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+ public static final String STAT_FILE = "stat.txt";\r
+\r
+ public Jronn() {\r
+ addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE,\r
+ "-f=H"));\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Map<String, Score> getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ Map<String, Score> sequences = null;\r
+ try {\r
+ InputStream inStream = new FileInputStream(new File(workDirectory,\r
+ getOutput()));\r
+ sequences = SequenceUtil.readJRonn(inStream);\r
+ inStream.close();\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ return sequences;\r
+ }\r
+\r
+ private static String getLibPath() {\r
+\r
+ String settings = ph.getProperty("jronn.jar.file");\r
+ if (compbio.util.Util.isEmpty(settings)) {\r
+ throw new NullPointerException(\r
+ "Please define jronn.jar.file property in Executable.properties file"\r
+ + "and initialize it with the location of jronn jar file");\r
+ }\r
+ if (new File(settings).isAbsolute()) {\r
+ // Jronn jar can be found so no actions necessary\r
+ // no further actions is necessary\r
+ return settings;\r
+ }\r
+ return compbio.engine.client.Util.convertToAbsolute(settings);\r
+ }\r
+\r
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), getError());\r
}\r
- return sequences;\r
- }\r
\r
- private static String getLibPath() {\r
+ @Override\r
+ public Jronn setInput(String inFile) {\r
+ super.setInput(inFile);\r
+ cbuilder.setParam("-i=" + inFile);\r
+ return this;\r
+ }\r
\r
- String settings = ph.getProperty("jronn.jar.file");\r
- if (compbio.util.Util.isEmpty(settings)) {\r
- throw new NullPointerException(\r
- "Please define jronn.jar.file property in Executable.properties file"\r
- + "and initialize it with the location of jronn jar file");\r
+ @Override\r
+ public Jronn setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ cbuilder.setParam("-o=" + outFile);\r
+ return this;\r
}\r
- if (new File(settings).isAbsolute()) {\r
- // Jronn jar can be found so no actions necessary\r
- // no further actions is necessary\r
- return settings;\r
+\r
+ @Override\r
+ public Limit<Jronn> getLimit(String presetName) {\r
+ if (limits == null) {\r
+ limits = getLimits();\r
+ }\r
+ Limit<Jronn> limit = null;\r
+ if (limits != null) {\r
+ // this returns default limit if preset is undefined!\r
+ limit = limits.getLimitByName(presetName);\r
+ }\r
+ // If limit is not defined for a particular preset, then return default\r
+ // limit\r
+ if (limit == null) {\r
+ log.debug("Limit for the preset " + presetName\r
+ + " is not found. Using default");\r
+ limit = limits.getDefaultLimit();\r
+ }\r
+ return limit;\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<Jronn> getLimits() {\r
+ // synchronise on static field\r
+ synchronized (log) {\r
+ if (limits == null) {\r
+ limits = Util.getLimits(this.getClass());\r
+ }\r
+ }\r
+ return limits;\r
}\r
- return compbio.engine.client.Util.convertToAbsolute(settings);\r
- }\r
-\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- return Arrays.asList(getOutput(), getError());\r
- }\r
-\r
- @Override\r
- public Jronn setInput(String inFile) {\r
- super.setInput(inFile);\r
- cbuilder.setParam("-i=" + inFile);\r
- return this;\r
- }\r
-\r
- @Override\r
- public Jronn setOutput(String outFile) {\r
- super.setOutput(outFile);\r
- cbuilder.setParam("-o=" + outFile);\r
- return this;\r
- }\r
-\r
- @Override\r
- public Limit<Jronn> getLimit(String presetName) {\r
- if (limits == null) {\r
- limits = getLimits();\r
+\r
+ @Override\r
+ public Class<? extends Executable<?>> getType() {\r
+ return this.getClass();\r
}\r
- Limit<Jronn> limit = null;\r
- if (limits != null) {\r
- // this returns default limit if preset is undefined!\r
- limit = limits.getLimitByName(presetName);\r
+\r
+ public static String getStatFile() {\r
+ return STAT_FILE;\r
}\r
- // If limit is not defined for a particular preset, then return default\r
- // limit\r
- if (limit == null) {\r
- log.debug("Limit for the preset " + presetName\r
- + " is not found. Using default");\r
- limit = limits.getDefaultLimit();\r
+\r
+ public void setNCore(int ncoreNumber) {\r
+ if (ncoreNumber < 1 || ncoreNumber > 100) {\r
+ throw new IndexOutOfBoundsException(\r
+ "Number of cores must be within 1 and 100 ");\r
+ }\r
+ this.ncoreNumber = ncoreNumber;\r
+ cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
}\r
- return limit;\r
- }\r
-\r
- @Override\r
- public LimitsManager<Jronn> getLimits() {\r
- // synchronise on static field\r
- synchronized (log) {\r
- if (limits == null) {\r
- limits = Util.getLimits(this.getClass());\r
- }\r
+\r
+ int getNCore() {\r
+ return ncoreNumber;\r
}\r
- return limits;\r
- }\r
-\r
- @Override\r
- public Class<? extends Executable<?>> getType() {\r
- return this.getClass();\r
- }\r
-\r
- public static String getStatFile() {\r
- return STAT_FILE;\r
- }\r
-\r
- public void setNCore(int ncoreNumber) {\r
- if (ncoreNumber < 1 || ncoreNumber > 100) {\r
- throw new IndexOutOfBoundsException(\r
- "Number of cores must be within 1 and 100 ");\r
+\r
+ @Override\r
+ public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
+ // If number of cores is provided, set it for the cluster execution\r
+ // only!\r
+ if (provider == Executable.ExecProvider.Cluster) {\r
+ int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
+ cpunum = (cpunum == 0) ? 1 : cpunum;\r
+ setNCore(cpunum);\r
+ } else {\r
+ // Limit number of cores to 1 for ANY execution which does not set\r
+ // Ncores explicitly using setNCore method or is run on local VM\r
+ if (ncoreNumber == 0) {\r
+ setNCore(1);\r
+ }\r
+ }\r
+ return super.getParameters(provider);\r
}\r
- this.ncoreNumber = ncoreNumber;\r
- cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
- }\r
-\r
- int getNCore() {\r
- return ncoreNumber;\r
- }\r
-\r
- @Override\r
- public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
- // If number of cores is provided, set it for the cluster execution only!\r
- if (provider == Executable.ExecProvider.Cluster) {\r
- int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
- cpunum = (cpunum==0) ? 1 : cpunum; \r
- setNCore(cpunum);\r
- } else { \r
- // Limit number of cores to 1 for ANY execution which does not set\r
- // Ncores explicitly using setNCore method or is run on local VM\r
- if(ncoreNumber==0) {\r
- setNCore(1);\r
- }\r
- }\r
- return super.getParameters(provider);\r
- }\r
\r
}\r
import java.io.InputStream;\r
import java.util.HashSet;\r
import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
\r
import org.testng.annotations.Test;\r
\r
FileInputStream fio;\r
try {\r
fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
- List<AnnotatedSequence> aseqs = SequenceUtil.readJRonn(fio);\r
+ Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
assertNotNull(aseqs);\r
assertEquals(aseqs.size(), 3);\r
- AnnotatedSequence aseq = aseqs.get(0);\r
+ Score aseq = aseqs.get(0);\r
assertNotNull(aseq);\r
- assertNotNull(aseq.getAnnotation());\r
+ assertNotNull(aseq.getScores());\r
// System.out.println(aseq);\r
- assertEquals(aseq.getAnnotation().length, aseq.getSequence()\r
- .length());\r
+ assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
fio.close();\r
} catch (FileNotFoundException e) {\r
e.printStackTrace();\r
try {\r
fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ "disembl.out");\r
- List<MultiAnnotatedSequence<DisemblResultAnnot>> aseqs = SequenceUtil\r
+ Map<FastaSequence, Set<Score>> aseqs = SequenceUtil\r
.readDisembl(fio);\r
assertNotNull(aseqs);\r
\r
import java.io.IOException;\r
import java.text.ParseException;\r
import java.util.Arrays;\r
+import java.util.HashSet;\r
\r
import javax.xml.bind.ValidationException;\r
\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.data.sequence.ConservationMethod;\r
-import compbio.data.sequence.MultiAnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<ConservationMethod> annotations = confAAcon.getResults();\r
+ HashSet<Score> annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 1);\r
+ assertEquals(annotations.size(), 1);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<ConservationMethod> annotations = confAAcon.getResults();\r
+ HashSet<Score> annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 13);\r
+ assertEquals(annotations.size(), 13);\r
assertEquals(al1.getResults(), annotations);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- MultiAnnotatedSequence<ConservationMethod> annotations = confAAcon.getResults();\r
+ HashSet<Score> annotations = confAAcon.getResults();\r
assertNotNull(annotations);\r
- assertEquals(annotations.getAnnotations().size(), 3);\r
+ assertEquals(annotations.size(), 3);\r
assertEquals(al1.getResults(), annotations);\r
\r
} catch (JobSubmissionException e) {\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.text.ParseException;\r
-import java.util.List;\r
+import java.util.HashSet;\r
\r
import javax.xml.bind.ValidationException;\r
\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.data.sequence.AnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
\r
public class DisemblTester {\r
\r
- public static String test_outfile = "TO1381.disembl.out";\r
+ public static String test_outfile = "TO1381.disembl.out";\r
\r
- private Disembl disembl;\r
+ private Disembl disembl;\r
\r
- @BeforeMethod(alwaysRun = true)\r
- void init() {\r
- disembl = new Disembl();\r
- disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
- }\r
+ @BeforeMethod(alwaysRun = true)\r
+ void init() {\r
+ disembl = new Disembl();\r
+ disembl.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ }\r
\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_runner })\r
- public void testRunOnCluster() {\r
- assertFalse(SysPrefs.isWindows,\r
- "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<Disembl> confDisembl = Configurator\r
- .configureExecutable(disembl,\r
- Executable.ExecProvider.Cluster);\r
- JobRunner runner = JobRunner.getInstance(confDisembl);\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnCluster() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<Disembl> confDisembl = Configurator\r
+ .configureExecutable(disembl,\r
+ Executable.ExecProvider.Cluster);\r
+ JobRunner runner = JobRunner.getInstance(confDisembl);\r
\r
- assertNotNull(runner, "Runner is NULL");\r
- runner.executeJob();\r
- // assertNotNull("JobId is null", jobId1);\r
- JobStatus status = runner.getJobStatus();\r
- assertTrue(status == JobStatus.PENDING\r
- || status == JobStatus.RUNNING,\r
- "Status of the process is wrong!");\r
- JobInfo info = runner.getJobInfo();\r
- assertNotNull(info, "JobInfo is null");\r
- StatisticManager sm = new StatisticManager(info);\r
- assertNotNull(sm, "Statictic manager is null");\r
- try {\r
+ assertNotNull(runner, "Runner is NULL");\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue(status == JobStatus.PENDING\r
+ || status == JobStatus.RUNNING,\r
+ "Status of the process is wrong!");\r
+ JobInfo info = runner.getJobInfo();\r
+ assertNotNull(info, "JobInfo is null");\r
+ StatisticManager sm = new StatisticManager(info);\r
+ assertNotNull(sm, "Statictic manager is null");\r
+ try {\r
\r
- String exits = sm.getExitStatus();\r
- assertNotNull("Exit status is null", exits);\r
- // cut 4 trailing zeros from the number\r
- int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
- .intValue();\r
- assertEquals(0, exitsInt);\r
- System.out.println(sm.getAllStats());\r
+ String exits = sm.getExitStatus();\r
+ assertNotNull("Exit status is null", exits);\r
+ // cut 4 trailing zeros from the number\r
+ int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
+ .intValue();\r
+ assertEquals(0, exitsInt);\r
+ System.out.println(sm.getAllStats());\r
\r
- } catch (ParseException e) {\r
- e.printStackTrace();\r
- fail("Parse Exception: " + e.getMessage());\r
- }\r
- //assertFalse(runner.cleanup());\r
- assertTrue(sm.hasExited());\r
- assertFalse(sm.wasAborted());\r
- assertFalse(sm.hasDump());\r
- assertFalse(sm.hasSignaled());\r
+ } catch (ParseException e) {\r
+ e.printStackTrace();\r
+ fail("Parse Exception: " + e.getMessage());\r
+ }\r
+ // assertFalse(runner.cleanup());\r
+ assertTrue(sm.hasExited());\r
+ assertFalse(sm.wasAborted());\r
+ assertFalse(sm.hasDump());\r
+ assertFalse(sm.hasSignaled());\r
\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (DrmaaException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (DrmaaException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ }\r
}\r
- }\r
\r
- /**\r
- * This tests fails from time to time depending on the cluster load or some\r
- * other factors. Any client code has to adjust for this issue\r
- */\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_runner })\r
- public void testRunOnClusterAsync() {\r
- assertFalse(SysPrefs.isWindows,\r
- "Cluster execution can only be in unix environment");\r
- try {\r
- ConfiguredExecutable<Disembl> confDisembl = Configurator\r
- .configureExecutable(disembl,\r
- Executable.ExecProvider.Cluster);\r
- AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);\r
- String jobId = aengine.submitJob(confDisembl);\r
- assertNotNull(jobId, "Runner is NULL");\r
- // let drmaa to start\r
- Thread.sleep(500);\r
- JobStatus status = aengine.getJobStatus(jobId);\r
- while (status != JobStatus.FINISHED) {\r
- System.out.println("Job Status: " + status);\r
- Thread.sleep(1000);\r
- status = aengine.getJobStatus(jobId);\r
- ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
- .getResults(jobId);\r
- assertNotNull(result);\r
- System.out.println("RES:" + result);\r
- // Some times the job could be removed from the cluster accounting \r
- // before it has been reported to finish. Make sure \r
- // to stop waiting in such case\r
- if (status == JobStatus.UNDEFINED) {\r
- break;\r
+ /**\r
+ * This tests fails from time to time depending on the cluster load or some\r
+ * other factors. Any client code has to adjust for this issue\r
+ */\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnClusterAsync() {\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ try {\r
+ ConfiguredExecutable<Disembl> confDisembl = Configurator\r
+ .configureExecutable(disembl,\r
+ Executable.ExecProvider.Cluster);\r
+ AsyncExecutor aengine = Configurator.getAsyncEngine(confDisembl);\r
+ String jobId = aengine.submitJob(confDisembl);\r
+ assertNotNull(jobId, "Runner is NULL");\r
+ // let drmaa to start\r
+ Thread.sleep(500);\r
+ JobStatus status = aengine.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ System.out.println("Job Status: " + status);\r
+ Thread.sleep(1000);\r
+ status = aengine.getJobStatus(jobId);\r
+ ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
+ .getResults(jobId);\r
+ assertNotNull(result);\r
+ System.out.println("RES:" + result);\r
+ // Some times the job could be removed from the cluster\r
+ // accounting\r
+ // before it has been reported to finish. Make sure\r
+ // to stop waiting in such case\r
+ if (status == JobStatus.UNDEFINED) {\r
+ break;\r
+ }\r
+ }\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
}\r
- }\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
}\r
- }\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testRunLocally() {\r
- try {\r
- ConfiguredExecutable<Disembl> confDisembl = Configurator\r
- .configureExecutable(disembl, Executable.ExecProvider.Local);\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocally() {\r
+ try {\r
+ ConfiguredExecutable<Disembl> confDisembl = Configurator\r
+ .configureExecutable(disembl, Executable.ExecProvider.Local);\r
\r
- // For local execution use relative\r
- LocalRunner lr = new LocalRunner(confDisembl);\r
- lr.executeJob();\r
- ConfiguredExecutable<?> al1 = lr.waitForResult();\r
- assertNotNull(al1.getResults());\r
- List<AnnotatedSequence> al2 = confDisembl.getResults();\r
- assertNotNull(al2);\r
- assertEquals(al2.size(), 3);\r
- assertEquals(al1.getResults(), al2);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+ // For local execution use relative\r
+ LocalRunner lr = new LocalRunner(confDisembl);\r
+ lr.executeJob();\r
+ ConfiguredExecutable<?> al1 = lr.waitForResult();\r
+ assertNotNull(al1.getResults());\r
+ HashSet<Score> al2 = confDisembl.getResults();\r
+ assertNotNull(al2);\r
+ assertEquals(al2.size(), 3);\r
+ assertEquals(al1.getResults(), al2);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
}\r
- }\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void readStatistics() {\r
- try {\r
- ConfiguredExecutable<Disembl> confDisembl = Configurator\r
- .configureExecutable(disembl, Executable.ExecProvider.Local);\r
- // For local execution use relavive\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void readStatistics() {\r
+ try {\r
+ ConfiguredExecutable<Disembl> confDisembl = Configurator\r
+ .configureExecutable(disembl, Executable.ExecProvider.Local);\r
+ // For local execution use relavive\r
\r
- AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
- String jobId = sexec.submitJob(confDisembl);\r
- FilePuller fw = FilePuller.newFilePuller(confDisembl\r
- .getWorkDirectory()\r
- + File.separator + Jronn.getStatFile(),\r
- FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
- int count = 0;\r
- long position = 0;\r
- fw.waitForFile(4);\r
- JobStatus status = sexec.getJobStatus(jobId);\r
- while (status != JobStatus.FINISHED) {\r
- if (fw.hasMoreData()) {\r
- ChunkHolder ch = fw.pull(position);\r
- String chunk = ch.getChunk();\r
- position = ch.getNextPosition();\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confDisembl);\r
+ String jobId = sexec.submitJob(confDisembl);\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confDisembl.getWorkDirectory() + File.separator\r
+ + Jronn.getStatFile(),\r
+ FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(4);\r
+ JobStatus status = sexec.getJobStatus(jobId);\r
+ while (status != JobStatus.FINISHED) {\r
+ if (fw.hasMoreData()) {\r
+ ChunkHolder ch = fw.pull(position);\r
+ String chunk = ch.getChunk();\r
+ position = ch.getNextPosition();\r
+ }\r
+ count++;\r
+ // Make sure the loop is terminated if the job fails\r
+ if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
+ break;\r
+ }\r
+ Thread.sleep(300);\r
+ status = sexec.getJobStatus(jobId);\r
+ }\r
+ assertTrue(count > 1);\r
+ ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
+ assertNotNull(al.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
}\r
- count++;\r
- // Make sure the loop is terminated if the job fails\r
- if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {\r
- break;\r
- }\r
- Thread.sleep(300);\r
- status = sexec.getJobStatus(jobId);\r
- }\r
- assertTrue(count > 1);\r
- ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
- assertNotNull(al.getResults());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
}\r
- }\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testPersistance() {\r
- try {\r
- Disembl disembl = new Disembl();\r
- disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
- .setOutput("outtt.txt");\r
- assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
- assertEquals(disembl.getError(), "errrr.txt");\r
- assertEquals(disembl.getOutput(), "outtt.txt");\r
- ConfiguredExecutable<Disembl> cDisembl = Configurator\r
- .configureExecutable(disembl, Executable.ExecProvider.Local);\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testPersistance() {\r
+ try {\r
+ Disembl disembl = new Disembl();\r
+ disembl.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+ .setOutput("outtt.txt");\r
+ assertEquals(disembl.getInput(), AllTestSuit.test_input);\r
+ assertEquals(disembl.getError(), "errrr.txt");\r
+ assertEquals(disembl.getOutput(), "outtt.txt");\r
+ ConfiguredExecutable<Disembl> cDisembl = Configurator\r
+ .configureExecutable(disembl, Executable.ExecProvider.Local);\r
\r
- SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);\r
- sexec.executeJob();\r
- ConfiguredExecutable<?> al = sexec.waitForResult();\r
- assertNotNull(al.getResults());\r
- // Save run configuration\r
- assertTrue(cDisembl.saveRunConfiguration());\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cDisembl);\r
+ sexec.executeJob();\r
+ ConfiguredExecutable<?> al = sexec.waitForResult();\r
+ assertNotNull(al.getResults());\r
+ // Save run configuration\r
+ assertTrue(cDisembl.saveRunConfiguration());\r
\r
- // See if loaded configuration is the same as saved\r
- RunConfiguration loadedRun = RunConfiguration\r
- .load(new FileInputStream(new File(cDisembl\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertEquals(((ConfExecutable<Disembl>) cDisembl)\r
- .getRunConfiguration(), loadedRun);\r
- // Load run configuration as ConfExecutable\r
- ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl\r
- .loadRunConfiguration(new FileInputStream(new File(cDisembl\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
- assertNotNull(resurrectedCDisembl);\r
- assertEquals(resurrectedCDisembl.getExecutable().getInput(),\r
- AllTestSuit.test_input);\r
- assertEquals(resurrectedCDisembl.getExecutable().getError(),\r
- "errrr.txt");\r
- assertEquals(resurrectedCDisembl.getExecutable().getOutput(),\r
- "outtt.txt");\r
- // See in details whether executables are the same\r
- assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cDisembl\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertEquals(\r
+ ((ConfExecutable<Disembl>) cDisembl).getRunConfiguration(),\r
+ loadedRun);\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<Disembl> resurrectedCDisembl = (ConfiguredExecutable<Disembl>) cDisembl\r
+ .loadRunConfiguration(new FileInputStream(new File(cDisembl\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCDisembl);\r
+ assertEquals(resurrectedCDisembl.getExecutable().getInput(),\r
+ AllTestSuit.test_input);\r
+ assertEquals(resurrectedCDisembl.getExecutable().getError(),\r
+ "errrr.txt");\r
+ assertEquals(resurrectedCDisembl.getExecutable().getOutput(),\r
+ "outtt.txt");\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCDisembl.getExecutable(), disembl);\r
\r
- ConfiguredExecutable<Disembl> resJronn = Configurator\r
- .configureExecutable(resurrectedCDisembl.getExecutable(),\r
- Executable.ExecProvider.Local);\r
+ ConfiguredExecutable<Disembl> resJronn = Configurator\r
+ .configureExecutable(resurrectedCDisembl.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
\r
- sexec = Configurator.getSyncEngine(resJronn,\r
- Executable.ExecProvider.Local);\r
- sexec.executeJob();\r
- al = sexec.waitForResult();\r
- assertNotNull(al);\r
+ sexec = Configurator.getSyncEngine(resJronn,\r
+ Executable.ExecProvider.Local);\r
+ sexec.executeJob();\r
+ al = sexec.waitForResult();\r
+ assertNotNull(al);\r
\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
}\r
- }\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
- public void testConfigurationLoading() {\r
- try {\r
- RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
- .getRunnerOptions(Disembl.class);\r
- assertNotNull(disemblConfig);\r
- assertTrue(disemblConfig.getArguments().size() > 0);\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testConfigurationLoading() {\r
+ try {\r
+ RunnerConfig<Disembl> disemblConfig = ConfExecutable\r
+ .getRunnerOptions(Disembl.class);\r
+ assertNotNull(disemblConfig);\r
+ assertTrue(disemblConfig.getArguments().size() > 0);\r
\r
- PresetManager<Disembl> disemblPresets = ConfExecutable\r
- .getRunnerPresets(Disembl.class);\r
- assertNull(disemblPresets); // there is no presets\r
+ PresetManager<Disembl> disemblPresets = ConfExecutable\r
+ .getRunnerPresets(Disembl.class);\r
+ assertNull(disemblPresets); // there is no presets\r
\r
- LimitsManager<Disembl> disemblLimits = ConfExecutable\r
- .getRunnerLimits(Disembl.class);\r
- assertNotNull(disemblLimits);\r
- assertTrue(disemblLimits.getLimits().size() > 0);\r
- disemblLimits.validate(disemblPresets);\r
+ LimitsManager<Disembl> disemblLimits = ConfExecutable\r
+ .getRunnerLimits(Disembl.class);\r
+ assertNotNull(disemblLimits);\r
+ assertTrue(disemblLimits.getLimits().size() > 0);\r
+ disemblLimits.validate(disemblPresets);\r
\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ValidationException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
}\r
- }\r
\r
}\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.text.ParseException;\r
-import java.util.List;\r
+import java.util.Map;\r
\r
import javax.xml.bind.ValidationException;\r
\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.data.sequence.AnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
}\r
\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_runner })\r
- public void testRunOnCluster() {\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnCluster() {\r
assertFalse(SysPrefs.isWindows,\r
"Cluster execution can only be in unix environment");\r
try {\r
ConfiguredExecutable<Jronn> confJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
+ .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
JobRunner runner = JobRunner.getInstance(confJronn);\r
\r
assertNotNull(runner, "Runner is NULL");\r
assertNotNull("Exit status is null", exits);\r
// cut 4 trailing zeros from the number\r
int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
- .intValue();\r
+ .intValue();\r
assertEquals(0, exitsInt);\r
System.out.println(sm.getAllStats());\r
\r
e.printStackTrace();\r
fail("Parse Exception: " + e.getMessage());\r
}\r
- //assertFalse(runner.cleanup());\r
+ // assertFalse(runner.cleanup());\r
assertTrue(sm.hasExited());\r
assertFalse(sm.wasAborted());\r
assertFalse(sm.hasDump());\r
* This tests fails from time to time depending on the cluster load or some\r
* other factors. Any client code has to adjust for this issue\r
*/\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_runner })\r
- public void testRunOnClusterAsync() {\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnClusterAsync() {\r
assertFalse(SysPrefs.isWindows,\r
- "Cluster execution can only be in unix environment");\r
+ "Cluster execution can only be in unix environment");\r
try {\r
ConfiguredExecutable<Jronn> confJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
+ .configureExecutable(jronn, Executable.ExecProvider.Cluster);\r
AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);\r
String jobId = aengine.submitJob(confJronn);\r
assertNotNull(jobId, "Runner is NULL");\r
Thread.sleep(1000);\r
status = aengine.getJobStatus(jobId);\r
ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine\r
- .getResults(jobId);\r
+ .getResults(jobId);\r
assertNotNull(result);\r
System.out.println("RES:" + result);\r
- // Some times the job could be removed from the cluster accounting \r
- // before it has been reported to finish. Make sure \r
+ // Some times the job could be removed from the cluster\r
+ // accounting\r
+ // before it has been reported to finish. Make sure\r
// to stop waiting in such case\r
if (status == JobStatus.UNDEFINED) {\r
break;\r
}\r
}\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocally() {\r
try {\r
ConfiguredExecutable<Jronn> confJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Local);\r
+ .configureExecutable(jronn, Executable.ExecProvider.Local);\r
\r
// For local execution use relative\r
LocalRunner lr = new LocalRunner(confJronn);\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- List<AnnotatedSequence> al2 = confJronn.getResults();\r
+ Map<String, Score> al2 = confJronn.getResults();\r
assertNotNull(al2);\r
assertEquals(al2.size(), 3);\r
assertEquals(al1.getResults(), al2);\r
}\r
}\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testRunLocallyOnTwoCpu() {\r
try {\r
jronn.setNCore(2);\r
ConfiguredExecutable<Jronn> confJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Local);\r
- \r
+ .configureExecutable(jronn, Executable.ExecProvider.Local);\r
+\r
// For local execution use relative\r
LocalRunner lr = new LocalRunner(confJronn);\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- List<AnnotatedSequence> al2 = confJronn.getResults();\r
+ Map<String, Score> al2 = confJronn.getResults();\r
assertNotNull(al2);\r
assertEquals(al2.size(), 3);\r
assertEquals(al1.getResults(), al2);\r
}\r
}\r
\r
- \r
- @Test(groups = { AllTestSuit.test_group_runner })\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void readStatistics() {\r
try {\r
ConfiguredExecutable<Jronn> confJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Local);\r
+ .configureExecutable(jronn, Executable.ExecProvider.Local);\r
// For local execution use relavive\r
\r
AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);\r
String jobId = sexec.submitJob(confJronn);\r
- FilePuller fw = FilePuller.newFilePuller(confJronn\r
- .getWorkDirectory()\r
- + File.separator + Jronn.getStatFile(),\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confJronn.getWorkDirectory() + File.separator\r
+ + Jronn.getStatFile(),\r
FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
int count = 0;\r
long position = 0;\r
}\r
}\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testPersistance() {\r
try {\r
Jronn jronn = new Jronn();\r
jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
- .setOutput("outtt.txt");\r
+ .setOutput("outtt.txt");\r
assertEquals(jronn.getInput(), AllTestSuit.test_input);\r
assertEquals(jronn.getError(), "errrr.txt");\r
assertEquals(jronn.getOutput(), "outtt.txt");\r
ConfiguredExecutable<Jronn> cJronn = Configurator\r
- .configureExecutable(jronn, Executable.ExecProvider.Local);\r
+ .configureExecutable(jronn, Executable.ExecProvider.Local);\r
\r
SyncExecutor sexec = Configurator.getSyncEngine(cJronn);\r
sexec.executeJob();\r
\r
// See if loaded configuration is the same as saved\r
RunConfiguration loadedRun = RunConfiguration\r
- .load(new FileInputStream(new File(cJronn\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ .load(new FileInputStream(new File(cJronn\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
assertEquals(\r
((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),\r
loadedRun);\r
// Load run configuration as ConfExecutable\r
ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn\r
- .loadRunConfiguration(new FileInputStream(new File(cJronn\r
- .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ .loadRunConfiguration(new FileInputStream(new File(cJronn\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
assertNotNull(resurrectedCMuscle);\r
assertEquals(resurrectedCMuscle.getExecutable().getInput(),\r
AllTestSuit.test_input);\r
assertEquals(resurrectedCMuscle.getExecutable().getError(),\r
"errrr.txt");\r
assertEquals(resurrectedCMuscle.getExecutable().getOutput(),\r
- "outtt.txt");\r
+ "outtt.txt");\r
// See in details whether executables are the same\r
assertEquals(resurrectedCMuscle.getExecutable(), jronn);\r
\r
ConfiguredExecutable<Jronn> resJronn = Configurator\r
- .configureExecutable(resurrectedCMuscle.getExecutable(),\r
- Executable.ExecProvider.Local);\r
+ .configureExecutable(resurrectedCMuscle.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
\r
sexec = Configurator.getSyncEngine(resJronn,\r
Executable.ExecProvider.Local);\r
}\r
}\r
\r
- @Test(groups = { AllTestSuit.test_group_runner })\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
public void testConfigurationLoading() {\r
try {\r
RunnerConfig<Jronn> jronnConfig = ConfExecutable\r
- .getRunnerOptions(Jronn.class);\r
+ .getRunnerOptions(Jronn.class);\r
assertNotNull(jronnConfig);\r
assertTrue(jronnConfig.getArguments().size() > 0);\r
\r
PresetManager<Jronn> jronnPresets = ConfExecutable\r
- .getRunnerPresets(Jronn.class);\r
+ .getRunnerPresets(Jronn.class);\r
assertNull(jronnPresets); // there is no presets\r
\r
LimitsManager<Jronn> jronnLimits = ConfExecutable\r
- .getRunnerLimits(Jronn.class);\r
+ .getRunnerLimits(Jronn.class);\r
assertNotNull(jronnLimits);\r
assertTrue(jronnLimits.getLimits().size() > 0);\r
jronnLimits.validate(jronnPresets);\r
import java.io.OutputStream;\r
import java.util.ArrayList;\r
import java.util.List;\r
+import java.util.Set;\r
\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.ClustalAlignmentUtil;\r
+import compbio.data.sequence.Score;\r
\r
public class IOHelper {\r
\r
}\r
}\r
\r
+ /**\r
+ * Outputs AAcon results into the file represented by the outStream\r
+ * \r
+ * @param outStream\r
+ * @param result\r
+ * the AACon scores to output\r
+ */\r
+ static void writeOut(OutputStream outStream, Set<Score> result) {\r
+ try {\r
+ Score.write(result, outStream);\r
+ } catch (IOException e) {\r
+ System.err\r
+ .println("Problems writing output file! Stack trace is below: ");\r
+ e.printStackTrace();\r
+ } finally {\r
+ if (outStream != null) {\r
+ try {\r
+ outStream.close();\r
+ } catch (IOException ignored) {\r
+ // e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
}\r
import java.net.URL;\r
import java.util.Arrays;\r
import java.util.List;\r
+import java.util.Set;\r
import java.util.logging.Level;\r
import java.util.logging.Logger;\r
\r
import javax.xml.ws.Service;\r
import javax.xml.ws.WebServiceException;\r
\r
+import compbio.data.msa.Annotation;\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.sequence.Alignment;\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.metadata.JobSubmissionException;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
}\r
Alignment alignment = null;\r
if (inputFile != null) {\r
+ OutputStream outStream = null;\r
+ if (outFile != null) {\r
+ outStream = IOHelper.getOutStream(outFile);\r
+ } else {\r
+ // this stream is going to be closed later which is fine as\r
+ // std.out will not be\r
+ outStream = System.out;\r
+ }\r
if (service == Services.AAConWS) {\r
- System.out.println("calc conserv!");\r
+ Set<Score> result = analize(inputFile, ((Annotation<T>) msaws),\r
+ preset, customOptions);\r
+ IOHelper.writeOut(outStream, result);\r
} else {\r
-\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
- OutputStream outStream = null;\r
- if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
- } else {\r
- // this stream is going to be closed later which is fine as\r
- // std.out will not be\r
- outStream = System.out;\r
- }\r
IOHelper.writeOut(outStream, alignment);\r
- // stream is closed in the method no need to close it here\r
}\r
+\r
+ // stream is closed in the method no need to close it here\r
}\r
\r
boolean listParameters = CmdHelper.listParameters(cmd);\r
((Closeable) msaws).close();\r
log.fine("Disconnected successfully!");\r
}\r
+ /**\r
+ * Calculate conservation for sequences loaded from the file\r
+ * \r
+ * @param wsproxy\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws UnknownFileFormatException\r
+ */\r
+ <T> Set<Score> analize(File file, Annotation<T> wsproxy, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+\r
+ List<FastaSequence> fastalist = null;\r
+ Set<Score> scores = null;\r
+ try {\r
+ fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out\r
+ .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = wsproxy.customAnalize(fastalist, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = wsproxy.presetAnalize(fastalist, preset);\r
+ } else {\r
+ jobId = wsproxy.analize(fastalist);\r
+ }\r
+ Thread.sleep(1000);\r
+ scores = wsproxy.getAnnotation(jobId);\r
+\r
+ } catch (IOException e) {\r
+ System.err\r
+ .println("Exception while reading the input file. "\r
+ + "Check that the input file contains a list of fasta formatted sequences! "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (JobSubmissionException e) {\r
+ System.err\r
+ .println("Exception while submitting job to a web server. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException ignored) {\r
+ // ignore and propagate an interruption\r
+ Thread.currentThread().interrupt();\r
+ } catch (WrongParameterException e) {\r
+ System.err\r
+ .println("Exception while parsing the web method input parameters. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err\r
+ .println("Exception while attempting to read the input file "\r
+ + "Exception details are below:");\r
+ System.out.println(e.getMessage());\r
+ e.printStackTrace();\r
+ }\r
+ return scores;\r
+ }\r
\r
/**\r
* Connects to a web service by the host and the service name\r
--- /dev/null
+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+\r
+import javax.annotation.Resource;\r
+import javax.jws.WebService;\r
+import javax.xml.ws.WebServiceContext;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.Annotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.Util;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.disorder.Jronn;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
+public class JronnWS implements Annotation<Jronn> {\r
+\r
+ // Ask for resource injection\r
+ @Resource\r
+ WebServiceContext wsContext;\r
+\r
+ private static Logger statLog = Logger.getLogger("JronnWS-stats");\r
+\r
+ private static Logger log = Logger.getLogger(JronnWS.class);\r
+\r
+ private static final RunnerConfig<Jronn> aaconOptions = Util\r
+ .getSupportedOptions(Jronn.class);\r
+\r
+ private static final PresetManager<Jronn> aaconPresets = Util\r
+ .getPresets(Jronn.class);\r
+\r
+ ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ Jronn jronn = new Jronn();\r
+ jronn.setInput("fasta.in").setOutput("aacon.out");\r
+ return Configurator.configureExecutable(jronn, sequences);\r
+ }\r
+\r
+ @Override\r
+ public HashSet<Score> getAnnotation(String jobId)\r
+ throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
+ .getResults(jobId);\r
+ HashSet<Score> mas = aacon.getResults();\r
+ log.trace(jobId + " getConservation : " + mas);\r
+ return mas;\r
+ }\r
+ /*\r
+ * @SuppressWarnings("unchecked") public JalviewAnnotation\r
+ * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
+ * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
+ * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
+ */\r
+\r
+ @Override\r
+ public Limit<Jronn> getLimit(String presetName) {\r
+ return new Jronn().getLimit(presetName);\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<Jronn> getLimits() {\r
+ return new Jronn().getLimits();\r
+ }\r
+\r
+ @Override\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+ WSUtil.validateJobId(jobId);\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+ + Jronn.getStatFile();\r
+ return WSUtil.pullFile(file, position);\r
+ }\r
+\r
+ @Override\r
+ public boolean cancelJob(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.cancelJob(jobId);\r
+ }\r
+\r
+ @Override\r
+ public JobStatus getJobStatus(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.getJobStatus(jobId);\r
+ }\r
+\r
+ @Override\r
+ public PresetManager<Jronn> getPresets() {\r
+ return aaconPresets;\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<Jronn> getRunnerOptions() {\r
+ return aaconOptions;\r
+ }\r
+\r
+ String analize(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
+ Limit<Jronn> limit) throws JobSubmissionException {\r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\r
+\r
+ compbio.runner.Util.writeInput(sequences, confExec);\r
+ AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+ String jobId = engine.submitJob(confExec);\r
+ return jobId;\r
+ }\r
+\r
+ @Override\r
+ public String analize(List<FastaSequence> sequences)\r
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Jronn> confAAcon = init(sequences);\r
+\r
+ // set default conservation method to fastest - SHENKIN\r
+ // TODO: This violates encapsulation, should be moved to the runners\r
+ // level.\r
+ // confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
+ return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String customAnalize(List<FastaSequence> sequences,\r
+ List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
+ // Could not do that! Space separated values\r
+ // will all be treated as keys! thus duplicates removed\r
+ // String params = cbuilder.getCommand();\r
+ List<String> params = WSUtil.getCommands(options,\r
+ AACon.KEY_VALUE_SEPARATOR);\r
+ confJronn.addParameters(params);\r
+ return analize(sequences, confJronn, null, "customAnalize",\r
+ getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String presetAnalize(List<FastaSequence> sequences,\r
+ Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
+ confJronn.addParameters(preset.getOptions());\r
+ Limit<Jronn> limit = getLimit(preset.getName());\r
+ return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
+ }\r
+\r
+}\r
git://source.jalview.org / jabaws.git / commitdiff