static void Main(string[] args)
{
try
{
ArgCollection argCollection = ArgCollection.GetInstance(args);
if (argCollection.ExtractOptionalFlag("help"))
{
Console.WriteLine("");
Console.WriteLine(UsageMessage);
Console.WriteLine(HelpMessage);
return;
}
string optimizerName = argCollection.ExtractOptional <string>("optimizer", "BrentThenGrid");
string keepTestName = argCollection.ExtractOptional <string>("keepTest", "AlwaysKeep");
string skipRowIndexFileNameOrNull = argCollection.ExtractOptional <string>("skipRowIndexFile", null);
argCollection.CheckNoMoreOptions();
string treeFileName = argCollection.ExtractNext <string>("treeFile");
string predictorFileName = argCollection.ExtractNext <string>("predictorFile");
string targetFileName = argCollection.ExtractNext <string>("targetFile");
string leafDistributionName = argCollection.ExtractNext <string>("leafDistribution");
string nullDataGeneratorName = argCollection.ExtractNext <string>("nullDataGenerator");
string niceName = argCollection.ExtractNext <string>("niceName");
string outputDirectory = argCollection.ExtractNext <string>("outputDirectory");
RangeCollection pieceIndexRangeCollection = argCollection.ExtractNext <RangeCollection>("pieceIndexRange");
int pieceCount = argCollection.ExtractNext <int>("pieceCount");
RangeCollection nullIndexRangeCollection = argCollection.ExtractNext <RangeCollection>("nullIndexRange");
argCollection.CheckThatEmpty();
if (!PhyloDDriver.ValidateDistribution(leafDistributionName))
{
Console.WriteLine("{0} is not a recognized distribution name. Please choose a name from the following list:", leafDistributionName);
foreach (string name in PhyloDDriver.GetDistributionNames())
{
Console.WriteLine("\t{0}", name);
}
throw new ArgumentException("Invalid distribution name.");
}
RangeCollection skipRowIndexRangeCollectionOrNull = (null == skipRowIndexFileNameOrNull) || skipRowIndexFileNameOrNull == "null" ? null : RangeCollection.Parse(File.ReadAllText(skipRowIndexFileNameOrNull));
KeepTest <Dictionary <string, string> > keepTest = KeepTest <Dictionary <string, string> > .GetInstance(null, keepTestName);
SpecialFunctions.CheckCondition(pieceIndexRangeCollection.IsBetween(0, pieceCount - 1), "pieceIndex must be at least 0 and less than pieceCount");
SpecialFunctions.CheckCondition(nullIndexRangeCollection.IsBetween(-1, int.MaxValue), "nullIndex must be at least -1");
PhyloTree aPhyloTree = PhyloTree.GetInstance(treeFileName, null);
ModelScorer modelScorer = ModelScorer.GetInstance(aPhyloTree, leafDistributionName, optimizerName);
ModelEvaluator modelEvaluator = ModelEvaluator.GetInstance(leafDistributionName, modelScorer);
PhyloDDriver driver = PhyloDDriver.GetInstance();
driver.Run(
modelEvaluator,
predictorFileName, targetFileName,
leafDistributionName, nullDataGeneratorName,
keepTest, skipRowIndexRangeCollectionOrNull,
niceName,
outputDirectory,
pieceIndexRangeCollection, pieceCount,
nullIndexRangeCollection,
optimizerName);
//Console.Write("Press enter to exist.");
//Console.Read();
}
catch (Exception exception)
{
Console.WriteLine("");
Console.WriteLine(exception.Message);
if (exception.InnerException != null)
{
Console.WriteLine(exception.InnerException.Message);
}
Console.WriteLine("");
Console.WriteLine(UsageMessage);
throw;
}
}
/// <summary>
/// Does the work.
/// </summary>
public override void DoWork()
{
// get our input data and null the field to make sure we don't serialize it back
InputData inputData = mInputData;
mInputData = null;
// get the job-specific names of input files
FileDefCollection fileDefs = Job.FileDefs;
string treeFileName = Utility.GetNamedFileDef(fileDefs, Constants.TreeFileDefName).LocalName;
string predictorFileName = Utility.GetNamedFileDef(fileDefs, Constants.PredictorFileDefName).LocalName;
string targetFileName = Utility.GetNamedFileDef(fileDefs, Constants.TargetFileDefName).LocalName;
string skipRowIndexFileName = Utility.GetNamedFileDef(fileDefs, Constants.SkipRowIndexFileDefName).LocalName;
// construct RangeCollections
RangeCollection pieceIndexRangeCollection = RangeCollection.Parse(inputData.PieceIndexRange);
RangeCollection nullIndexRangeCollection = RangeCollection.Parse(inputData.NullIndexRange);
RangeCollection skipRowIndexRangeCollection;
FileInfo fileInfo = new FileInfo(skipRowIndexFileName);
if (fileInfo.Length > 0)
{
skipRowIndexRangeCollection = RangeCollection.Parse(File.ReadAllText(skipRowIndexFileName));
}
else
{
skipRowIndexRangeCollection = null;
}
// do the rest
PhyloTree aPhyloTree = PhyloTree.GetInstance(treeFileName, null);
ModelScorer modelScorer =
ModelScorer.GetInstance(aPhyloTree, inputData.LeafDistributionName, inputData.OptimizerName);
ModelEvaluator modelEvaluator = ModelEvaluator.GetInstance(inputData.LeafDistributionName, modelScorer);
KeepTest <Dictionary <string, string> > keepTest =
KeepTest <Dictionary <string, string> > .GetInstance(null, inputData.KeepTestName);
PhyloDDriver driver = PhyloDDriver.GetInstance();
// create a name for the temporary job sandbox. This directory gets created by driver.Run(...)
string agentOutputDirectoryName =
Path.Combine(Environment.CurrentDirectory, String.Format(CultureInfo.InvariantCulture, "{0}.{1}", Job.JobId, Task.TaskId));
// save the standard out and standard error in memory streams
using (MemoryStream streamOut = new MemoryStream(), streamError = new MemoryStream())
{
try
{
// redirect the outputs
using (
StreamWriter writerOut = new StreamWriter(streamOut),
writerError = new StreamWriter(streamError))
{
Console.SetOut(writerOut);
Console.SetError(writerError);
try
{
// run the model
string outputFileName = driver.Run(
modelEvaluator,
predictorFileName, targetFileName,
inputData.LeafDistributionName, inputData.NullDataGeneratorName,
keepTest, skipRowIndexRangeCollection,
inputData.NiceName,
agentOutputDirectoryName,
pieceIndexRangeCollection, inputData.PieceCount,
nullIndexRangeCollection,
inputData.OptimizerName);
// this is the expected output file name -- save this so it can be written on the master side with the same name.
mOutputFileName = Path.GetFileName(outputFileName);
mLocalOutputFileName = Path.Combine(inputData.LocalOutputDirectoryName, mOutputFileName);
// get the output data
string fullOutputPath = Path.Combine(agentOutputDirectoryName, mOutputFileName);
if (!File.Exists(fullOutputPath))
{
TaskResult.FailureReason = TaskFailureReason.MissingOutput;
TaskResult.FailureMessage = String.Format(CultureInfo.CurrentCulture, "Cannot find output file '{0}'", targetFileName);
TaskResult.Status = TaskAssignmentStatus.Failed;
}
using (StreamReader outputData = new StreamReader(fullOutputPath))
{
mOutputData = outputData.ReadToEnd();
}
}
finally
{
// this finally is to make sure we delete the folder
// get rid of the sandbox
Directory.Delete(agentOutputDirectoryName, true);
}
}
}
finally
{
// this finally is to make sure we get console output
Encoding encoding = Encoding.Default;
TaskResult.StandardOutput = encoding.GetString(streamOut.GetBuffer());
TaskResult.StandardError = encoding.GetString(streamError.GetBuffer());
}
}
}