Exemple #1
0
        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;
            }
        }
Exemple #2
0
        /// <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());
                }
            }
        }