/// <returns>True if item was added. False if it already existed in the range.</returns>
override public bool TryAdd(Dictionary <string, string> row, string fileName)
{
Helper.CheckCondition(row.ContainsKey("rowIndex"), string.Format(@"When auditing tabulation a ""rowIndex"" column is required. (File ""{0}"")", fileName));
Helper.CheckCondition(row.ContainsKey("rowCount"), string.Format(@"When auditing tabulation a ""rowCount"" column is required. (File ""{0}"")", fileName));
RangeCollection rowIndexRange = RangeCollection.Parse(row["rowIndex"]);
long rowCount = long.Parse(row["rowCount"]);
Helper.CheckCondition(rowIndexRange.IsBetween(0, rowCount - 1), string.Format(@"rowIndex must be at least zero and less than rowCount (File ""{0}"")", fileName));
if (RowCountSoFar == long.MinValue)
{
RowCountSoFar = rowCount;
}
else
{
Helper.CheckCondition(RowCountSoFar == rowCount, string.Format("A different row count was at rowIndex {0} in file {1}", rowIndexRange, fileName));
}
bool tryAdd = RowIndexRangeCollection.TryAddRangeCollection(rowIndexRange);
return(tryAdd);
}
static void Main(string[] args)
{
try {
// before using the ArgCollection class, let the DigipedeClient grab its args.
DigipedeClient client = new DigipedeClient();
args = client.ProcessArguments(args, true);
ArgCollection argCollection = ArgCollection.GetInstance(args);
// show help, if requested
if (argCollection.ExtractOptionalFlag("help"))
{
Console.WriteLine("");
Console.WriteLine(UsageMessage);
Console.WriteLine(HelpMessage);
return;
}
// fail if the DigipedeClient doesn't have the args
SpecialFunctions.CheckCondition(client.IsInitialized, "Digipede Client didn't initialize.");
string keepTestName = argCollection.ExtractOptional("keepTest", "AlwaysKeep");
string skipRowIndexFileNameOrNull = argCollection.ExtractOptional <string>("skipRowIndexFile", null);
string optimizerName = argCollection.ExtractOptional("optimizer", "BrentThenGrid");
argCollection.CheckNoMoreOptions();
int pieceCount = argCollection.ExtractNext <int>("pieceCount");
//int taskPerJobCount = argCollection.ExtractNext<int>("taskPerJobCount"); -- we're not using this -- keep it in case we want to put it back
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 outputDirectoryName = argCollection.ExtractNext <string>("outputDirectory");
RangeCollection nullIndexRangeCollection = argCollection.ExtractNext <RangeCollection>("nullIndexRange");
SpecialFunctions.CheckCondition(nullIndexRangeCollection.IsBetween(-1, int.MaxValue), "nullIndex must be at least -1");
argCollection.CheckThatEmpty();
Directory.CreateDirectory(outputDirectoryName);
// Define a JobTemplate for PhyloD.
JobTemplate jobTemplate = CreateJobTemplate();
// Require 32 bit (ensures we use WOW64 on 64-bit machines) since SpecialFunctions.dll built for x86.
jobTemplate.Control.UseWow64On64Bit = true;
// allow task failures (all but one failure will result in job success)
jobTemplate.JobDefaults.MaxFailures = pieceCount - 1;
// allow multiple concurrent tasks (one for each core); each isolated in its own process.
jobTemplate.Control.Concurrency = ApplicationConcurrency.MultiplePerCore;
jobTemplate.Control.ProcessHostingOptions = HostingOptions.ManySingleUse;
// create a Job based on that JobTemplate
Job job = jobTemplate.NewJob();
// add job-specific data / files
FileDefCollection fileDefs = job.FileDefs;
// files
Utility.GetNamedFileDef(fileDefs, Constants.TreeFileDefName).RemoteName = treeFileName;
Utility.GetNamedFileDef(fileDefs, Constants.PredictorFileDefName).RemoteName = predictorFileName;
Utility.GetNamedFileDef(fileDefs, Constants.TargetFileDefName).RemoteName = targetFileName;
// skipRowIndex file is more complicated because it may not exist, but the JobTemplate requires it.
FileDef fileDef = Utility.GetNamedFileDef(fileDefs, Constants.SkipRowIndexFileDefName);
if (skipRowIndexFileNameOrNull == null || skipRowIndexFileNameOrNull == "null")
{
// stream an empty file
fileDef.Stream = new MemoryStream(0);
}
else
{
// stream the actual file
fileDef.LocalName = skipRowIndexFileNameOrNull;
}
// Create the tasks for the template
for (int pieceIndex = 0; pieceIndex < pieceCount; pieceIndex++)
{
// Create a Task for this piece
Task task = job.NewTask();
// Create an InputData object to encapsulate all input data in one place
InputData inputData = new InputData(optimizerName, keepTestName, leafDistributionName, nullDataGeneratorName,
niceName, outputDirectoryName, pieceIndex, pieceCount, nullIndexRangeCollection.ToString());
// create a Worker for this task
task.Worker = new PhyloDWorker(inputData);
}
// Wire events to catch result data. Note that retrieving data isn't necessary here --
// data can be requested in a server call from another process.
job.TaskCompleted += job_TaskCompleted;
// Write an event to catch any monitoring errors
client.MonitoringError += client_MonitoringError;
// submit the job
SubmissionResult sr = client.SubmitJob(jobTemplate, job);
Console.WriteLine("Submitted job {0} with {1} tasks.", sr.JobId, job.Tasks.Count);
// wait for the result
JobStatusSummary jss = client.WaitForJobWithStatus(sr.JobId);
Console.WriteLine("Job finished with status of {0}", jss.Status);
}
catch (Exception exception)
{
Console.WriteLine("");
Console.WriteLine(exception.Message);
if (exception.InnerException != null)
{
Console.WriteLine(exception.InnerException.Message);
}
Console.WriteLine("");
Console.WriteLine(UsageMessage);
throw;
}
}
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;
}
}