public void SetSymbolCharMatrix(string name, string[,] value)
{
clsRCmdLog.LogRComment(string.Format("RdnConnectorClass.SetSymbolCharMatrix:{0}", name));
var sym = _engine.CreateCharacterMatrix(value);
_engine.SetSymbol(name, sym);
}
private void SetupDotNetToRConverters()
{
SetupDotNetToRConverter(typeof(void), p => null);
SetupDotNetToRConverter(typeof(string), p => engine.CreateCharacter((string)p));
SetupDotNetToRConverter(typeof(string[]), p => engine.CreateCharacterVector((string[])p));
SetupDotNetToRConverter(typeof(List <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(IList <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(ICollection <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(IEnumerable <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(string[, ]), p => engine.CreateCharacterMatrix((string[, ])p));
SetupDotNetToRConverter(typeof(int), p => engine.CreateInteger((int)p));
SetupDotNetToRConverter(typeof(int[]), p => engine.CreateIntegerVector((int[])p));
SetupDotNetToRConverter(typeof(List <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(IList <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(ICollection <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(IEnumerable <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(int[, ]), p => engine.CreateIntegerMatrix((int[, ])p));
SetupDotNetToRConverter(typeof(bool), p => engine.CreateLogical((bool)p));
SetupDotNetToRConverter(typeof(bool[]), p => engine.CreateLogicalVector((bool[])p));
SetupDotNetToRConverter(typeof(List <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(IList <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(ICollection <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(IEnumerable <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(bool[, ]), p => engine.CreateLogicalMatrix((bool[, ])p));
SetupDotNetToRConverter(typeof(double), p => engine.CreateNumeric((double)p));
SetupDotNetToRConverter(typeof(double[]), p => engine.CreateNumericVector((double[])p));
SetupDotNetToRConverter(typeof(List <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(IList <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(ICollection <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(IEnumerable <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(double[, ]), p => engine.CreateNumericMatrix((double[, ])p));
SetupDotNetToRConverter(typeof(DateTime), p => engine.CreatePosixct((DateTime)p));
SetupDotNetToRConverter(typeof(DateTime[]), p => engine.CreatePosixctVector((DateTime[])p));
SetupDotNetToRConverter(typeof(List <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(IList <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(ICollection <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(IEnumerable <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(DateTime[, ]), p => engine.CreatePosixctMatrix((DateTime[, ])p));
SetupDotNetToRConverter(typeof(TimeSpan), p => engine.CreateDiffTime((TimeSpan)p));
SetupDotNetToRConverter(typeof(TimeSpan[]), p => engine.CreateDiffTimeVector((TimeSpan[])p));
SetupDotNetToRConverter(typeof(List <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(IList <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(ICollection <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(IEnumerable <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(TimeSpan[, ]), p => engine.CreateDiffTimeMatrix((TimeSpan[, ])p));
}
private void runTask()
{
string basedir = AppDomain.CurrentDomain.BaseDirectory;
string mapPath = basedir + "/tmp/";
// string mapPath = HttpContext.Current.Server.MapPath("~/tmp/");
REngine engine = Utils.getREngineInstance();
string primer3path = System.Web.Configuration.WebConfigurationManager.AppSettings["primer3Home"];
string processNum = System.Web.Configuration.WebConfigurationManager.AppSettings["processNum"];
string isDeleteTempDir = System.Web.Configuration.WebConfigurationManager.AppSettings["deleteTempDir"];
while (true)
{
if (task_queue.Count != 0)
{
Application.Lock();
CustomTask customTask = (CustomTask)task_queue.Dequeue();
Application.UnLock();
customTask.waitQueue = 0;
Object[] task_queue_array = task_queue.ToArray();
for (int i = 0; i < task_queue_array.Length; i++)
{
CustomTask tmpTask = (CustomTask)task_queue_array[i];
tmpTask.waitQueue = i + 1;
}
Application["running_task"] = customTask;
string fileName = customTask.url;
fileName = basedir + "/" + customTask.url;
DataTable dt = read_primer_sequence(fileName);
string[,] primerMat = getPrimerMat(dt);
customTask.status = "preparing ...";
WriteLog(customTask.key, customTask);
CharacterMatrix primer = engine.CreateCharacterMatrix(primerMat);
string rand_file = System.IO.Path.GetRandomFileName();
string tmp_path = mapPath + rand_file;
//string primer3path = "D:/Install/primer3-win-bin-2.3.6";
if (Directory.Exists(tmp_path))
{
DirectoryInfo di = new DirectoryInfo(tmp_path);
di.Delete(true);
}
else if (File.Exists(tmp_path))
{
FileInfo fi = new FileInfo(tmp_path);
fi.Delete();
}
Directory.CreateDirectory(tmp_path);
engine.Evaluate("library(xlsx)");
customTask.percent = 8;
string script_path = basedir + "/primer_dimer_check.R";
script_path = script_path.Replace(@"\", @"/");
engine.Evaluate("source(\"" + script_path + "\")");
customTask.percent = 10;
engine.SetSymbol("primer", primer);
engine.SetSymbol("tmp_dir", engine.CreateCharacter(tmp_path));
engine.SetSymbol("primer", primer);
engine.SetSymbol("primer3dir", engine.CreateCharacter(primer3path));
int?nProcess = Convert.ToInt32(processNum);
if (nProcess != null)
{
engine.SetSymbol("nprocess", engine.CreateInteger(Convert.ToInt32(nProcess)));
}
else
{
engine.SetSymbol("nprocess", engine.CreateInteger(4));
}
engine.SetSymbol("outputfile", engine.CreateCharacter(fileName));
string[] bat_cmds = engine.Evaluate("prepare_bat(tmp_dir,primer,primer3dir,nprocess)").AsCharacter().ToArray();
customTask.status = "dimer calculating ...";
customTask.percent = 20;
WriteLog(customTask.key, customTask);
AutoResetEvent[] resets = new AutoResetEvent[bat_cmds.Length];
for (int i = 0; i < bat_cmds.Length; i++)
{
resets[i] = new AutoResetEvent(false);
Global.ThreadTransfer transfer = new Global.ThreadTransfer(bat_cmds[i], resets[i]);
Thread thread = new Thread(new ParameterizedThreadStart(run_cmd));
thread.Start(transfer);
}
foreach (var v in resets)
{
v.WaitOne();
customTask.percent += 60 / resets.Length;
}
customTask.status = "result generating ...";
customTask.percent = 80;
WriteLog(customTask.key, customTask);
engine.Evaluate("output_result(tmp_dir,primer,outputfile)");
if (isDeleteTempDir == "true")
{
DirectoryInfo di = new DirectoryInfo(tmp_path);
di.Delete(true);
}
customTask.status = "complete";
customTask.percent = 100;
WriteLog(customTask.key, customTask);
Application["running_task"] = null;
}
}
}
