// * Process all schemas in file
// * @param staging Staging object
// * @param fileName name of file
// * @param is InputStream
// * @param singleLineNumber if not null, only process this line number
// * @return IntegrationResult
public static IntegrationUtils.IntegrationResult processSchema_MultiTask(TNMStagingCSharp.Src.Staging.Staging staging, String fileName, Stream inputStream, int singleLineNumber) //throws IOException, InterruptedException
{
// set up a mapping of output field positions in the CSV file
Dictionary <CsOutput, int> mappings = new Dictionary <CsOutput, int>(100);
mappings[CsOutput.AJCC6_T] = 42;
mappings[CsOutput.AJCC6_TDESCRIPTOR] = 43;
mappings[CsOutput.AJCC6_N] = 44;
mappings[CsOutput.AJCC6_NDESCRIPTOR] = 45;
mappings[CsOutput.AJCC6_M] = 46;
mappings[CsOutput.AJCC6_MDESCRIPTOR] = 47;
mappings[CsOutput.AJCC6_STAGE] = 48;
mappings[CsOutput.AJCC7_T] = 49;
mappings[CsOutput.AJCC7_TDESCRIPTOR] = 50;
mappings[CsOutput.AJCC7_N] = 51;
mappings[CsOutput.AJCC7_NDESCRIPTOR] = 52;
mappings[CsOutput.AJCC7_M] = 53;
mappings[CsOutput.AJCC7_MDESCRIPTOR] = 54;
mappings[CsOutput.AJCC7_STAGE] = 55;
mappings[CsOutput.SS1977_T] = 56;
mappings[CsOutput.SS1977_N] = 57;
mappings[CsOutput.SS1977_M] = 58;
mappings[CsOutput.SS1977_STAGE] = 59;
mappings[CsOutput.SS2000_T] = 60;
mappings[CsOutput.SS2000_N] = 61;
mappings[CsOutput.SS2000_M] = 62;
mappings[CsOutput.SS2000_STAGE] = 63;
mappings[CsOutput.STOR_AJCC6_T] = 64;
mappings[CsOutput.STOR_AJCC6_TDESCRIPTOR] = 65;
mappings[CsOutput.STOR_AJCC6_N] = 66;
mappings[CsOutput.STOR_AJCC6_NDESCRIPTOR] = 67;
mappings[CsOutput.STOR_AJCC6_M] = 68;
mappings[CsOutput.STOR_AJCC6_MDESCRIPTOR] = 69;
mappings[CsOutput.STOR_AJCC6_STAGE] = 70;
mappings[CsOutput.STOR_AJCC7_T] = 71;
mappings[CsOutput.STOR_AJCC7_TDESCRIPTOR] = 72;
mappings[CsOutput.STOR_AJCC7_N] = 73;
mappings[CsOutput.STOR_AJCC7_NDESCRIPTOR] = 74;
mappings[CsOutput.STOR_AJCC7_M] = 75;
mappings[CsOutput.STOR_AJCC7_MDESCRIPTOR] = 76;
mappings[CsOutput.STOR_AJCC7_STAGE] = 77;
mappings[CsOutput.STOR_SS1977_STAGE] = 78;
mappings[CsOutput.STOR_SS2000_STAGE] = 79;
// go over each file
int processedCases = 0;
int iLineNumber = 0;
//int iLineCounter = 0;
MultiTasksExecutor thisMultiTasksExecutor = new MultiTasksExecutor();
thisMultiTasksExecutor.AddAction(new MultiTasksExecutor.ActionCallBack(MultiTask_TaskCompute));
int iThreads = thisMultiTasksExecutor.GetNumThreads();
mMultiTask_Staging = staging;
miMultiTask_FailedCases = 0;
miMultiTask_ThreadProcessedCases = 0;
thisMultiTasksExecutor.StartTasks();
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
if (singleLineNumber >= 0)
{
IntegrationUtils.WritelineToLog("Starting " + fileName + ", line # " + singleLineNumber + "...");
}
else
{
IntegrationUtils.WritelineToLog("Starting " + fileName + " [" + (iThreads + 1) + " threads]");
}
// loop over each line in the file
TextReader reader = new StreamReader(inputStream);
String line = reader.ReadLine();
while (line != null)
{
iLineNumber++;
if (iLineNumber >= 0)
{
processedCases++;
// split the CSV record
String[] values = line.Split(",".ToCharArray());
// if a single line was requested, skip all other lines
if (singleLineNumber >= 0 && singleLineNumber != iLineNumber)
{
continue;
}
if (values.Length != 80)
{
IntegrationUtils.WritelineToLog("Line " + iLineNumber + " has " + values.Length + " cells; it should be 80.");
}
else
{
MultiTask_DataObj obj = new MultiTask_DataObj();
obj.mMappings = mappings;
obj.mValues = values;
obj.msFileName = fileName;
obj.miLineNum = iLineNumber;
thisMultiTasksExecutor.AddDataItem(obj);
/*
* iLineCounter++;
* if (iLineCounter > 50000)
* {
* IntegrationUtils.WritelineToLog("Time: " + stopwatch.Elapsed.TotalMilliseconds + " ms.");
* iLineCounter = 0;
* }
*/
}
}
line = reader.ReadLine();
}
thisMultiTasksExecutor.WaitForCompletion();
stopwatch.Stop();
String perMs = String.Format("{0,12:F4}", ((float)stopwatch.Elapsed.TotalMilliseconds / processedCases)).Trim();
IntegrationUtils.WritelineToLog("Completed " + processedCases + " cases for " + fileName + " in " + TNMStaging_UnitTestApp.Src.Staging.IntegrationUtils.GenerateTotalTimeString(stopwatch) + " (" + perMs + " ms/case).");
IntegrationUtils.WritelineToLog("Threads Completed " + miMultiTask_ThreadProcessedCases + " cases.");
if (miMultiTask_FailedCases > 0)
{
IntegrationUtils.WritelineToLog("There were " + miMultiTask_FailedCases + " failures.");
}
else
{
IntegrationUtils.WritelineToLog("");
}
IntegrationUtils.WritelineToLog("-----------------------------------------------");
inputStream.Close();
return(new IntegrationUtils.IntegrationResult(processedCases, miMultiTask_FailedCases));
}
// * Process all schemas in TNM file
// * @param staging Staging object
// * @param fileName name of file
// * @param is InputStream
// * @param singleLineNumber if not null, only process this line number
// * @return IntegrationResult
public static IntegrationUtils.IntegrationResult processTNMSchema(TNMStagingCSharp.Src.Staging.Staging staging, String fileName, Stream inputStream, int singleLineNumber, bool bJSONFormat) //throws IOException, InterruptedException
{
Dictionary <TnmOutput, String> output_values = null;
Dictionary <TnmInput, String> input_values = null;
// initialize the threads pool
int n = Math.Min(9, Environment.ProcessorCount + 1);
ThreadPool.SetMaxThreads(n, n);
// go over each file
int processedCases = 0;
int iLineNumber = 0;
//int iLineCounter = 0;
MultiTasksExecutor thisMultiTasksExecutor = new MultiTasksExecutor();
thisMultiTasksExecutor.AddAction(new MultiTasksExecutor.ActionCallBack(MultiTask_TaskCompute));
int iThreads = thisMultiTasksExecutor.GetNumThreads();
mMultiTask_Staging = staging;
miMultiTask_FailedCases = 0;
miMultiTask_ThreadProcessedCases = 0;
thisMultiTasksExecutor.StartTasks();
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
if (singleLineNumber >= 0)
{
System.Diagnostics.Trace.WriteLine("Starting " + fileName + ", line # " + singleLineNumber + " [" + n + " threads]");
}
else
{
System.Diagnostics.Trace.WriteLine("Starting " + fileName + " [" + (iThreads + 1) + " threads]");
}
// loop over each line in the file
TextReader reader = new StreamReader(inputStream);
String line = reader.ReadLine();
String input_line = "";
String output_line = "";
String[] input_strs;
String[] output_strs;
String[] entries;
String sExpectedResult = "";
bool bStageThis = true;
while (line != null)
{
iLineNumber++;
if (iLineNumber >= 0)
{
bStageThis = true;
if (bJSONFormat)
{
bStageThis = false;
if (line.IndexOf("input=") >= 0)
{
input_line = line.Trim();
}
if (line.IndexOf("expectedOutput=") >= 0)
{
output_line = line.Trim();
}
if (output_line.Length > 0)
{
bStageThis = true;
input_values = new Dictionary <TnmInput, String>();
output_values = new Dictionary <TnmOutput, String>();
input_line = input_line.Substring(7, input_line.Length - 8).Trim();
output_line = output_line.Substring(16, output_line.Length - 17).Trim();
input_strs = input_line.Split(",".ToCharArray());
output_strs = output_line.Split(",".ToCharArray());
// set up a mapping of output field positions in the CSV file
foreach (String s in input_strs)
{
entries = s.Split("=".ToCharArray());
if (entries.Length == 2)
{
entries[0] = entries[0].Trim();
entries[1] = entries[1].Trim();
foreach (TnmInput inp in TnmInput.Values)
{
if (inp.toString() == entries[0])
{
input_values.Add(inp, entries[1]);
}
}
}
else
{
System.Diagnostics.Trace.WriteLine("Line " + iLineNumber + " has " + entries.Length + " cells; it should be 2. (" + input_line + ")");
}
}
foreach (String s in output_strs)
{
entries = s.Split("=".ToCharArray());
if (entries.Length == 2)
{
entries[0] = entries[0].Trim();
entries[1] = entries[1].Trim();
foreach (TnmOutput outp in TnmOutput.Values)
{
if (outp.toString() == entries[0])
{
output_values.Add(outp, entries[1]);
}
}
}
else
{
System.Diagnostics.Trace.WriteLine("Line " + iLineNumber + " has " + entries.Length + " cells; it should be 2. (" + output_line + ")");
}
}
}
}
else
{
input_values = new Dictionary <TnmInput, String>();
output_values = new Dictionary <TnmOutput, String>();
// Each line is a comma delimited string.
input_strs = line.Split(",".ToCharArray());
if (input_strs.Length == 54)
{
String sVal = "";
for (int i = 0; i < 54; i++)
{
sVal = input_strs[i].Trim();
if (sVal.Length > 0)
{
TnmInput in_key = TnmInput.PRIMARY_SITE;
TnmOutput out_key = TnmOutput.DERIVED_VERSION;
switch (i)
{
case 0: in_key = TnmInput.PRIMARY_SITE; break;
case 1: in_key = TnmInput.HISTOLOGY; break;
case 2: in_key = TnmInput.DX_YEAR; break;
case 3: in_key = TnmInput.BEHAVIOR; break;
case 4: in_key = TnmInput.GRADE; break;
case 5: in_key = TnmInput.SEX; break;
case 6: in_key = TnmInput.AGE_AT_DX; break;
case 7: in_key = TnmInput.RX_SUMM_SURGERY; break;
case 8: in_key = TnmInput.RX_SUMM_RADIATION; break;
case 9: in_key = TnmInput.REGIONAL_NODES_POSITIVE; break;
case 10: in_key = TnmInput.CLIN_T; break;
case 11: in_key = TnmInput.CLIN_N; break;
case 12: in_key = TnmInput.CLIN_M; break;
case 13: in_key = TnmInput.CLIN_STAGE_GROUP_DIRECT; break;
case 14: in_key = TnmInput.PATH_T; break;
case 15: in_key = TnmInput.PATH_N; break;
case 16: in_key = TnmInput.PATH_M; break;
case 17: in_key = TnmInput.PATH_STAGE_GROUP_DIRECT; break;
case 18: in_key = TnmInput.SSF1; break;
case 19: in_key = TnmInput.SSF2; break;
case 20: in_key = TnmInput.SSF3; break;
case 21: in_key = TnmInput.SSF4; break;
case 22: in_key = TnmInput.SSF5; break;
case 23: in_key = TnmInput.SSF6; break;
case 24: in_key = TnmInput.SSF7; break;
case 25: in_key = TnmInput.SSF8; break;
case 26: in_key = TnmInput.SSF9; break;
case 27: in_key = TnmInput.SSF10; break;
case 28: in_key = TnmInput.SSF11; break;
case 29: in_key = TnmInput.SSF12; break;
case 30: in_key = TnmInput.SSF13; break;
case 31: in_key = TnmInput.SSF14; break;
case 32: in_key = TnmInput.SSF15; break;
case 33: in_key = TnmInput.SSF16; break;
case 34: in_key = TnmInput.SSF17; break;
case 35: in_key = TnmInput.SSF18; break;
case 36: in_key = TnmInput.SSF19; break;
case 37: in_key = TnmInput.SSF20; break;
case 38: in_key = TnmInput.SSF21; break;
case 39: in_key = TnmInput.SSF22; break;
case 40: in_key = TnmInput.SSF23; break;
case 41: in_key = TnmInput.SSF24; break;
case 42: in_key = TnmInput.SSF25; break;
case 43: out_key = TnmOutput.DERIVED_VERSION; break;
case 44: out_key = TnmOutput.CLIN_STAGE_GROUP; break;
case 45: out_key = TnmOutput.PATH_STAGE_GROUP; break;
case 46: out_key = TnmOutput.COMBINED_STAGE_GROUP; break;
case 47: out_key = TnmOutput.COMBINED_T; break;
case 48: out_key = TnmOutput.COMBINED_N; break;
case 49: out_key = TnmOutput.COMBINED_M; break;
case 50: out_key = TnmOutput.SOURCE_T; break;
case 51: out_key = TnmOutput.SOURCE_N; break;
case 52: out_key = TnmOutput.SOURCE_M; break;
}
if (i <= 42)
{
input_values.Add(in_key, sVal);
}
else if (i <= 52)
{
output_values.Add(out_key, sVal);
}
}
}
sExpectedResult = input_strs[53];
}
else
{
System.Diagnostics.Trace.WriteLine("Error: Line " + iLineNumber + " has " + input_strs.Length + " entries.");
}
}
if (bStageThis)
{
processedCases++;
MultiTask_DataObj obj = new MultiTask_DataObj();
obj.mInputValues = input_values;
obj.mOutputValues = output_values;
obj.mbJSONFormat = bJSONFormat;
obj.msExpectedResult = sExpectedResult;
obj.msFileName = fileName;
obj.miLineNum = iLineNumber;
thisMultiTasksExecutor.AddDataItem(obj);
// DEBUG
/*
* iLineCounter++;
* if (iLineCounter >= 50000)
* {
* IntegrationUtils.WritelineToLog("Line: " + iLineNumber + " Time: " + stopwatch.Elapsed.TotalMilliseconds + " ms.");
* iLineCounter = 0;
* }
*/
input_line = "";
output_line = "";
}
}
line = reader.ReadLine();
}
thisMultiTasksExecutor.WaitForCompletion();
stopwatch.Stop();
String perMs = String.Format("{0,12:F4}", ((float)stopwatch.Elapsed.TotalMilliseconds / processedCases)).Trim();
IntegrationUtils.WritelineToLog("Completed " + processedCases + " cases for " + fileName + " in " + TNMStaging_UnitTestApp.Src.Staging.IntegrationUtils.GenerateTotalTimeString(stopwatch) + " (" + perMs + " ms/case).");
IntegrationUtils.WritelineToLog("Threads Completed " + miMultiTask_ThreadProcessedCases + " cases.");
if (miMultiTask_FailedCases > 0)
{
System.Diagnostics.Trace.WriteLine("There were " + miMultiTask_FailedCases + " failures.");
}
else
{
System.Diagnostics.Trace.WriteLine("");
}
System.Diagnostics.Trace.WriteLine("-----------------------------------------------");
inputStream.Close();
return(new IntegrationUtils.IntegrationResult(processedCases, miMultiTask_FailedCases));
}