public IEnumerable <object> Get()
{
logData.Info("Get Assay Function is called");
// getting back the assaytypes from the database table( AssayTypes)
using (var repo = new AssayRepository())
{
try
{
List <DisplayClass> objectAssay = new List <DisplayClass>();
var assaynamesobj = repo.GetAssay();
foreach (var assaytype in assaynamesobj)
{
DisplayClass ds = new DisplayClass();
ds.Id = assaytype.ID;
ds.TypeId = assaytype.TypeId;
ds.AssayName = assaytype.AssayName;
objectAssay.Add(ds);
}
logData.Info("Get Assay Function is finished");
return(objectAssay);
}
catch (SqlException odbcEx)
{
Console.WriteLine(odbcEx.Message);
logData.Error(odbcEx.Message);
return(null);
}
}
}
public CurveFile Transform(string jsonMessages, string AssayName)
{
var delim = new[] { '"' };
jsonMessages = Regex.Unescape(jsonMessages);
jsonMessages = jsonMessages.TrimEnd(delim).TrimStart(delim);
AssayName = Regex.Unescape(AssayName);
AssayName = AssayName.TrimEnd(delim).TrimStart(delim);
dynamic data = JObject.Parse(jsonMessages);
long AssayDBID = 0;
using (var repo = new AssayRepository())
{
AssayDBID = repo.GetAssayID(AssayName);
}
CurveFile toReturn = JsonConvert.DeserializeObject <CurveFile>(jsonMessages);
toReturn.AssayDBID = AssayDBID;
//Extract extension from file name
ExtractExtensionService helper = new ExtractExtensionService();
string[] fullFileName = new string[2];
fullFileName = helper.ExtractExt(toReturn);
return(toReturn);
}
public AssayController(AssayRepository repository, PurchaseRepository pu_repository, IHubContext <PrintHub> hub, IOptionsSnapshot <WorkOption> option, IHostingEnvironment env)
{
r = repository;
pu_r = pu_repository;
_hub = hub;
_hostingEnvironment = env;
this.option = option.Value;
}
// POST: api/HashValues
public IEnumerable <int> Post()
{
List <int> exists = new List <int>();
List <string> hashedValues = new List <string>();
for (var i = 0; i < HttpContext.Current.Request.Files.Count; i++)
{
List <string> hashValues = new List <string>();
HttpPostedFile file = HttpContext.Current.Request.Files.Get(i);
string filename = file.FileName;
Debug.WriteLine(file);
Debug.WriteLine(filename);
using (var repo = new AssayRepository())
{
try
{
var fileStream = file.InputStream;
SHA1Managed sha = new SHA1Managed();
byte[] checksum = sha.ComputeHash(fileStream);
string sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
var hashValuesObj = repo.GetReport();
foreach (var hashtype in hashValuesObj)
{
hashedValues.Add(hashtype.HashValue);
}
Debug.WriteLine(hashedValues);
if (hashedValues.Contains(sendCheckSum))
{
exists.Add(1);
}
else
{
exists.Add(0);
}
Debug.WriteLine(exists);
// return exists;
}
catch (Exception e)
{
Console.WriteLine(e.Message);
logData.Error(e.Message);
return(null);
}
}
// return exists;
}
return(exists);
}
public string GetAssayInDB()
{
IEnumerable <long> container = null;
List <AssayType> assayContainer = new List <AssayType>();
List <AssayType> toReturn = new List <AssayType>();
using (var repo = new CurveFilesRepository())
{
container = repo.GetUniqueTypeID();
}
var assayRepo = new AssayRepository();
foreach (var item in container)
{
assayContainer.Add(assayRepo.GetAssayUsingTypeID(item));
}
return(JsonConvert.SerializeObject(assayContainer));
}
public string Get()
{
log.Info("getAssay method is called");
IEnumerable <AssayType> container = null;
var toReturn = new List <AssayCount>();
var repo = new AssayRepository();
var curveRepo = new CurveFilesRepository();
container = repo.GetAssay();
foreach (var item in container)
{
toReturn.Add(new AssayCount
{
assay = item,
fileCount = curveRepo.GetCountOfCurve(item.TypeId)
});
}
log.Info("getAssay method is finished");
return(JsonConvert.SerializeObject(toReturn));
}
// GET: api/AssayNamesReportFile
public IEnumerable <object> Get()
{
logData.Info("Get Assay Name from Report File Function is called");
// getting assay id from the database table( ReportFile)
using (var repo = new AssayRepository())
{
try
{
List <DisplayClass> objectAssay = new List <DisplayClass>();
List <long> ids = new List <long>();
List <long> typeId = new List <long>();
List <string> assayNames = new List <string>();
var assayobject = repo.GetAssayNameFromReportFile();
foreach (var assayName in assayobject)
{
DisplayClass ds = new DisplayClass();
ids.Add(assayName.AssayTypeId);
ds.Id = assayName.AssayTypeId;
}
//Using the assayId getting back the assay names
foreach (var assayid in ids)
{
DisplayClass ds = new DisplayClass();
ds.AssayName = repo.GetAssayName(assayid);
ds.TypeId = repo.GetTypeIdWithID(assayid);
objectAssay.Add(ds);
}
return(objectAssay);
}
catch (SqlException odbcEx)
{
Console.WriteLine(odbcEx.Message);
logData.Error(odbcEx.Message);
return(null);
}
}
}
public string Get(Boolean IsGolden, string Tag, string AssayVersion, string SoftwareVersion, int AssayID)
{
long AssayDBID;
string AssayName = "";
//Assay name is specified
if (AssayID != -1)
{
using (var repo = new AssayRepository())
{
AssayDBID = repo.GetTypeIdWithID(AssayID);
AssayName = repo.GetAssayName(AssayID);
}
}
else
{
AssayDBID = -1;
}
var files = new List <Pair>();
if (Tag == "undefined")
{
Tag = "";
}
if (AssayVersion == "undefined")
{
AssayVersion = "";
}
if (SoftwareVersion == "undefined")
{
SoftwareVersion = "";
}
using (var repo = new CurveFilesRepository())
{
var tempContainer = repo.GetSpecifiedFile(IsGolden, Tag, AssayVersion, SoftwareVersion, AssayDBID);
if (tempContainer.Count <CurveFile>() == 0)
{
return(JsonConvert.SerializeObject("No Matching Curve File Found"));
}
else
{
var service = new CurveDataPointService();
var assayRepo = new AssayRepository();
foreach (var temp in tempContainer)
{
var container = service.getCurveData(temp.Data, temp.FullFileName);
if (AssayDBID == -1)
{
AssayName = assayRepo.GetAssayNameUsingTypeID(temp.AssayDBID);
}
files.Add(new Pair
{
AssayName = AssayName,
curveFile = temp,
data = container.dataSet,
FileType = container.FileType
});
}
}
}
return(JsonConvert.SerializeObject(files));
}
// POST: api/ExtractAssayName
public IEnumerable <string> Post()
{
/* lock (ControllerSync)
* {
*/
List <string> assayNames = new List <string>();
for (var i = 0; i < HttpContext.Current.Request.Files.Count; i++)
{
int flag = 0;
logData.Info("Get all files from the staged area to extract assayname");
HttpPostedFile file = HttpContext.Current.Request.Files.Get(i);
string filename = file.FileName;
var tempPathToStore = Path.GetTempPath();
tempPathToStore += "assaynames";
System.IO.Directory.CreateDirectory(tempPathToStore);
//save the file in temp folder
file.SaveAs(tempPathToStore + file.FileName);
//getting the path of stored file
var tempStoredPath = tempPathToStore + file.FileName;
var tempfilename = filename.Replace(".pdf", ".txt");
string pathToText = System.IO.Path.Combine(tempPathToStore, tempfilename);
//Convert PDF file to Text file
SautinSoft.PdfFocus f = new SautinSoft.PdfFocus();
f.OpenPdf(tempStoredPath);
if (f.PageCount > 0)
{
int count = 0;
try
{
string line;
//getting assaynames from database
var repo = new AssayRepository();
List <string> assaylist1 = new List <string>();
//string[] assayFromDb;
var assaynamesobj = repo.GetAssay();
foreach (var assaytype in assaynamesobj)
{
string assayname = assaytype.AssayShortName;
assaylist1.Add(assayname);
}
string[] assaylistFromDB = assaylist1.ToArray();
foreach (var ind in assaylistFromDB)
{
Debug.WriteLine(ind);
}
//string[] assaylist1 = { "AC2", "AC2 250 (1)", "AdV/hMPV/RV", "Babesia", "C. diff", "CT", "CT 250", "DENV", "dHBV", "dHCV", "dHIV", "DNA60", "Flu A/B/RSV", "GBS", "GC", "GC 250 (6)", "GT HPV", "HEV", "HPV", "HPV 250 (14)", "HSV 1&2", "LDT RT TMA-1", "LDT RT TMA-2", "LDT RT TMA-3", "LDT TMA-1", "LDT TMA-2", "LDT TMA-3", "LDT1", "M gen", "MRSA", "OADNA55", "OADNA58", "OADNA62", "OADNA65", "Paraflu", "Parvo/HAV", "PSA 100", "QCDNAIC", "QCFluPPR", "QCRNAIC", "qHBV", "qHCV", "qHIV-1", "RNA60", "RNA60-10uL", "TRICH", "TRICH 250 (10)", "Ultrio Elite", "WNV", "ZIKV", "ZIKV (51)" };
string[] assaylist2 = { "AC2 100 (21)", "AC2 250 (1)", "AdV/hMPV/RV (102)", "Babesia (50)", "C. diff (108)", "CT 100 (22)", "CT 250 (5)", "DENV (36)", "dHBV (97)", "dHCV (98)", "dHIV (99)", "DNA60 (1507)", "Flu A/B/RSV (101)", "GBS (106)", "GC 100 (23)", "GC 250 (6)", "GT HPV (20)", "HEV (39)", "HPV 100 (24)", "HPV 250 (14)", "HSV 1&2 (40)", "LDT RT TMA-1 (90)", "LDT RT TMA-2 (91)", "LDT RT TMA-3 (92)", "LDT TMA-1 (95)", "LDT TMA-2 (88)", "LDT TMA-3 (89)", "LDT1 (1001)", "M gen (43)", "MRSA (107)", "OADNA55 (1505)", "OADNA58 (1506)", "OADNA62 (1508)", "OADNA65 (1509)", "Paraflu (103)", "Parvo/HAV (29)", "PSA 100 (31)", "QCDNAIC (1501)", "QCFluPPR (1503)", "QCRNAIC (1502)", "qHBV (34)", "qHCV (32)", "qHIV-1 (28)", "RNA60 (1510)", "RNA60-10uL (1512)", "TRICH 100 (9)", "TRICH 250 (10)", "Ultrio Elite (25)", "WNV (4)", "ZIKV (52)", "ZIKV (51)" };
int result = f.ToText(pathToText);
if (result == 0)
{
var lineCount = File.ReadLines(pathToText).Count();
Debug.WriteLine(lineCount);
FileStream inFile = new FileStream(pathToText, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
using (StreamReader sr = new StreamReader(inFile))
{
while ((line = sr.ReadLine()) != null)
{
count++;
foreach (string word in assaylist1)
{
if (line.Contains(word))
{
var indexOfAssay = Array.IndexOf(assaylistFromDB, word);
var assayNameExtracted = assaylist2[indexOfAssay];
assayNames.Add(assayNameExtracted);
flag = 1;
break;
}
}
if (flag == 1)
{
break;
}
}
Debug.WriteLine(count);
if (count == lineCount)
{
var assayNameExtracted = "Choose AssayName";
assayNames.Add(assayNameExtracted);
}
}
if (assayNames[i] == "")
{
assayNames.Add("Choose AssayName");
}
}
logData.Info("Returning the assay name");
}
catch (Exception e)
{
logData.Error(e.Message);
}
f.ClosePdf();
}
else
{
assayNames.Add("Choose AssayName");
}
}
return(assayNames);
// }
}
public string getAssayFromFile(Byte[] byteFile, string fileName)
{
var delim = new[] { '"' };
fileName = Regex.Unescape(fileName);
fileName = fileName.TrimEnd(delim).TrimStart(delim);
var tempPath = Path.GetTempPath();
var tempPathFile = Path.Combine(tempPath, fileName);
File.WriteAllBytes(tempPathFile, byteFile);
var repo = new AssayRepository();
var typeID = "";
using (var streamReader = new StreamReader(tempPathFile))
{
var firstLine = streamReader.ReadLine();
var secondLine = streamReader.ReadLine();
if (firstLine == null || secondLine == null)
{
return("Invalid");
}
var lowerFirstLine = firstLine.ToLower();
string[] seperatedValueFirst = lowerFirstLine.Split(',');
if (lowerFirstLine.Contains("sampleid") &&
(lowerFirstLine.Contains("testorderid") || lowerFirstLine.Contains("testorder id")))
{
//RPTool files
if (seperatedValueFirst.Length == 9)
{
List <string> firstColHolder = new List <string>();
var newStream = new StreamReader(tempPathFile);
while (!newStream.EndOfStream)
{
var newLine = newStream.ReadLine();
String[] seperatedVal = newLine.Split(',');
firstColHolder.Add(seperatedVal[0]);
}
//check the string with number
for (var index = 0; index < firstColHolder.Count; index++)
{
var charArr = firstColHolder[index].ToCharArray();
if (Char.IsNumber(charArr[0]))
{
typeID = charArr[0].ToString();
typeID = typeID.Insert(1, charArr[1].ToString());
var toReturn = repo.GetAssayNameUsingTypeID(Int32.Parse(typeID));
return(toReturn);
}
}
}
//TCycle and some versions of .curve
if (lowerFirstLine.Contains("cyclenum"))
{
String[] seperatedValue = secondLine.Split(',');
//TCYC
if (seperatedValue.Length != 15)
{
typeID = seperatedValue[7];
}
//.Curve
else
{
typeID = seperatedValue[6];
}
var toReturn = repo.GetAssayNameUsingTypeID(Int32.Parse(typeID));
//If assay are outdated
if (toReturn == "")
{
return("Invalid-Outdated");
}
return(toReturn);
}
//Fluorescence curve
else if (lowerFirstLine.Contains("rtf"))
{
String[] seperatedValue = secondLine.Split(';');
var Assay = seperatedValue[2];
String[] assayNumber = seperatedValue[2].Split(',');
var AssayDBID = assayNumber[0];
var toReturn = repo.GetAssayNameUsingTypeID(Int32.Parse(AssayDBID));
//If assay are outdated
if (toReturn == "")
{
return("Invalid-Outdated");
}
return(toReturn);
}
}
//validates FLUO.csv file
else if (seperatedValueFirst.Length == 19)
{
var typeIDStr = seperatedValueFirst[8];
var toReturn = repo.GetAssayNameUsingTypeID(Int32.Parse(typeIDStr));
//If assay are outdated
if (toReturn == "")
{
return("Invalid-Outdated");
}
return(toReturn);
}
//validates LUMI.csv file
else
{
var typeIDStr = "";
if (seperatedValueFirst.Length > 5)
{
if (seperatedValueFirst[5] != null)
{
var numOfDataPts = seperatedValueFirst[5];
typeIDStr = seperatedValueFirst[Int32.Parse(numOfDataPts) + 8];
}
else
{
return("Invalid");
}
var toReturn = repo.GetAssayNameUsingTypeID(Int32.Parse(typeIDStr));
//If assay are outdated
if (toReturn == "")
{
return("Invalid-Outdated");
}
return(toReturn);
}
}
}
return("Invalid");
}
public PairResponse ValidateFile(Byte [] byteFile, string fileName, string AssayName)
{
var delim = new[] { '"' };
AssayName = Regex.Unescape(AssayName);
AssayName = AssayName.TrimEnd(delim).TrimStart(delim);
var tempPath = Path.GetTempPath();
var tempPathFile = Path.Combine(tempPath, fileName);
File.WriteAllBytes(tempPathFile, byteFile);
using (var streamReader = new StreamReader(tempPathFile))
{
var firstLine = streamReader.ReadLine();
var secondLine = streamReader.ReadLine();
var lowerFirstLine = firstLine.ToLower();
string lowerSecondLine = "";
if (secondLine != null)
{
lowerSecondLine = secondLine.ToLower();
}
else
{
return(new PairResponse {
Indicator = false, message = "^Curve File has no content"
});
}
long TypeId;
//parse
String[] seperatedValue = firstLine.Split(',');
//validates TCYC, .curve, LUMI.RPTool, FLUO.RPTool
if (lowerFirstLine.Contains("sampleid") &&
(lowerFirstLine.Contains("testorderid") || lowerFirstLine.Contains("testorder id")))
{
using (var repo = new AssayRepository())
{
TypeId = repo.GetAssayTypeId(AssayName);
}
//RPTool files
if (seperatedValue.Length == 9)
{
List <string> firstColHolder = new List <string>();
var newStream = new StreamReader(tempPathFile);
while (!newStream.EndOfStream)
{
var newLine = newStream.ReadLine();
String[] seperatedVal = newLine.Split(',');
firstColHolder.Add(seperatedVal[0]);
}
//check the string with number
for (var index = 0; index < firstColHolder.Count; index++)
{
var charArr = firstColHolder[index].ToCharArray();
if (Char.IsNumber(charArr[0]))
{
//TODO get index 0 and 1 and combine them
string typeID = charArr[0].ToString();
typeID = typeID.Insert(1, charArr[1].ToString());
return(new PairResponse {
Indicator = true, message = ""
});
}
}
return(new PairResponse {
Indicator = false, message = "^Curve does not match Assay type"
});
}
//TCycle curve
if (lowerFirstLine.Contains("cyclenum"))
{
if (TypeId > 99)
{
if (lowerSecondLine.Contains(AssayName.ToLower()) && lowerSecondLine != null)
{
return(new PairResponse {
Indicator = true, message = ""
});
}
}
return(new PairResponse {
Indicator = false, message = "^Curve does not match Assay type"
});
//Fluorescence curve
}
else if (lowerFirstLine.Contains("rtf"))
{
if (TypeId < 100 && lowerSecondLine != null)
{
return(new PairResponse {
Indicator = true, message = ""
});
}
else
{
return(new PairResponse {
Indicator = false, message = "^Curve does not match Assay type"
});
}
}
//Else
else if (lowerFirstLine.Contains("rfu"))
{
if (TypeId < 100 && lowerSecondLine != null)
{
return(new PairResponse {
Indicator = true, message = ""
});
}
else
{
return(new PairResponse {
Indicator = false, message = "^Curve does not match Assay type"
});
}
}
}
//validates FLUO.csv file
else if (seperatedValue.Length == 19)
{
//TODO validate if mapped correctly
var typeIDStr = seperatedValue[8];
return(new PairResponse {
Indicator = true, message = ""
});
}
//validates LUMI.csv file
else
{
var typeIDStr = "";
if (seperatedValue.Length > 5)
{
if (seperatedValue[5] != null)
{
var numOfDataPts = seperatedValue[5];
typeIDStr = seperatedValue[Int32.Parse(numOfDataPts) + 8];
return(new PairResponse {
Indicator = true, message = ""
});
}
else
{
return(new PairResponse {
Indicator = false, message = "^Invalid Curve File"
});
}
}
}
}
return(new PairResponse {
Indicator = false, message = "^Invalid Curve File"
});
}
