public string SaveFiles(byte[] contents, string filename, out int fileId)
{
fileId = 0;
var barcodeId = -1;
var row = 'A';
var col = -1;
ParseFileName(filename, out barcodeId, out row, out col);
// invalid filename
if (barcodeId == -1)
{
return(FileUploadErrorKeys.InvalidFileName);
}
// load up the barcode, from db
var barcode = _repositoryFactory.BarcodeRepository.GetNullableById(barcodeId);
if (barcode == null)
{
return(FileUploadErrorKeys.InvalidBarcode);
}
// check db for existing file
var existingFile = _repositoryFactory.BarcodeFileRepository.Queryable.FirstOrDefault(a => a.Barcode == barcode && a.WellColumn == col && a.WellRow == row);
// check the file system
if (File.Exists(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename)) || existingFile != null)
{
return(FileUploadErrorKeys.DuplicateFile);
}
if (WriteFile(filename, contents, string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId)))
{
var bfile = new BarcodeFile()
{
Barcode = barcode,
WellColumn = col,
WellRow = row,
Uploaded = true
};
_repositoryFactory.BarcodeFileRepository.EnsurePersistent(bfile);
fileId = bfile.Id;
return(string.Empty);
}
return(FileUploadErrorKeys.WriteError);
}
// run the validation, calculate the quality results
private void ValidatePhred(BarcodeFile bcf)
{
//var files = _repositoryFactory.BarcodeFileRepository.Queryable.Where(a => a.Barcode.Id == bcf.Barcode.Id && !a.Validated).ToList();
var start = 0;
var end = 0;
var numbers = ReadPhredFile(bcf.Barcode.Id, bcf);
FindIndexes(numbers, out start, out end);
bcf.Start = start;
bcf.End = end;
bcf.DateTimeValidated = DateTime.Now;
bcf.Validated = true;
}
private int[] ReadPhredFile(int barcode, BarcodeFile barcodeFile)
{
var path = string.Format(@"{0}\output\{1}\{2}", _storageLocation, barcode, barcodeFile.ValidationFileName);
if (File.Exists(path))
{
var lines = File.ReadAllLines(path);
lines[0] = string.Empty;
var line = string.Join(" ", lines);
var values = line.Split(new string[] { " " }, StringSplitOptions.RemoveEmptyEntries);
var numbers = new int[values.Count()];
for (var i = 0; i < values.Count(); i++)
{
numbers[i] = Convert.ToInt32(values[i].Trim());
}
return(numbers);
}
return(new int[0]);
}
/*
* This is apparently the method that scans the "uploadLocation", and copies the files to
* the raw directory for either PhRed processing or user download.
*/
public void ScanFiles()
{
//var uploadLocation = @"\\do-files\cgfdata";
//var uploadLocation = @"C:\Users\lai\Dropbox\Documents\Projects\Cgf\cgf\Cgf Data\data";
var re = new Regex(@"^Backup$");
foreach (var directory in Directory.EnumerateDirectories(_uploadLocation).Where(d => !re.IsMatch(Path.GetFileName(d))))
{
foreach (var file in Directory.EnumerateFiles(directory))
{
var start = file.LastIndexOf('\\') + 1;
var filename = file.Substring(start);
var barcodeId = -1;
var row = 'A';
var col = -1;
ParseFileName(filename, out barcodeId, out row, out col);
if (barcodeId != -1)
{
// load up the barcode, from db
var barcode = _repositoryFactory.BarcodeRepository.GetNullableById(barcodeId);
if (barcode != null)
{
if (!Directory.Exists(string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId)))
{
Directory.CreateDirectory(string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId));
}
if (File.Exists(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename)))
{
File.Delete(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename));
}
// move the file into permanent storage, over write any existing files
File.Move(file, string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename));
// This is probably the best place to add the logic that updates non-sequencing
// jobs so that they can be downloaded directly by the user without any further
// processing.
// save the record into the database
var barcodeFile = barcode.BarcodeFiles.FirstOrDefault(a => a.WellColumn == col && a.WellRow == row);
if (barcodeFile == null)
{
barcodeFile = new BarcodeFile()
{
Barcode = barcode, WellColumn = col, WellRow = row, Uploaded = true
};
}
else
{
// resets all the values so that phred runs again and displays the right values
barcodeFile.DateTimeValidated = null;
barcodeFile.Validated = false;
barcodeFile.Uploaded = true;
barcodeFile.Start = 0;
barcodeFile.End = 0;
}
_repositoryFactory.BarcodeFileRepository.EnsurePersistent(barcodeFile);
/*
* 2013-01-17 by kjt: Added logic to bypass need for validation
* if Barcode.UserJobPlate.UserJob.JobType.HasSequencing is false,
* since PhRed os only required on jobs with jobtypes that have sequencing.
*/
var hasSequencing = barcode.UserJobPlate.UserJob.JobType.HasSequencing;
if (!hasSequencing)
{
//Skip Validation And Allow For Download
SkipValidationAndAllowForDownload(barcode);
}
} // end if barcode != null
// however, if the barcode was null we end up here.
} // end if barcode != -1
} // end for each file in directory
Directory.Delete(directory);
} // end for each directory.
} // end method ScanFiles().
// run the validation, calculate the quality results
private void ValidatePhred(BarcodeFile bcf)
{
//var files = _repositoryFactory.BarcodeFileRepository.Queryable.Where(a => a.Barcode.Id == bcf.Barcode.Id && !a.Validated).ToList();
var start = 0;
var end = 0;
var numbers = ReadPhredFile(bcf.Barcode.Id, bcf);
FindIndexes(numbers, out start, out end);
bcf.Start = start;
bcf.End = end;
bcf.DateTimeValidated = DateTime.Now;
bcf.Validated = true;
}
private int[] ReadPhredFile(int barcode, BarcodeFile barcodeFile)
{
var path = string.Format(@"{0}\output\{1}\{2}", _storageLocation, barcode, barcodeFile.ValidationFileName);
if (File.Exists(path))
{
var lines = File.ReadAllLines(path);
lines[0] = string.Empty;
var line = string.Join(" ", lines);
var values = line.Split(new string[] { " " }, StringSplitOptions.RemoveEmptyEntries);
var numbers = new int[values.Count()];
for (var i = 0; i < values.Count(); i++)
{
numbers[i] = Convert.ToInt32(values[i].Trim());
}
return numbers;
}
return new int[0];
}
/*
* This is apparently the method that scans the "uploadLocation", and copies the files to
* the raw directory for either PhRed processing or user download.
*/
public void ScanFiles()
{
//var uploadLocation = @"\\do-files\cgfdata";
//var uploadLocation = @"C:\Users\lai\Dropbox\Documents\Projects\Cgf\cgf\Cgf Data\data";
var re = new Regex(@"^Backup$");
foreach(var directory in Directory.EnumerateDirectories(_uploadLocation).Where(d => !re.IsMatch(Path.GetFileName(d))))
{
foreach(var file in Directory.EnumerateFiles(directory))
{
var start = file.LastIndexOf('\\') + 1;
var filename = file.Substring(start);
var barcodeId = -1;
var row = 'A';
var col = -1;
ParseFileName(filename, out barcodeId, out row, out col);
if (barcodeId != -1)
{
// load up the barcode, from db
var barcode = _repositoryFactory.BarcodeRepository.GetNullableById(barcodeId);
if (barcode != null)
{
if (!Directory.Exists(string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId)))
{
Directory.CreateDirectory(string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId));
}
if (File.Exists(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename)))
{
File.Delete(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename));
}
// move the file into permanent storage, over write any existing files
File.Move(file, string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename));
// This is probably the best place to add the logic that updates non-sequencing
// jobs so that they can be downloaded directly by the user without any further
// processing.
// save the record into the database
var barcodeFile = barcode.BarcodeFiles.FirstOrDefault(a => a.WellColumn == col && a.WellRow == row);
if (barcodeFile == null)
{
barcodeFile = new BarcodeFile() {Barcode = barcode, WellColumn = col, WellRow = row, Uploaded = true };
}
else
{
// resets all the values so that phred runs again and displays the right values
barcodeFile.DateTimeValidated = null;
barcodeFile.Validated = false;
barcodeFile.Uploaded = true;
barcodeFile.Start = 0;
barcodeFile.End = 0;
}
_repositoryFactory.BarcodeFileRepository.EnsurePersistent(barcodeFile);
/*
* 2013-01-17 by kjt: Added logic to bypass need for validation
* if Barcode.UserJobPlate.UserJob.JobType.HasSequencing is false,
* since PhRed os only required on jobs with jobtypes that have sequencing.
*/
var hasSequencing = barcode.UserJobPlate.UserJob.JobType.HasSequencing;
if (!hasSequencing)
{
//Skip Validation And Allow For Download
SkipValidationAndAllowForDownload(barcode);
}
} // end if barcode != null
// however, if the barcode was null we end up here.
} // end if barcode != -1
} // end for each file in directory
Directory.Delete(directory);
} // end for each directory.
}
public string SaveFiles(byte[] contents, string filename, out int fileId)
{
fileId = 0;
var barcodeId = -1;
var row = 'A';
var col = -1;
ParseFileName(filename, out barcodeId, out row, out col);
// invalid filename
if (barcodeId == -1)
{
return FileUploadErrorKeys.InvalidFileName;
}
// load up the barcode, from db
var barcode = _repositoryFactory.BarcodeRepository.GetNullableById(barcodeId);
if (barcode == null)
{
return FileUploadErrorKeys.InvalidBarcode;
}
// check db for existing file
var existingFile = _repositoryFactory.BarcodeFileRepository.Queryable.FirstOrDefault(a => a.Barcode == barcode && a.WellColumn == col && a.WellRow == row);
// check the file system
if (File.Exists(string.Format(@"{0}\raw\{1}\{2}", _storageLocation, barcodeId, filename)) || existingFile != null)
{
return FileUploadErrorKeys.DuplicateFile;
}
if (WriteFile(filename, contents, string.Format(@"{0}\raw\{1}", _storageLocation, barcodeId)))
{
var bfile = new BarcodeFile()
{
Barcode = barcode,
WellColumn = col,
WellRow = row,
Uploaded = true
};
_repositoryFactory.BarcodeFileRepository.EnsurePersistent(bfile);
fileId = bfile.Id;
return string.Empty;
}
return FileUploadErrorKeys.WriteError;
}
