public static bool ProcessGDCUploadReport(string fileName)
{
if (!File.Exists(fileName))
{
Console.WriteLine("File not found, Upload Report file from GDC: " + fileName);
return(false);
}
int counter = 0;
string line;
try
{
using (StreamReader file = new StreamReader(fileName))
{
while ((line = file.ReadLine()) != null)
{
string[] parts = line.Split('\t');
if (parts.Length > 1)
{
if (parts[2] == "submitted_unaligned_reads")
{
counter++;
SeqFileInfo newDataFile = new SeqFileInfo
{
Id = parts[0],
Related_case = parts[1],
EType = parts[2],
Submitter_id = parts[4],
ReadyForUpload = false
};
var tempSUR = new SUR();
if (GDCmetadata.SURdictionary.TryGetValue(parts[4], out tempSUR))
{
newDataFile.DataFileName = tempSUR.file_name;
newDataFile.DataFileSize = tempSUR.file_size;
}
Program.SeqDataFiles.Add(counter, newDataFile);
}
}
}
file.Close();
}
}
catch
{
Console.WriteLine("Exception while processing upload report from the gdc: " + fileName);
Console.WriteLine("Counter = " + counter.ToString());
return(false);
}
return(true);
}
public static Dictionary <string, SUR> SURdictionary = new Dictionary <string, SUR>(); // container for submitted unaligned reads entities
// public static List<ReadGroup> ReadGroupList = new List<ReadGroup>(); // list for read_group objects - do not need at this time
public static bool LoadGDCJsonObjects(string inputString)
{
try
{
gdc_jsonObjects = JsonConvert.DeserializeObject <List <GDCjson> >(inputString, new GDCConverter());
}
catch
{
return(false);
}
SURdictionary.Clear();
foreach (GDCjson gdcJsonOject in gdc_jsonObjects)
{
if (gdcJsonOject.type == "submitted_unaligned_reads")
{
SubmittedUnalignedReads temp1 = new SubmittedUnalignedReads();
temp1 = gdcJsonOject as SubmittedUnalignedReads;
SUR temp2 = new SUR()
{
submitter_id = temp1.submitter_id,
file_name = temp1.file_name,
file_size = temp1.file_size,
md5sum = temp1.md5sum,
project_id = temp1.project_id
};
SURdictionary.Add(temp1.submitter_id, temp2);
}
// *** at this time we have no use for read_group objects, so do not load them
//else if (gdcJsonOject.type == "read_group")
//{
// ReadGroup temp1 = new ReadGroup();
// temp1 = gdcJsonOject as ReadGroup;
// ReadGroupList.Add(temp1);
//}
}
gdc_jsonObjects.Clear();
return(true);
}