public TCGADatatableBuilderUI()
{
InitializeComponent();
rootDir.SetDirectoryArgument("TCGARoot", "TCGA Data Root");
targetFile.FileArgument = new SaveFileArgument("Target Data", "tsv");
lbDataTypes.Items.AddRange(TCGATechnology.GetTechnologyNames().ToArray());
lbSampleTypes.Items.AddRange(TCGASampleCode.GetSampleCodes().OrderBy(m => m.Code).ToList().ConvertAll(m => string.Format("{0}, {1}", m.ShortLetterCode, m.Definition)).ToArray());
this.Text = Constants.GetSQHTitle(title, version);
}
public override bool PrepareOptions()
{
if (!Directory.Exists(this.TCGADirectory))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", this.TCGADirectory));
return(false);
}
try
{
TCGATechnology.Parse(this.DataType);
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
foreach (var tumor in this.TumorTypes)
{
var tumordir = this.TCGADirectory + "/" + tumor;
if (!Directory.Exists(tumordir))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", tumordir));
return(false);
}
}
if (TCGASampleCodeStrings == null || TCGASampleCodeStrings.Count == 0)
{
TCGASampleCodeStrings = (from v in TCGASampleCode.GetSampleCodes()
select v.ShortLetterCode).ToList();
}
else
{
try
{
GetTCGASampleCodes();
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
}
try
{
GetTechnology();
}
catch (Exception ex)
{
ParsingErrors.Add(ex.Message);
return(false);
}
if (this.Platforms == null || this.Platforms.Count == 0)
{
var tec = GetTechnology();
this.Platforms = (from tumor in TumorTypes
let dir = Path.Combine(this.TCGADirectory, tumor)
let tecdir = tec.GetTechnologyDirectory(dir)
from subdir in Directory.GetDirectories(tecdir)
select Path.GetFileName(subdir)).Distinct().OrderBy(m => m).ToList();
}
return(true);
}