public void TestRead()
{
var samples = new BreastCancerSampleItemFormat("Source Name").ReadFromFile("../../../data/E-TABM-158.sdrf.txt");
Assert.AreEqual(130, samples.Count);
var s = samples[0];
Assert.AreEqual("A-AFFY-76", s.Platform);
Assert.AreEqual("E-TABM-158", s.Dataset);
Assert.AreEqual("LBL_POP_W405609.F03.CEL", s.Sample);
Assert.AreEqual("s0100", s.SourceName);
Assert.AreEqual(string.Empty, s.SampleTitle);
Assert.AreEqual(string.Empty, s.Patient);
Assert.AreEqual("breast cancer", s.Disease);
Assert.AreEqual("Neg", s.FamilyHistory);
Assert.AreEqual("1", s.Stage);
Assert.AreEqual("3", s.Grade);
Assert.AreEqual(StatusValue.POSITIVE, s.ER);
Assert.AreEqual(StatusValue.POSITIVE, s.PR);
Assert.AreEqual(StatusValue.NEGATIVE, s.HER2);
Assert.AreEqual(StatusValue.NEGATIVE, s.P53);
Assert.AreEqual(StatusValue.NEGATIVE, s.HormonalTherapy);
Assert.AreEqual(StatusValue.NEGATIVE, s.ChemotherapyTreatment);
Assert.AreEqual(StatusValue.POSITIVE, s.RadiationTreatment);
Assert.AreEqual(StatusValue.NEGATIVE, s.Recurrence);
Assert.AreEqual(StatusValue.NEGATIVE, s.AliveAtEndpoint);
}
public void TestRead2()
{
var samples = new BreastCancerSampleItemFormat("Source Name").ReadFromFile("../../../data/E-MTAB-365.sdrf.txt");
Assert.AreEqual(1843, samples.Count);
var s = samples[1];
Assert.AreEqual("A-AFFY-44", s.Platform);
Assert.AreEqual("E-MTAB-365", s.Dataset);
Assert.AreEqual("170706-09.CEL", s.Sample);
Assert.AreEqual("CIT_DSOA_101", s.SourceName);
Assert.AreEqual(string.Empty, s.SampleTitle);
Assert.AreEqual(string.Empty, s.Patient);
Assert.AreEqual("breast carcinoma", s.Disease);
Assert.AreEqual(StatusValue.NA, s.FamilyHistory);
Assert.AreEqual(string.Empty, s.Stage);
Assert.AreEqual(string.Empty, s.Grade);
Assert.AreEqual(StatusValue.POSITIVE, s.ER);
Assert.AreEqual(StatusValue.NEGATIVE, s.PR);
Assert.AreEqual(StatusValue.NEGATIVE, s.HER2);
Assert.AreEqual(StatusValue.NA, s.P53);
Assert.AreEqual(StatusValue.NA, s.HormonalTherapy);
Assert.AreEqual(StatusValue.NA, s.ChemotherapyTreatment);
Assert.AreEqual(StatusValue.NA, s.RadiationTreatment);
Assert.AreEqual(StatusValue.NA, s.Recurrence);
Assert.AreEqual(StatusValue.NA, s.AliveAtEndpoint);
}
public override IEnumerable<string> Process(string rootDirectory)
{
var subdirs = SampleUtils.GetDatasets(rootDirectory);
var format = new BreastCancerSampleItemFormat();
List<BreastCancerSampleItem> total = new List<BreastCancerSampleItem>();
foreach (var subdir in subdirs)
{
var parser = ParserFactory.GetParserInDirectory(subdir);
var dirname = Path.GetFileName(subdir);
Console.WriteLine(dirname);
Dictionary<string, BreastCancerSampleItem> flist = new Dictionary<string, BreastCancerSampleItem>();
parser.ParseDataset(subdir, flist);
total.AddRange(flist.Values);
var sampleFile = subdir + @"\" + dirname + ".sample";
format.WriteToFile(sampleFile, flist.Values.ToList());
}
var htmlFile = rootDirectory + "\\" + Path.GetFileNameWithoutExtension(rootDirectory) + "_SampleInformation.html";
new BreastCancerSampleItemHtmlWriter().WriteToFile(htmlFile, total);
var excelFile = Path.ChangeExtension(htmlFile, ".xls");
new BreastCancerSampleItemExcelWriter().WriteToFile(excelFile, total);
return new string[] { htmlFile, excelFile };
}
