public void DownloadClinicalData(string tumor, SpiderTreeNode node, string targetDir, IProgressCallback callback = null)
{
TCGASpider.DownloadFiles(node, targetDir, null, callback);
//var gzfile = string.Format("clinical_{0}.tar.gz", tumor);
//var uri = string.Format("{0}/{1}", node.Uri, gzfile);
//var targetFile = string.Format("{0}/{1}", targetDir, gzfile);
//if (!WebUtils.DownloadFile(uri, targetFile, callback))
//{
// TCGASpider.DownloadFiles(node, targetDir, null, callback);
// return;
//}
//else
//{
// UncompressFile(targetDir, targetDir, targetFile, true);
//}
}
public override IEnumerable <string> Process()
{
Progress.SetMessage("Getting tree from TCGA ...");
var node = TCGASpider.GetDirectoryTree("tumor", TCGASpider.RootUrl, true);
var name = string.Format("TCGA_directory_{0:yyyyMMdd}", DateTime.Now);
var treeFile = Path.Combine(options.OutputDirectory, name + ".tree");
node.PrintToFile(treeFile);
var fileName = Path.Combine(options.OutputDirectory, name + ".xml");
Progress.SetMessage("Saving data to " + fileName + " ...");
new SpiderTreeNodeXmlFormat().WriteToFile(fileName, node);
Progress.SetMessage("Done.");
Progress.End();
return(new[] { fileName, treeFile });
}
