public static void PrintToFile(this SpiderTreeNode node, string fileName)
{
using (StreamWriter sw = new StreamWriter(fileName))
{
node.Print(sw);
}
}
public static void FillDirectoryTree(SpiderTreeNode node, bool recursive)
{
node.Print(Console.Out);
if (node.Name.Contains(".Level_") || node.Name.Contains(".mage-tab."))
{
return;
}
var content = WebUtils.DownloadHtml(node.Uri);
//Console.WriteLine(content);
HtmlDocument doc = new HtmlDocument();
doc.LoadHtml(content);
foreach (HtmlNode link in doc.DocumentNode.SelectNodes("//a[@href]"))
{
HtmlAttribute att = link.Attributes["href"];
var curlink = att.Value;
if (curlink.StartsWith("/") || !curlink.EndsWith("/") || curlink.Equals("lost+found/"))
{
continue;
}
string cururi;
if (node.Uri.EndsWith("/"))
{
cururi = node.Uri + curlink;
}
else
{
cururi = node.Uri + "/" + curlink;
}
var curname = curlink.TrimEnd('/');
var lastModified = link.NextSibling.InnerText.Trim();
lastModified = lastModified.Substring(0, lastModified.Length - 1).Trim();
node.Nodes.Add(new SpiderTreeNode()
{
Name = curname,
Uri = cururi,
LastModified = lastModified,
Depth = node.Depth + 1
});
}
if (recursive)
{
foreach (var subnode in node.Nodes)
{
FillDirectoryTree(subnode, true);
}
}
}
public static void FillDirectoryTree(SpiderTreeNode node, bool recursive)
{
node.Print(Console.Out);
if (node.Name.Contains(".Level_") || node.Name.Contains(".mage-tab."))
{
return;
}
var content = WebUtils.DownloadHtml(node.Uri);
//Console.WriteLine(content);
HtmlDocument doc = new HtmlDocument();
doc.LoadHtml(content);
foreach (HtmlNode link in doc.DocumentNode.SelectNodes("//a[@href]"))
{
HtmlAttribute att = link.Attributes["href"];
var curlink = att.Value;
if (curlink.StartsWith("/") || !curlink.EndsWith("/") || curlink.Equals("lost+found/"))
{
continue;
}
string cururi;
if (node.Uri.EndsWith("/"))
{
cururi = node.Uri + curlink;
}
else
{
cururi = node.Uri + "/" + curlink;
}
var curname = curlink.TrimEnd('/');
var lastModified = link.NextSibling.InnerText.Trim();
lastModified = lastModified.Substring(0, lastModified.Length - 1).Trim();
node.Nodes.Add(new SpiderTreeNode()
{
Name = curname,
Uri = cururi,
LastModified = lastModified,
Depth = node.Depth + 1
});
}
if (recursive)
{
foreach (var subnode in node.Nodes)
{
FillDirectoryTree(subnode, true);
}
}
}
public static void DownloadFiles(SpiderTreeNode node, string targetDir, Action <List <DownloadItem> > filterFile, IProgressCallback callback = null)
{
List <DownloadItem> items = GetDownloadFiles(node, targetDir, filterFile);
foreach (var item in items)
{
if (!WebUtils.DownloadFile(item.Url, item.TargetFile, callback))
{
throw new Exception(string.Format("Download {0} to {1} failed!", item.Url, item.TargetFile));
}
}
}
public static void Print(this SpiderTreeNode node, TextWriter writer)
{
for (int i = 1; i < node.Depth; i++)
{
writer.Write("->");
}
writer.WriteLine("{0}:[{1}]", node.Name, node.LastModified);
foreach (var subnode in node.Nodes)
{
subnode.Print(writer);
}
}
public static SpiderTreeNode GetDirectoryTree(string name, string uri, bool recursive)
{
var result = new SpiderTreeNode()
{
Name = name,
Uri = uri,
Depth = 1
};
FillDirectoryTree(result, recursive);
return(result);
}
public static SpiderTreeNode GetDirectoryTree(string name, string uri, bool recursive)
{
var result = new SpiderTreeNode()
{
Name = name,
Uri = uri,
Depth = 1
};
FillDirectoryTree(result, recursive);
return result;
}
private void btnLoad_Click(object sender, EventArgs e)
{
if (!File.Exists(xmlFile.FullName))
{
MessageBox.Show(this, string.Format("Xml file {0} not exists", xmlFile.FullName));
return;
}
_lastXml = xmlFile.FullName;
_rootNode = new SpiderTreeNodeXmlFormat().ReadFromFile(xmlFile.FullName);
_tumors = (from node in _rootNode.Nodes
select node.Name as object).Distinct().ToList();
FillTumor();
}
public static List <DownloadItem> GetDownloadFiles(SpiderTreeNode node, string targetDir, Action <List <DownloadItem> > filterFile)
{
List <DownloadItem> result = new List <DownloadItem>();
var content = WebUtils.DownloadHtml(node.Uri);
HtmlDocument doc = new HtmlDocument();
doc.LoadHtml(content);
var links = new List <string>();
foreach (HtmlNode link in doc.DocumentNode.SelectNodes("//a[@href]"))
{
HtmlAttribute att = link.Attributes["href"];
var curlink = att.Value;
if (curlink.EndsWith("/") || curlink.StartsWith("?"))
{
continue;
}
string cururi;
if (node.Uri.EndsWith("/"))
{
cururi = node.Uri + curlink;
}
else
{
cururi = node.Uri + "/" + curlink;
}
var targetFile = new FileInfo(targetDir + "/" + curlink).FullName;
result.Add(new DownloadItem()
{
Url = cururi,
TargetFile = targetFile,
RetryCount = 0
});
}
if (null != filterFile)
{
filterFile(result);
}
FilterExists(result);
return(result);
}
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);
//}
}
private void btnLoad_Click(object sender, EventArgs e)
{
if (!File.Exists(xmlFile.FullName))
{
MessageBox.Show(this, string.Format("Xml file {0} not exists", xmlFile.FullName));
return;
}
_lastXml = xmlFile.FullName;
_rootNode = new SpiderTreeNodeXmlFormat().ReadFromFile(xmlFile.FullName);
_tumors = (from node in _rootNode.Nodes
select node.Name as object).Distinct().ToList();
FillTumor();
}
private void DownloadLevel3Data(SpiderTreeNode m, string currDir)
{
if (m.Nodes.Any(n => TCGAUtils.IsLevel3(n.Name)))
{
m.Nodes.RemoveAll(n => TCGAUtils.IsLevel1(n.Name) || TCGAUtils.IsLevel2(n.Name));
}
else //download level2 data
{
m.Nodes.RemoveAll(n => TCGAUtils.IsLevel1(n.Name));
}
m.MarkHighestVersionNodes();
foreach (var node in m.Nodes)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
var fDir = currDir + "/" + node.Name;
var compressed = fDir + ".tar.gz";
var compressedMd5 = fDir + ".tar.gz.md5";
var parentDir = Path.GetDirectoryName(currDir);
var parentFDir = parentDir + "/" + node.Name;
var parentFComparessed = parentFDir + ".tar.gz";
var parentFComparessedMd5 = parentFDir + ".tar.gz.md5";
if (Directory.Exists(parentFDir))
{
Directory.Move(parentFDir, fDir);
}
if (File.Exists(parentFComparessed))
{
File.Move(parentFComparessed, compressed);
}
if (File.Exists(parentFComparessedMd5))
{
File.Move(parentFComparessedMd5, compressedMd5);
}
if (node.IsPreviousVersion)
{
if (Directory.Exists(fDir))
{
Progress.SetMessage("Deleting previous version : " + fDir);
Directory.GetFiles(fDir).ToList().ForEach(File.Delete);
Directory.Delete(fDir);
}
if (!File.Exists(compressed))
continue;
File.Delete(compressed);
File.Delete(compressedMd5);
}
else
{
Progress.SetMessage("Processing {0}.{1} ...", m.Name, node.Name);
var bDownload = !File.Exists(compressed);
var bTar = bDownload || !Directory.Exists(fDir);
if (bDownload)
{
var uri = node.Uri.Substring(0, node.Uri.Length - 1) + ".tar.gz";
if (!WebUtils.DownloadFile(uri, compressed, this.Progress))
{
throw new Exception(string.Format("Downloading {0} failed", uri));
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
WebUtils.DownloadFile(uri + ".md5", compressedMd5);
var downloadedMD5 = HashUtils.GetMD5Hash(compressed, true, false);
var trueMD5 = File.ReadAllText(compressedMd5).Split(new[] { '\t', ' ' })[0];
if (!downloadedMD5.Equals(trueMD5))
{
throw new Exception(string.Format("MD5 of file {0} doesn't equal to server provided MD5, downloading failed!\nYou may consider to delete the file and try again, or you may download and de-compress it by youself.", compressed));
}
}
UncompressFile(currDir, fDir, compressed, bTar);
}
}
}
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 static void DownloadFiles(SpiderTreeNode node, string targetDir, Action<List<DownloadItem>> filterFile, IProgressCallback callback = null)
{
List<DownloadItem> items = GetDownloadFiles(node, targetDir, filterFile);
foreach (var item in items)
{
if (!WebUtils.DownloadFile(item.Url, item.TargetFile, callback))
{
throw new Exception(string.Format("Download {0} to {1} failed!", item.Url, item.TargetFile));
}
}
}
public static List<DownloadItem> GetDownloadFiles(SpiderTreeNode node, string targetDir, Action<List<DownloadItem>> filterFile)
{
List<DownloadItem> result = new List<DownloadItem>();
var content = WebUtils.DownloadHtml(node.Uri);
HtmlDocument doc = new HtmlDocument();
doc.LoadHtml(content);
var links = new List<string>();
foreach (HtmlNode link in doc.DocumentNode.SelectNodes("//a[@href]"))
{
HtmlAttribute att = link.Attributes["href"];
var curlink = att.Value;
if (curlink.EndsWith("/") || curlink.StartsWith("?"))
{
continue;
}
string cururi;
if (node.Uri.EndsWith("/"))
{
cururi = node.Uri + curlink;
}
else
{
cururi = node.Uri + "/" + curlink;
}
var targetFile = new FileInfo(targetDir + "/" + curlink).FullName;
result.Add(new DownloadItem()
{
Url = cururi,
TargetFile = targetFile,
RetryCount = 0
});
}
if (null != filterFile)
{
filterFile(result);
}
FilterExists(result);
return result;
}
private void DownloadLevel3Data(SpiderTreeNode m, string currDir)
{
if (m.Nodes.Any(n => TCGAUtils.IsLevel3(n.Name)))
{
m.Nodes.RemoveAll(n => TCGAUtils.IsLevel1(n.Name) || TCGAUtils.IsLevel2(n.Name));
}
else //download level2 data
{
m.Nodes.RemoveAll(n => TCGAUtils.IsLevel1(n.Name));
}
m.MarkHighestVersionNodes();
foreach (var node in m.Nodes)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
var fDir = currDir + "/" + node.Name;
var compressed = fDir + ".tar.gz";
var compressedMd5 = fDir + ".tar.gz.md5";
var parentDir = Path.GetDirectoryName(currDir);
var parentFDir = parentDir + "/" + node.Name;
var parentFComparessed = parentFDir + ".tar.gz";
var parentFComparessedMd5 = parentFDir + ".tar.gz.md5";
if (Directory.Exists(parentFDir))
{
Directory.Move(parentFDir, fDir);
}
if (File.Exists(parentFComparessed))
{
File.Move(parentFComparessed, compressed);
}
if (File.Exists(parentFComparessedMd5))
{
File.Move(parentFComparessedMd5, compressedMd5);
}
if (node.IsPreviousVersion)
{
if (Directory.Exists(fDir))
{
Progress.SetMessage("Deleting previous version : " + fDir);
Directory.GetFiles(fDir).ToList().ForEach(File.Delete);
Directory.Delete(fDir);
}
if (!File.Exists(compressed))
{
continue;
}
File.Delete(compressed);
File.Delete(compressedMd5);
}
else
{
Progress.SetMessage("Processing {0}.{1} ...", m.Name, node.Name);
var bDownload = !File.Exists(compressed);
var bTar = bDownload || !Directory.Exists(fDir);
if (bDownload)
{
var uri = node.Uri.Substring(0, node.Uri.Length - 1) + ".tar.gz";
if (!WebUtils.DownloadFile(uri, compressed, this.Progress))
{
throw new Exception(string.Format("Downloading {0} failed", uri));
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
WebUtils.DownloadFile(uri + ".md5", compressedMd5);
var downloadedMD5 = HashUtils.GetMD5Hash(compressed, true, false);
var trueMD5 = File.ReadAllText(compressedMd5).Split(new[] { '\t', ' ' })[0];
if (!downloadedMD5.Equals(trueMD5))
{
throw new Exception(string.Format("MD5 of file {0} doesn't equal to server provided MD5, downloading failed!\nYou may consider to delete the file and try again, or you may download and de-compress it by youself.", compressed));
}
}
UncompressFile(currDir, fDir, compressed, bTar);
}
}
}
