/// <summary>
///
/// </summary>
public override void Retrieve()
{
// If we last retrieved data less than a minute ago, don't do it again
if ((LastRetrievalTime + new TimeSpan(0, 1, 0)) > DateTime.Now)
{
return;
}
if (MakeInstanceDir())
{
Preferences.PreferenceSet Prefs = Preferences.PreferenceSet.Instance;
// Download FAHlog.txt
WebRequest httpc1 = (WebRequest)WebRequest.Create(this._URL + "/" + this.RemoteFAHLogFilename);
httpc1.Credentials = new NetworkCredential(_Username, _Password);
httpc1.Method = WebRequestMethods.Http.Get;
httpc1.CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore);
if (Prefs.UseProxy)
{
httpc1.Proxy = new WebProxy(Prefs.ProxyServer, Prefs.ProxyPort);
if (Prefs.UseProxyAuth)
{
httpc1.Proxy.Credentials = new NetworkCredential(Prefs.ProxyUser, Prefs.ProxyPass);
}
}
else
{
httpc1.Proxy = null;
}
try
{
WebResponse r1 = (WebResponse)httpc1.GetResponse();
String FAHLog_txt = base.BaseDirectory + LocalFAHLog;
StreamWriter sw1 = new StreamWriter(FAHLog_txt, false);
StreamReader sr1 = new StreamReader(r1.GetResponseStream(), Encoding.ASCII);
sw1.Write(sr1.ReadToEnd());
sw1.Flush();
sw1.Close();
sr1.Close();
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
}
// Download unitinfo.txt
WebRequest httpc2 = (WebRequest)WebRequest.Create(this._URL + "/" + this.RemoteUnitInfoFilename);
httpc2.Credentials = new NetworkCredential(_Username, _Password);
httpc2.Method = WebRequestMethods.Http.Get;
httpc2.CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore);
if (Prefs.UseProxy)
{
httpc2.Proxy = new WebProxy(Prefs.ProxyServer, Prefs.ProxyPort);
if (Prefs.UseProxyAuth)
{
httpc2.Proxy.Credentials = new NetworkCredential(Prefs.ProxyUser, Prefs.ProxyPass);
}
}
else
{
httpc2.Proxy = null;
}
try
{
WebResponse r2 = (WebResponse)httpc2.GetResponse();
String UnitInfo_txt = base.BaseDirectory + LocalUnitInfo;
StreamWriter sw2 = new StreamWriter(UnitInfo_txt, false);
StreamReader sr2 = new StreamReader(r2.GetResponseStream(), Encoding.ASCII);
sw2.Write(sr2.ReadToEnd());
sw2.Flush();
sw2.Close();
sr2.Close();
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
}
base.Retrieve();
}
}
/// <summary>
/// Retrieve the log and unit info files from the configured FTP location
/// </summary>
public override void Retrieve()
{
DateTime Start = Debug.ExecStart;
// If last retrieval was less than a minute ago, don't do it again
if ((LastRetrievalTime + new TimeSpan(0, 1, 0)) > DateTime.Now)
{
return;
}
if (MakeInstanceDir())
{
Preferences.PreferenceSet Prefs = Preferences.PreferenceSet.Instance;
// Download FAHlog.txt
FtpWebRequest ftpc1 = (FtpWebRequest)FtpWebRequest.Create("ftp://" + this._Server + this._Path + this.RemoteFAHLogFilename);
ftpc1.Method = WebRequestMethods.Ftp.DownloadFile;
if ((_Username != "") && (_Username != null))
{
if (_Username.Contains("\\"))
{
String[] UserParts = _Username.Split('\\');
ftpc1.Credentials = new NetworkCredential(UserParts[1], _Password, UserParts[0]);
}
else
{
ftpc1.Credentials = new NetworkCredential(_Username, _Password);
}
}
ftpc1.CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore);
if (Prefs.UseProxy)
{
ftpc1.Proxy = new WebProxy(Prefs.ProxyServer, Prefs.ProxyPort);
if (Prefs.UseProxyAuth)
{
ftpc1.Proxy.Credentials = new NetworkCredential(Prefs.ProxyUser, Prefs.ProxyPass);
}
}
else
{
ftpc1.Proxy = null;
}
FtpWebResponse ftpr1;
try
{
ftpr1 = (FtpWebResponse)ftpc1.GetResponse();
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
return;
}
String FAHLog_txt = base.BaseDirectory + LocalFAHLog;
StreamWriter sw1 = new StreamWriter(FAHLog_txt, false);
StreamReader sr1 = new StreamReader(ftpr1.GetResponseStream(), Encoding.ASCII);
sw1.Write(sr1.ReadToEnd());
sw1.Flush();
sw1.Close();
sr1.Close();
// Download unitinfo.txt
FtpWebRequest ftpc2 = (FtpWebRequest)FtpWebRequest.Create("ftp://" + this._Server + this._Path + this.RemoteUnitInfoFilename);
if ((_Username != "") && (_Username != null))
{
if (_Username.Contains("\\"))
{
String[] UserParts = _Username.Split('\\');
ftpc2.Credentials = new NetworkCredential(UserParts[1], _Password, UserParts[0]);
}
else
{
ftpc2.Credentials = new NetworkCredential(_Username, _Password);
}
}
ftpc2.Method = System.Net.WebRequestMethods.Ftp.DownloadFile;
ftpc2.CachePolicy = new RequestCachePolicy(RequestCacheLevel.NoCacheNoStore);
if (Prefs.UseProxy)
{
ftpc2.Proxy = new WebProxy(Prefs.ProxyServer, Prefs.ProxyPort);
if (Prefs.UseProxyAuth)
{
ftpc2.Proxy.Credentials = new NetworkCredential(Prefs.ProxyUser, Prefs.ProxyPass);
}
}
else
{
ftpc2.Proxy = null;
}
System.Net.FtpWebResponse ftpr2;
try
{
ftpr2 = (System.Net.FtpWebResponse)ftpc2.GetResponse();
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception {1}.", Debug.FunctionName, Ex.Message), null);
return;
}
String UnitInfo_txt = base.BaseDirectory + LocalUnitInfo;
StreamWriter sw2 = new StreamWriter(UnitInfo_txt, false);
StreamReader sr2 = new StreamReader(ftpr2.GetResponseStream(), Encoding.ASCII);
sw2.Write(sr2.ReadToEnd());
sw2.Flush();
sw2.Close();
sr2.Close();
base.Retrieve();
}
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
}
/// <summary>
/// Download project information from Stanford University (psummaryC.html)
/// </summary>
/// <param name="State">Null in this implementation</param>
public void DownloadFromStanford(Object State /* null */)
{
DateTime Start = Debug.ExecStart;
lock (this)
{
Preferences.PreferenceSet Prefs = Preferences.PreferenceSet.Instance;
WebRequest wrq = (WebRequest)WebRequest.Create("http://vspx27.stanford.edu/psummaryC.html");
wrq.Method = WebRequestMethods.Http.Get;
WebResponse wrs;
StreamReader sr1;
if (Prefs.UseProxy)
{
wrq.Proxy = new WebProxy(Prefs.ProxyServer, Prefs.ProxyPort);
if (Prefs.UseProxyAuth)
{
wrq.Proxy.Credentials = new NetworkCredential(Prefs.ProxyUser, Prefs.ProxyPass);
}
}
else
{
wrq.Proxy = null;
}
// TODO: Handle timeouts and errors
try
{
wrs = (WebResponse)wrq.GetResponse();
sr1 = new StreamReader(wrs.GetResponseStream(), Encoding.ASCII);
if ((wrs == null) || (sr1 == null))
{
throw new IOException("The web response or stream was null");
}
}
catch (WebException ExWeb)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw WebException {1}.", Debug.FunctionName, ExWeb.Message), null);
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return;
}
catch (IOException ExIO)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw IOException {1}.", Debug.FunctionName, ExIO.Message), null);
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return;
}
catch (Exception Ex)
{
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw WebException {1}.", Debug.FunctionName, Ex.Message), null);
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return;
}
HTMLparser pSummary = new HTMLparser();
String sSummaryPage = sr1.ReadToEnd();
pSummary.Init(sSummaryPage);
// Locate the table
HTMLchunk oChunk = null;
// Parse until returned oChunk is null indicating we reached end of parsing
while ((oChunk = pSummary.ParseNext()) != null)
{
if (oChunk.sTag.ToLower() == "tr")
{
Protein p = new Protein();
while (((oChunk = pSummary.ParseNext()) != null) && (oChunk.sTag.ToLower() != "td"))
{
; // Do nothing!
}
// Skip the empty attributes
oChunk = pSummary.ParseNext();
try
{
#region Parse Code for HTML Table
// Suck out the project number
p.ProjectNumber = Int32.Parse(oChunk.oHTML.ToString());
// Skip the closing tag, opening tags and attributes
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.ServerIP = oChunk.oHTML.ToString().Trim();
// Skip the closing tag, opening tags and attributes
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.WorkUnitName = oChunk.oHTML.ToString().Trim();
// Skip the closing tag, opening tags and attributes
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.NumAtoms = Int32.Parse(oChunk.oHTML.ToString());
// Skip the closing tag, opening tags and attributes
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.PreferredDays = Int32.Parse(oChunk.oHTML.ToString().Substring(0, oChunk.oHTML.IndexOf('.')).Trim());
// Skip the closing tag, opening tags and attributes
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
try
{
p.MaxDays = Int32.Parse(oChunk.oHTML.ToString().Substring(0, oChunk.oHTML.IndexOf('.')).Trim());
}
catch
{
p.MaxDays = 0;
}
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.Credit = Int32.Parse(oChunk.oHTML.ToString().Substring(0, oChunk.oHTML.IndexOf('.')).Trim());
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.Frames = Int32.Parse(oChunk.oHTML.ToString().Trim());
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.Core = oChunk.oHTML.ToString();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.Description = oChunk.oParams["href"].ToString();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
oChunk = pSummary.ParseNext();
p.Contact = oChunk.oHTML.ToString();
#endregion
if (this.ContainsKey(p.ProjectNumber))
{
this[p.ProjectNumber] = p;
}
else
{
this.Add(p.ProjectNumber, p);
}
}
catch (Exception Ex)
{
// Ignore this row of the table - unparseable
ClassLogger.LogException(LogLevel.Warn, String.Format("{0} threw exception while parsing HTML: {1}", Debug.FunctionName, Ex.Message), null);
}
}
}
if (this.Count > 0)
{
OnNFOUpdated(new NFOUpdatedEventArgs());
}
}
SaveToCSV(_LocalNFOFile);
ClassLogger.Log(LogLevel.Trace, String.Format("{0} loaded {1} proteins from Stanford", Debug.FunctionName, ProteinCollection.Instance.Count), "");
ClassLogger.Log(LogLevel.Trace, String.Format("{0} Execution Time: {1}", Debug.FunctionName, Debug.GetExecTime(Start)), "");
return;
}