private void ListHistoryVersion()
{
string VersionIDURL = "<a href='WikiHistory.aspx?PageName={0}&VID={1}'>{1}</a>";
string strSQL = string.Format("select pagehistoryid,modifydate,modifiedby from wiki_pagehistory where pagename='{0}' order by modifydate desc", m_PageName);;
//DBInterface.ConnectDB();
IDataReader result = DBInterface.QuerySQL(strSQL);
int i = 0;
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcVersion = new TableCell();
tcVersion.Text = string.Format(VersionIDURL, m_PageName, result.GetValue(0).ToString());
tcVersion.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcVersion);
TableCell tcVersionTime = new TableCell();
tcVersionTime.Text = result.GetDateTime(1).ToString("MM/dd/yy H:mm:ss zzz");
tcVersionTime.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcVersionTime);
TableCell tcEditor = new TableCell();
tcEditor.Text = result.GetString(2);
tcEditor.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcEditor);
if (i == 0 && m_VersionID == "")
{
m_VersionID = result.GetValue(0).ToString();
trCaption.BackColor = System.Drawing.Color.LightBlue;
}
else if (m_VersionID == result.GetValue(0).ToString())
{
trCaption.BackColor = System.Drawing.Color.LightBlue;
}
tbVersionList.Rows.Add(trCaption);
i += 1;
}
result.Close();
}
DBInterface.CloseDB();
}
private void LoadVersionContent()
{
string strSQL = string.Format("select pagecontent from wiki_pagehistory where pagehistoryid='{0}' ", m_VersionID);;
//DBInterface.ConnectDB();
IDataReader result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
while (result.Read())
{
WikiTextFormatter wf = new WikiTextFormatter();
litContent.Text = wf.FormatPageForDisplay(result.GetString(0));
}
result.Close();
}
DBInterface.CloseDB();
}
private void GetPeptideFamily(string PeptideSeq)
{
string PepIDURL = "<a href='PeptideInfo.aspx?QType=Peptide+ID&QValue={0}'>{1}</a>";
string strSQL = string.Format("select p.peptide_cop_id,p.peptide_sequence,p.molecular_weight, t.score from peptide_tbl p,TABLE(blastp_match('{0}',cursor(select peptide_cop_id, peptide_sequence from peptide_tbl))) t where p.peptide_cop_id = t.T_SEQ_ID", PeptideSeq);
//DBInterface.ConnectDB();
IDataReader result = DBInterface.QuerySQL(strSQL);
int i = 0;
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcPepID = new TableCell();
tcPepID.Text = string.Format(PepIDURL, result.GetString(0), result.GetString(0));
tcPepID.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPepID);
TableCell tcSequence = new TableCell();
tcSequence.Text = result.GetString(1);
tcSequence.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcSequence);
TableCell tcMW = new TableCell();
tcMW.Text = result.GetDouble(2).ToString();
tcMW.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcMW);
TableCell tcScore = new TableCell();
tcScore.Text = result.GetValue(3).ToString();
tcScore.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcScore);
tbPeptides.Rows.Add(trCaption);
i += 1;
}
result.Close();
}
DBInterface.CloseDB();
}
private void LoadNewPages()
{
string PageNameURL = "<a href='COPaWikiDefault.aspx?PageName={0}'>{0}</a>";
//string strSQL = "select * from (select a.pagename,a.lastmodified,a.modifiedby from wiki_pages a where ((a.pagename like '%%') order by lastmodified desc) where rownum<10";
string strSQL = "select * from (select a.pagename, a.lastmodified, a.modifiedby from wiki_pages a where not regexp_like(a.pagename, '^([A-Z0-9]{6}(-[0-9]+)?|[0-9]+|[A-Z]+)$') order by a.lastmodified desc) where rownum < 10";
if (DBInterface.DbType == "MySql")
{
strSQL = "select a.pagename,a.lastmodified,a.modifiedby from wiki_pages a where not ((a.pagename like 'CoPro%' or a.pagename like 'CoPep%' ) and length(a.pagename)=13) order by lastmodified desc limit 10";
}
//DBInterface.ConnectDB();
IDataReader result = DBInterface.QuerySQL(strSQL);
int i = 0;
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcPagename = new TableCell();
tcPagename.Text = string.Format(PageNameURL, result.GetString(0));
tcPagename.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPagename);
TableCell tcLastModifiedTime = new TableCell();
tcLastModifiedTime.Text = result.GetDateTime(1).ToLongDateString();
tcLastModifiedTime.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcLastModifiedTime);
TableCell tcEditor = new TableCell();
tcEditor.Text = result.GetString(2);
tcEditor.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcEditor);
tbNewPages.Rows.Add(trCaption);
i += 1;
}
result.Close();
}
string ProteinIDURL = "<a href='ProteinInfo.aspx?QType=Protein+ID&QValue={0}'>{1}</a>";
strSQL = "select * from (select a.pagename,b.protein_name,a.lastmodified,a.modifiedby from wiki_pages a, protein_tbl b where trim(b.protein_cop_id) = trim(a.pagename) order by lastmodified desc) where rownum<10";
if (DBInterface.DbType == "MySql")
{
strSQL = "select a.pagename,b.protein_name,a.lastmodified,a.modifiedby from wiki_pages a, protein_tbl b where a.pagename like 'IPI%' and trim(b.protein_cop_id) = trim(a.pagename) order by lastmodified desc limit 10";
}
//DBInterface.ConnectDB();
result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcPagename = new TableCell();
tcPagename.Text = string.Format(ProteinIDURL, result.GetString(0), result.GetString(0));
tcPagename.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPagename);
TableCell tcLastModifiedTime = new TableCell();
tcLastModifiedTime.Text = result.GetDateTime(2).ToLongDateString();
tcLastModifiedTime.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcLastModifiedTime);
TableCell tcEditor = new TableCell();
tcEditor.Text = result.GetString(3);
tcEditor.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcEditor);
tbProteinPages.Rows.Add(trCaption);
}
result.Close();
}
string PeptideIDURL = "<a href='PeptideInfo.aspx?QType=Peptide+ID&QValue={0}'>{1}</a>";
strSQL = "select * from (select a.pagename,b.peptide_sequence,a.lastmodified,a.modifiedby from wiki_pages a, peptide_tbl b where trim(b.peptide_sequence) = trim(a.pagename) order by lastmodified desc) where rownum<10";
if (DBInterface.DbType == "MySql")
{
strSQL = "select a.pagename,b.peptide_sequence,a.lastmodified,a.modifiedby from wiki_pages a, peptide_tbl b where a.pagename like 'CoPep%' and trim(b.peptide_cop_id) = trim(a.pagename) order by lastmodified desc limit 10";
}
result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcPagename = new TableCell();
tcPagename.Text = string.Format(PeptideIDURL, result.GetString(0), result.GetString(0));
tcPagename.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPagename);
TableCell tcLastModifiedTime = new TableCell();
tcLastModifiedTime.Text = result.GetDateTime(2).ToLongDateString();
tcLastModifiedTime.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcLastModifiedTime);
TableCell tcEditor = new TableCell();
tcEditor.Text = result.GetString(3);
tcEditor.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcEditor);
tbPeptidePages.Rows.Add(trCaption);
}
result.Close();
}
string SpectrumURL = "<a href='SpectrumInfo.aspx?QValue={0}' Target='_blank'>{0}</a>";
strSQL = "select a.pagename,b.instrumentation,a.lastmodified,a.modifiedby from wiki_pages a, spectrum_tbl b where to_char(b.spectrum_seq) = a.pagename and rownum < 10 order by lastmodified desc";
if (DBInterface.DbType == "MySql")
{
strSQL = "select a.pagename,b.instrumentation,a.lastmodified,a.modifiedby from wiki_pages a, spectrum_tbl b where to_char(b.spectrum_seq) = a.pagename order by lastmodified desc limit 10";
}
result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
while (result.Read())
{
TableRow trCaption = new TableRow();
TableCell tcPagename = new TableCell();
tcPagename.Text = string.Format(SpectrumURL, result.GetString(0));
tcPagename.HorizontalAlign = HorizontalAlign.Left;
trCaption.Cells.Add(tcPagename);
TableCell tcLastModifiedTime = new TableCell();
tcLastModifiedTime.Text = result.GetDateTime(2).ToLongDateString();
tcLastModifiedTime.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcLastModifiedTime);
TableCell tcEditor = new TableCell();
tcEditor.Text = result.GetString(3);
tcEditor.HorizontalAlign = HorizontalAlign.Right;
trCaption.Cells.Add(tcEditor);
tbSpectrumPages.Rows.Add(trCaption);
}
result.Close();
}
DBInterface.CloseDB();
}
protected void btUpload_Click(object sender, EventArgs e)
{
//if (this.tbUserID.Text == "")
//{
// this.lbEmailMessage1.Text = "Required field.";
// return;
//}
//else
// this.lbEmailMessage1.Text = "*";
if (!this.RegularExpressionValidator2.IsValid || !this.RegularExpressionValidator1.IsValid)
{
return;
//validation group for mzMl or raw file
}
if (!cbUseURL.Checked && !this.InputFile1.HasFile)
{
return;
}
if (cbUseURL.Checked && this.tbURL.Text == "")
{
this.lbMessage.Text = "You need to upload a local file or provide the URL of a file in the web.";
return;
}
string FileName = "";
string SingleFileName = "";
if (cbUseURL.Checked)
{
FileName = this.tbURL.Text;
SingleFileName = FileName.Substring(FileName.LastIndexOf("/") + 1);
}
else
{
FileName = this.InputFile1.FileName;
SingleFileName = FileName;
}
string strSQL = "insert into search_task (task_user,upload_filename,search_model,report_filename) values ('{0}','{1}','{2}','{3}')";
string strReportName = SingleFileName.Substring(0, SingleFileName.LastIndexOf(".")) + ".txt";
strSQL = string.Format(strSQL, DBInterface.SQLValidString(this.tbUserID.Text), DBInterface.SQLValidString(FileName), this.ddlModels.Text, DBInterface.SQLValidString(strReportName));
//DBInterface.ConnectDB();
string taskID = "";
if (DBInterface.UpdateSQL(strSQL) > 0)
{
strSQL = "select task_seq from search_task where task_user='******' and upload_filename = '{1}' order by task_seq desc";
strSQL = string.Format(strSQL, DBInterface.SQLValidString(this.tbUserID.Text), DBInterface.SQLValidString(FileName));
IDataReader result = DBInterface.QuerySQL(strSQL);
if (result != null)
{
result.Read();
taskID = result.GetValue(0).ToString();
}
DBInterface.CloseDB();
string UploadPath = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + taskID + "\\";
DirectoryInfo newpath = new DirectoryInfo(UploadPath);
if (!newpath.Exists)
{
newpath.Create();
}
if (!cbUseURL.Checked)
{
string TargeFile = UploadPath + FileName;
this.InputFile1.MoveTo(TargeFile, Brettle.Web.NeatUpload.MoveToOptions.Overwrite);
}
//***save the searching conditions in files***
SearchingParameters mySP = new SearchingParameters();
if (cbUseDefault.Checked)
{
mySP.ConfidenceLevel = 0.95F;
mySP.DistinctPeptide = 1;
mySP.LibraryModule = this.ddlModels.Text;
mySP.OnlyTop1 = true;
mySP.Peptidetolerance = 2;
mySP.PTMShift = 0;
mySP.SlideSize = 1;
mySP.ScoreCriteria = "|0;-1";
mySP.UseNoiseLibrary = true;
mySP.UseStatisticalMode = true;
mySP.HighResolution = false;
mySP.PeptideToleranceHR = 20;
mySP.IsotopePeaks = 2;
mySP.BonusDetaMz = false;
mySP.CustomizedLibraryFDR = false;
mySP.UniquePeptide = 0;
mySP.UsePTMModule = false;
}
else
{
try
{
mySP.ConfidenceLevel = float.Parse(this.ddl_Threshold.Text.Substring(0, this.ddl_Threshold.Text.Length - 1)) / 100;
if (mySP.ConfidenceLevel >= 1 || mySP.ConfidenceLevel <= 0)
{
lbMessage.Text = "The peptide confidence should be set in the range 0%-100%.";
return;
}
}
catch
{
lbMessage.Text = "The peptide confidence setting is out of range.";
return;
}
mySP.DistinctPeptide = int.Parse(this.ddl_DistinctPepties.Text); // sc.DistinctPeptide;
mySP.UniquePeptide = int.Parse(this.ddl_UniquePeptides.Text);
mySP.LibraryModule = this.ddlModels.Text; // GetModuleName(sc.searchModule);
mySP.OnlyTop1 = true; // sc.bOnlyTop1;
mySP.Peptidetolerance = float.Parse(this.ddl_PrecursorTolerance.Text); //sc.fPrecursorWindow;
mySP.PTMShift = float.Parse(this.ddl_PTMshift.Text); // sc.fPTMShift;
string Criterias = "|0;-1";
//foreach (SearchingThreadPair stp in sc.NormalSearchCondition)
//{
// Criterias += string.Format("|{0};{1}", stp.MatchScore, stp.DetaDecoyScore);
//}
mySP.ScoreCriteria = Criterias;
mySP.SlideSize = int.Parse(this.ddl_SlideSize.Text); // sc.iSlideSize;
mySP.UseNoiseLibrary = this.cbUseNDP.Checked; // sc.bUseNoiseLibrary;
mySP.UseStatisticalMode = true; // sc.bStatisticSearching;
mySP.HighResolution = this.cbHighResolution.Checked;
mySP.PeptideToleranceHR = float.Parse(this.ddlHRPrecursorTolerance.Text);
mySP.IsotopePeaks = int.Parse(this.ddlIsotopePeaks.Text);
mySP.BonusDetaMz = this.cbBonusMS.Checked;
mySP.CustomizedLibraryFDR = false;
mySP.UsePTMModule = false;
}
string sclocation = UploadPath + "searchcondition.xml";
mySP.SaveSettings(sclocation);
//*****************************************
strSQL = "update search_task set task_status=1 where task_seq=" + taskID;
if (DBInterface.UpdateSQL(strSQL) > 0)
{
if (cbUseURL.Checked)
{
informationShow.Text = @"<div id='helpNote' class='collapse'>";
informationBtn.Text = @"<button type='button' class='close button collapsed' data-toggle='collapse' data-target='#helpNote'>×</button>";
lbMessage.Text = "You URL resource has been submitted. The task ID is <a href=\"SearchReport.aspx?QType=" + this.tbUserID.Text + "&QValue=" + taskID + "\" style=\"font-size: large; color: #FF0000\" >" + taskID + "</a>.";
//this.cbUseURL.Checked = false;
}
else
{
lbMessage.Text = "You mzML file has been successfully uploaded. The task ID is <a href=\"SearchReport.aspx?QType=" + this.tbUserID.Text + "&QValue=" + taskID + "\" style=\"font-size: large; color: #FF0000\" >" + taskID + "</a>.";
}
}
}
}