public List <SearchQuery> RetrieveUsersSearchQueries(string userid)
{
using (var db = new PerceptronDatabaseEntities())
{
return(db.SearchQueries.Where(x => x.UserId == userid).ToList());
}
}
//Stores Server Status
public List <SearchQuery> RetrieveSearchQueries()
{
using (var db = new PerceptronDatabaseEntities())
{
return(db.SearchQueries.ToList());
}
}
//Returns Progress
public int RetrieveQueryProgress(string qid)
{
using (var db = new PerceptronDatabaseEntities())
{
return(Convert.ToInt32(db.SearchQueries.Where(x => x.QueryId == qid).Select(x => x.Progress)));
}
}
public void StoreSearchFiles(SearchParametersDto param)
{
using (var db = new PerceptronDatabaseEntities())
{
db.SaveChanges();
}
}
public SearchParametersDto GetParameters(string qid)
{
SearchParametersDto searchParametersDto;
using (var db = new PerceptronDatabaseEntities())
{
var searchParameters = from b in db.SearchParameters
where b.QueryId == qid
select b;
var ptmFixed = (from b in db.PtmFixedModifications
where b.QueryId == qid
select b.ModificationCode).ToList();
var ptmVariable = (from b in db.PtmVariableModifications
where b.QueryId == qid
select b.ModificationCode).ToList();
var files = (from b in db.SearchFiles
where b.QueryId == qid
select b).ToList();
var fileType = files.Select(b => b.FileType).ToArray();
var fileName = files.Select(b => b.FileName).ToArray();
searchParametersDto = searchParameters.Any() ? GetSearchParametersDtoModel(searchParameters.First(), ptmVariable, ptmFixed, fileType, fileName) : new SearchParametersDto();
}
return(searchParametersDto);
}
//Store Query Parameters
public void StoreSearchParameters(SearchParametersDto param)
{
using (var db = new PerceptronDatabaseEntities())
{
db.SearchQueries.Add(param.SearchQuerry);
db.SearchParameters.Add(param.SearchParameters);
db.SearchFiles.AddRange(param.SearchFiles);
//db.PtmFixedModifications.AddRange(param.FixedMods);
//db.PtmVariableModifications.AddRange(param.VarMods);
db.SaveChanges();
}
}
public List <ScanResults> Scan_Results(string qid)
{
qid = qid.Trim('"');
var scanResults = new List <ScanResults>();
using (var db = new PerceptronDatabaseEntities())
{
var sqlConnection1 =
new SqlConnection(
"Server= CHIRAGH-I; Database= PerceptronDatabase; Integrated Security=SSPI;");
var cmd = new SqlCommand
{
CommandText =
"SELECT *\nFROM SearchResults E\nWHERE E.QueryId = '" + qid +
"' AND ABS(E.score - (SELECT max(E2.score) FROM SearchResults E2 Where E2.QueryId=E.QueryId AND E2.FileId = E.FileId)) <= 0.01",
CommandType = CommandType.Text,
Connection = sqlConnection1
};
sqlConnection1.Open();
var t = db.SearchFiles.Where(x => x.QueryId == qid).ToList();
int j = 0;
var dataReader = cmd.ExecuteReader();
while (dataReader.Read())
{
if (j == t.Count())
{
break;
}
int startPos = t[j].FileName.LastIndexOf("C:\\inetpub\\wwwroot\\PerceptronAPI\\App_Data\\") + "C:\\inetpub\\wwwroot\\PerceptronAPI\\App_Data\\".Length;
int length = t[j].FileName.Length - startPos;
t[j].FileName = t[j].FileName.Substring(startPos, length);
var temp = new ScanResults
{
FileId = dataReader["FileId"].ToString(),
FileName = t[j].FileName,
Frags = 1,
Mods = 1,
MolW = (double)dataReader["Mw"],
Truncation = "No",
ProteinId = dataReader["Header"].ToString(),
Score = (double)dataReader["Score"]
};
++j;
scanResults.Add(temp);
}
dataReader.Close();
cmd.Dispose();
sqlConnection1.Close();
}
return(scanResults);
}
public stat stat()
{
var temp = new stat();
using (var db = new PerceptronDatabaseEntities())
{
var sqlConnection1 =
new SqlConnection(
"Server= CHIRAGH-I; Database= PerceptronDatabase; Integrated Security=SSPI;");
var cmd = new SqlCommand
{
CommandText =
"SELECT count( distinct UserId) as one FROM SearchQueries",
CommandType = CommandType.Text,
Connection = sqlConnection1
};
sqlConnection1.Open();
int j = 0;
var dataReader = cmd.ExecuteReader();
while (dataReader.Read())
{
temp.user = dataReader["one"].ToString();
}
dataReader.Close();
cmd.Dispose();
sqlConnection1.Close();
}
using (var db = new PerceptronDatabaseEntities())
{
var sqlConnection1 =
new SqlConnection(
"Server= CHIRAGH-I; Database= PerceptronDatabase; Integrated Security=SSPI;");
var cmd = new SqlCommand
{
CommandText =
"Select count( QueryId) as two FROM SearchResults",
CommandType = CommandType.Text,
Connection = sqlConnection1
};
sqlConnection1.Open();
int j = 0;
var dataReader = cmd.ExecuteReader();
while (dataReader.Read())
{
temp.search = dataReader["two"].ToString();
}
dataReader.Close();
cmd.Dispose();
sqlConnection1.Close();
}
return(temp);
}
public ResultsDto RetrieveResultByRid(string rid)
{
using (var db = new PerceptronDatabaseEntities())
{
return(new ResultsDto
{
InsilicioLeft = db.ResultInsilicoMatchLefts.Where(x => x.ResultId == rid).ToList(),
InsilicoRight = db.ResultInsilicoMatchRights.Where(x => x.ResultId == rid).ToList(),
PtmSites = db.ResultPtmSites.Where(x => x.ResultId == rid).ToList(),
Results = db.SearchResults.First(x => x.ResultId == rid)
});
}
}
public int Set_Progress(string qid, int progress)
{
using (var db = new PerceptronDatabaseEntities())
{
var result = db.SearchQueries.SingleOrDefault(b => b.QueryId == qid);
if (result != null)
{
result.Progress = progress.ToString();
db.SaveChanges();
}
}
return(1);
}
public List <SearchQueryDto> ServerStatus()
{
List <SearchQueryDto> searchQueryList;
using (var db = new PerceptronDatabaseEntities())
{
var query = (from b in db.SearchQueries
where b.Progress == Constants.QueryNotStarted
select b).ToList();
var query1 = query.Select(GetSearchQueryDto);
searchQueryList = query1.Any() ? query1.ToList() : new List <SearchQueryDto>();
}
return(searchQueryList);
}
public List <SummaryResults> Summary_results(string qid, string fid)
{
qid = qid.Trim('"');
var summaryResults = new List <SummaryResults>();
var db = new PerceptronDatabaseEntities();
using (new PerceptronDatabaseEntities())
{
var sqlConnection1 =
new SqlConnection(
"Server= CHIRAGH-I; Database= PerceptronDatabase; Integrated Security=SSPI;");
var cmd = new SqlCommand
{
CommandText =
"SELECT *\nFROM SearchResults E\nWHERE E.QueryId = '" + qid + "' AND E.fileid = '" + fid + "' ORDER BY E.Score DESC ",
CommandType = CommandType.Text,
Connection = sqlConnection1
};
sqlConnection1.Open();
int j = 0;
var dataReader = cmd.ExecuteReader();
while (dataReader.Read())
{
var temp = new SummaryResults
{
ProteinId = dataReader["Header"].ToString(),
Mods = 2,
MolW = (double)dataReader["Mw"],
ProteinName = "Protein " + j,
ProteinRank = 1,
ResultId = dataReader["ResultId"].ToString(),
Score = (double)dataReader["Score"],
TerminalMods = "no"
};
++j;
summaryResults.Add(temp);
}
dataReader.Close();
cmd.Dispose();
sqlConnection1.Close();
}
return(summaryResults);
}
//public string GetEmailFromUserId(string id)
//{
// string email;
// using (var db = new PerceptronContext())
// {
// var query = from b in db.SearchQueryTable
// where b.UserId == id
// select b.Email;
// email = query.Any() ? query.First() : Constants.EmailNotFound;
// }
// return email;
//}
public string StoreResults(SearchResultsDto res, string fileName, int fileId)
{
string message = Constants.ResultsSotredSuccessfully; //Spelling mistake?#PROBLEM_DETECTED
using (var db = new PerceptronDatabaseEntities())
{
var executionTime = GetExecutionTimeModel(res, fileName);
db.ExecutionTimes.Add(executionTime);
//db.SaveChanges();
foreach (ProteinDto protein in res.FinalProt)
{
var resId = Guid.NewGuid();
var headerTag = GetHeaderTag(protein.Header);
var searchResult = GetSearchResultModel(res.QueryId, fileId, headerTag, protein, resId);
db.SearchResults.Add(searchResult);
//db.SaveChanges();
if (protein.PtmParticulars == null)
{
continue;
}
foreach (var ptmSite in protein.PtmParticulars)
{
var resultPtmSites = GetResultPtmSitesModel(resId, ptmSite);
db.ResultPtmSites.Add(resultPtmSites);
//db.SaveChanges();
}
var resultInsilicoMatchLeft = GetResultInsilicoMatchLeftModel(resId, protein.InsilicoDetails.PeaklistMassLeft);
db.ResultInsilicoMatchLefts.Add(resultInsilicoMatchLeft);
//db.SaveChanges();
var resultInsilicoMatchRight = GetResultInsilicoMatchLeftModel(resId, protein.InsilicoDetails.PeaklistMassRight);
db.ResultInsilicoMatchLefts.Add(resultInsilicoMatchRight); //#PROBLEM_DETECTED??? Why this-->ResultInsilicoMatchLeftTable WHy not ResultInsilicoMatchRights
//db.SaveChanges();
}
db.SaveChanges();
}
return(message);
}
public ResultViewDto retrieve_searchview_db(string qid)
{
using (var db = new PerceptronDatabaseEntities())
{
return(new ResultViewDto
{
Paramters = new SearchParametersDto
{
SearchParameters = db.SearchParameters.First(x => x.QueryId == qid),
FixedMods = db.PtmFixedModifications.Where(x => x.QueryId == qid).ToList(),
SearchFiles = db.SearchFiles.Where(x => x.QueryId == qid).ToList(),
SearchQuerry = db.SearchQueries.First(x => x.QueryId == qid),
VarMods = db.PtmVariableModifications.Where(x => x.QueryId == qid).ToList()
},
ExecutionTime = db.ExecutionTimes.First(x => x.QueryId == qid),
Results =
db.SearchResults.Where(x => x.QueryId == qid)
.Select(x => RetrieveResultByRid(x.ResultId))
.ToList()
});
}
}
public DetailedResults Detailed_Results(string qid, string rid)
{
var detiledResults = new DetailedResults();
using (new PerceptronDatabaseEntities())
{
var sqlConnection1 =
new SqlConnection(
"Server= CHIRAGH-I; Database= PerceptronDatabase; Integrated Security=SSPI;");
var cmd = new SqlCommand
{
CommandText =
"SELECT QueryId \nFROM SearchResults \nWHERE ResultId = '" + rid + "'",
CommandType = CommandType.Text,
Connection = sqlConnection1
};
sqlConnection1.Open();
var dataReader = cmd.ExecuteReader();
while (dataReader.Read())
{
qid = dataReader["QueryId"].ToString();
}
dataReader.Close();
cmd.Dispose();
sqlConnection1.Close();
}
using (var db = new PerceptronDatabaseEntities())
{
var searchParameters = db.SearchParameters.Where(x => x.QueryId == qid).ToList();
var searchResult = db.SearchResults.Where(x => x.ResultId == rid).ToList();
var resultInsilicoLeft = db.ResultInsilicoMatchLefts.Where(x => x.ResultId == rid).ToList();
var resultInsilicoRight = db.ResultInsilicoMatchRights.Where(x => x.ResultId == rid).ToList();
var ptmVarmod = db.PtmVariableModifications.Where(x => x.QueryId == qid).ToList();
var ptmFixedmod = db.PtmFixedModifications.Where(x => x.QueryId == qid).ToList();
var ptmSite = db.ResultPtmSites.Where(x => x.ResultId == rid).ToList();
var execTime = db.ExecutionTimes.Where(x => x.QueryId == qid).ToList();
var searchQuery = db.SearchQueries.Where(x => x.QueryId == qid).ToList();
if (searchParameters.Count != 0)
{
detiledResults.Paramters.SearchParameters = searchParameters.Any() ? GetSearchParametersDtoModel(searchParameters.First()) : new SearchParameter();
}
detiledResults.Paramters.FixedMods = ptmFixedmod;
detiledResults.Paramters.VarMods = ptmVarmod;
if (searchQuery.Count != 0)
{
detiledResults.Paramters.SearchQuerry = searchQuery.First();
}
detiledResults.Results.InsilicioLeft = resultInsilicoLeft;
detiledResults.Results.InsilicoRight = resultInsilicoRight;
detiledResults.Results.PtmSites = ptmSite;
if (searchResult.Count != 0)
{
detiledResults.Results.Results = searchResult.First();
}
if (execTime.Count != 0)
{
detiledResults.ExecutionTime = execTime.First();
}
}
return(detiledResults);
}
