public string GetAvailableNetworks([FromQuery] CoexpParams coexpdata)
{
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetAvailableNetworks(coexpdata);
return(response);
}
public string GetModuleTOMGenes([FromQuery] CoexpParams coexpdata)
{
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetModuleTOMGenes(coexpdata);
return(response);
}
public string GetNetworkCategories()
{
//getNetworkCategories()
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetNetworkCategories();
return(response);
}
public string GetCellTypeFromTissue([FromQuery] CoexpParams coexpdata)
{
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetCellTypeFromTissue(coexpdata);
response = response.Replace("_row", "Cell Type");
return(response);
}
public string PostGetModuleTOMGraph([FromBody] CoexpParams coexpdata)
{
/////////////////////////////////////////////////
// 2. If, at least one gene has been found, we make a request to CoExp R
/////////////////////////////////////////////////
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetModuleTOMGraph(coexpdata);
return(response);
}
public string PostReportOnGenesMultipleTissue([FromBody] CoexpParams coexpdata)
{
//category = which.one
//network = tissue
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.ReportOnGenesMultipleTissue(coexpdata);
string parsed_response = response.Replace("go.report", "go_report");
parsed_response = parsed_response.Replace("pd.genes", "pd_genes");
parsed_response = parsed_response.Replace("cell.type.pred", "cell_type_pred");
//parsed_response = parsed_response.Replace("p.val.mods", "p_val_mods");
parsed_response = parsed_response.Replace("tissue", "network");
return(parsed_response);
}
public string GetGOFromTissue([FromQuery] CoexpParams coexpdata)
{
//category = which.one
//network = tissue
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetGOFromTissue(coexpdata);
//REPLACE CHARACTERS
string parsed_response = response.Replace("query.number", "query_number");
parsed_response = parsed_response.Replace("p.value", "p_value");
parsed_response = parsed_response.Replace("term.size", "term_size");
parsed_response = parsed_response.Replace("query.size", "query_size");
parsed_response = parsed_response.Replace("overlap.size", "overlap_size");
parsed_response = parsed_response.Replace("term.id", "term_id");
parsed_response = parsed_response.Replace("subgraph.number", "subgraph_number");
parsed_response = parsed_response.Replace("term.name", "term_name");
parsed_response = parsed_response.Replace("relative.depth", "relative_depth");
parsed_response = parsed_response.Replace(",", ", ");
return(parsed_response);
}
public string PostGlobalReportOnGenes([FromBody] CoexpParams coexpdata)
{
string parsed_response;
//////////////////////////////////////////////
//// 1. First, we check all typed genes
//////////////////////////////////////////////
//var provider = new PhysicalFileProvider(_hostingEnvironment.WebRootPath);
//var genesfileInfo = provider.GetFileInfo("data/genes.txt");
////Read all ensembl genes from a .csv file.
//string csvData = System.IO.File.ReadAllText(genesfileInfo.PhysicalPath);
////Convert both ensembl and typed genes into two different lists
//IEnumerable<string> genes;
//IEnumerable<string> ensembleData = csvData.Split("\r\n");
//ensembleData = String.Join(',',ensembleData).Split(',');
//if (coexpdata.Genes.Contains(", ")){
// genes = coexpdata.Genes.Split(", ");
//}
//else if (coexpdata.Genes.Contains(",")){
// genes = coexpdata.Genes.Split(",");
//}
//else{
// genes = coexpdata.Genes.Split(" ");
//}
////Using LINQ we check whether the genes typed exist
//if(genes.Any(x => ensembleData.Contains(x))) {
// IEnumerable<string> genesFound = genes.Where(p => ensembleData.Any(l => p == l)).ToList();
// IEnumerable<string> genesNotFound = genes.Where(p => !genesFound.Any(p2 => p == p2)).ToList();
// if (genesNotFound.Count() > 0)
// {
// parsed_response = String.Format("The following {0} genes from your list have not been found on Ensembl: {1}.\n\nWould you like to continue the request?",
// genesNotFound.Count(),
// String.Join(",", genesNotFound));
// //parsed_response = "[{\"message\":\""+ parsed_response + "\",\"genes\":\""+ String.Join(',', genesFound)+ "\"}]";
// parsed_response = JsonConvert.SerializeObject(new
// {
// message = parsed_response,
// genes = String.Join(",", genesFound),
// multipleData = coexpdata.MultipleSelectionData
// });
// }
// else
// {
/////////////////////////////////////////////////
// 2. If, at least one gene has been found, we make a request to CoExp R
/////////////////////////////////////////////////
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GlobalReportOnGenes(coexpdata);
parsed_response = response.Replace("go.report", "go_report");
parsed_response = parsed_response.Replace("pd.genes", "pd_genes");
parsed_response = parsed_response.Replace("cell.type.pred", "cell_type_pred");
//parsed_response = parsed_response.Replace("p.val.mods", "p_val_mods");
parsed_response = parsed_response.Replace("tissue", "network");
// }
//}else
//{
// parsed_response = "Please, check your gene list. None of your genes has been found on Ensembl.";
//}
return(parsed_response);
}
