public string GetModuleTOMGenes(CoexpParams coexpdata)
{
//Set the URL with parameters. This URL will allow us to establish a communication with
//CoExp R application API (published using Plumber R package)
if (coexpURL == ProductionEnv)
{
coexpURL += "GetModuleTOMGenes";
PostData = "{\"network\":\"" + coexpdata.Network +
"\",\"category\":\"" + coexpdata.Category +
"\",\"module\":\"" + coexpdata.ModuleColor + "\"}";
}
else
{
coexpURL += "getModuleTOMGenes";
PostData = "{\"tissue\":\"" + coexpdata.Network +
"\",\"which.one\":\"" + coexpdata.Category +
"\",\"module\":\"" + coexpdata.ModuleColor + "\"}";
}
//Make the request
var finalResponse = _adapter.POSTHttpRequestJSON(coexpURL, PostData);
//Return the response
return(finalResponse);
}
public string GetModuleTOMGenes([FromQuery] CoexpParams coexpdata)
{
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetModuleTOMGenes(coexpdata);
return(response);
}
public string GetAvailableNetworks([FromQuery] CoexpParams coexpdata)
{
CoExpRepository repository = new CoExpRepository(_hostingEnvironment);
string response = repository.GetAvailableNetworks(coexpdata);
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 IActionResult Annotated(CoexpParams coexpParams)
{
try
{
return(View(coexpParams));
}
catch (Exception e)
{
ErrorViewModel errorModel = new ErrorViewModel()
{
Message = e.Message
};
return(View("Error", errorModel));
}
}
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);
}
/// <summary>
/// Method to obtain data from 'getAvailableNetworks' API method. This method makes a GET request.
/// </summary>
/// <param name="coexpdata">Data to be sent to 'getAvailableNetworks' CoExp API method</param>
/// <returns>Response received from 'getAvailableNetworks' CoExp API method</returns>
public string GetAvailableNetworks(CoexpParams coexpdata)
{
//Set the URL with parameters. This URL will allow us to establish a communication with
//CoExp R application API (published using Plumber R package)
if (coexpURL == ProductionEnv)
{
coexpURL += "GetAvailableNetworks";
}
else
{
coexpURL += "getAvailableNetworks";
}
PostData = "{\"category\":\"" + coexpdata.Category + "\"}";
//Make the request
var finalResponse = _adapter.POSTHttpRequestJSON(coexpURL, PostData);
//Return the response
return(finalResponse);
}
public string GetModuleTOMGraph(CoexpParams coexpdata)
{
if (coexpURL == ProductionEnv)
{
coexpURL += "GetModuleTOMGraph";
PostData = "{\"network\":\"" + coexpdata.Network +
"\",\"category\":\"" + coexpdata.Category +
"\",\"module\":\"" + coexpdata.ModuleColor + "\",\"topgenes\":\"" + coexpdata.TopGenes + "\"}";
}
else
{
coexpURL += "getModuleTOMGraph";
PostData = "{\"tissue\":\"" + coexpdata.Network +
"\",\"which.one\":\"" + coexpdata.Category +
"\",\"module\":\"" + coexpdata.ModuleColor + "\",\"topgenes\":\"" + coexpdata.TopGenes + "\"}";
}
//Make the request
var finalResponse = _adapter.POSTHttpRequestJSON(coexpURL, PostData);
return(finalResponse.ToString());
}
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 GlobalReportOnGenes(CoexpParams coexpdata)
{
//Declare initial variables
string categoriesLabel = string.Empty;
string localCategory;
string networks = string.Empty;
string localNetworks;
string finalResponse;
string[] categoryData;
//Remove parenthesis
coexpdata.MultipleSelectionData = coexpdata.MultipleSelectionData.Replace("{", "");
coexpdata.MultipleSelectionData = coexpdata.MultipleSelectionData.Replace("}", "");
var categories = (coexpdata.MultipleSelectionData).Split("**");
foreach (var category in categories)
{
if (category != String.Empty)
{
categoryData = category.Split("|");
localCategory = categoryData[0];
if (categoriesLabel.Length == 0)
{
categoriesLabel = categoryData[0];
}
else
{
categoriesLabel = categoriesLabel + "," + categoryData[0];
}
if (categoryData[1].Substring(categoryData[1].Length - 1, 1) == (","))
{
localNetworks = categoryData[1].Remove(categoryData[1].Length - 2);
if (networks.Length > 0)
{
networks = networks + "," + categoryData[1].Remove(categoryData[1].Length - 2);
}
else
{
networks = categoryData[1].Remove(categoryData[1].Length - 2);
}
}
else
{
localNetworks = categoryData[1];
if (networks.Length > 0)
{
networks = networks + "," + categoryData[1];
}
else
{
networks = categoryData[1];
}
}
if (localNetworks.Split(",").Length > 1)
{
for (var i = 0; i < localNetworks.Split(",").Length - 1; i++)
{
categoriesLabel = categoriesLabel + "," + localCategory;
}
}
}
}
if (coexpURL == ProductionEnv)
{
coexpURL += "GlobalReportOnGenes";
PostData = "{\"categories\":\"" + categoriesLabel + "\",\"networks\":\"" + networks + "\",\"genes\":\"" + coexpdata.Genes + "\"}";
}
else
{
coexpURL += "globalReportOnGenes";
PostData = "{\"categories\":\"" + categoriesLabel + "\",\"tissues\":\"" + networks + "\",\"genes\":\"" + coexpdata.Genes + "\"}";
}
//Make the request
finalResponse = _adapter.POSTHttpRequestJSON(coexpURL, PostData);
return(finalResponse);
}
/**************************************************************/
/********************* POST METHODS ***************************/
/**************************************************************/
public string ReportOnGenesMultipleTissue(CoexpParams coexpdata)
{
//Set the URL with parameters. This URL will allow us to establish a communication with
//CoExp R application API (published using Plumber R package)
var finalResponse = string.Empty;
//"**CoExpROSMAP**probad,ad,**gtexv6**AntCingCortex"
var categories = (coexpdata.MultipleSelectionData).Split("**,");
List <JArray> responses = new List <JArray>();
JArray finalJSONresponse = new JArray();
string localResponse;
foreach (var category in categories)
{
if (category != String.Empty)
{
var categoryData = category.Split("|");
var categoryLabel = categoryData[0];
var networks = string.Empty;
if (categoryData[1].Substring(categoryData[1].Length - 1, 1) == (","))
{
networks = categoryData[1].Remove(categoryData[1].Length - 2);
}
else
{
networks = categoryData[1];
}
if (networks.Contains("**"))
{
networks = networks.Remove(networks.Length - 2);
}
if (coexpURL == ProductionEnv)
{
coexpURL += "ReportOnGenesMultipleTissue";
PostData = "{\"networks\":\"" + networks + "\",\"category\":\"" + categoryLabel + "\",\"genes\":\"" + coexpdata.Genes + "\"}";
}
else
{
coexpURL += "reportOnGenesMultipleTissue";
PostData = "{\"tissues\":\"" + networks + "\",\"which.one\":\"" + categoryLabel + "\",\"genes\":\"" + coexpdata.Genes + "\"}";
}
//Make the request
localResponse = _adapter.POSTHttpRequestJSON(coexpURL, PostData);
if (!localResponse.Contains("error"))
{
JObject item = JObject.Parse(localResponse);
responses.Add((JArray)item.SelectToken("report"));
}
else
{
finalResponse = localResponse;
break;
}
}
}
//finalJSONresponse = responses[0];
if (finalResponse == string.Empty)
{
foreach (JArray response in responses)
{
foreach (var e in response)
{
finalJSONresponse.Add(e);
}
}
return(finalJSONresponse.ToString());
}
else
{
//Return the response
return(finalResponse);
}
}
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);
}
public string GetTreeMenuData()
{
try
{
dynamic jsonCategories = JsonConvert.DeserializeObject(GetNetworkCategories());
List <TreeMenuNode> nodes = new List <TreeMenuNode>();
//List<Network> networks = new List<Network>();
int categoryID = 1;
int networkID = 100;
TreeMenuNode all = new TreeMenuNode()
{
id = "0",
name = "All",
pid = string.Empty
};
nodes.Add(all);
foreach (var categoryName in jsonCategories)
{
TreeMenuNode category = new TreeMenuNode()
{
name = categoryName,
id = categoryID.ToString(),
pid = "0",
label = categoryName
};
nodes.Add(category);
CoexpParams coexpParams = new CoexpParams()
{
Category = category.name
};
dynamic jsonNetworks = JsonConvert.DeserializeObject(GetAvailableNetworks(coexpParams));
foreach (var networkName in jsonNetworks)
{
TreeMenuNode network = new TreeMenuNode()
{
name = networkName,
id = networkID.ToString(),
pid = categoryID.ToString(),
label = categoryName
};
nodes.Add(network);
networkID++;
}
categoryID++;
networkID = 100;
}
var jsonAllData = JsonConvert.SerializeObject(nodes);
return(jsonAllData);
}
catch (Exception ex)
{
return("Problems with web service connection. " + ex.Message);
}
}
