public async Task <IActionResult> analyseMcode([FromBody] ModifierInputObject input)
{
return(await runAnalysis(input, "mcode"));
}
public async Task <IActionResult> analysecorrelationClique([FromBody] ModifierInputObject input)
{
return(await runAnalysis(input, "correlationClique"));
}
public async Task <IActionResult> analysediffCoEx([FromBody] ModifierInputObject input)
{
return(await runAnalysis(input, "diffCoEx"));
}
public async Task <IActionResult> analyseCliqueSum([FromBody] ModifierInputObject input)
{
return(await runAnalysis(input, "cliqueSum"));
}
public async Task <IActionResult> deleteFiles([FromBody] ModifierInputObject input)
{
RScriptRunner.deleteFiles(input.id);
return(Ok(input.id));
}
public async Task <IActionResult> saveFiles([FromBody] ModifierInputObject input)
{
string id = RScriptRunner.saveFiles(input.expressionMatrixContent, input.probeMapContent, input.networkContent);
return(Ok(id));
}
public async Task <IActionResult> analyseMd([FromBody] ModifierInputObject input)
{
return(Ok("Got some input!: " + input.group1Label));
}
public static async Task <string> RunFromCmd(Config rconfig, string filename, ModifierInputObject modifierInputObject, string methodOfAnalysis, string id)
{
string sampleGroup1 = "";
string sampleGroup2 = "";
foreach (string s1 in modifierInputObject.sampleGroup1)
{
sampleGroup1 = sampleGroup1 + ";" + s1;
}
foreach (string s2 in modifierInputObject.sampleGroup2)
{
sampleGroup2 = sampleGroup2 + ";" + s2;
}
string result = string.Empty;
string error = string.Empty;
try
{
var info = new ProcessStartInfo();
info.FileName = rconfig.rExePath; // @"C:\Program Files\R\R-3.4.1\bin\Rscript.exe";
info.WorkingDirectory = rconfig.rLibPath; //@"C:\Program Files\R\R-3.4.1\bin";
info.Arguments =
Path.Combine(Directory.GetCurrentDirectory(), "RCode", filename) + " "
+ sampleGroup1 + " " + sampleGroup2 + " "
+ modifierInputObject.group1Label + " " + modifierInputObject.group2Label + " "
+ methodOfAnalysis + " "
+ Path.Combine(Directory.GetCurrentDirectory(), "RCode")
+ " " + id;
info.RedirectStandardInput = false;
info.RedirectStandardOutput = true;
info.RedirectStandardError = true;
info.UseShellExecute = false;
info.CreateNoWindow = true;
using (var proc = new Process())
{
proc.StartInfo = info;
proc.Start();
error = proc.StandardError.ReadToEnd();
result = proc.StandardOutput.ReadToEnd();
}
if (error.ToUpper().Contains("ERROR") || result.ToUpper().Contains("ERROR"))
{
throw new Exception("Error in R script: " + result + error);
}
return(result);
}
catch (Exception ex)
{
throw new Exception("R Script failed: " + error, ex);
}
}
