//#################################################################################################
public static string DownloadAndProcessGEOProfiles(List <Classes.Content> clist)
{
string zipName = Path.Combine(zipPath, Program.GuidString + ".zip");
ClearDirectory(tmpPath);
Directory.CreateDirectory(tmpPath);
Directory.CreateDirectory(zipPath);
Directory.CreateDirectory(dataPath);
Directory.CreateDirectory(processedPath);
foreach (string GDS_accession in clist.Where(cont => cont.download).Select(cont => cont.accession).Distinct())
{
string filename = $"{GDS_accession}_full.soft.gz";
if (!Classes.web_scraper.download_soft_file(GDS_accession, Path.Combine(zipPath, $"{GDS_accession}_full.soft.gz")))
{
LogController.LogError($"Could not download entry for {GDS_accession}"); continue;
}
MoveAndExtractFiles(zipPath, dataPath);
Classes.PythonProcess.filter_GEOProfiles_soft(Path.Combine(dataPath, $"{GDS_accession}_full.soft"),
Path.Combine(processedPath, $"{GDS_accession}_identifier.soft"),
Path.Combine(processedPath, $"{GDS_accession}_data.soft"));
}
ZipFile.CreateFromDirectory(processedPath, zipName);
ClearDirectory(dataPath);
ClearDirectory(processedPath);
return(zipName);
}
//#################################################################################################
public IActionResult LoadSessionFromFile(Models.SessionModel sessionModel)
{
Program.sessionModel.validationMessage = String.Empty;
Program.sessionModel.valError = false;
if ((sessionModel.file != null && !sessionModel.file.FileName.EndsWith(".xml")) ||
(!String.IsNullOrEmpty(sessionModel.fileName) && !sessionModel.fileName.EndsWith(".xml")))
{
Program.sessionModel.validationMessage = HelperController.GetMessage("Session.Err.WrongType").txt;
Program.sessionModel.valError = true;
return(Session());
}
if (sessionModel.file != null)
{
try
{
var result = new StringBuilder();
using (var reader = new StreamReader(sessionModel.file.OpenReadStream()))
{
while (reader.Peek() >= 0)
{
result.AppendLine(reader.ReadLine());
}
}
var filestring = result.ToString();
Program.indexModel.FilterList = GetFiltersFromXml(Controllers.XmlController.GetXml(filestring));
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("SessionController.Err.LoadSessionFromFile(Model)1").txt, ex.ToString()));
Program.sessionModel.validationMessage = HelperController.GetMessage("SessionController.Err.LoadSessionFromFile(Model)1").ext;
Program.sessionModel.valError = true;
return(Session());
}
}
else
{
try
{
Program.indexModel.FilterList = GetFiltersFromXml(Controllers.XmlController.GetXml(HelperController.ConvertBase64ToUtf8(sessionModel.fileString)));
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("SessionController.Err.LoadSessionFromFile(Model)2").txt, ex.ToString()));
Program.sessionModel.validationMessage = HelperController.GetMessage("SessionController.Err.LoadSessionFromFile(Model)2").ext;
Program.sessionModel.valError = true;
return(Session());
}
}
Program.sessionModel.validationMessage = HelperController.GetMessage("SessionController.Inf.LoadSessionFromFile(Model)").txt;
return(Session());
}
//#################################################################################################
public static XmlDocument GetXml(string str)
{
XmlDocument xDoc = new XmlDocument();
try
{
xDoc.LoadXml(str);
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("XmlController.Err.GetXml").txt, ex.ToString()));
throw;
}
return(xDoc);
}
public static bool IsValid(string str)
{
if (!String.IsNullOrEmpty(str))
{
try
{
XmlDocument xDoc = GetXml(str);
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("XmlController.Err.IsValid").txt, ex.ToString()));
throw;
}
}
return(true);
}
//#################################################################################################
public IActionResult Index()
{
LogController.Begin();
try
{
if (false && Program.indexModel.FilterList == null)
{
Program.indexModel.FilterList = Controllers.SessionController.LoadSession();
}
}
catch (Exception ex)
{
Program.indexModel.FilterList = new Classes.FList();
LogController.LogError(ex.ToString());
}
ViewData["Preview"] = GEOMiner.Controllers.HelperController.GetMessage("Index.Inf.Preview").txt;
LogController.End();
return(View("~/Views/Home/Index.cshtml", Program.indexModel));
}
public IActionResult Start(Models.IndexModel model, string action)
{
LogController.Begin();
if (model.FilterList == null | (model.FilterList != null && model.FilterList.flist == null))
{
var msg = HelperController.GetMessage("Index.Err.NoFilter");
LogController.LogError(msg.txt);
Program.indexModel.ExceptionMessage = msg.txt;
return(RedirectToAction("Index", "Home"));
}
SessionController.SaveSession(model.FilterList);
Program.indexModel.ExceptionMessage = model.ExceptionMessage;
Program.indexModel.ErrorFilterList = model.ErrorFilterList;
if (!String.IsNullOrEmpty(action) && action != "Start")
{
Program.indexModel.FilterList.Remove(action);
return(RedirectToAction("Index", "Home"));
}
Program.indexModel.FilterList = new Classes.FList(model.FilterList);
//da "GetContent" nicht statisch
try
{
queryController qController = new queryController();
Program.indexModel.ContentList = new List <Classes.Content>();
Program.indexModel.ContentList = qController.GetContent(Program.indexModel.FilterList.flist);
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("Helper.Err.QueryController").txt, ex.ToString()));
Program.indexModel.ExceptionMessage = HelperController.GetMessage("Helper.Err.QueryController").ext;
}
return(RedirectToAction("Index", "Home"));
}
//#################################################################################################
public static Classes.FList LoadSessionFromFile(string file, bool usedef)
{
XmlDocument doc = new XmlDocument();
try
{
doc = Controllers.FileController.LoadXmlFromFile(file);
if (doc.ChildNodes.Count == 0 && usedef)
{
return(LoadSessionFromFile("DefaultFilters.xml", false));
}
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("SessionController.Err.LoadSessionFromFile(string,bool)").txt, ex.ToString()));
throw;
}
return(GetFiltersFromXml(doc));
}
//#################################################################################################
public static Message GetMessage(string msgcode)
{
try
{
Controllers.LogController.Begin();
StartZeit = DateTime.Now;
LogController.LogMessage(string.Format("GetMessage: MsgCode: '{0}', Language:'{1}'", msgcode, language));
Message msg = new Message();
string strFilename = Path.Combine("Config", "Messages.xml");
XmlTextReader reader = new XmlTextReader("Messages.xml");
XmlDocument doc = new XmlDocument();
try
{
doc.Load(strFilename);
}
catch
{
if (System.IO.File.Exists(strFilename))
{
Controllers.LogController.LogError($"Error loading {strFilename}.");
}
else
{
Controllers.LogController.LogError($"Could not load {strFilename}. File does not exist");
}
}
XmlNode messages = doc.SelectSingleNode("messages");
foreach (XmlNode node in messages.SelectNodes("message"))
{
if (node.SelectSingleNode("msgcode") == null)
{
continue;
}
if (!node.SelectSingleNode("msgcode").InnerText.ToLower().Equals(msgcode.ToLower()))
{
continue;
}
if (node.SelectSingleNode("text") != null)
{
if (node.SelectSingleNode(string.Format("text/{0}", language)) != null)
{
msg.txt = node.SelectSingleNode("text/" + language).InnerText;
}
}
if (msg.txt == "" || msg.txt == null)
{
msg.txt = string.Format("{0} for lanuage '{1}' isn't available.", msgcode, language);
LogController.LogError(string.Format("{0} for lanuage '{1}' isn't available.", msgcode, language));
}
if (node.SelectSingleNode("extern") != null)
{
if (node.SelectSingleNode(string.Format("extern/{0}", language)) != null)
{
msg.ext = node.SelectSingleNode("extern/" + language).InnerText;
}
}
if (node.SelectSingleNode("type") != null)
{
msg.type = node.SelectSingleNode("type").Value;
}
else
{
msg.type = "default";
}
break;
}
Controllers.LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
return(msg);
} catch
{
Controllers.LogController.LogError("Message could not be produced");
Message msg = new Message();
msg.txt = "'Empty'";
return(msg);
}
}
//#################################################################################################
public IActionResult UploadFile(Models.UploadModel uploadModel)
{
try
{
Controllers.LogController.Begin();
StartZeit = DateTime.Now;
Program.uploadModel.ExceptionMessage = null;
Program.uploadModel.Step = 1;
Directory.CreateDirectory(tmpPath);
Directory.CreateDirectory(dataPath);
Directory.CreateDirectory(csvPath);
Directory.CreateDirectory(processedPath);
if (uploadModel.file != null)
{
try
{
using (var stream = System.IO.File.Create(Path.Combine(dataPath, uploadModel.file.FileName)))
{
uploadModel.file.CopyTo(stream);
}
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("UploadController.Err.UploadFile1").txt, ex.ToString()));
Program.uploadModel.ExceptionMessage = HelperController.GetMessage("UploadController.Err.UploadFile1").ext;
return(Upload());
}
}
else
{
try
{
if (uploadModel.fileString.IndexOf("data:") >= 0)
{
uploadModel.fileString = Regex.Replace(uploadModel.fileString, "data:([^,]+)", String.Empty);
uploadModel.fileString = uploadModel.fileString.Remove(0, 1);
}
System.IO.File.WriteAllBytesAsync(Path.Combine(dataPath, uploadModel.fileName), Convert.FromBase64String(uploadModel.fileString));
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("UploadController.Err.UploadFile2").txt, ex.ToString()));
Program.uploadModel.ExceptionMessage = HelperController.GetMessage("UploadController.Err.UploadFile2").ext;
return(Upload());
}
}
Program.uploadModel.FileList = new List <Classes.File>();
FileController.MoveAndExtractFiles(dataPath, csvPath);
FileController.MoveAndExtractFiles(csvPath, processedPath);
LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
return(Preview(processedPath));
}
catch (Exception ex)
{
LogController.LogError(String.Format(HelperController.GetMessage("UploadController.Err.Total").txt, ex.ToString()));
Program.uploadModel.ExceptionMessage = HelperController.GetMessage("UploadController.Err.Total").ext;
FileController.ClearDirectory(@"C:\temp\tmp_upload_" + Program.GuidString);
Program.uploadModel.FileList = null;
return(Upload());
}
}
