public List <Classes.Content> GetContent(List <Classes.Filter> flist)
{
LogController.Begin();
StartZeit = DateTime.Now;
eSearch = new Classes.ESearch(Program.indexModel.database.KeyName);
eSummary = new Classes.ESummary(Program.indexModel.database.KeyName);
try
{
PassQuery(flist, eSearch);
} // fills Webenvironment and Ids
catch
{
Controllers.LogController.LogError($"Query via Flist failed with {flist.Count()} elements");
throw;
};
try
{
PassWebEnv(this.WebEnvironment, eSummary);
} // fills titles and summaries
catch (Exception ex)
{
Controllers.LogController.LogError($"Query via WebENv failed with {this.WebEnvironment} for utility 'esummary', ERROR: {ex.ToString()}");
throw;
};
LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
return(GetContent());
}
//#################################################################################################
public void PassQuery(List <GEOMiner.Classes.Filter> inputs, Classes.EUtilities u)
{
LogController.Begin();
StartZeit = DateTime.Now;
string query = "&term=";
List <String> existFilters = new List <String>();
foreach (GEOMiner.Classes.Filter input in inputs)
{
if (existFilters.Contains(input.name))
{
continue;
}
if (query != "&term=")
{
query = query + "+AND+";
}
Classes.Filter tmp = input;
foreach (GEOMiner.Classes.Filter i in inputs)
{
if (i.id != input.id && i.name == input.name)
{
tmp.value = tmp.value + "," + i.value;
}
}
query = query + tmp.GetValueForQuery(Program.indexModel.database.KeyName);
existFilters.Add(input.name);
}
query = query.Trim().Replace(' ', '+');
query = FormulateRequest(query, u.EType, Program.indexModel.database.KeyName);
try
{
(this.WebEnvironment, this.IDs) = u.SendRequest(query);
}
catch (Exception ex)
{
Controllers.LogController.LogError($"Query failed with {query} for utility '{u.EType}' , ERROR: {ex.ToString()} ");
};
LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
}
//#################################################################################################
public void PassWebEnv(String keys, Classes.EUtilities u)
{
LogController.Begin();
StartZeit = DateTime.Now;
// WebEnv keys best be stored as fully realised request Strings as soon as they get parsed
String query = this.FormulateRequest(keys, u.EType, Program.indexModel.database.KeyName);
try
{
this.summaries = u.SendRequest_(query);
}
catch
{
Controllers.LogController.LogError($"Query failed with {query} for utility '{u.EType}' ");
};
LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
}
//#################################################################################################
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 String FormulateRequest(String request, String request_type = "esearch", String database = "geoprofiles", String version = "&version=2.0")
{
LogController.Begin();
StartZeit = DateTime.Now;
String base_address = $"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/{request_type}.fcgi?db={database}{version}&retmax=1000";
String authenticators = "&tools=GEOMiner&[email protected]&api_key=284c0c6aaa88d90d532e60eed8446e68ce09";
String url = base_address + request + authenticators;
if (this.WebEnvironment == null)
{
url = url + "&usehistory=y";
}
Controllers.LogController.LogMessage($"Parsed url: {url}");
LogController.End(String.Format("verstrichene Zeit: {0}", DateTime.Now - StartZeit));
return(url);
}
//#################################################################################################
public static void MoveAndExtractFiles(string source, string destination)
{
LogController.Begin();
foreach (FileInfo fi in new DirectoryInfo(source).GetFiles())
{
var newName = ExtractFiles(fi.FullName);
if (newName != null && fi.Extension == ".zip")
{
var t = Path.GetFileName(newName);
MoveAndExtractFiles(Path.Combine(source, Path.GetFileName(newName)), destination);
continue;
}
if (newName != null)
{
var t = Path.Combine(source, Path.GetFileName(newName));
if (new FileInfo(Path.Combine(destination, Path.GetFileName(newName))).Exists)
{
System.IO.File.Delete(Path.Combine(destination, Path.GetFileName(newName)));
}
System.IO.File.Move(Path.Combine(source, Path.GetFileName(newName)), Path.Combine(destination, Path.GetFileName(newName)));
continue;
}
if (new FileInfo(Path.Combine(destination, fi.Name)).Exists)
{
System.IO.File.Delete(Path.Combine(destination, Path.GetFileName(newName)));
}
System.IO.File.Move(fi.FullName, Path.Combine(destination, fi.Name));
//Program.uploadModel.FileList.Add(fi);
}
foreach (DirectoryInfo di in new DirectoryInfo(source).GetDirectories())
{
MoveAndExtractFiles(di.FullName, destination);
}
LogController.End();
}
//#################################################################################################
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());
}
}
