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 List <Classes.Content> GetContent()
{
LogController.Begin();
StartZeit = DateTime.Now;
List <Classes.Content> ret = new List <Classes.Content>();
if (summaries == null)
{
return(ret);
}
var s = summaries.GetEnumerator();
while (s.MoveNext())
{
DateTime start = DateTime.Now;
var el = s.Current;
var newContent = new Classes.Content();
int c;
Int32.TryParse(el.Attribute("uid").Value, out c);
newContent.ID = c;
using (XmlReader reader = el.CreateReader())
{
while (reader.Read())
{
switch (reader.NodeType, reader.Name, Program.indexModel.database.KeyName)
{
//#################################################################################################
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 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 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 AddFilter(string filtername)
{
LogController.Begin();
Program.indexModel.ErrorFilterList = null;
Program.indexModel.ExceptionMessage = null;
if (!String.IsNullOrEmpty(filtername))
{
try
{
if (Program.indexModel.FilterList == null)
{
Program.indexModel.FilterList = new Classes.FList();
}
Program.indexModel.FilterList.Add(new Classes.Filter(filtername, ""));
}
catch (Exception ex)
{
Program.indexModel.ErrorFilterList = ex.Message;
}
}
return(RedirectToAction("Index", "Home"));
}
public IActionResult SaveToCsv(Models.IndexModel indexModel, int newSite = -1, int newCps = -1)
{
LogController.Begin();
Program.indexModel.ErrorFilterList = indexModel.ErrorFilterList;
Program.indexModel.ExceptionMessage = indexModel.ExceptionMessage;
int num = 0;
//change only the actual shown part of the contentlist
for (int i = 0 + Program.indexModel.cps * Program.indexModel.actSite; i < Program.indexModel.ContentList.Count && i < Program.indexModel.cps * (Program.indexModel.actSite + 1); i++)
{
int j = i % Program.indexModel.cps;
Program.indexModel.ContentList[i].download = indexModel.PartialContentList[j].download;
if (Program.indexModel.ContentList[i].download)
{
num++;
}
}
if (num > 5)
{
Program.indexModel.ExceptionMessage = HelperController.GetMessage("Index.Err.ToManyFiles").txt;
return(RedirectToAction("Index", "Home"));
}
if (newSite >= 0)
{
return(SetActSite(newSite));
}
if (newCps >= 0)
{
return(SetCps(newCps));
}
switch (Program.indexModel.database.KeyName)
{
case ("geoprofiles"):
var zipFile = FileController.DownloadAndProcessGEOProfiles(Program.indexModel.ContentList);
if (zipFile != null && System.IO.File.Exists(zipFile))
{
var bArray = System.IO.File.ReadAllBytes(zipFile);
return(File(bArray, "application/octet-stream", "export.zip"));
}
else
{
Controllers.LogController.LogError($"Zipfile could not be accessed at {zipFile}");
}
//break;
var csv = FileController.WriteListToCsv(Program.indexModel.ContentList);
if (csv != null)
{
var bArray = System.Text.Encoding.UTF8.GetBytes(csv.ToString());
return(File(bArray, "application/octet-stream", "export.csv"));
}
break;
case ("gds"):
var processedPath = FileController.DowloadAndProcessGDS(Program.indexModel.ContentList);
if (processedPath != null)
{
return(RedirectToAction("Upload", "Upload"));
}
break;
}
return(RedirectToAction("Index", "Home"));
}
