public ValidateLimits()
{
// dbLimits = new MongoModel("Limits");
string relativepath = "/App_Data/system.conf";
string absolutedpath = HttpContext.Current.Server.MapPath(relativepath);
Filelimits = new DataFileManager(absolutedpath, "juanin");
}
/**
* Create a data file for the tests
*/
void CreateFile()
{
if (!File.Exists(path))
{
File.Create(path).Dispose();
}
DataFileManager.ResetFile(path);
}
public async Task ThenThePageContentIncludesTheEpaoName()
{
var response = _context.Get <HttpResponseMessage>(ContextKeys.HttpResponse);
var actualContent = await response.Content.ReadAsStringAsync();
var json = DataFileManager.GetFile("course-epao.json");
var expectedApiResponse = JsonConvert.DeserializeObject <CourseEpao>(json);
actualContent.Should().Contain(HttpUtility.HtmlEncode(expectedApiResponse.Epao.Name));
}
public OmimVcfCreator(string inputPrefix, string refSeqPath, string outPath)
{
_inputPrefix = inputPrefix;
_outPath = outPath;
_compressedSequence = new CompressedSequence();
var reader = new CompressedSequenceReader(FileUtilities.GetReadStream(refSeqPath), _compressedSequence);
_renamer = _compressedSequence.Renamer;
_dataFileManager = new DataFileManager(reader, _compressedSequence);
_processedGeneSet = new HashSet <string>();
}
public async Task ThenThereIsARowForEachCourse()
{
var response = _context.Get <HttpResponseMessage>(ContextKeys.HttpResponse);
var actualContent = await response.Content.ReadAsStringAsync();
var json = DataFileManager.GetFile("course-list.json");
var expectedApiResponse = JsonConvert.DeserializeObject <CourseList>(json);
foreach (var course in expectedApiResponse.Courses)
{
actualContent.Should().Contain(HttpUtility.HtmlEncode(course.Title));
}
}
/// <summary>
/// constructor
/// </summary>
public PianoAnnotationSource(Stream transcriptCacheStream, CompressedSequenceReader compressedSequenceReader)
{
OverlappingTranscripts = new List <Transcript>();
_performanceMetrics = PerformanceMetrics.Instance;
_compressedSequence = new CompressedSequence();
_dataFileManager = new DataFileManager(compressedSequenceReader, _compressedSequence);
_dataFileManager.Changed += LoadData;
_renamer = _compressedSequence.Renamer;
_aminoAcids = new AminoAcids();
_vid = new VID();
LoadTranscriptCache(transcriptCacheStream, _renamer.NumRefSeqs, out _transcriptIntervalForest);
}
public IList <DataLine> GetDataLines(string filePath)
{
var dataLineDtos = DataFileManager.GetLines(filePath);
var dataLines = new List <DataLine>();
foreach (var dataLineDto in dataLineDtos)
{
DataLine dataLine;
dataLine = Mapper.Map <DataLine>(dataLineDto);
dataLines.Add(dataLine);
}
return(dataLines);
}
/**
* Select the next platform depending of the part of the body
*/
protected void AdaptProbabilities()
{
string playerName = PlayerPrefs.GetString("PlayerName");
Dictionary <string, float> data = DataFileManager.FindData(playerName);
if (data == null)
{
return;
}
float adjustment = 0.90f;
foreach (KeyValuePair <string, float> entry in data)
{
if (entry.Value >= 0.5)
{
int index1 = -1;
for (int i = 0; i < platformsList.Length; i++)
{
if (platformsList[i].name == entry.Key)
{
index1 = i;
break;
}
}
if (index1 != -1)
{
int index2 = -1;
for (int i = 0; i < platformsList.Length; i++)
{
if (platformsList[i].GetComponent <PrefabController>().myType == platformsList[index1].GetComponent <PrefabController>().myType&& platformsList[i].tag == "coinPlatform")
{
index2 = i;
break;
}
}
if (index2 != -1)
{
int diffWeight = System.Convert.ToInt32(platformsList[index1].GetComponent <PrefabController>().InitialSpawnWeight *(entry.Value * adjustment));
platformsList[index1].GetComponent <PrefabController>().Weight = platformsList[index1].GetComponent <PrefabController>().Weight - diffWeight;
platformsList[index2].GetComponent <PrefabController>().Weight = platformsList[index2].GetComponent <PrefabController>().Weight + diffWeight;
}
}
}
}
}
public async Task ThenTheSectorsAndLevelsAreAvailableToFilter()
{
var response = _context.Get <HttpResponseMessage>(ContextKeys.HttpResponse);
var actualContent = await response.Content.ReadAsStringAsync();
var json = DataFileManager.GetFile("courses.json");
var expectedApiResponse = JsonConvert.DeserializeObject <TrainingCourses>(json);
foreach (var sector in expectedApiResponse.Sectors)
{
actualContent.Should().Contain(HttpUtility.HtmlEncode(sector.Route));
}
foreach (var level in expectedApiResponse.Levels)
{
actualContent.Should().Contain($"Level {level.Code} - {HttpUtility.HtmlEncode(level.Name)}");
}
}
public MustGenotypeExtractor(string compressedSeqPath, string oneKGenomeVcf, string clinvarVcf, string cosmicVcf, bool isHg19 = false)
{
_compressedSequence = new CompressedSequence();
_dataFileManager = new DataFileManager(new CompressedSequenceReader(FileUtilities.GetReadStream(compressedSeqPath), _compressedSequence), _compressedSequence);
_assembly = _compressedSequence.GenomeAssembly == GenomeAssembly.GRCh37 && isHg19? GenomeAssembly.hg19:_compressedSequence.GenomeAssembly;
if (_assembly == GenomeAssembly.Unknown)
{
throw new Exception("Genome assembly must be either GRCh37 or GRCh38");
}
if (_compressedSequence.GenomeAssembly == GenomeAssembly.GRCh38 && isHg19)
{
throw new Exception("reference sequence is GRCh38 while generating hg19 files");
}
_oneKGenomeReader = string.IsNullOrEmpty(oneKGenomeVcf)? null: GZipUtilities.GetAppropriateStreamReader(oneKGenomeVcf);
_clinvarReader = string.IsNullOrEmpty(clinvarVcf) ? null : GZipUtilities.GetAppropriateStreamReader(clinvarVcf);
_cosmicReader = string.IsNullOrEmpty(cosmicVcf) ? null : GZipUtilities.GetAppropriateStreamReader(cosmicVcf);
}
private void DeleteButton_Click(object sender, EventArgs e)
{
var currentItem = ServerList.Text;
if (string.IsNullOrEmpty(currentItem))
{
MessageBox.Show("There is no server to delete.");
return;
}
var item = DataFileManager.Data.AllServers.FirstOrDefault(x => x.Name == currentItem);
if (item == null)
{
RefreshServerList();
return;
}
DataFileManager.Data.AllServers.Remove(item);
DataFileManager.SaveData();
RefreshServerList();
}
/**
* Unit test of the AddNewPlayer function
*/
void TestAddNewPlayer()
{
print("TestAddNewPlayer...");
int id;
PlayerData newPlayer;
CreateFile();
//Player not in the file
id = DataFileManager.NextId("Test", path);
Assert.AreEqual(1, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 1!"));
//Add a player
newPlayer = new PlayerData("Test", 1, 2, 3, 4, 0, 0, 1, 0, 0);
DataFileManager.AddNewPlayer(newPlayer, path);
id = DataFileManager.NextId("Test", path);
Assert.AreEqual(2, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 2!"));
id = DataFileManager.NextId("Test2", path);
Assert.AreEqual(1, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 1!"));
//Add an other game for the player
newPlayer = new PlayerData("Test", 1, 2, 3, 4, 0, 0, 0, 1, 0);
DataFileManager.AddNewPlayer(newPlayer, path);
id = DataFileManager.NextId("Test", path);
Assert.AreEqual(3, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 3!"));
//Add an other player
newPlayer = new PlayerData("Test2", 1, 2, 3, 4, 0, 0, 0, 1, 0);
DataFileManager.AddNewPlayer(newPlayer, path);
id = DataFileManager.NextId("Test", path);
Assert.AreEqual(3, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 3!"));
id = DataFileManager.NextId("Test2", path);
Assert.AreEqual(2, id, string.Format("<color=#{0:X2}{1:X2}{2:X2}>{3}</color>", (byte)(255), (byte)(0), (byte)(0), "...FAILED : Value should be 2!"));
DeleteFile();
}
/// <summary>
/// Check if username and password is valid, if it is, sets sessions and formauth to true
/// </summary>
/// <param name="username">The user name</param>
/// <param name="password">The User password</param>
/// <returns>Index View if valid user, Login view if invalid user</returns>
/// <author>Galaviz Alejos Luis Angel</author>
public ActionResult Login(string username, string password)
{
if (username == "" || password == "")
{
this.Redirect("/Login");
}
//Check the user on the database
//usertable = new UserTable();
BsonDocument doc = usertable.Login(username, password);
ProfileTable profiletable = new ProfileTable();
//If the return is null, is an invalid user
if (doc != null)
{
//User Password time validation
if (doc["_id"].AsObjectId.ToString() != "52e95ab907719e0d40637d96")
{
JObject userInformation = JsonConvert.DeserializeObject <JObject>(usertable.GetRow(doc["_id"].AsObjectId.ToString()));
if (userInformation["lastChgPassword"] != null)
{
try
{
DateTime d1 = DateTime.ParseExact(userInformation["lastChgPassword"].ToString(), "dd/MM/yyyy HH:mm:ss", null);
DateTime d2 = DateTime.Now;
systemSettingsTable = new SystemSettingsTable();
JArray cantDays = JsonConvert.DeserializeObject <JArray>(systemSettingsTable.Get("name", "daysChangePassword"));
string days = (from mov in cantDays select(string) mov["days"]).First().ToString();
TimeSpan time = d2 - d1;
int NrOfDays = time.Days;
if (int.Parse(days) <= NrOfDays)
{
ViewBag.Message = "Timeout";
ViewData["timeout"] = "Timeout";
List <string> backgrounds = Design.getBackgrounds();
return(View("Index", backgrounds));
}
}
catch (Exception ex)
{
ViewBag.Error = true;
ViewBag.Message = ex.ToString();
ViewData["timeout"] = ex.ToString();
List <string> backgrounds = Design.getBackgrounds();
return(View("Index", backgrounds));
}
}
else
{
try
{
JObject user = JsonConvert.DeserializeObject <JObject>(usertable.GetRow(doc["_id"].AsObjectId.ToString()));
user["lastChgPassword"] = DateTime.Now.ToString("dd/MM/yyyy HH:mm:ss");
usertable.saveRow(JsonConvert.SerializeObject(user), user["_id"].ToString());
}
catch (Exception ex)
{
// throw new Exception(ex.ToString());
//return Redirect("~/Home");
}
//END - User Password time validation
}
}
DataFileManager Filelimits;
string filepath = "/App_Data/system.conf";
string absolutedpath = Server.MapPath(filepath);
Filelimits = new DataFileManager(absolutedpath, "juanin");
if (!Filelimits.empty())
{
//Set user name (to show on the upper right corner of the system)
this.Session["LoggedUser"] = "";
try
{
this.Session["Semaphores"] = DateTime.Now.ToString("dd/MM/yyyy HH:mm:ss");
HttpCookie aCookiesem = new HttpCookie("semaphores");
aCookiesem.Value = Session["Semaphores"].ToString();
aCookiesem.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookiesem);
}
catch (Exception ex)
{
}
this.Session["Username"] = "";
try
{
this.Session["Username"] = doc["name"].AsString;
this.Session["LoggedUser"] += doc["name"].AsString;
try
{
this.Session["LoggedUser"] += " " + doc["lastname"].AsString;
}
catch (Exception e) { /*Ignored*/ }
}
catch (Exception e) { /*Ignored*/ }
//If needed for user transactions
this.Session["_id"] = doc["_id"].AsObjectId;
HttpCookie aCookie2 = new HttpCookie("_id2");
aCookie2.Value = doc["_id"].AsObjectId.ToString();
aCookie2.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookie2);
//Check if there exist the image extension registry on database, if it exist, sets the relative
//path
try
{
if (!string.IsNullOrEmpty(doc["imgext"].ToString()))
{
//Relative path to save images
string relativepath = string.Format("\\Uploads\\Images\\{0}.{1}",
Session["_id"].ToString(), doc["imgext"].ToString());
//Check if profile picture file exists on the server
if (System.IO.File.Exists(Server.MapPath(relativepath)))
{
//if it exist, sets the profile picture url
this.Session["ProfilePicture"] = Url.Content(relativepath);
HttpCookie aCookie4 = new HttpCookie("_picture");
aCookie4.Value = Url.Content(relativepath);
aCookie4.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookie4);
}
else
{
//Set picture to default
this.Session["ProfilePicture"] = null;
}
}
}
catch (Exception e) { /*Ignored*/ }
string usuarioid = Session["_id"].ToString();
String profileid = usertable.getRowString(usuarioid);
JObject rowArray = JsonConvert.DeserializeObject <JObject>(profileid);
var jdatos = "";
if (rowArray["permissionsHTK"] != null)
{
string arraypermisos = rowArray["permissionsHTK"].ToString();
JObject allp = JsonConvert.DeserializeObject <JObject>(arraypermisos);
jdatos = JsonConvert.SerializeObject(allp);
this.Session["Permissions"] = jdatos.ToString();
}
else
{
string idpro = rowArray["profileId"].ToString();
String profiles = profiletable.GetRow(idpro);
JObject rowArraypro = JsonConvert.DeserializeObject <JObject>(profiles);
string arraypermisos = rowArraypro["permissionsHTK"].ToString();
JObject allp = JsonConvert.DeserializeObject <JObject>(arraypermisos);
jdatos = JsonConvert.SerializeObject(allp);
this.Session["Permissions"] = jdatos.ToString();
}
try
{
this.Session["PermissionsClient"] = Filelimits["scenario"]["modules"].ToString();
string filedata = Filelimits["scenario"]["modules"].ToString();
HttpCookie aCookiep = new HttpCookie("permissionsclient");
aCookiep.Value = Filelimits["scenario"]["modules"].ToString();
aCookiep.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookiep);
}
catch (Exception ex)
{
this.Session["PermissionsClient"] = "";
}
HttpCookie aCookie = new HttpCookie("permissions");
aCookie.Value = jdatos.ToString();
aCookie.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookie);
HttpCookie aCookie1 = new HttpCookie("_loggeduser");
aCookie1.Value = Session["LoggedUser"].ToString();
aCookie1.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookie1);
HttpCookie aCookie3 = new HttpCookie("_username");
aCookie3.Value = Session["Username"].ToString();
aCookie3.Expires = DateTime.Now.AddDays(10);
Response.Cookies.Add(aCookie3);
//Sets the login authorization
FormsAuthentication.SetAuthCookie("User", false);
TimeSpan time = FormsAuthentication.Timeout;
// FormsAuthentication.Timeout.Subtract(time);
//Redirect Index
FormsAuthentication.Timeout.Subtract(time);
/* TimeSpan time2= TimeSpan.Parse("00:04:00");
* FormsAuthentication.Timeout.Add(time2);
* string horasuma2 = DateTime.Now.ToString("HH:mm:ss");
* TimeSpan timenow = TimeSpan.Parse(horasuma2);
* int total = time2.Minutes - timenow.Minutes;*/
return(Redirect("~/Home"));
}
else
{
ViewBag.Error = true;
ViewBag.Message = "Error de Permisos";
List <string> backgrounds = Design.getBackgrounds();
return(View("Index", backgrounds));
}
}
else
{
//Set error and return to login page
ViewBag.Error = true;
ViewBag.Message = "Error de Login";
List <string> backgrounds = Design.getBackgrounds();
return(View("Index", backgrounds));
}
}
// constructor
public CreateSupplementaryDatabase(
string compressedReferencePath,
string nsdBaseFileName,
string dbSnpFileName = null,
string cosmicVcfFile = null,
string cosmicTsvFile = null,
string clinVarFileName = null,
string oneKGenomeAfFileName = null,
string evsFileName = null,
string exacFileName = null,
List <string> customFiles = null,
string dgvFileName = null,
string oneKSvFileName = null,
string clinGenFileName = null,
string chrWhiteList = null)
{
_nsdBaseFileName = nsdBaseFileName;
_dataSources = new List <DataSourceVersion>();
_iSupplementaryDataItemList = new List <IEnumerator <SupplementaryDataItem> >();
_supplementaryIntervalList = new List <SupplementaryInterval>();
Console.WriteLine("Creating supplementary annotation files... Data version: {0}, schema version: {1}", SupplementaryAnnotationCommon.DataVersion, SupplementaryAnnotationCommon.SchemaVersion);
_compressedSequence = new CompressedSequence();
var compressedSequenceReader = new CompressedSequenceReader(FileUtilities.GetReadStream(compressedReferencePath), _compressedSequence);
_renamer = _compressedSequence.Renamer;
_dataFileManager = new DataFileManager(compressedSequenceReader, _compressedSequence);
if (!string.IsNullOrEmpty(chrWhiteList))
{
Console.WriteLine("Creating SA for the following chromosomes only:");
foreach (var refSeq in chrWhiteList.Split(','))
{
InputFileParserUtilities.ChromosomeWhiteList.Add(_renamer.GetEnsemblReferenceName(refSeq));
Console.Write(refSeq + ",");
}
Console.WriteLine();
}
else
{
InputFileParserUtilities.ChromosomeWhiteList = null;
}
if (dbSnpFileName != null)
{
AddSourceVersion(dbSnpFileName);
var dbSnpReader = new DbSnpReader(new FileInfo(dbSnpFileName), _renamer);
var dbSnpEnumerator = dbSnpReader.GetEnumerator();
_iSupplementaryDataItemList.Add(dbSnpEnumerator);
}
if (cosmicVcfFile != null && cosmicTsvFile != null)
{
AddSourceVersion(cosmicVcfFile);
var cosmicReader = new MergedCosmicReader(cosmicVcfFile, cosmicTsvFile, _renamer);
var cosmicEnumerator = cosmicReader.GetEnumerator();
_iSupplementaryDataItemList.Add(cosmicEnumerator);
}
if (oneKGenomeAfFileName != null)
{
AddSourceVersion(oneKGenomeAfFileName);
var oneKGenReader = new OneKGenReader(new FileInfo(oneKGenomeAfFileName), _renamer);
var oneKGenEnumerator = oneKGenReader.GetEnumerator();
_iSupplementaryDataItemList.Add(oneKGenEnumerator);
}
if (oneKSvFileName != null)
{
if (oneKGenomeAfFileName == null)
{
AddSourceVersion(oneKSvFileName);
}
var oneKGenSvReader = new OneKGenSvReader(new FileInfo(oneKSvFileName), _renamer);
var oneKGenSvEnumerator = oneKGenSvReader.GetEnumerator();
_iSupplementaryDataItemList.Add(oneKGenSvEnumerator);
}
if (evsFileName != null)
{
AddSourceVersion(evsFileName);
var evsReader = new EvsReader(new FileInfo(evsFileName), _renamer);
var evsEnumerator = evsReader.GetEnumerator();
_iSupplementaryDataItemList.Add(evsEnumerator);
}
if (exacFileName != null)
{
AddSourceVersion(exacFileName);
var exacReader = new ExacReader(new FileInfo(exacFileName), _renamer);
var exacEnumerator = exacReader.GetEnumerator();
_iSupplementaryDataItemList.Add(exacEnumerator);
}
if (clinVarFileName != null)
{
AddSourceVersion(clinVarFileName);
var clinVarReader = new ClinVarXmlReader(new FileInfo(clinVarFileName), compressedSequenceReader, _compressedSequence);
var clinVarList = clinVarReader.ToList();
clinVarList.Sort();
Console.WriteLine($"{clinVarList.Count} clinvar items read form XML file");
IEnumerator <ClinVarItem> clinVarEnumerator = clinVarList.GetEnumerator();
_iSupplementaryDataItemList.Add(clinVarEnumerator);
}
if (dgvFileName != null)
{
AddSourceVersion(dgvFileName);
var dgvReader = new DgvReader(new FileInfo(dgvFileName), _renamer);
var dgvEnumerator = dgvReader.GetEnumerator();
_iSupplementaryDataItemList.Add(dgvEnumerator);
}
if (clinGenFileName != null)
{
AddSourceVersion(clinGenFileName);
var clinGenReader = new ClinGenReader(new FileInfo(clinGenFileName), _renamer);
var clinGenEnumerator = clinGenReader.GetEnumerator();
_iSupplementaryDataItemList.Add(clinGenEnumerator);
}
if (customFiles != null)
{
foreach (var customFile in customFiles)
{
AddSourceVersion(customFile);
var customReader = new CustomAnnotationReader(new FileInfo(customFile), _renamer);
var customEnumerator = customReader.GetEnumerator();
_iSupplementaryDataItemList.Add(customEnumerator);
}
}
// initializing the IEnumerators in the list
foreach (var iDataEnumerator in _iSupplementaryDataItemList)
{
if (!iDataEnumerator.MoveNext())
{
_iSupplementaryDataItemList.Remove(iDataEnumerator);
}
}
_additionalItemsList = new List <SupplementaryDataItem>();
}
