//[Authorize(Roles = "ReadGenome")]
public JsonResult PartialIndex(Guid?id, int page, int pageSize)
{
JsonResult jr = new JsonResult();
pageSize = pageSize == 100 ? 101 : pageSize;
using (GeneXContext context = new GeneXContext())
{
IQueryable <SNPDTO> query = context.SNP
.Where(m => m.GenomeId == id.Value)
.Join(context.SNPedia,
c => c.ClusterId,
d => d.ClusterId,
(c, d) => new SNPDTO()
{
ClusterId = c.ClusterId,
ChromosomeType = c.ChromosomeType,
Chromosome = c.Chromosome,
Allele1 = c.Allele1,
Allele2 = c.Allele2,
SNPId = c.SNPId,
Position = c.Position,
Notes = d.Notes
}).Where(m => !(m.Notes == null || m.Notes.Trim() == string.Empty))
.OrderBy(m => m.Chromosome)
.ThenBy(m => m.Position)
.Skip(page * pageSize)
.Take(pageSize);
jr.Data = query.ToList();
}
jr.JsonRequestBehavior = JsonRequestBehavior.AllowGet;
return(jr);
}
public ActionResult Index(Guid?id)
{
GenomeViewModel gvm = new GenomeViewModel();
if (id != null)
{
using (GeneXContext context = new GeneXContext())
{
Genome g = context.Genome.Where(m => m.GenomeId == id.Value).FirstOrDefault();
if (g != null)
{
gvm.Id = g.GenomeId;
gvm.Name = g.Name;
}
}
FileInfo fi = new FileInfo(Path.Combine(ServerMapPath, id.ToString() + ".txt"));
if (fi.Exists)
{
gvm.DataFileExists = true;
gvm.DateTime = fi.LastWriteTime;
}
}
return(View(gvm));
}
public ActionResult Index()
{
IndexViewModel ivm = new IndexViewModel();
using (GeneXContext cs = new GeneXContext())
{
var claim = ((System.Security.Claims.ClaimsPrincipal) this.User).Claims.Where(m => m.Type == "http://schemas.xmlsoap.org/ws/2005/05/identity/claims/nameidentifier").FirstOrDefault();
if (claim != null)
{
string id = claim.Value;
List <Guid> genomeIds = (from gp in cs.GenomePermission where gp.UserId == new Guid(id) && gp.PermissionId == Model.Constants.Permissions.Ids.Owner select gp.GenomeId).ToList();
List <Genome> results = (from g in cs.Genome where genomeIds.Contains(g.GenomeId) select g).ToList();
foreach (Genome g in results)
{
ivm.Genomes.Add(g.GenomeId, g.Name);
}
}
}
return(View(ivm));
}
public ActionResult Add(string Name)
{
using (GeneXContext context = new GeneXContext())
{
Genome g = new Genome();
g.GenomeId = Guid.NewGuid();
g.Name = Name;
context.Genome.Add(g);
context.SaveChanges();
GenomePermission gp = new GenomePermission();
gp.GenomeId = g.GenomeId;
gp.GenomePermissionId = Guid.NewGuid();
gp.OrganizationId = User.Identity.GetUserGroupId();
gp.UserId = User.Identity.GetUserGuid();
gp.PermissionId = Constants.Permissions.Ids.Owner;
context.GenomePermission.Add(gp);
context.SaveChanges();
}
return(RedirectToAction("Index", "Home"));
}
protected void Application_Start()
{
AreaRegistration.RegisterAllAreas();
GlobalConfiguration.Configure(WebApiConfig.Register);
FilterConfig.RegisterGlobalFilters(GlobalFilters.Filters);
RouteConfig.RegisterRoutes(RouteTable.Routes);
BundleConfig.RegisterBundles(BundleTable.Bundles);
//GlobalFilters.Filters.Add(new System.Web.Mvc.AuthorizeAttribute());
AntiForgeryConfig.UniqueClaimTypeIdentifier = ClaimTypes.NameIdentifier;
Database.SetInitializer(new MigrateDatabaseToLatestVersion <GeneXContext, GeneX.Model.Migrations.Configuration>());
Database.SetInitializer(new MigrateDatabaseToLatestVersion <Db, GeneX.Security.Migrations.Configuration>());
GeneXContext context = new GeneXContext();
context.Database.Initialize(false);
context.Database.CreateIfNotExists();
Db securityContext = new Db();
securityContext.Database.Initialize(false);
securityContext.Database.CreateIfNotExists();
}
// TODO: Fix the Calls to include Either FormValues Dictionary or DTO.
public ActionResult Index(Guid?id, HttpPostedFileBase file)
{
if (file == null || file.ContentLength == 0 || file.ContentType == null || string.IsNullOrEmpty(file.FileName) || file.InputStream == null)
{
this.ModelState.AddModelError("PostedFile", "Must attach file.");
return(View());
}
if (file.ContentLength > 0)
{
string path = Path.Combine(ServerMapPath, id.ToString() + ".txt");
string fileName = Path.GetFileName(file.FileName);
if (fileName.EndsWith(".zip"))
{
string tempPath = Path.Combine(ServerMapPath, id.ToString() + ".zip");
string extractPath = Path.Combine(ServerMapPath, id.ToString());
file.SaveAs(tempPath);
System.IO.Compression.ZipFile.ExtractToDirectory(tempPath, extractPath);
string[] names = Directory.GetFiles(extractPath);
if (names.Length != 1)
{
throw new FileLoadException("Zip file must only contain one file.");
}
System.IO.File.Move(names[0], path);
}
List <SNP> snps = new List <SNP>();
int i = 0;
using (StreamReader sr = new StreamReader(path))
{
GeneXContext context = new GeneXContext();
while (sr.Peek() >= 0)
{
string line = sr.ReadLine();
if (line.StartsWith("#", true, CultureInfo.InvariantCulture))
{
continue;
}
string[] parsed = line.Split("\t".ToCharArray());
string tmp = parsed[0];
SNP snp = context.SNP.Where(m => m.ClusterId == tmp && m.GenomeId == id.Value).FirstOrDefault();
int chromosome = 0;
string chromosomeType;
if (parsed[1].ToUpper().Equals("X") || parsed[1].ToUpper().Equals("Y"))
{
chromosome = 23;
chromosomeType = parsed[1].ToUpper();
}
else if (parsed[1].ToUpper().Equals("MT"))
{
chromosome = 0;
chromosomeType = "MT";
}
else
{
chromosome = int.Parse(parsed[1]);
chromosomeType = "A";
}
char?allele1 = null;
char?allele2 = null;
if (parsed[3].Length > 0)
{
allele1 = parsed[3][0];
}
if (parsed[3].Length > 1)
{
allele2 = parsed[3][0];
}
if (snp == null)
{
context.SNP.Add(new SNP {
SNPId = Guid.NewGuid(), GenomeId = id.Value, ClusterId = parsed[0], Chromosome = chromosome, ChromosomeType = chromosomeType, Position = int.Parse(parsed[2]), Genotype = parsed[3], Allele1 = allele1.ToString(), Allele2 = allele2.ToString()
});
}
else
{
snp.ChromosomeType = chromosomeType;
snp.Genotype = parsed[3];
}
++i;
if (i % 1000 == 0)
{
context.SaveChanges();
context.Dispose();
context = new GeneXContext();
}
}
context.SaveChanges();
context.Dispose();
}
}
return(RedirectToAction("Index", "Home"));
}
public ActionResult Index(Guid?id, HttpPostedFileBase file)
{
if (file == null || file.ContentLength == 0 || file.ContentType == null || string.IsNullOrEmpty(file.FileName) || file.InputStream == null)
{
this.ModelState.AddModelError("PostedFile", "Must attach file.");
return(View());
}
if (file.ContentLength > 0)
{
string fileName = Path.GetFileName(file.FileName);
string path = Path.Combine(ServerMapPath, id.ToString() + ".txt");
file.SaveAs(path);
List <SNPedia> snps = new List <SNPedia>();
int i = 0;
using (StreamReader sr = new StreamReader(path))
{
GeneXContext context = new GeneXContext();
while (sr.Peek() >= 0)
{
string line = sr.ReadLine();
if (line.StartsWith("#", true, CultureInfo.InvariantCulture) || string.IsNullOrWhiteSpace(line))
{
continue;
}
string[] parsed = line.Split("\t".ToCharArray());
string chrome = parsed[0];
string reference = parsed[1];
string chiptype = parsed[2];
int pos = int.Parse(parsed[3]);
string toParse = parsed[8];
int chromosome = -1;
string chromosomeType;
string notes = toParse.Substring(toParse.IndexOf("Note=") + 5).Replace("\"", string.Empty);
int cidStart = toParse.IndexOf("ID=") + 6;
int cidEnd = toParse.IndexOf(";", cidStart);
string cid = toParse.Substring(cidStart, cidEnd - cidStart);
if (chrome.Contains("MT"))
{
chromosomeType = "MT";
chromosome = 0;
}
else if (chrome.Contains("X"))
{
chromosomeType = "X";
chromosome = 23;
}
else if (chrome.Contains("Y"))
{
chromosomeType = "Y";
chromosome = 23;
}
else
{
chromosomeType = "A";
if (!int.TryParse(chrome.Substring(3), out chromosome))
{
// Not Human
continue;
}
}
SNPedia snpedia = context.SNPedia.Where(m => m.Position == pos && m.Chromosome == chromosome && m.ChromosomeType == chromosomeType).FirstOrDefault();
if (snpedia == null)
{
context.SNPedia.Add(new SNPedia {
SNPediaId = Guid.NewGuid(), ClusterId = cid, Chromosome = chromosome, ChromosomeType = chromosomeType, Position = pos, ChipType = chiptype, Source = reference, Notes = notes
});
}
++i;
if (i % 1000 == 0)
{
context.SaveChanges();
context.Dispose();
context = new GeneXContext();
}
}
context.SaveChanges();
context.Dispose();
}
}
return(RedirectToAction("Index", "Home"));
}
