private MapComponent GetMapComponentFromViewModel(MapComponentViewModel mapcomponentvm)
{
MapComponent mapcomponent = null;
if (mapcomponentvm.Id > 0)
{
ValidateMapComponentGenotype(mapcomponentvm.Id, mapcomponentvm.GenotypeId);
mapcomponent = u_repo.GetMapComponent(mapcomponentvm.Id);
mapcomponentvm.ToMapComponent(mapcomponent);
}
else
{
mapcomponent = mapcomponentvm.ToMapComponent();
mapcomponent.isRemoved = false;
}
if (mapcomponent.GenotypeId.HasValue)
{
mapcomponent.Genotype = u_repo.GetGenotype(mapcomponent.GenotypeId.Value);
}
if (mapcomponent.Map == null)
{
mapcomponent.Map = u_repo.GetMap(mapcomponent.MapId);
}
return(mapcomponent);
}
private void GetDefaultValues(CrossPlan crossPlan, IPlantBreedingRepo repo)
{
if (crossPlan.Id > 0 && !crossPlan.GenotypeId.HasValue)
{
CrossPlan old = repo.GetCrossPlan(crossPlan.Id);
if (!crossPlan.GenotypeId.HasValue)
{
crossPlan.GenotypeId = old.GenotypeId;
}
}
if (crossPlan.FemaleParentId.HasValue && crossPlan.FemaleParent == null)
{
crossPlan.FemaleParent = repo.GetGenotype(crossPlan.FemaleParentId.Value);
}
if (crossPlan.MaleParentId.HasValue && crossPlan.MaleParent == null)
{
crossPlan.MaleParent = repo.GetGenotype(crossPlan.MaleParentId.Value);
}
if (crossPlan.OriginId.HasValue && crossPlan.OriginId == null)
{
crossPlan.Origin = repo.GetOrigin(crossPlan.OriginId.Value);
}
if (crossPlan.CrossTypeId.HasValue && crossPlan.CrossType == null)
{
crossPlan.CrossType = repo.GetCrossType(crossPlan.CrossTypeId.Value);
}
crossPlan.Genus = repo.GetGenus(crossPlan.GenusId);
}
public PhenotypeEntryViewModel GetPhenotypeSummary(int genotypeId)
{
Genotype genotype = u_repo.GetGenotype(genotypeId);
List <Fate> possibleFates = u_repo.GetFates().OrderBy(t => t.Order).ToList();
PhenotypeEntryViewModel vm = GenotypePhenotypeEntry(genotype, possibleFates);
return(vm);
}
/// <summary>
/// Updates a genotype from a crossplan
/// </summary>
/// <param name="cp"></param>
public Genotype GenotypeFromCrossPlan(CrossPlan cp)
{
if (!cp.GenotypeId.HasValue)
{
//TODO: Throw error
}
Genotype genotype = u_repo.GetGenotype(cp.GenotypeId.Value);
if (genotype != null)
{
genotype.UpdateFromCrossPlan(cp);
}
return(genotype);
}
/// <summary>
/// Builds a pedigree tree for a Genotype. A Pedigree tree is a BST-like structure of parents for that genotype.
/// </summary>
/// <param name="id">The ID of the Genotype to build a Pedigree from.</param>
/// <returns>The root node of the Pedigree Tree, or null if the ID doesn't find a match.</returns>
public static TreeNode <Genotype> BuildPedigreeTree(this Genotype target, IPlantBreedingRepo repo)
{
if (target == null)
{
throw new ArgumentNullException("target");
}
Genotype root = repo.GetGenotype(target.Id);
Tuple <Genotype, Genotype> parents = repo.GetGenotypeParents(target);
var node = new TreeNode <Genotype> {
Data = root
};
if (parents != null && parents.Item1 != null)
{
// Left side is always the male.
node.Left = BuildPedigreeTree(parents.Item1, repo);
}
if (parents != null && parents.Item2 != null)
{
// Right side is always the female.
node.Right = BuildPedigreeTree(parents.Item2, repo);
}
return(node);
}
public ReportViewModel GetSelectionSummaryReport(SelectionSummaryReport vm)
{
string reportName = Properties.Settings.Default.ReportNameSelectionSummary;
var genotype = u_repo.GetGenotype(vm.GenotypeId);
string reportTitle = $"{genotype.Name} Phenotype Summary";
return(vm.ToReportViewModel(reportName, reportTitle));
}
public SelectionSummaryViewModel GetSelectionSummary(int id)
{
Genotype genotype = u_repo.GetGenotype(id);
IEnumerable <Family> families = u_repo.GetQueryableFamilies(t => t.MaleParent == genotype.Id || t.FemaleParent == genotype.Id).ToList();
IEnumerable <FamilyUseViewModel> fuvms = families.ToFamilyUseViewModel(genotype);
PhenotypeEntryViewModel pdvm = GetPhenotypeEntry(id);
SelectionSummaryViewModel ssvm = genotype.ToSelectionSummaryViewModel(pdvm, fuvms);
return(ssvm);
}
public void SaveOrderProduct(OrderProductViewModel orderProduct)
{
var op = OrderProductViewModel.ToOrderProduct(orderProduct);
op.Genotype = u_repo.GetGenotype(op.GenotypeId);
op.Material = u_repo.GetMaterials().SingleOrDefault(m => m.Id == op.MaterialId);
u_repo.SaveOrderProduct(op);
var savedVM = OrderProductViewModel.Create(op);
savedVM.CopyTo(orderProduct);
}
/// <summary>
/// Displays selection summary detail view for given genotype.
/// </summary>
/// <param name="id">
/// Id of genotype to display selection summary for.
/// </param>
/// <returns>
/// Detail view for selection summary.
/// </returns>
public ActionResult Detail(int?id)
{
if (!id.HasValue)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
SelectionSummaryViewModel ssvm = s_repo.GetSelectionSummary(id.Value);
if (ssvm == null)
{
return(HttpNotFound());
}
ViewBag.GenusId = m_repo.GetGenotype(id.Value).Family.GenusId;
ViewBag.FlatTypes = new SelectList(m_repo.GetFlatTypes(), "Id", "Label");
return(View(ssvm));
}
public ActionResult Tree(int?id)
{
if (!id.HasValue)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
//Constants needed by the tree
int treeSize = 15;
int index = 1; //Current location in the array
//root of tree, child to build off of
Genotype root = m_repo.GetGenotype(id.Value);
if (root == null)
{
return(new HttpStatusCodeResult(HttpStatusCode.BadRequest));
}
//Tree to pass to page
List <Genotype> tree = new List <Genotype>();
List <Family> fams = new List <Family>();
//fill list to handle off array errors
for (int i = 0; i < treeSize; i++)
{
tree.Add(new Genotype {
GivenName = ""
});
}
//fill list to handle off array errors
for (int i = 0; i < treeSize; i++)
{
fams.Add(new Family());
}
//add male parent
tree.Insert(index, root);
fams.Insert(index, m_repo.GetFamily(root.FamilyId));
//Increment index
index++;
//Get root parents
Tuple <Genotype, Genotype> parents = m_repo.GetGenotypeParents(root);
//different iteration to handle 0 index
//Female is always first in the tuple
if (parents.Item1 != null)
{
tree.Insert(index, parents.Item1);
fams.Insert(index, m_repo.GetFamily(parents.Item1.FamilyId));
}
else
{
tree.Insert(index, new Genotype {
GivenName = ""
});
fams.Insert(index, new Family()
{
});
}
//Male is second
if (parents.Item2 != null)
{
tree.Insert(index + 1, parents.Item2);
fams.Insert(index + 1, m_repo.GetFamily(parents.Item2.FamilyId));
}
else
{
tree.Insert(index + 1, new Genotype {
GivenName = ""
});
fams.Insert(index + 1, new Family()
{
});
}
//Tree population, through grandparents (index 8), start at father (index 2)
for (int i = 2; i < 8; i++)
{
if (!tree[i].Id.Equals(0)) //if parent is not null
{
parents = m_repo.GetGenotypeParents(tree[i]); //get parents
}
else
{
parents = new Tuple <Genotype, Genotype>(item1: null, item2: null); //new tuple with null genotypes
}
addParents(ref index, ref tree, ref fams, parents);
}
//Send list to view
tree.RemoveAt(0);
fams.RemoveAt(0);
//tree.RemoveRange(15, tree.Count - 15);
ViewBag.genotypeList = tree;
ViewBag.families = fams;
ViewBag.Genotype = root;
return(View());
}
public AccessionViewModel GetAccessionViewModel(int id)
{
Genotype genotype = u_repo.GetGenotype(id);
if (genotype == null)
{
return(null);
}
IEnumerable <MapComponent> mapComponents = genotype.MapComponents.OrderBy(t => t.Map.EvaluationYear);
var accession = genotype.ToAccessionViewModel();
if (accession.IsBase.Equals(true))
{
accession.Year = null;
accession.Note = null;
}
accession.MapComponents = mapComponents.Where(t => t.Map.Retired == false).OrderByDescending(t => t.Map.PlantingYear).ToList();
accession.MapComponentsRetired = mapComponents.Where(t => t.Map.Retired == true).OrderByDescending(t => t.Map.PlantingYear).ToList();
return(accession);
}
public ActionResult Index(int?pageSize, int?genotypeId, string filter, int page = 1, string messageResult = "")
{
int defaultPage = 1;
int baseIdResult = 0;
int genotypeIdResult = 0;
bool successfullResult = true;
string filterResult = filter;
if (!pageSize.HasValue)
{
if (SessionManager.SessionPageSize.HasValue)
{
pageSize = SessionManager.SessionPageSize;
}
else
{
pageSize = Properties.Settings.Default.PageSize;
}
}
SetPageSizeViewBag();
SessionManager.SessionPageSize = pageSize.Value;
int genusId = SessionManager.GetGenusId().Value;
IPagedList <AccessionIndexViewModel> pageOfAccessions = null;
try
{
pageOfAccessions = a_repo.GetPageInIndex(pageSize.Value, genotypeId, filter, page, genusId);
}
catch (SearchException e)
{
successfullResult = false;
messageResult = e.Message;
}
if (successfullResult == false)
{
try
{
pageOfAccessions = a_repo.GetPageInIndex(pageSize.Value, defaultPage, genusId);
}
catch (SearchException)
{
return(RedirectToAction("Create"));
//return new HttpStatusCodeResult(HttpStatusCode.BadRequest);
}
}
Genotype genotypeSearched = null;
if (!genotypeId.HasValue && !filter.IsNullOrWhiteSpace())
{
genotypeSearched = m_repo.GetGenotypes(filter, genusId, 1).FirstOrDefault();
}
else if (genotypeId.HasValue)
{
genotypeSearched = m_repo.GetGenotype(genotypeId.Value);
}
if (genotypeSearched != null)
{
successfullResult = true;
genotypeIdResult = genotypeSearched.Id;
if (genotypeSearched.Family.BaseGenotypeId.HasValue && pageOfAccessions.HasAny(t => t.Id == genotypeSearched.Family.BaseGenotypeId))
{
baseIdResult = genotypeSearched.Family.BaseGenotypeId.Value;
}
else
{
baseIdResult = genotypeSearched.Id;
}
}
ViewBag.GenusId = genusId;
ViewBag.GenotypeId = genotypeIdResult;
ViewBag.BaseId = baseIdResult;
ViewBag.SuccessfulSearch = successfullResult;
ViewBag.Filter = filter;
ViewBag.SearchErrorMessage = messageResult;
ViewBag.PageSize = pageSize.Value.ToString();
ViewBag.CurrentDate = DateTime.Now;
return(View(pageOfAccessions));
}