public void Constructor()
{
TaxonSearchCriteria searchCriteria;
searchCriteria = new TaxonSearchCriteria();
Assert.IsNotNull(searchCriteria);
}
/// <summary>
/// Cache taxon list information about all valid taxa.
/// </summary>
private void LoadTaxonListInformation()
{
// Get taxa.
ITaxonSearchCriteria searchCriteria = new TaxonSearchCriteria();
searchCriteria.IsValidTaxon = true;
TaxonList taxa = CoreData.TaxonManager.GetTaxa(mContext, searchCriteria);
// Init new taxon information items.
foreach (ITaxon taxon in taxa)
{
var taxonListInformation = new TaxonListInformation
{
CommonName = taxon.CommonName,
Id = taxon.Id,
CategoryId = taxon.Category.Id,
ParentCategoryId = taxon.Category.ParentId,
ScientificName = taxon.ScientificName
};
mTaxonInformationCache.TaxonInformation[taxon.Id] = taxonListInformation;
}
// Add species fact information.
//GetLandscapeTypeSpeciesFactsToCache();
//GetOrganismGroupSpeciesFactsToCache();
GetRedListCategorySpeciesFactsToCache();
//GetRedListCriteriaSpeciesFactsToCache();
//GetRedListTaxonCategorySpeciesFactsToCache();
//GetSwedishOccurrenceSpeciesFactsToCache();
//GetRedListOldCategorySpeciesFactsToCache();
}
private TaxonSearchCriteria GetSearchCriteria(Boolean refresh)
{
if (_searchCriteria.IsNull() || refresh)
{
_searchCriteria = new TaxonSearchCriteria();
}
return(_searchCriteria);
}
public List <ITaxon> GetChildTaxa(int[] parentTaxonIds)
{
var searchCriteria = new TaxonSearchCriteria()
{
TaxonIds = new List <int>(parentTaxonIds),
TaxonCategoryIds = new List <int> {
(int)TaxonCategoryId.Species
},
Scope = TaxonSearchScope.AllChildTaxa
};
return(CoreData.TaxonManager.GetTaxa(UserContext, searchCriteria));
}
/// <summary>
/// Get a list with corresponding taxon from taxon ids
/// </summary>
/// <param name="taxonIds">The taxon ids.</param>
/// <returns></returns>
private List <ITaxon> GetMatches(List <Int32> taxonIds)
{
var searchCriteria = new TaxonSearchCriteria();
searchCriteria.TaxonIds = new List <int>();
searchCriteria.IsValidTaxon = true;
foreach (Int32 id in taxonIds)
{
searchCriteria.TaxonIds.Add(id);
}
TaxonList taxa = CoreData.TaxonManager.GetTaxa(_user, searchCriteria);
return((List <ITaxon>)taxa.GetGenericList());
}
/// <summary>
/// Load information about suitable parent taxa.
/// </summary>
/// <param name="userContext">User context.</param>
private void LoadTaxonInformation(IUserContext userContext)
{
ITaxonSearchCriteria searchCriteria;
List <Int32> taxonIds;
TaxonList parentTaxa;
TaxonNameList allTaxonNames;
_italicStringsInAutomaticTaxonomicParagraph = new List <String>();
if (_suitableParents.IsEmpty() && _taxon.IsNotNull())
{
searchCriteria = new TaxonSearchCriteria();
taxonIds = new List <Int32>();
taxonIds.Add(_taxon.Id);
searchCriteria.TaxonIds = taxonIds;
searchCriteria.Scope = TaxonSearchScope.AllParentTaxa;
parentTaxa = CoreData.TaxonManager.GetTaxa(userContext, searchCriteria);
_suitableParents = new TaxonList();
foreach (ITaxon parent in parentTaxa)
{
if ((parent.Category.Id == (Int32)(TaxonCategoryId.Kingdom)) ||
(parent.Category.Id == (Int32)(TaxonCategoryId.Phylum)) ||
(parent.Category.Id == (Int32)(TaxonCategoryId.Class)) ||
(parent.Category.Id == (Int32)(TaxonCategoryId.Order)) ||
(parent.Category.Id == (Int32)(TaxonCategoryId.Family)))
{
if (parent.Id != (Int32)(TaxonId.Life))
{
_suitableParents.Add(parent);
}
}
}
}
if (_synonyms.IsEmpty() && _taxon.IsNotNull())
{
_synonyms = new TaxonNameList();
allTaxonNames = CoreData.TaxonManager.GetTaxonNames(userContext, _taxon);
foreach (ITaxonName name in allTaxonNames)
{
if ((name.Category.Id == 0) &&
(name.Status.Id == 0) &&
(!name.IsRecommended) &&
(name.Name != _taxon.ScientificName))
{
_italicStringsInAutomaticTaxonomicParagraph.Add(name.Name);
_synonyms.Add(name);
}
}
}
}
public void Add_Filter_Data()
{
IUserContext userContext = CoreData.UserManager.GetCurrentUser();
var searchCriteria = new TaxonSearchCriteria();
searchCriteria.IsValidTaxon = true;
searchCriteria.TaxonIds = new List <int>();
searchCriteria.TaxonIds.Add(1);
searchCriteria.TaxonIds.Add(2);
searchCriteria.TaxonIds.Add(3);
searchCriteria.TaxonIds.Add(4);
var taxa = CoreData.TaxonManager.GetTaxa(userContext, searchCriteria);
Assert.AreEqual(4, taxa.Count);
}
/// <summary>
/// Updates the reference relations.
/// </summary>
/// <param name="taxon">The source taxon.</param>
/// <param name="guid">The unique identifier.</param>
/// <param name="newReferenceList">The new reference list.</param>
/// <param name="applyMode">The apply mode.</param>
public void UpdateReferenceRelations(
ITaxon taxon,
string guid,
ReferenceViewModel[] newReferenceList,
ReferenceApplyMode applyMode)
{
ReferenceRelationList allReferenceRelationItemsToCreate = new ReferenceRelationList();
ReferenceRelationList allReferenceRelationItemsToDelete = new ReferenceRelationList();
ReferenceRelationList createReferenceRelationItems;
ReferenceRelationList deleteReferenceRelationItems;
// Handle source taxon reference relations
createReferenceRelationItems = GetReferenceRelationsThatWillBeCreated(guid, newReferenceList, ReferenceApplyMode.OnlySelected);
deleteReferenceRelationItems = GetReferenceRelationsThatWillBeDeleted(guid, newReferenceList, ReferenceApplyMode.OnlySelected);
allReferenceRelationItemsToCreate.AddRange(createReferenceRelationItems);
allReferenceRelationItemsToDelete.AddRange(deleteReferenceRelationItems);
if (applyMode != ReferenceApplyMode.OnlySelected)
{
// Get all child taxa
ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
taxonSearchCriteria.TaxonIds = new List <int>();
taxonSearchCriteria.TaxonIds.Add(taxon.Id);
taxonSearchCriteria.Scope = TaxonSearchScope.AllChildTaxa;
TaxonList taxonList = CoreData.TaxonManager.GetTaxa(user, taxonSearchCriteria);
taxonList.Remove(taxon);
foreach (ITaxon childTaxon in taxonList)
{
createReferenceRelationItems = GetReferenceRelationsThatWillBeCreated(childTaxon.Guid, newReferenceList, applyMode);
deleteReferenceRelationItems = GetReferenceRelationsThatWillBeDeleted(childTaxon.Guid, newReferenceList, applyMode);
allReferenceRelationItemsToCreate.AddRange(createReferenceRelationItems);
allReferenceRelationItemsToDelete.AddRange(deleteReferenceRelationItems);
}
}
if (allReferenceRelationItemsToCreate.Count > 0 || allReferenceRelationItemsToDelete.Count > 0)
{
using (ITransaction transaction = user.StartTransaction())
{
CoreData.ReferenceManager.DeleteReferenceRelations(user, allReferenceRelationItemsToDelete);
CoreData.ReferenceManager.CreateReferenceRelations(user, allReferenceRelationItemsToCreate);
transaction.Commit();
}
}
}
/// <summary>
/// Updates the cache by getting all relations and all taxa from Taxon service
/// and create a TaxonRelationTree.
/// This method is thread safe.
/// </summary>
/// <param name="userContext">The user context.</param>
public static void UpdateCache(IUserContext userContext)
{
lock (LockingTarget)
{
Debug.WriteLine("Start update Cache {0}", DateTime.Now);
ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
var allTaxa = CoreData.TaxonManager.GetTaxa(userContext, taxonSearchCriteria);
TaxonRelationSearchCriteria searchCriteria = new TaxonRelationSearchCriteria();
TaxonRelationList allRelations = CoreData.TaxonManager.GetTaxonRelations(userContext, searchCriteria);
TaxonRelationList = allRelations;
CachedTaxonRelationTree = TaxonRelationsTreeManager.CreateTaxonRelationsTree(
userContext,
allRelations,
allTaxa);
CacheLastUpdatedTime = DateTime.Now;
Debug.WriteLine("End update Cache {0}", DateTime.Now);
DyntaxaLogger.WriteMessage("DyntaxaTree updated {0}", DateTime.Now);
}
}
public void CreateCompleteTaxonRelationsTree()
{
using (ShimsContext.Create())
{
LoginApplicationUserAndSetSessionVariables();
SetSwedishLanguage();
IUserContext userContext = ApplicationUserContextSV;
ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
var allTaxa = CoreData.TaxonManager.GetTaxa(userContext, taxonSearchCriteria);
TaxonRelationSearchCriteria searchCriteria = new TaxonRelationSearchCriteria();
var allRelations = CoreData.TaxonManager.GetTaxonRelations(userContext, searchCriteria);
var tree = TaxonRelationsTreeManager.CreateTaxonRelationsTree(userContext, allRelations, allTaxa, false);
//1012265
//1011617
//6001191 ensam
var edges = tree.GetAllChildAndParentEdges(266838);
string graphviz = GraphvizManager.CreateGraphvizFormatRepresentation(edges);
// find suspicious hybrids
List <ITaxonRelationsTreeNode> invalidHybrids;
// find root nodes
tree.RootNodes = new HashSet <ITaxonRelationsTreeNode>();
tree.ValidRootNodes = new HashSet <ITaxonRelationsTreeNode>();
foreach (var node in tree.AllTreeNodes)
{
tree.RootNodes.Add(node.RootNode);
if (node.RootNode.Taxon.IsValid)
{
tree.ValidRootNodes.Add(node.RootNode);
}
}
}
}
public void SplitGraphTest()
{
using (ShimsContext.Create())
{
//Arrange
LoginApplicationUserAndSetSessionVariables();
SetSwedishLanguage();
IUserContext userContext = ApplicationUserContextSV;
const int lumpSplitTaxonId = 2755;
//TaxonIdBefore: 233285
//TaxonIdAfter: 2755
ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
TaxonList allTaxa = CoreData.TaxonManager.GetTaxa(userContext, taxonSearchCriteria);
TaxonRelationSearchCriteria searchCriteria = new TaxonRelationSearchCriteria();
TaxonRelationList allRelations = CoreData.TaxonManager.GetTaxonRelations(userContext, searchCriteria);
TaxonRelationsTree tree = TaxonRelationsTreeManager.CreateTaxonRelationsTree(userContext, allRelations,
allTaxa, false);
var edges = tree.GetAllChildAndParentEdges(lumpSplitTaxonId);
var edges2 = tree.GetAllValidChildAndParentEdges(lumpSplitTaxonId);
List <ITaxonRelationsTreeNode> sourceNodes = new List <ITaxonRelationsTreeNode> {
tree.GetTreeNode(lumpSplitTaxonId)
};
GraphVizFormat graphVizFormat = new GraphVizFormat()
{
ShowLumpsAndSplits = true,
ShowRelationId = false
};
string graphRepresentation2 = GraphvizManager.CreateGraphvizFormatRepresentation(
userContext,
tree,
edges2,
sourceNodes,
graphVizFormat);
int x = 8;
}
}
/// <summary>
/// Get all child taxon
/// </summary>
/// <param name="parentTaxaIds">Id of parent taxon</param>
/// <returns></returns>
public List <TaxonSearchResultItemViewModel> GetChildTaxa(int[] parentTaxaIds)
{
var searchCriteria = new TaxonSearchCriteria()
{
TaxonIds = new List <int>(parentTaxaIds),
TaxonCategoryIds = new List <int> {
(int)TaxonCategoryId.Species
},
Scope = TaxonSearchScope.AllChildTaxa
};
var taxa = CoreData.TaxonManager.GetTaxa(_user, searchCriteria);
var resultList = (from t in taxa select TaxonSearchResultItemViewModel.CreateFromTaxon(t, false)).Distinct().ToList();
var speciesFactManager = new SpeciesFactManager(_user);
var protectedTaxonList = speciesFactManager.GetProtectedTaxons();
// Set protection level for each taxon; public or not
resultList.ForEach(t => t.SpeciesProtectionLevel = protectedTaxonList.Any(ptl => ptl.Id == t.TaxonId) ? SpeciesProtectionLevelEnum.Protected1 : SpeciesProtectionLevelEnum.Public);
return(resultList);
}
/// <summary>
/// Update invalid taxaidlist cache if not present
/// </summary>
/// <returns></returns>
private HashSet <int> UpdateInvalidTaxaIdListCache()
{
ITaxonSearchCriteria searchCriteria = new TaxonSearchCriteria()
{
IsValidTaxon = false
};
var taxonList = CoreData.TaxonManager.GetTaxa(mUserContext, searchCriteria);
var taxaListTaxonIdsSet = new HashSet <int>();
foreach (var taxon in taxonList)
{
taxaListTaxonIdsSet.Add(taxon.Id);
}
AspNetCache.AddCachedObject(
"allInvalidTaxaIds",
taxaListTaxonIdsSet,
DateTime.Now + new TimeSpan(0, 24, 0, 0),
CacheItemPriority.Normal);
return(taxaListTaxonIdsSet);
}
public TaxonSearchCriteriaTest()
{
_searchCriteria = null;
}
public void ValidateTaxonRelationsTree()
{
using (ShimsContext.Create())
{
LoginApplicationUserAndSetSessionVariables();
SetSwedishLanguage();
IUserContext userContext = ApplicationUserContextSV;
ITaxonSearchCriteria taxonSearchCriteria = new TaxonSearchCriteria();
var allTaxa = CoreData.TaxonManager.GetTaxa(userContext, taxonSearchCriteria);
TaxonRelationSearchCriteria searchCriteria = new TaxonRelationSearchCriteria();
var allRelations = CoreData.TaxonManager.GetTaxonRelations(userContext, searchCriteria);
var tree = TaxonRelationsTreeManager.CreateTaxonRelationsTree(userContext, allRelations, allTaxa, false);
List <ITaxonRelationsTreeNode> collectiveTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> hybridTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> artkomplexTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> validCollectiveTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> validHybridTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> validArtkomplexTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> possiblyInvalidCollectiveTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> possiblyInvalidHybridTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> possiblyInvalidArtkomplexTaxa = new List <ITaxonRelationsTreeNode>();
List <ITaxonRelationsTreeNode> notYetHandledHybridTaxa = new List <ITaxonRelationsTreeNode>();
foreach (var node in tree.AsDepthFirstNodeIterator())
{
if (node.Taxon.Category.Id == 27)
{
collectiveTaxa.Add(node);
// Kollektivtaxon ska ha 0 eller flera barn?
// MainChildren = 0 && SecondaryChildren >= 0
if (node.ValidMainChildren == null)
{
validCollectiveTaxa.Add(node);
}
else
{
possiblyInvalidCollectiveTaxa.Add(node);
}
}
if (node.Taxon.Category.Id == 21)
{
hybridTaxa.Add(node);
// Hybrider ska ha exakt 1 primär förälder precis som alla andra taxon.
// När alla Hybrider har hanterats i revisioner (Mora är på gång att ta tag i det så ska den ha
// 1 primär relation oftast under ett släkte (minsta gemensamma nämnaren för föräldrarna)
// men ibland även högre upp. Tyvärr verkar det ligga någon regel i Dyntaxa som
// förhindrar vissa av dessa saker. För släktet Anodonta kan jag t ex inte lägga till
// ett artkomplex (möjligen samma för hybrider) som sekundär förälder.
// 2 eller flera sekundära föräldrar. Oftast till arter.
// Hybrider ska ha exakt 2 sekundära föräldrar.
// och exakt 1 primär förälder.
if (node.ValidMainParents != null && node.ValidMainParents.Count == 1 &&
node.ValidSecondaryParents != null && node.ValidSecondaryParents.Count >= 2)
{
validHybridTaxa.Add(node);
}
else
{
notYetHandledHybridTaxa.Add(node);
//possiblyInvalidHybridTaxa.Add(node);
}
}
if (node.Taxon.Category.Id == 28)
{
artkomplexTaxa.Add(node);
// Artkomplex ska ha 0 eller fler barn?
// MainChildren = 0 && SecondaryChildren >= 0
if (node.ValidMainChildren == null)
{
validArtkomplexTaxa.Add(node);
}
else
{
possiblyInvalidArtkomplexTaxa.Add(node);
}
if (node.ValidSecondaryChildren != null && node.ValidSecondaryChildren.Count == 1)
{
int z = 8;
}
}
}
int t = 8;
}
}
