/// <summary>
/// Convert a list of WebSpeciesFact instances
/// to a SpeciesFactList.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="webSpeciesFacts">List of WebSpeciesFact instances.</param>
/// <returns>List of SpeciesFact instances.</returns>
protected override SpeciesFactList GetSpeciesFacts(
IUserContext userContext,
List <WebSpeciesFact> webSpeciesFacts)
{
SpeciesFactList speciesFacts;
FactorList factors = CoreData.FactorManager.GetFactors(userContext);
IndividualCategoryList individualCategories = CoreData.FactorManager.GetIndividualCategories(userContext);
PeriodList periods = CoreData.FactorManager.GetPeriods(userContext);
speciesFacts = null;
if (webSpeciesFacts.IsNotEmpty())
{
speciesFacts = new SpeciesFactList();
foreach (WebSpeciesFact webSpeciesFact in webSpeciesFacts)
{
if (webSpeciesFact.QualityId <= (int)SpeciesFactQualityId.Acceptable)
{
speciesFacts.Add(GetSpeciesFact(webSpeciesFact, factors, individualCategories, periods));
}
// else: Bad quality, do not use this species fact.
}
}
return(speciesFacts);
}
/// <summary>
/// Method that returns a filtered version of this species fact list.
/// The filtering is done on individual categories.
/// </summary>
/// <param name="individualCategories">Individual categories for the requested species facts.</param>
/// <returns>A filtered species fact list.</returns>
public SpeciesFactList GetSpeciesFacts(IndividualCategoryList individualCategories)
{
if (individualCategories == null)
{
throw new ArgumentException("CategoryList is null", "individualCategories");
}
SpeciesFactList filteredList = new SpeciesFactList();
if (this.IsNotEmpty())
{
foreach (ISpeciesFact fact in this)
{
foreach (IIndividualCategory category in individualCategories)
{
if (fact.IndividualCategory.Id == category.Id)
{
filteredList.Add(fact);
break;
}
}
}
}
return(filteredList);
}
/// <summary>
/// Convert a list of WebSpeciesFact instances
/// to a SpeciesFactList.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="webSpeciesFacts">List of WebSpeciesFact instances.</param>
/// <returns>List of SpeciesFact instances.</returns>
protected virtual SpeciesFactList GetSpeciesFacts(IUserContext userContext, List <WebSpeciesFact> webSpeciesFacts)
{
SpeciesFactList speciesFacts;
FactorList factors = CoreData.FactorManager.GetFactors(userContext);
IndividualCategoryList individualCategories = CoreData.FactorManager.GetIndividualCategories(userContext);
PeriodList periods = CoreData.FactorManager.GetPeriods(userContext);
ReferenceList references;
SpeciesFactQualityList speciesFactQualities = CoreData.SpeciesFactManager.GetSpeciesFactQualities(userContext);
List <Int32> referenceIds, taxonIds;
TaxonList taxa;
speciesFacts = null;
if (webSpeciesFacts.IsNotEmpty())
{
referenceIds = GetReferenceIds(webSpeciesFacts);
references = CoreData.ReferenceManager.GetReferences(userContext, referenceIds);
taxonIds = GetTaxonIds(webSpeciesFacts);
taxa = CoreData.TaxonManager.GetTaxa(userContext, taxonIds);
speciesFacts = new SpeciesFactList();
foreach (WebSpeciesFact webSpeciesFact in webSpeciesFacts)
{
speciesFacts.Add(GetSpeciesFact(userContext, webSpeciesFact, factors, individualCategories, periods, references, speciesFactQualities, taxa));
}
}
return(speciesFacts);
}
/// <summary>
/// Set individual categories for specified locale.
/// </summary>
/// <param name="individualCategories">Individual categories.</param>
/// <param name="locale">Locale.</param>
protected override void SetIndividualCategories(IndividualCategoryList individualCategories,
ILocale locale)
{
lock (IndividualCategories)
{
IndividualCategories[locale.ISOCode] = individualCategories;
}
}
/// <summary>
/// Add individual category to search criteria.
/// </summary>
/// <param name="individualCategory">The individual category.</param>
public void Add(IIndividualCategory individualCategory)
{
if (IndividualCategories.IsNull())
{
IndividualCategories = new IndividualCategoryList();
}
IndividualCategories.Add(individualCategory);
}
/// <summary>
/// Remove individual categories from current species fact data set scope.
/// The species facts in the data set are updated
/// to the new species fact data set scope.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="selection">Changed scope of the data set.</param>
public virtual void RemoveSelection(IUserContext userContext,
IndividualCategoryList selection)
{
ISpeciesFactDataSetSelection newSelection;
newSelection = new SpeciesFactDataSetSelection();
newSelection.IndividualCategories.Merge(selection);
RemoveSelection(userContext, newSelection);
}
/// <summary>
/// Create a species fact data set selection instance.
/// </summary>
public SpeciesFactDataSetSelection()
{
_factors = new FactorList(true);
_hosts = new TaxonList(true);
_individualCategories = new IndividualCategoryList(true);
_periods = new PeriodList(true);
_references = new ReferenceList(true);
_taxa = new TaxonList(true);
}
/// <summary>
/// Get individual categories for specified locale.
/// </summary>
/// <param name="locale">Locale.</param>
/// <returns>Individual categories for specified locale.</returns>
protected virtual IndividualCategoryList GetIndividualCategories(ILocale locale)
{
IndividualCategoryList individualCategories = null;
if (IndividualCategories.ContainsKey(locale.ISOCode))
{
individualCategories = (IndividualCategoryList)(IndividualCategories[locale.ISOCode]);
}
return(individualCategories);
}
/// <summary>
/// Default constructor
/// </summary>
public SpeciesFactSearchCriteria()
{
FactorDataTypes = new FactorDataTypeList();
Factors = new FactorList();
FieldSearchCriteria = new SpeciesFactFieldSearchCriteriaList();
Hosts = new TaxonList();
IndividualCategories = new IndividualCategoryList();
Periods = new PeriodList();
References = new ReferenceList();
Taxa = new TaxonList();
}
/// <summary>
/// Create a species fact data set instance.
/// </summary>
public SpeciesFactDataSet()
{
Factors = new FactorList(true);
Hosts = new TaxonList(true);
IndividualCategories = new IndividualCategoryList(true);
Periods = new PeriodList(true);
References = new ReferenceList(true);
_selection = new SpeciesFactDataSetSelection();
_selectionCopy = new SpeciesFactDataSetSelection();
SpeciesFacts = new SpeciesFactList();
Taxa = new TaxonList(true);
}
/// <summary>
/// Get individual categories for specified locale.
/// </summary>
/// <param name="locale">Locale.</param>
/// <returns>Individual categories for specified locale.</returns>
protected override IndividualCategoryList GetIndividualCategories(ILocale locale)
{
IndividualCategoryList individualCategories = null;
lock (IndividualCategories)
{
if (IndividualCategories.ContainsKey(locale.ISOCode))
{
individualCategories = (IndividualCategoryList)(IndividualCategories[locale.ISOCode]);
}
}
return(individualCategories);
}
/// <summary>
/// Remove factors, hosts, individual categories, periods or
/// taxa from current species fact data set scope.
/// The species facts in the data set are updated
/// to the new species fact data set scope.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="selection">Changed scope of the data set.</param>
public virtual void RemoveSelection(IUserContext userContext,
ISpeciesFactDataSetSelection selection)
{
FactorList factors;
IndividualCategoryList individualCategories;
PeriodList periods;
ReferenceList references;
TaxonList hosts, taxa;
// Check arguments.
selection.CheckNotNull("selection");
// Update selection with existing scope.
factors = new FactorList();
factors.Merge(_selection.Factors);
factors.Remove(selection.Factors);
selection.Factors = factors;
hosts = new TaxonList();
hosts.Merge(_selection.Hosts);
hosts.Remove(selection.Hosts);
selection.Hosts = hosts;
individualCategories = new IndividualCategoryList();
individualCategories.Merge(_selection.IndividualCategories);
individualCategories.Remove(selection.IndividualCategories);
selection.IndividualCategories = individualCategories;
periods = new PeriodList();
periods.Merge(_selection.Periods);
periods.Remove(selection.Periods);
selection.Periods = periods;
references = new ReferenceList();
references.Merge(_selection.References);
references.Remove(selection.References);
selection.References = references;
taxa = new TaxonList();
taxa.Merge(_selection.Taxa);
taxa.Remove(selection.Taxa);
selection.Taxa = taxa;
// Update species fact data set.
UpdateSelection(userContext, selection);
}
/// <summary>
/// Read rows from the excel xml format.
/// Overridden by each class that inherits this class.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name='xmlDoc'>The xml document that the row node will be read from.</param>
/// <param name="nsmgr">Namespacemanager containing all namespaces used by the excel compatible xml format</param>
protected override void ReadExcelXmlRows(IUserContext userContext,
XmlDocument xmlDoc,
XmlNamespaceManager nsmgr)
{
IndividualCategoryList individualCategories;
XmlNode dataNode;
XmlNodeList rowNodes;
rowNodes = xmlDoc.SelectNodes("/ss:Workbook/ss:Worksheet/ss:Table/ss:Row", nsmgr);
individualCategories = new IndividualCategoryList();
foreach (XmlNode rowNode in rowNodes)
{
dataNode = rowNode.SelectSingleNode("ss:Cell/ss:Data", nsmgr);
individualCategories.Add(CoreData.FactorManager.GetIndividualCategory(userContext, dataNode.InnerText.WebParseInt32()));
}
IndividualCategories = individualCategories;
}
/// <summary>
/// Convert a list of WebIndividualCategory instances
/// to a IndividualCategoryList.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="webIndividualCategories">List of WebIndividualCategory instances.</param>
/// <returns>Individual categories.</returns>
private IndividualCategoryList GetIndividualCategories(IUserContext userContext,
List <WebIndividualCategory> webIndividualCategories)
{
IndividualCategoryList individualCategories;
individualCategories = null;
if (webIndividualCategories.IsNotEmpty())
{
individualCategories = new IndividualCategoryList();
foreach (WebIndividualCategory webIndividualCategory in webIndividualCategories)
{
individualCategories.Add(GetIndividualCategory(userContext, webIndividualCategory));
}
individualCategories.Sort();
}
return(individualCategories);
}
/// <summary>
/// Reset species fact data set to no species facts.
/// This method is used when species fact data set selection
/// does not contain both factors and taxa.
/// </summary>
/// <param name="selection">
/// Scope of the data set is defined by this
/// species fact data set selection.
/// </param>
private void Reset(ISpeciesFactDataSetSelection selection)
{
Factors = new FactorList(true);
Factors.Merge(selection.Factors);
Hosts = new TaxonList(true);
Hosts.Merge(selection.Hosts);
IndividualCategories = new IndividualCategoryList(true);
IndividualCategories.Merge(selection.IndividualCategories);
Periods = new PeriodList(true);
Periods.Merge(selection.Periods);
References = new ReferenceList(true);
References.Merge(selection.References);
SpeciesFacts = new SpeciesFactList(true);
Taxa = new TaxonList();
Taxa.Merge(selection.Taxa);
// Save selection information.
_selection = (ISpeciesFactDataSetSelection)(selection.Clone());
_selectionCopy = (ISpeciesFactDataSetSelection)(selection.Clone());
}
public void RemoveSelectionIndividualCategories()
{
FactorList factors;
IFactor factor1, factor2;
IndividualCategoryList individualCategories1, individualCategories2;
Int32 speciesFactCount;
ITaxon taxon1, taxon2;
TaxonList taxa;
factor1 = CoreData.FactorManager.GetFactor(GetUserContext(), FactorId.SwedishHistory);
factor2 = CoreData.FactorManager.GetFactor(GetUserContext(), FactorId.SwedishOccurrence);
taxon1 = CoreData.TaxonManager.GetTaxon(GetUserContext(), TaxonId.DrumGrasshopper);
taxon2 = CoreData.TaxonManager.GetTaxon(GetUserContext(), TaxonId.Wolverine);
factors = new FactorList();
factors.Add(factor1);
factors.Add(factor2);
taxa = new TaxonList();
taxa.Add(taxon1);
taxa.Add(taxon2);
GetDataSet(true).AddSelection(GetUserContext(), factors);
GetDataSet().AddSelectionTaxa(GetUserContext(), taxa);
individualCategories1 = CoreData.FactorManager.GetIndividualCategories(GetUserContext());
GetDataSet().AddSelection(GetUserContext(), individualCategories1);
Assert.IsFalse(GetDataSet().Factors.IsEmpty());
Assert.IsFalse(GetDataSet().SpeciesFacts.IsEmpty());
speciesFactCount = GetDataSet().SpeciesFacts.Count;
individualCategories2 = new IndividualCategoryList();
individualCategories2.Add(individualCategories1[1]);
individualCategories2.Add(individualCategories1[2]);
GetDataSet().RemoveSelection(GetUserContext(), individualCategories2);
Assert.IsTrue(speciesFactCount > GetDataSet().SpeciesFacts.Count);
individualCategories2 = null;
GetDataSet().RemoveSelection(GetUserContext(), individualCategories2);
}
/// <summary>
/// Set individual categories for specified locale.
/// </summary>
/// <param name="individualCategories">Individual categories.</param>
/// <param name="locale">Locale.</param>
protected virtual void SetIndividualCategories(IndividualCategoryList individualCategories,
ILocale locale)
{
IndividualCategories[locale.ISOCode] = individualCategories;
}
/// <summary>
/// Convert a WebSpeciesFact instance into
/// an ISpeciesFact instance.
/// </summary>
/// <param name="webSpeciesFact">A WebSpeciesFact instance.</param>
/// <param name="factors">List of factors.</param>
/// <param name="individualCategories">List of individual categories.</param>
/// <param name="periods">List of periods.</param>
/// <returns>An ISpeciesFact instance.</returns>
private ISpeciesFact GetSpeciesFact(
WebSpeciesFact webSpeciesFact,
FactorList factors,
IndividualCategoryList individualCategories,
PeriodList periods)
{
IFactor factor;
IPeriod period;
ISpeciesFact speciesFact;
ITaxon host, taxon;
factor = factors.Get(webSpeciesFact.FactorId);
if (webSpeciesFact.IsHostSpecified)
{
host = new Data.Taxon();
host.Id = webSpeciesFact.HostId;
}
else
{
if (factor.IsTaxonomic)
{
host = new Data.Taxon {
Id = (int)TaxonId.Life
};
}
else
{
host = null;
}
}
if (webSpeciesFact.IsPeriodSpecified)
{
period = periods.Get(webSpeciesFact.PeriodId);
}
else
{
period = null;
}
taxon = new Data.Taxon();
taxon.Id = webSpeciesFact.TaxonId;
speciesFact = new SpeciesFact(
webSpeciesFact.Id,
taxon,
individualCategories.Get(webSpeciesFact.IndividualCategoryId),
factor,
host,
period,
webSpeciesFact.FieldValue1,
webSpeciesFact.IsFieldValue1Specified,
webSpeciesFact.FieldValue2,
webSpeciesFact.IsFieldValue2Specified,
webSpeciesFact.FieldValue3,
webSpeciesFact.IsFieldValue3Specified,
webSpeciesFact.FieldValue4,
webSpeciesFact.IsFieldValue4Specified,
webSpeciesFact.FieldValue5,
webSpeciesFact.IsFieldValue5Specified,
null,
null,
webSpeciesFact.ModifiedBy,
webSpeciesFact.ModifiedDate);
return(speciesFact);
}
/// <summary>
/// Convert a WebSpeciesFact instance into
/// an ISpeciesFact instance.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="webSpeciesFact">A WebSpeciesFact instance.</param>
/// <param name="factors">List of factors.</param>
/// <param name="individualCategories">List of individual categories.</param>
/// <param name="periods">List of periods.</param>
/// <param name="references">List of references.</param>
/// <param name="speciesFactQualities">List of species fact qualities.</param>
/// <param name="taxa">Taxa that are used in the species facts.</param>
/// <returns>An ISpeciesFact instance.</returns>
private ISpeciesFact GetSpeciesFact(IUserContext userContext,
WebSpeciesFact webSpeciesFact,
FactorList factors,
IndividualCategoryList individualCategories,
PeriodList periods,
ReferenceList references,
SpeciesFactQualityList speciesFactQualities,
TaxonList taxa)
{
IFactor factor;
IPeriod period;
ISpeciesFact speciesFact;
ITaxon host, taxon;
factor = factors.Get(webSpeciesFact.FactorId);
if (webSpeciesFact.IsHostSpecified)
{
#if EXAMINE_PROBLEM
if (!(taxa.Contains(webSpeciesFact.HostId)))
{
throw new Exception("Host with id = " + webSpeciesFact.HostId + " is not in taxon list." + webSpeciesFact.GetString());
}
#endif
host = taxa.Get(webSpeciesFact.HostId);
}
else
{
if (factor.IsTaxonomic)
{
host = CoreData.TaxonManager.GetTaxon(userContext, 0);
}
else
{
host = null;
}
}
if (webSpeciesFact.IsPeriodSpecified)
{
#if EXAMINE_PROBLEM
if (!(periods.Contains(webSpeciesFact.PeriodId)))
{
throw new Exception("Period with id = " + webSpeciesFact.PeriodId + " is not in period list." + webSpeciesFact.GetString());
}
#endif
period = periods.Get(webSpeciesFact.PeriodId);
}
else
{
period = null;
}
#if EXAMINE_PROBLEM
if (!(taxa.Contains(webSpeciesFact.TaxonId)))
{
throw new Exception("Taxon with id = " + webSpeciesFact.TaxonId + " is not in taxon list." + webSpeciesFact.GetString());
}
#endif
taxon = taxa.Get(webSpeciesFact.TaxonId);
#if EXAMINE_PROBLEM
if (!(individualCategories.Contains(webSpeciesFact.IndividualCategoryId)))
{
throw new Exception("Individual category with id = " + webSpeciesFact.IndividualCategoryId + " is not in individual category list." + webSpeciesFact.GetString());
}
if (!(speciesFactQualities.Contains(webSpeciesFact.QualityId)))
{
throw new Exception("Quality with id = " + webSpeciesFact.QualityId + " is not in quality list." + webSpeciesFact.GetString());
}
if (!(references.Contains(webSpeciesFact.ReferenceId)))
{
throw new Exception("Reference with id = " + webSpeciesFact.ReferenceId + " is not in reference list." + webSpeciesFact.GetString());
}
#endif
speciesFact = CoreData.SpeciesFactManager.GetSpeciesFact(userContext,
webSpeciesFact.Id,
taxon,
individualCategories.Get(webSpeciesFact.IndividualCategoryId),
factor,
host,
period,
webSpeciesFact.FieldValue1,
webSpeciesFact.IsFieldValue1Specified,
webSpeciesFact.FieldValue2,
webSpeciesFact.IsFieldValue2Specified,
webSpeciesFact.FieldValue3,
webSpeciesFact.IsFieldValue3Specified,
webSpeciesFact.FieldValue4,
webSpeciesFact.IsFieldValue4Specified,
webSpeciesFact.FieldValue5,
webSpeciesFact.IsFieldValue5Specified,
speciesFactQualities.Get(webSpeciesFact.QualityId),
references.Get(webSpeciesFact.ReferenceId),
webSpeciesFact.ModifiedBy,
webSpeciesFact.ModifiedDate);
return(speciesFact);
}
/// <summary>
/// Update information about which factors, hosts,
/// individual categories, periods, references and taxa
/// that are used in the species facts.
/// </summary>
/// <param name="userContext">
/// Information about the user that makes this method call.
/// </param>
/// <param name="selection">
/// Scope of the data set is defined by this
/// species fact data set selection.
/// </param>
/// <param name="speciesFacts">Species facts.</param>
private void UpdateScope(IUserContext userContext,
ISpeciesFactDataSetSelection selection,
SpeciesFactList speciesFacts)
{
Factors = new FactorList(true);
Factors.AddRange(selection.Factors);
Hosts = new TaxonList(true);
Hosts.AddRange(selection.Hosts);
IndividualCategories = new IndividualCategoryList(true);
IndividualCategories.AddRange(selection.IndividualCategories);
Periods = new PeriodList(true);
Periods.AddRange(selection.Periods);
References = new ReferenceList(true);
Taxa = new TaxonList(true);
Taxa.AddRange(selection.Taxa);
if (speciesFacts.IsNotEmpty())
{
foreach (ISpeciesFact speciesFact in speciesFacts)
{
Factors.Merge(speciesFact.Factor);
if (speciesFact.HasHost)
{
Hosts.Merge(speciesFact.Host);
}
IndividualCategories.Merge(speciesFact.IndividualCategory);
if (speciesFact.HasPeriod)
{
Periods.Merge(speciesFact.Period);
}
if (speciesFact.HasReference)
{
References.Merge(speciesFact.Reference);
}
Taxa.Merge(speciesFact.Taxon);
}
}
// Set default values if no values are entered.
if (Hosts.IsEmpty())
{
Hosts.Add(CoreData.TaxonManager.GetTaxon(userContext, TaxonId.Life));
}
if (IndividualCategories.IsEmpty())
{
IndividualCategories.Add(CoreData.FactorManager.GetDefaultIndividualCategory(userContext));
}
if (Periods.IsEmpty())
{
Periods.AddRange(CoreData.FactorManager.GetPeriods(userContext));
}
// Sort all lists.
Factors.Sort();
Hosts.Sort();
IndividualCategories.Sort();
Periods.Sort();
References.Sort();
Taxa.Sort();
}
/// <summary>
/// Method that returns a filtered version of this species fact list. The filtering is done on several parameters.
/// </summary>
/// <param name="individualCategories">Individual categories for the requested species facts.</param>
/// <param name="periods">Periods for the requested species facts.</param>
/// <param name="hosts">Hosts for the requested species facts.</param>
/// <param name="taxa">Taxa for the requested species facts.</param>
/// <param name="factors">Factors for the requested species facts.</param>
/// <returns>A species fact list.</returns>
public SpeciesFactList GetSpeciesFacts(IndividualCategoryList individualCategories,
PeriodList periods,
TaxonList hosts,
TaxonList taxa,
FactorList factors)
{
SpeciesFactList filteredList = new SpeciesFactList();
if (this.IsNotEmpty())
{
foreach (ISpeciesFact fact in this)
{
bool go = true;
if (fact.IndividualCategory != null)
{
if ((individualCategories != null) && (individualCategories.Count > 0))
{
if (!individualCategories.Exists(fact.IndividualCategory))
{
go = false;
}
}
}
if (go)
{
if (fact.Period != null)
{
if ((periods != null) && (periods.Count > 0))
{
if (!periods.Exists(fact.Period))
{
go = false;
}
}
}
}
if (go)
{
if (fact.Host != null)
{
// For the time being we only accept species facts that dont have a host.
go = false;
//if ((hosts != null) && (hosts.Count > 0))
//{
// if (!hosts.Exists(fact.Host))
// go = false;
//}
}
}
if (go)
{
if (fact.Taxon != null)
{
if ((taxa != null) && (taxa.Count > 0))
{
if (!taxa.Exists(fact.Taxon))
{
go = false;
}
}
}
}
if (go)
{
if (fact.Factor != null)
{
if ((factors != null) && (factors.Count > 0))
{
if (!factors.Exists(fact.Factor))
{
go = false;
}
}
}
}
if (go)
{
filteredList.Add(fact);
}
}
}
return(filteredList);
}
