public RParentChild( LinksDataSet dsLinks, LinksDataSet.tblRelatedStructureRow drLeft )
{
//ImportDataSet dsImport, , LinksDataSet.tblRelatedStructureRow drRight
if ( dsLinks == null ) throw new ArgumentNullException("dsLinks");
if ( drLeft == null ) throw new ArgumentNullException("drLeft");
if ( dsLinks.tblSubject.Count == 0 ) throw new InvalidOperationException("tblSubject must NOT be empty before assigning R values from it.");
_dsLinks = dsLinks;
_drLeft = drLeft;
_idRelatedLeft = _drLeft.ID;
_drBare1 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S1);
_drBare2 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S2);
Trace.Assert(_drBare1.Generation != _drBare2.Generation, "The generation should not be the same for a parent-child relationship.");
_multipleBirth = MultipleBirth.No;
_isMZ = Tristate.No;
//For IAssignPass1
_rImplicitPass1 = RCoefficients.ParentChild;
_rImplicit2004 = RCoefficients.ParentChild;
_rExplicitOldestSibVersion = null;
_rExplicitYoungestSibVersion = null;
_rExplicitPass1 = RCoefficients.ParentChild;
_rPass1 = RCoefficients.ParentChild;
//For IAssignPass2
_rImplicit = RCoefficients.ParentChild;
_rImplicitSubject = RCoefficients.ParentChild;
_rImplicitMother = RCoefficients.ParentChild;
_rExplicit = RCoefficients.ParentChild;
_rFull = RCoefficients.ParentChild;
_rPeek = RCoefficients.ParentChild;
}
public RGen2Cousins( LinksDataSet dsLinks, LinksDataSet.tblRelatedStructureRow drLeft )
{
//ImportDataSet dsImport, , LinksDataSet.tblRelatedStructureRow drRight
if ( dsLinks == null ) throw new ArgumentNullException("dsLinks");
if ( drLeft == null ) throw new ArgumentNullException("drLeft");
if ( dsLinks.tblSubject.Count == 0 ) throw new InvalidOperationException("tblSubject must NOT be empty before assigning R values from it.");
_dsLinks = dsLinks;
_idRelatedLeft = drLeft.ID;
_drBare1 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S1);
_drBare2 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S2);
Trace.Assert(_drBare1.Generation == (byte)Generation.Gen2, "The generation should be Gen2.");
Trace.Assert(_drBare2.Generation == (byte)Generation.Gen2, "The generation should be Gen2.");
_multipleBirth = MultipleBirth.No;
_isMZ = Tristate.No;
LinksDataSet.tblRelatedValuesRow drValuesOfGen1Housemates = Gen1HousematesValues(_drBare1.SubjectTag, _drBare2.SubjectTag);//RelatedValues.Retrieve(_dsLinks, _path,
//For IAssignPass1
if ( drValuesOfGen1Housemates.IsRImplicitPass1Null() ) _rImplicitPass1 = null;
else _rImplicitPass1 = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RImplicitPass1);
if ( drValuesOfGen1Housemates.IsRImplicit2004Null() ) _rImplicit2004 = null;
else _rImplicit2004 = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RImplicit2004);
_rExplicitOldestSibVersion = null;
_rExplicitYoungestSibVersion = null;
if ( drValuesOfGen1Housemates.IsRExplicitPass1Null() ) _rExplicitPass1 = null;
else _rExplicitPass1 = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RExplicitPass1);
if ( drValuesOfGen1Housemates.IsRPass1Null() ) _rPass1 = null;
else _rPass1 = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RPass1); ;
//For IAssignPass2
if ( drValuesOfGen1Housemates.IsRImplicitNull() ) _rImplicit = null;
else _rImplicit = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RImplicit);
if ( drValuesOfGen1Housemates.IsRImplicitSubjectNull() ) _rImplicitSubject = null;
else _rImplicitSubject = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RImplicitSubject);
if ( drValuesOfGen1Housemates.IsRImplicitMotherNull() ) _rImplicitMother = null;
else _rImplicitMother = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RImplicitMother);
if ( drValuesOfGen1Housemates.IsRExplicitNull() ) _rExplicit = null;
else _rExplicit = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RExplicit);
if ( drValuesOfGen1Housemates.IsRNull() ) _r= null;
else _r= (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.R);
if ( drValuesOfGen1Housemates.IsRFullNull() ) _rFull = null;
else _rFull = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RFull);
if ( drValuesOfGen1Housemates.IsRPeekNull() ) _rPeek = null;
else _rPeek = (float)(RCoefficients.ParentChild * RCoefficients.ParentChild * drValuesOfGen1Housemates.RPeek);
}
public override IDeepCopyable CopyTo(IDeepCopyable other)
{
var dest = other as Patient;
if (dest != null)
{
base.CopyTo(dest);
if (Identifier != null)
{
dest.Identifier = new List <Hl7.Fhir.Model.Identifier>(Identifier.DeepCopy());
}
if (Name != null)
{
dest.Name = new List <Hl7.Fhir.Model.HumanName>(Name.DeepCopy());
}
if (Telecom != null)
{
dest.Telecom = new List <Hl7.Fhir.Model.Contact>(Telecom.DeepCopy());
}
if (Gender != null)
{
dest.Gender = (Hl7.Fhir.Model.CodeableConcept)Gender.DeepCopy();
}
if (BirthDateElement != null)
{
dest.BirthDateElement = (Hl7.Fhir.Model.FhirDateTime)BirthDateElement.DeepCopy();
}
if (Deceased != null)
{
dest.Deceased = (Hl7.Fhir.Model.Element)Deceased.DeepCopy();
}
if (Address != null)
{
dest.Address = new List <Hl7.Fhir.Model.Address>(Address.DeepCopy());
}
if (MaritalStatus != null)
{
dest.MaritalStatus = (Hl7.Fhir.Model.CodeableConcept)MaritalStatus.DeepCopy();
}
if (MultipleBirth != null)
{
dest.MultipleBirth = (Hl7.Fhir.Model.Element)MultipleBirth.DeepCopy();
}
if (Photo != null)
{
dest.Photo = new List <Hl7.Fhir.Model.Attachment>(Photo.DeepCopy());
}
if (Contact != null)
{
dest.Contact = new List <Hl7.Fhir.Model.Patient.ContactComponent>(Contact.DeepCopy());
}
if (Animal != null)
{
dest.Animal = (Hl7.Fhir.Model.Patient.AnimalComponent)Animal.DeepCopy();
}
if (Communication != null)
{
dest.Communication = new List <Hl7.Fhir.Model.CodeableConcept>(Communication.DeepCopy());
}
if (CareProvider != null)
{
dest.CareProvider = new List <Hl7.Fhir.Model.ResourceReference>(CareProvider.DeepCopy());
}
if (ManagingOrganization != null)
{
dest.ManagingOrganization = (Hl7.Fhir.Model.ResourceReference)ManagingOrganization.DeepCopy();
}
if (Link != null)
{
dest.Link = new List <Hl7.Fhir.Model.Patient.PatientLinkComponent>(Link.DeepCopy());
}
if (ActiveElement != null)
{
dest.ActiveElement = (Hl7.Fhir.Model.FhirBoolean)ActiveElement.DeepCopy();
}
return(dest);
}
else
{
throw new ArgumentException("Can only copy to an object of the same type", "other");
}
}
private float? _rPass1 = float.NaN; // float.NaN;
#endregion Fields
#region Constructors
public RGen1Pass1( ImportDataSet dsImport, LinksDataSet dsLinks, LinksDataSet.tblRelatedStructureRow drLeft, LinksDataSet.tblRelatedStructureRow drRight )
{
if ( dsImport == null ) throw new ArgumentNullException("dsImport");
if ( dsLinks == null ) throw new ArgumentNullException("dsLinks");
if ( drLeft == null ) throw new ArgumentNullException("drLeft");
if ( drRight == null ) throw new ArgumentNullException("drRight");
if ( dsImport.tblLinks2004Gen1.Count == 0 ) throw new InvalidOperationException("tblLinks2004Gen1 must NOT be empty before assigning R values from it.");
if ( dsLinks.tblMzManual.Count == 0 ) throw new InvalidOperationException("tblMzManual must NOT be empty before assigning R values from it.");
if ( dsLinks.tblSubject.Count == 0 ) throw new InvalidOperationException("tblSubject must NOT be empty before assigning R values from it.");
if ( dsLinks.tblRosterGen1.Count == 0 ) throw new InvalidOperationException("tblRosterGen1 must NOT be empty before assigning R values from it.");
if ( dsLinks.tblMarkerGen1.Count == 0 ) throw new InvalidOperationException("tblMarkerGen2 must NOT be empty before assigning R values from it.");
if ( dsLinks.tblSubjectDetails.Count == 0 ) throw new InvalidOperationException("tblSubjectDetails must NOT be empty before assigning R values from it.");
_dsImport = dsImport;
_dsLinks = dsLinks;
_drLeft = drLeft;
_drRight = drRight;
_idRelatedLeft = _drLeft.ID;
_idRelatedRight = _drRight.ID;
_drSubjectDetails1 = _dsLinks.tblSubjectDetails.FindBySubjectTag(drLeft.SubjectTag_S1);
_drSubjectDetails2 = _dsLinks.tblSubjectDetails.FindBySubjectTag(drLeft.SubjectTag_S2);
_extendedID = _drLeft.tblSubjectRowByFK_tblRelatedStructure_tblSubject_Subject1.ExtendedID;
//LinksDataSet.tblRosterGen1Row drRoster = _dsLinks.tblRosterGen1.FindByRelatedID(drLeft.ID);
//Tristate rosterShareBiomom = (Tristate)drRoster.ShareBiomom;
//Tristate rosterShareBiodad = (Tristate)drRoster.ShareBiodad;
//if ( drRoster.IsRNull() ) _rRoster = null;
//else _rRoster = (float)drRoster.R;
if ( _drSubjectDetails1.BirthOrderInNls <= _drSubjectDetails2.BirthOrderInNls ) {//This is the way it usually is. Remember that twins were assigned tied birth orders
_idRelatedOlderAboutYounger = _idRelatedLeft;
_idRelatedYoungerAboutOlder = _idRelatedRight;
}
else if ( _drSubjectDetails1.BirthOrderInNls > _drSubjectDetails2.BirthOrderInNls ) {
_idRelatedOlderAboutYounger = _idRelatedRight;
_idRelatedYoungerAboutOlder = _idRelatedLeft;
}
_dtMarkersGen1 = MarkerGen1.PairRelevantMarkerRows(_idRelatedLeft, _idRelatedRight, _dsLinks, _extendedID);
LinksDataSet.tblMzManualRow drMz = Retrieve.MzManualRecord(_drLeft.SubjectTag_S1, _drLeft.SubjectTag_S2, _dsLinks);
if ( drMz == null ) {
_multipleBirth = MultipleBirth.No;
_isMZ = Tristate.No;
_isRelatedInMzManual = Tristate.DoNotKnow;
}
else {
_multipleBirth = (MultipleBirth)drMz.MultipleBirthIfSameSex;
_isMZ = (Tristate)drMz.IsMz;
if ( drMz.IsRelatedNull() ) _isRelatedInMzManual = Tristate.DoNotKnow;
else if ( drMz.Related ) _isRelatedInMzManual = Tristate.Yes;
else _isRelatedInMzManual = Tristate.No;
}
MarkerEvidence explicitBiomomFromOlder = ReduceShareBioparentToOne(MarkerType.ShareBiomom, ItemYears.Gen1ShareBioparent.Length, _idRelatedOlderAboutYounger);
MarkerEvidence explicitBiodadFromOlder = ReduceShareBioparentToOne(MarkerType.ShareBiodad, ItemYears.Gen1ShareBioparent.Length, _idRelatedOlderAboutYounger);
MarkerEvidence explicitBiomomFromYounger = ReduceShareBioparentToOne(MarkerType.ShareBiomom, ItemYears.Gen1ShareBioparent.Length, _idRelatedYoungerAboutOlder);
MarkerEvidence explicitBiodadFromYounger = ReduceShareBioparentToOne(MarkerType.ShareBiodad, ItemYears.Gen1ShareBioparent.Length, _idRelatedYoungerAboutOlder);
MarkerEvidence biomomInHH1979 = MarkerGen1.RetrieveParentMarkerMultiYear(_idRelatedOlderAboutYounger, MarkerType.Gen1BiomomInHH, 1979, Bioparent.Mom, _dtMarkersGen1);
MarkerEvidence biodadInHH1979 = MarkerGen1.RetrieveParentMarkerMultiYear(_idRelatedOlderAboutYounger, MarkerType.Gen1BiodadInHH, 1979, Bioparent.Dad, _dtMarkersGen1);
MarkerEvidence biomomDeathAge = MarkerGen1.RetrieveParentMarkerSingleYear(_idRelatedOlderAboutYounger, MarkerType.Gen1BiomomDeathAge, Bioparent.Mom, _dtMarkersGen1);
MarkerEvidence biodadDeathAge = MarkerGen1.RetrieveParentMarkerSingleYear(_idRelatedOlderAboutYounger, MarkerType.Gen1BiodadDeathAge, Bioparent.Dad, _dtMarkersGen1);
_explicitShareBiomomPass1 = CommonFunctions.TranslateEvidenceToTristate(explicitBiomomFromOlder, explicitBiomomFromYounger);
_explicitShareBiodadPass1 = CommonFunctions.TranslateEvidenceToTristate(explicitBiodadFromOlder, explicitBiodadFromYounger);
_implicitShareBiomomPass1 = ImplicitShareBioparent(inHH1979: biomomInHH1979, deathAge: biomomDeathAge);
_implicitShareBiodadPass1 = ImplicitShareBioparent(inHH1979: biodadInHH1979, deathAge: biodadDeathAge);
_shareBiomomPass1 = CommonFunctions.TakePriority(_explicitShareBiomomPass1, _implicitShareBiomomPass1);
_shareBiodadPass1 = CommonFunctions.TakePriority(_explicitShareBiodadPass1, _implicitShareBiodadPass1);
_rExplicitOldestSibVersion = CalculateRExplicitSingleSibVersion(explicitBiomomFromOlder, explicitBiodadFromOlder);
_rExplicitYoungestSibVersion = CalculateRExplicitSingleSibVersion(explicitBiomomFromYounger, explicitBiodadFromYounger);
_rExplicitPass1 = CommonFunctions.TranslateToR(shareBiomom: _explicitShareBiomomPass1, shareBiodad: _explicitShareBiodadPass1, mustDecide: false);
_rImplicitPass1 = CommonFunctions.TranslateToR(shareBiomom: _implicitShareBiomomPass1, shareBiodad: _implicitShareBiodadPass1, mustDecide: false);
_rImplicit2004 = RetrieveRImplicit2004();
_rPass1 = CalculateRFull(shareBiomom: _shareBiomomPass1, shareBiodad: _shareBiodadPass1,
multiple: _multipleBirth, isMZ: _isMZ, isRelatedInMZManual: _isRelatedInMzManual, idRelated: _idRelatedLeft, dtRoster: _dsLinks.tblRosterGen1);
}
public static float? CalculateRFull( Tristate shareBiomom, Tristate shareBiodad, MultipleBirth multiple, Tristate isMZ, Tristate isRelatedInMZManual, Int32 idRelated, LinksDataSet.tblRosterGen1DataTable dtRoster )
{
float? rRoster = CalculateRRoster(idRelated, dtRoster);
if ( isMZ == BaseAssembly.Tristate.Yes ) {
return RCoefficients.MzTrue;
}
else if ( isRelatedInMZManual == Tristate.No ) {
return RCoefficients.NotRelated; //Of the 21 Gen1 subjects in tblMZManual with Related=0, 17 ended up with R=0 (as of 11/9/2012). 1 was assigned R=.5; 3 were assigned R=NULL (which I want to override now here, looking at the DOB differences).
}
else if ( isMZ == BaseAssembly.Tristate.DoNotKnow && isRelatedInMZManual == Tristate.Yes ) {
Trace.Assert(multiple == MultipleBirth.Twin || multiple == MultipleBirth.Trip || multiple == MultipleBirth.TwinOrTrip, "To be assigned full sib, they've got to be assigned to be a twin/trip.");
return RCoefficients.MzAmbiguous;
}
else if ( multiple == MultipleBirth.Twin || multiple == MultipleBirth.Trip || multiple == MultipleBirth.TwinOrTrip ) {
return RCoefficients.SiblingFull;
}
else if ( rRoster.HasValue ) {
return rRoster;
}
else {
//The implicits & explicits were already combined to get the values of shareBiomom & shareBiodad.
return CommonFunctions.TranslateToR(shareBiomom: shareBiomom, shareBiodad: shareBiodad, mustDecide: false);
}
}
public RGen2Pass1( ImportDataSet dsImport, LinksDataSet dsLinks, LinksDataSet.tblRelatedStructureRow drLeft, LinksDataSet.tblRelatedStructureRow drRight )
{
if ( dsImport == null ) throw new ArgumentNullException("dsImport");
if ( dsLinks == null ) throw new ArgumentNullException("dsLinks");
if ( drLeft == null ) throw new ArgumentNullException("drLeft");
if ( drRight == null ) throw new ArgumentNullException("drRight");
if ( dsImport.tblLinks2004Gen2.Count == 0 ) throw new InvalidOperationException("tblLinks2004Gen2 must NOT be empty before assigning R values from it.");
if ( dsLinks.tblMzManual.Count == 0 ) throw new InvalidOperationException("tblMzManual must NOT be empty before assigning R values from it.");
if ( dsLinks.tblSubject.Count == 0 ) throw new InvalidOperationException("tblSubject must NOT be empty before assigning R values from it.");
if ( dsLinks.tblSubjectDetails.Count == 0 ) throw new InvalidOperationException("tblSubjectDetails must NOT be empty before assigning R values from it.");
if ( dsLinks.tblMarkerGen2.Count == 0 ) throw new InvalidOperationException("tblMarkerGen2 must NOT be empty before assigning R values from it.");
_dsImport = dsImport;
_dsLinks = dsLinks;
_drLeft = drLeft;
_drRight = drRight;
_idRelatedLeft = _drLeft.ID;
_idRelatedRight = _drRight.ID;
_drBare1 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S1);
_drBare2 = _dsLinks.tblSubject.FindBySubjectTag(drLeft.SubjectTag_S2);
_drSubjectDetails1 = _dsLinks.tblSubjectDetails.FindBySubjectTag(drLeft.SubjectTag_S1);
_drSubjectDetails2 = _dsLinks.tblSubjectDetails.FindBySubjectTag(drLeft.SubjectTag_S2);
_extendedID = _drLeft.tblSubjectRowByFK_tblRelatedStructure_tblSubject_Subject1.ExtendedID;
if ( _drSubjectDetails1.BirthOrderInNls <= _drSubjectDetails2.BirthOrderInNls ) {//This is the way it usually is. Recall twins were assigned tied birth orders
_idRelatedOlderAboutYounger = _idRelatedLeft;
_idRelatedYoungerAboutOlder = _idRelatedRight;
}
else if ( _drSubjectDetails1.BirthOrderInNls > _drSubjectDetails2.BirthOrderInNls ) {
_idRelatedOlderAboutYounger = _idRelatedRight;
_idRelatedYoungerAboutOlder = _idRelatedLeft;
}
_dtMarkersGen2 = MarkerGen2.PairRelevantMarkerRows(_idRelatedLeft, _idRelatedRight, _dsLinks, _extendedID);
LinksDataSet.tblMzManualRow drMzManual = Retrieve.MzManualRecord(_drBare1, _drBare2, _dsLinks);
if ( drMzManual == null ) {
_multipleBirth = MultipleBirth.No;
_isMZ = Tristate.No;
}
else {
_multipleBirth = (MultipleBirth)drMzManual.MultipleBirthIfSameSex;
_isMZ = (Tristate)drMzManual.IsMz;
}
MarkerEvidence babyDaddyDeathDate = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyDeathDate, _dtMarkersGen2);
MarkerEvidence babyDaddyAlive = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyAlive, _dtMarkersGen2);
MarkerEvidence babyDaddyInHH = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyInHH, _dtMarkersGen2);
MarkerEvidence babyDaddyLeftHHDate = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyLeftHHDate, _dtMarkersGen2);
MarkerEvidence babyDaddyDistanceFromHH = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyDistanceFromHH, _dtMarkersGen2);
MarkerEvidence babyDaddyAsthma = MarkerGen2.RetrieveBiodadMarkerFromGen1(_idRelatedOlderAboutYounger, MarkerType.BabyDaddyAsthma, _dtMarkersGen2);
_rImplicitPass1 = CalculateRImplicitPass1(babyDaddyDeathDate, babyDaddyAlive, babyDaddyInHH, babyDaddyLeftHHDate, babyDaddyDistanceFromHH, babyDaddyAsthma);
//_rImplicit not set;
_rImplicit2004 = RetrieveRImplicit2004();
_rExplicitOldestSibVersion = CalculateRExplicitOldestSibVersion();
_rExplicitYoungestSibVersion = CalculateRExplicitYoungestSibVersion();
_rExplicitPass1 = CalculateRExplicitPass1(_isMZ, _multipleBirth);
//_rExplicit not set;
_rPass1 = CalculateRPass1();
//_r not set;
//_rPeek not set;
}
private float? CalculateRExplicitPass1( Tristate isMZ, MultipleBirth multipleBirth )
{
float? rExplicitPreTwin = null;
if ( !RExplicitOldestSibVersion.HasValue && !RExplicitYoungestSibVersion.HasValue )
rExplicitPreTwin = null;
else if ( !RExplicitOldestSibVersion.HasValue )
rExplicitPreTwin = RExplicitYoungestSibVersion.Value;
else if ( !RExplicitYoungestSibVersion.HasValue )
rExplicitPreTwin = RExplicitOldestSibVersion.Value;
else if ( RExplicitOldestSibVersion.Value == RExplicitYoungestSibVersion.Value )
rExplicitPreTwin = RExplicitOldestSibVersion.Value;
else if ( RExplicitOldestSibVersion.Value == RCoefficients.SiblingAmbiguous )
rExplicitPreTwin = RExplicitYoungestSibVersion.Value;
else if ( RExplicitYoungestSibVersion.Value == RCoefficients.SiblingAmbiguous )
rExplicitPreTwin = RExplicitOldestSibVersion.Value;
else if ( RExplicitOldestSibVersion.Value == RCoefficients.SiblingFull && RExplicitYoungestSibVersion.Value == RCoefficients.SiblingHalf )
rExplicitPreTwin = RCoefficients.SiblingAmbiguous;
else if ( RExplicitYoungestSibVersion.Value == RCoefficients.SiblingFull && RExplicitOldestSibVersion.Value == RCoefficients.SiblingHalf )
rExplicitPreTwin = RCoefficients.SiblingAmbiguous;
else
throw new InvalidOperationException("All condition should have been caught.");
return ExplicitAgreementWithTwins(isMZ, multipleBirth, rExplicitPreTwin);
//return rExplicitPreTwin;
}
internal static float? ExplicitAgreementWithTwins( Tristate isMz, MultipleBirth multipleBirth, float? newRExplicit )
{
if ( !newRExplicit.HasValue )
return null;
else if ( isMz == Tristate.Yes ) {
Trace.Assert(newRExplicit >= RCoefficients.SiblingFull, "If the pair has been identified as MZ, their RExplicit should be >= .5.");
return RCoefficients.MzTrue;
}
else if ( isMz == Tristate.DoNotKnow ) {
Trace.Assert(newRExplicit >= RCoefficients.SiblingAmbiguous, "If the pair has been identified as an ambiguous MZ, their RExplicit should be >= .5.");
return RCoefficients.MzAmbiguous;
}
else if ( multipleBirth == MultipleBirth.Trip || multipleBirth == MultipleBirth.Twin || multipleBirth == MultipleBirth.TwinOrTrip ) {
Trace.Assert(newRExplicit >= RCoefficients.SiblingFull, "If the pair has been identified as Twin/Trip, their RExplicit should be >= .5.");
return newRExplicit;
}
else {
return newRExplicit;
}
}
public override ErrorList Validate()
{
var result = new ErrorList();
result.AddRange(base.Validate());
if (Identifier != null)
{
Identifier.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Name != null)
{
Name.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Telecom != null)
{
Telecom.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Gender != null)
{
result.AddRange(Gender.Validate());
}
if (BirthDateElement != null)
{
result.AddRange(BirthDateElement.Validate());
}
if (Deceased != null)
{
result.AddRange(Deceased.Validate());
}
if (Address != null)
{
Address.ForEach(elem => result.AddRange(elem.Validate()));
}
if (MaritalStatus != null)
{
result.AddRange(MaritalStatus.Validate());
}
if (MultipleBirth != null)
{
result.AddRange(MultipleBirth.Validate());
}
if (Photo != null)
{
Photo.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Contact != null)
{
Contact.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Animal != null)
{
result.AddRange(Animal.Validate());
}
if (Communication != null)
{
Communication.ForEach(elem => result.AddRange(elem.Validate()));
}
if (Provider != null)
{
result.AddRange(Provider.Validate());
}
if (Link != null)
{
Link.ForEach(elem => result.AddRange(elem.Validate()));
}
if (ActiveElement != null)
{
result.AddRange(ActiveElement.Validate());
}
return(result);
}
public Patient CreateFHIRPatientProfile()
{
Patient pt;
try
{
/*
*
* _patientFHIRProfile.NoIDHubPassword = password;
* _patientFHIRProfile.NoIDHubName = patientHub;
* _patientFHIRProfile.GenderChangeFlag = genderChangeFlag;
*
*/
pt = new Patient();
BiometricsCaptured = GetBiometricsCaptured();
// Add message status New, Return or Update
Meta meta = new Meta();
meta.Extension.Add(FHIRUtilities.MessageTypeExtension(NoIDStatus, NoIDType, CheckinDateTime));
meta.Extension.Add(FHIRUtilities.ClinicLocationExtension(ClinicArea, DevicePhysicalLocation));
if (FingerPrintMinutiasList.Count > 0)
{
meta.Extension.Add(FHIRUtilities.CaptureSummaryExtension(BiometricsCaptured,
FingerPrintMinutiasList[0].DeviceName,
FingerPrintMinutiasList[0].OriginalDpi,
FingerPrintMinutiasList[0].OriginalHeight,
FingerPrintMinutiasList[0].OriginalWidth)
);
}
meta.Extension.Add(FHIRUtilities.NoIDHubInfo(NoIDHubName, NoIDHubPassword));
if (GenderChangeFlag.ToLower().Contains("yes") == true || MultipleBirth.ToLower().Contains("no") == false)
{
meta.Extension.Add(FHIRUtilities.GenderAndTwinInfo(GenderChangeFlag, MultipleBirth));
}
pt.Meta = meta;
//TODO: Move fingerprint minutias to Identifier.Extension
Identifier idSession = new Identifier();
idSession.System = ServerName + "/fhir/SessionID";
if (SessionID == null || SessionID.Length == 0)
{
NewSession();
}
idSession.Value = SessionID;
pt.Identifier.Add(idSession);
if (BiometricExceptionMissingReason.Length > 0)
{
if (SecretQuestion1.Length > 0 && SecretAnswer1.Length > 0 && SecretQuestion2.Length > 0 && SecretAnswer2.Length > 0)
{
Identifier idBiometricException = new Identifier();
idBiometricException.System = ServerName + "/fhir/BiometricException";
idBiometricException.Value = "Biometric Exception Pathway";
Extension extBiometricException;
extBiometricException = FHIRUtilities.BiometricException(
BiometricExceptionMissingReason,
SecretQuestion1, SecretAnswer1,
SecretQuestion2, SecretAnswer2
);
idBiometricException.Extension.Add(extBiometricException);
pt.Identifier.Add(idBiometricException);
}
{
//throw an error back to the page.
}
}
ResourceReference managingOrganization = new ResourceReference(OrganizationName, DomainName);
pt.ManagingOrganization = managingOrganization;
// Add patient demographics
pt.Language = Language;
pt.BirthDate = BirthDate;
if (Gender.ToLower() == "f")
{
pt.Gender = AdministrativeGender.Female;
}
else if (Gender.ToLower() == "m")
{
pt.Gender = AdministrativeGender.Male;
}
else
{
pt.Gender = AdministrativeGender.Unknown;
}
if (!(MultipleBirth == null) && MultipleBirth.Length > 0)
{
if (MultipleBirth.ToLower().Substring(0, 2) == "no")
{
pt.MultipleBirth = new FhirString("No");
}
else if (MultipleBirth.ToLower() == "yes")
{
pt.MultipleBirth = new FhirString("Yes");
}
}
// Add patient name
HumanName ptName = new HumanName();
ptName.Given = new string[] { FirstName, MiddleName };
ptName.Family = LastName;
pt.Name = new List <HumanName> {
ptName
};
if (StreetAddress.Length > 0 || City.Length > 0 || State.Length > 0 || PostalCode.Length > 0)
{
Address address = new Address(); // Add patient address
address.Line = new string[] { StreetAddress, StreetAddress2 };
address.City = City;
address.State = State;
address.Country = Country;
address.PostalCode = PostalCode;
pt.Address.Add(address);
}
// Add patient contact information (phone numbers and email)
// TODO: make sure email and phone are valid.
// Validate phone with UI.
Patient.ContactComponent contact = new Patient.ContactComponent();
bool addContact = false;
if ((EmailAddress != null) && EmailAddress.Length > 0)
{
ContactPoint emailAddress = new ContactPoint(ContactPoint.ContactPointSystem.Email, ContactPoint.ContactPointUse.Home, EmailAddress);
contact.Telecom.Add(emailAddress);
addContact = true;
}
if ((PhoneHome != null) && PhoneHome.Length > 0)
{
ContactPoint phoneHome = new ContactPoint(ContactPoint.ContactPointSystem.Phone, ContactPoint.ContactPointUse.Home, PhoneHome);
contact.Telecom.Add(phoneHome);
addContact = true;
}
if ((PhoneCell != null) && PhoneCell.Length > 0)
{
ContactPoint phoneCell = new ContactPoint(ContactPoint.ContactPointSystem.Phone, ContactPoint.ContactPointUse.Mobile, PhoneCell);
contact.Telecom.Add(phoneCell);
addContact = true;
}
if ((PhoneWork != null) && PhoneWork.Length > 0)
{
ContactPoint phoneWork = new ContactPoint(ContactPoint.ContactPointSystem.Phone, ContactPoint.ContactPointUse.Work, PhoneWork);
contact.Telecom.Add(phoneWork);
addContact = true;
}
if (addContact)
{
pt.Contact.Add(contact);
}
//TODO: Change location of minutias in Patient FHIR profile from attached Photo.Extension to Identity.Extension
foreach (FingerPrintMinutias minutias in FingerPrintMinutiasList)
{
Attachment attach = new Attachment();
Media fingerprintMedia = FingerPrintFHIRMedia(minutias, minutias.DeviceName, minutias.OriginalDpi, minutias.OriginalHeight, minutias.OriginalWidth);
byte[] mediaBytes = FhirSerializer.SerializeToJsonBytes(fingerprintMedia, summary: SummaryType.Data);
attach.Data = mediaBytes;
pt.Photo.Add(attach);
}
}
catch (Exception ex)
{
BaseException = new Exception("Error in PatientProfile::CreateFHIRProfile(). Failed to create a new FHIR profile: " + ex.Message);
return(null);
}
return(pt);
}