/// <summary>
/// Get included objects
/// </summary>
protected override IEnumerable <Resource> GetReverseIncludes(Core.Model.Roles.Patient resource, IEnumerable <IncludeInstruction> reverseIncludePaths)
{
return(reverseIncludePaths.SelectMany(includeInstruction =>
{
switch (includeInstruction.Type)
{
case ResourceType.RelatedPerson:
// Load all related persons and convert them
var rpHandler = FhirResourceHandlerUtil.GetMappersFor(ResourceType.RelatedPerson).FirstOrDefault();
return resource.LoadCollection(o => o.Relationships)
.Where(o => o.ClassificationKey != RelationshipClassKeys.ContainedObjectLink &&
o.RelationshipRoleKey == null &&
this.GetRelatedPersonConceptUuids().Contains(o.RelationshipTypeKey.Value))
.Select(o => rpHandler.MapToFhir(o));
default:
this.m_tracer.TraceError($"{includeInstruction.Type} is not supported reverse include");
throw new InvalidOperationException(this.m_localizationService.GetString("error.type.NotSupportedException.userMessage"));
}
}));
}
/// <summary>
/// Map a patient object to FHIR.
/// </summary>
/// <param name="model">The patient to map to FHIR</param>
/// <returns>Returns the mapped FHIR resource.</returns>
protected override Patient MapToFhir(Core.Model.Roles.Patient model)
{
// If the model is being constructed as part of a bundle, then the caller
// should have included the bundle so we can add any related resources
var partOfBundle = model.GetAnnotations <Bundle>().FirstOrDefault();
var retVal = DataTypeConverter.CreateResource <Patient>(model);
retVal.Active = StatusKeys.ActiveStates.Contains(model.StatusConceptKey.Value);
retVal.Address = model.GetAddresses().Select(DataTypeConverter.ToFhirAddress).ToList();
if (model.DateOfBirth.HasValue)
{
switch (model.DateOfBirthPrecision.GetValueOrDefault())
{
case DatePrecision.Day:
retVal.BirthDate = model.DateOfBirth.Value.ToString("yyyy-MM-dd");
break;
case DatePrecision.Month:
retVal.BirthDate = model.DateOfBirth.Value.ToString("yyyy-MM");
break;
case DatePrecision.Year:
retVal.BirthDate = model.DateOfBirth.Value.ToString("yyyy");
break;
}
}
// Deceased precision
if (model.DeceasedDate.HasValue)
{
if (model.DeceasedDate == DateTime.MinValue)
{
retVal.Deceased = new FhirBoolean(true);
}
else
{
switch (model.DeceasedDatePrecision)
{
case DatePrecision.Day:
retVal.Deceased = new FhirDateTime(model.DeceasedDate.Value.Year, model.DeceasedDate.Value.Month, model.DeceasedDate.Value.Day);
break;
case DatePrecision.Month:
retVal.Deceased = new FhirDateTime(model.DeceasedDate.Value.Year, model.DeceasedDate.Value.Month);
break;
case DatePrecision.Year:
retVal.Deceased = new FhirDateTime(model.DeceasedDate.Value.Year);
break;
default:
retVal.Deceased = DataTypeConverter.ToFhirDateTime(model.DeceasedDate);
break;
}
}
}
if (model.GenderConceptKey.HasValue)
{
retVal.Gender = DataTypeConverter.ToFhirEnumeration <AdministrativeGender>(model.GenderConceptKey, "http://hl7.org/fhir/administrative-gender", true);
}
retVal.Identifier = model.Identifiers?.Select(DataTypeConverter.ToFhirIdentifier).ToList();
retVal.MultipleBirth = model.MultipleBirthOrder == 0 ? (DataType) new FhirBoolean(true) : model.MultipleBirthOrder.HasValue ? new Integer(model.MultipleBirthOrder.Value) : null;
retVal.Name = model.GetNames().Select(DataTypeConverter.ToFhirHumanName).ToList();
retVal.Telecom = model.GetTelecoms().Select(DataTypeConverter.ToFhirTelecom).ToList();
retVal.Communication = model.GetPersonLanguages().Select(DataTypeConverter.ToFhirCommunicationComponent).ToList();
foreach (var rel in model.GetRelationships().Where(o => !o.InversionIndicator))
{
if (rel.RelationshipTypeKey == EntityRelationshipTypeKeys.Contact)
{
var relEntity = rel.LoadProperty(o => o.TargetEntity);
if (relEntity is Core.Model.Entities.Person person)
{
var contact = new Patient.ContactComponent()
{
ElementId = $"{person.Key}",
Address = DataTypeConverter.ToFhirAddress(person.GetAddresses().FirstOrDefault()),
Relationship = new List <CodeableConcept>()
{
DataTypeConverter.ToFhirCodeableConcept(rel.RelationshipRoleKey, "http://terminology.hl7.org/CodeSystem/v2-0131"),
DataTypeConverter.ToFhirCodeableConcept(rel.RelationshipTypeKey, "http://terminology.hl7.org/CodeSystem/v2-0131")
}.OfType <CodeableConcept>().ToList(),
Name = DataTypeConverter.ToFhirHumanName(person.GetNames().FirstOrDefault()),
// TODO: Gender
Gender = DataTypeConverter.ToFhirEnumeration <AdministrativeGender>(person.GenderConceptKey, "http://hl7.org/fhir/administrative-gender"),
Telecom = person.GetTelecoms().Select(t => DataTypeConverter.ToFhirTelecom(t)).ToList()
};
var scoper = person.LoadCollection(o => o.Relationships).FirstOrDefault(o => o.RelationshipTypeKey == EntityRelationshipTypeKeys.Scoper);
if (scoper != null)
{
contact.Organization = DataTypeConverter.CreateNonVersionedReference <Hl7.Fhir.Model.Organization>(scoper.LoadProperty(o => o.TargetEntity));
}
DataTypeConverter.AddExtensions(person, contact);
retVal.Contact.Add(contact);
}
else if (relEntity is Core.Model.Entities.Organization org) // it *IS* an organization
{
var contact = new Patient.ContactComponent()
{
ElementId = $"{org.Key}",
Relationship = new List <CodeableConcept>()
{
DataTypeConverter.ToFhirCodeableConcept(rel.RelationshipRoleKey, "http://terminology.hl7.org/CodeSystem/v2-0131"),
DataTypeConverter.ToFhirCodeableConcept(rel.RelationshipTypeKey, "http://terminology.hl7.org/CodeSystem/v2-0131")
}.OfType <CodeableConcept>().ToList(),
Organization = DataTypeConverter.CreateNonVersionedReference <Hl7.Fhir.Model.Organization>(org)
};
retVal.Contact.Add(contact);
}
}
else if (rel.RelationshipTypeKey == EntityRelationshipTypeKeys.Scoper)
{
var scoper = rel.LoadProperty(o => o.TargetEntity);
retVal.ManagingOrganization = DataTypeConverter.CreateNonVersionedReference <Hl7.Fhir.Model.Organization>(scoper);
// If this is part of a bundle, include it
partOfBundle?.Entry.Add(new Bundle.EntryComponent
{
FullUrl = $"{MessageUtil.GetBaseUri()}/Organization/{scoper.Key}",
Resource = FhirResourceHandlerUtil.GetMapperForInstance(scoper).MapToFhir(scoper)
});
}
else if (rel.RelationshipTypeKey == EntityRelationshipTypeKeys.HealthcareProvider)
{
var practitioner = rel.LoadProperty(o => o.TargetEntity);
retVal.GeneralPractitioner.Add(DataTypeConverter.CreateVersionedReference <Practitioner>(practitioner));
// If this is part of a bundle, include it
partOfBundle?.Entry.Add(new Bundle.EntryComponent
{
FullUrl = $"{MessageUtil.GetBaseUri()}/Practitioner/{practitioner.Key}",
Resource = FhirResourceHandlerUtil.GetMapperForInstance(practitioner).MapToFhir(practitioner)
});
}
else if (rel.RelationshipTypeKey == EntityRelationshipTypeKeys.Replaces)
{
retVal.Link.Add(this.CreateLink <Patient>(rel.TargetEntityKey.Value, Patient.LinkType.Replaces));
}
else if (rel.RelationshipTypeKey == EntityRelationshipTypeKeys.Duplicate)
{
retVal.Link.Add(this.CreateLink <Patient>(rel.TargetEntityKey.Value, Patient.LinkType.Seealso));
}
else if (rel.RelationshipTypeKey == MDM_MASTER_LINK) // HACK: MDM Master Record
{
if (rel.SourceEntityKey.HasValue && rel.SourceEntityKey != model.Key)
{
retVal.Link.Add(this.CreateLink <Patient>(rel.SourceEntityKey.Value, Patient.LinkType.Seealso));
}
else // Is a local
{
retVal.Link.Add(this.CreateLink <Patient>(rel.TargetEntityKey.Value, Patient.LinkType.Refer));
}
}
else if (rel.ClassificationKey == EntityRelationshipTypeKeys.EquivalentEntity)
{
retVal.Link.Add(this.CreateLink <Patient>(rel.TargetEntityKey.Value, Patient.LinkType.Refer));
}
else if (partOfBundle != null) // This is part of a bundle and we need to include it
{
// HACK: This piece of code is used to add any RelatedPersons to the container bundle if it is part of a bundle
if (this.GetRelatedPersonConceptUuids().Contains(rel.RelationshipTypeKey.Value))
{
var relative = FhirResourceHandlerUtil.GetMapperForInstance(rel).MapToFhir(rel);
partOfBundle.Entry.Add(new Bundle.EntryComponent()
{
FullUrl = $"{MessageUtil.GetBaseUri()}/RelatedPerson/{rel.Key}",
Resource = relative
});
}
}
}
// Reverse relationships of family member?
var uuids = model.Relationships.Where(r => r.RelationshipTypeKey == MDM_MASTER_LINK).Select(r => r.SourceEntityKey).Union(new Guid?[] { model.Key }).ToArray();
var familyMemberConcepts = this.GetFamilyMemberUuids();
var reverseRelationships = this.m_erRepository.Find(o => uuids.Contains(o.TargetEntityKey) && familyMemberConcepts.Contains(o.RelationshipTypeKey.Value) && o.ObsoleteVersionSequenceId == null);
foreach (var rrv in reverseRelationships)
{
retVal.Link.Add(new Patient.LinkComponent
{
Type = Patient.LinkType.Seealso,
Other = DataTypeConverter.CreateNonVersionedReference <RelatedPerson>(rrv)
});
// If this is part of a bundle, include it
partOfBundle?.Entry.Add(new Bundle.EntryComponent
{
FullUrl = $"{MessageUtil.GetBaseUri()}/RelatedPerson/{rrv.Key}",
Resource = FhirResourceHandlerUtil.GetMappersFor(ResourceType.RelatedPerson).First().MapToFhir(rrv)
});
}
// Was this record replaced?
if (!retVal.Active.GetValueOrDefault())
{
var replacedRelationships = this.m_erRepository.Find(o => uuids.Contains(o.TargetEntityKey) && o.RelationshipTypeKey == EntityRelationshipTypeKeys.Replaces && o.ObsoleteVersionSequenceId == null);
foreach (var repl in replacedRelationships)
{
retVal.Link.Add(new Patient.LinkComponent()
{
Type = Patient.LinkType.ReplacedBy,
Other = DataTypeConverter.CreateNonVersionedReference <Patient>(repl.LoadProperty(o => o.SourceEntity)),
});
}
}
var photo = model.LoadCollection(o => o.Extensions).FirstOrDefault(o => o.ExtensionTypeKey == ExtensionTypeKeys.JpegPhotoExtension);
if (photo != null)
{
retVal.Photo = new List <Attachment>
{
new Attachment
{
ContentType = "image/jpg",
Data = photo.ExtensionValueXml
}
};
}
return(retVal);
}
/// <summary>
/// Get included objects
/// </summary>
protected override IEnumerable <Resource> GetIncludes(Core.Model.Roles.Patient resource, IEnumerable <IncludeInstruction> includePaths)
{
return(includePaths.SelectMany(includeInstruction =>
{
switch (includeInstruction.Type)
{
case ResourceType.Practitioner:
{
var rpHandler = FhirResourceHandlerUtil.GetMappersFor(ResourceType.Practitioner).FirstOrDefault();
switch (includeInstruction.JoinPath)
{
case "generalPractitioner":
return resource.LoadCollection(o => o.Relationships)
.Where(o => o.ClassificationKey != RelationshipClassKeys.ContainedObjectLink &&
o.RelationshipTypeKey == EntityRelationshipTypeKeys.HealthcareProvider &&
o.LoadProperty(r => r.TargetEntity) is Core.Model.Roles.Provider)
.Select(o => rpHandler.MapToFhir(o.TargetEntity));
default:
this.m_tracer.TraceError($"Cannot determine how to include {includeInstruction}");
throw new InvalidOperationException(this.m_localizationService.FormatString("error.type.InvalidOperation.cannotDetermine", new
{
param = includeInstruction
}));
}
}
case ResourceType.Organization:
{
// Load all related persons and convert them
var rpHandler = FhirResourceHandlerUtil.GetMappersFor(ResourceType.Organization).FirstOrDefault();
switch (includeInstruction.JoinPath)
{
case "managingOrganization":
return resource.LoadCollection(o => o.Relationships)
.Where(o => o.ClassificationKey != RelationshipClassKeys.ContainedObjectLink &&
o.RelationshipTypeKey == EntityRelationshipTypeKeys.Scoper &&
o.LoadProperty(r => r.TargetEntity) is Core.Model.Entities.Organization)
.Select(o => rpHandler.MapToFhir(o.TargetEntity));
case "generalPractitioner":
return resource.LoadCollection(o => o.Relationships)
.Where(o => o.ClassificationKey != RelationshipClassKeys.ContainedObjectLink &&
o.RelationshipTypeKey == EntityRelationshipTypeKeys.HealthcareProvider &&
o.LoadProperty(r => r.TargetEntity) is Core.Model.Entities.Organization)
.Select(o => rpHandler.MapToFhir(o.TargetEntity));
default:
this.m_tracer.TraceError($"Cannot determine how to include {includeInstruction}");
throw new InvalidOperationException(this.m_localizationService.FormatString("error.type.InvalidOperation.cannotDetermine", new
{
param = includeInstruction
}));
}
}
default:
this.m_tracer.TraceError($"{includeInstruction.Type} is not supported reverse include");
throw new InvalidOperationException(this.m_localizationService.GetString("error.type.NotSupportedException.userMessage"));
}
}));
}
/// <summary>
/// Maps a FHIR patient resource to an HDSI patient.
/// </summary>
/// <param name="resource">The resource.</param>
/// <returns>Returns the mapped model.</returns>
protected override Core.Model.Roles.Patient MapToModel(Patient resource)
{
Core.Model.Roles.Patient patient = null;
// Attempt to XRef
if (Guid.TryParse(resource.Id, out Guid key))
{
patient = this.m_repository.Get(key);
// Patient doesn't exist?
if (patient == null)
{
patient = new Core.Model.Roles.Patient
{
Key = key
};
}
}
else if (resource.Identifier.Any())
{
foreach (var ii in resource.Identifier.Select(DataTypeConverter.ToEntityIdentifier))
{
if (ii.LoadProperty(o => o.Authority).IsUnique)
{
patient = this.m_repository.Find(o => o.Identifiers.Where(i => i.AuthorityKey == ii.AuthorityKey).Any(i => i.Value == ii.Value)).FirstOrDefault();
}
if (patient != null)
{
break;
}
}
if (patient == null)
{
patient = new Core.Model.Roles.Patient
{
Key = Guid.NewGuid()
};
}
}
else
{
patient = new Core.Model.Roles.Patient
{
Key = Guid.NewGuid()
};
}
patient.Addresses = resource.Address.Select(DataTypeConverter.ToEntityAddress).ToList();
patient.CreationTime = DateTimeOffset.Now;
patient.GenderConceptKey = resource.Gender == null ? null : DataTypeConverter.ToConcept(new Coding("http://hl7.org/fhir/administrative-gender", Hl7.Fhir.Utility.EnumUtility.GetLiteral(resource.Gender)))?.Key;
patient.Identifiers = resource.Identifier.Select(DataTypeConverter.ToEntityIdentifier).ToList();
patient.LanguageCommunication = resource.Communication.Select(DataTypeConverter.ToLanguageCommunication).ToList();
patient.Names = resource.Name.Select(DataTypeConverter.ToEntityName).ToList();
patient.StatusConceptKey = resource.Active == null || resource.Active == true ? StatusKeys.Active : StatusKeys.Inactive;
patient.Telecoms = resource.Telecom.Select(DataTypeConverter.ToEntityTelecomAddress).OfType <EntityTelecomAddress>().ToList();
patient.Relationships = resource.Contact.Select(r => DataTypeConverter.ToEntityRelationship(r, resource)).ToList();
patient.Extensions = resource.Extension.Select(o => DataTypeConverter.ToEntityExtension(o, patient)).ToList();
patient.DateOfBirth = DataTypeConverter.ToDateTimeOffset(resource.BirthDate, out var dateOfBirthPrecision)?.DateTime;
// TODO: fix
// HACK: the date of birth precision CK only allows "Y", "M", or "D" for the precision value
patient.DateOfBirthPrecision = dateOfBirthPrecision == DatePrecision.Full ? DatePrecision.Day : dateOfBirthPrecision;
switch (resource.Deceased)
{
case FhirDateTime dtValue when !String.IsNullOrEmpty(dtValue.Value):
patient.DeceasedDate = DataTypeConverter.ToDateTimeOffset(dtValue.Value, out var datePrecision)?.DateTime;
// TODO: fix
// HACK: the deceased date precision CK only allows "Y", "M", or "D" for the precision value
patient.DeceasedDatePrecision = datePrecision == DatePrecision.Full ? DatePrecision.Day : datePrecision;
break;
case FhirBoolean boolValue when boolValue.Value.GetValueOrDefault():
// we don't have a field for "deceased indicator" to say that the patient is dead, but we don't know that actual date/time of death
// should find a better way to do this
patient.DeceasedDate = DateTime.MinValue;
patient.DeceasedDatePrecision = DatePrecision.Year;
break;
}
switch (resource.MultipleBirth)
{
case FhirBoolean boolBirth when boolBirth.Value.GetValueOrDefault():
patient.MultipleBirthOrder = 0;
break;
case Integer intBirth:
patient.MultipleBirthOrder = intBirth.Value;
break;
}
if (resource.GeneralPractitioner != null)
{
patient.Relationships.AddRange(resource.GeneralPractitioner.Select(r =>
{
var referenceKey = DataTypeConverter.ResolveEntity <Core.Model.Roles.Provider>(r, resource) as Entity ?? DataTypeConverter.ResolveEntity <Core.Model.Entities.Organization>(r, resource);
if (referenceKey == null)
{
this.m_tracer.TraceError("Can't locate a registered general practitioner");
throw new KeyNotFoundException(m_localizationService.FormatString("error.type.KeyNotFoundException.cannotLocateRegistered", new
{
param = "general practitioner"
}));
}
return(new EntityRelationship(EntityRelationshipTypeKeys.HealthcareProvider, referenceKey));
}));
}
if (resource.ManagingOrganization != null)
{
var referenceKey = DataTypeConverter.ResolveEntity <Core.Model.Entities.Organization>(resource.ManagingOrganization, resource);
if (referenceKey == null)
{
this.m_tracer.TraceError("Can't locate a registered managing organization");
throw new KeyNotFoundException(m_localizationService.FormatString("error.type.KeyNotFoundException.cannotLocateRegistered", new
{
param = "managing organization"
}));
}
patient.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.Scoper, referenceKey));
}
// Process contained related persons
foreach (var itm in resource.Contained.OfType <RelatedPerson>())
{
var er = FhirResourceHandlerUtil.GetMappersFor(ResourceType.RelatedPerson).First().MapToModel(itm) as Core.Model.Entities.EntityRelationship;
// Relationship bindings
er.ClassificationKey = RelationshipClassKeys.ContainedObjectLink;
er.SourceEntityKey = patient.Key;
// Now add rels to me
patient.Relationships.Add(er);
}
// Links
foreach (var lnk in resource.Link)
{
switch (lnk.Type.Value)
{
case Patient.LinkType.Replaces:
{
// Find the victim
var replacee = DataTypeConverter.ResolveEntity <Core.Model.Roles.Patient>(lnk.Other, resource);
if (replacee == null)
{
this.m_tracer.TraceError($"Cannot locate patient referenced by {lnk.Type} relationship");
throw new KeyNotFoundException(m_localizationService.FormatString("error.messaging.fhir.patientResource.cannotLocatePatient", new
{
param = lnk.Type
}));
}
replacee.StatusConceptKey = StatusKeys.Obsolete;
patient.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.Replaces, replacee));
break;
}
case Patient.LinkType.ReplacedBy:
{
// Find the new
var replacer = DataTypeConverter.ResolveEntity <Core.Model.Roles.Patient>(lnk.Other, resource);
if (replacer == null)
{
this.m_tracer.TraceError($"Cannot locate patient referenced by {lnk.Type} relationship");
throw new KeyNotFoundException(m_localizationService.FormatString("error.messaging.fhir.patientResource.cannotLocatePatient", new
{
param = lnk.Type
}));
}
patient.StatusConceptKey = StatusKeys.Obsolete;
patient.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.Replaces, patient)
{
HolderKey = replacer.Key
});
break;
}
case Patient.LinkType.Seealso:
{
var referee = DataTypeConverter.ResolveEntity <Entity>(lnk.Other, resource); // We use Entity here in lieu Patient since the code below can handle the MDM layer
// Is this a current MDM link?
if (referee.GetTag(FhirConstants.PlaceholderTag) == "true") // The referee wants us to become the data
{
patient.Key = referee.Key;
}
else if (referee.LoadCollection(o => o.Relationships).Any(r => r.RelationshipTypeKey == MDM_MASTER_LINK) &&
referee.GetTag("$mdm.type") == "M") // HACK: This is a master and someone is attempting to point another record at it
{
patient.Relationships.Add(new EntityRelationship()
{
RelationshipTypeKey = MDM_MASTER_LINK,
SourceEntityKey = referee.Key,
TargetEntityKey = patient.Key
});
}
else
{
patient.Relationships.Add(new EntityRelationship(EntityRelationshipTypeKeys.EquivalentEntity, referee));
}
break;
}
case Patient.LinkType.Refer: // This points to a more detailed view of the patient
{
var referee = DataTypeConverter.ResolveEntity <Entity>(lnk.Other, resource);
if (referee.GetTag("$mdm.type") == "M") // HACK: MDM User is attempting to point this at another Master (note: THE MDM LAYER WON'T LIKE THIS)
{
patient.Relationships.Add(new EntityRelationship(MDM_MASTER_LINK, referee));
}
else
{
this.m_tracer.TraceError($"Setting refer relationships to source of truth is not supported");
throw new NotSupportedException(m_localizationService.GetString("error.type.NotSupportedException.userMessage"));
}
break; // TODO: These are special cases of references
}
}
}
if (resource.Photo != null && resource.Photo.Any())
{
patient.Extensions.RemoveAll(o => o.ExtensionTypeKey == ExtensionTypeKeys.JpegPhotoExtension);
patient.Extensions.Add(new EntityExtension(ExtensionTypeKeys.JpegPhotoExtension, resource.Photo.First().Data));
}
return(patient);
}
