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fix(vr): fix time based partial date times #208

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merged 12 commits into from
Jan 22, 2025
+383 −130
Merged

fix(vr): fix time based partial date times #208

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5d8ee42
Refactored time to be better integrated into date setting
RobertScalfani Dec 9, 2024
e53e0b1
Added fhirdatetime support
RobertScalfani Dec 9, 2024
6a813fe
Adding tests for PDT
RobertScalfani Jan 17, 2025
c05210b
Test fixes
RobertScalfani Jan 22, 2025
53c9508
doc update
RobertScalfani Jan 22, 2025
18d23be
Remove 2.1 EOL from dotnet versions
smacadam Jan 22, 2025
e2e1afd
Only use dotnet 6 in github action
smacadam Jan 22, 2025
143a777
Redefine dotnet version matrix
smacadam Jan 22, 2025
94a7263
Testing multiple dotnet versions
smacadam Jan 22, 2025
815f282
Use multiple dotnet versions in matrix
smacadam Jan 22, 2025
0bf08cd
Only use dotnet 6 for dotnet test runner
smacadam Jan 22, 2025
7f79b97
Fix spacing in github action yml file
smacadam Jan 22, 2025
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81 changes: 44 additions & 37 deletions projects/BFDR/NatalityRecord_submissionProperties.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@
{
AddBirthDateToPatient(Subject, false);
}
Date newDate = UpdateFhirDate(Subject.BirthDateElement, value, PartialDateYearUrl, true);
Date newDate = UpdateFhirDateElement(Subject.BirthDateElement, value, PartialDateYearUrl, true);
if (newDate != null)
{
Subject.BirthDateElement = newDate;
Expand Down Expand Up @@ -197,7 +197,7 @@
{
AddBirthDateToPatient(Subject, false);
}
Date newDate = UpdateFhirDate(Subject.BirthDateElement, value, PartialDateMonthUrl, true);
Date newDate = UpdateFhirDateElement(Subject.BirthDateElement, value, PartialDateMonthUrl, true);
if (newDate != null)
{
Subject.BirthDateElement = newDate;
Expand All @@ -222,7 +222,7 @@
{
AddBirthDateToPatient(Subject, false);
}
Date newDate = UpdateFhirDate(Subject.BirthDateElement, value, PartialDateDayUrl, true);
Date newDate = UpdateFhirDateElement(Subject.BirthDateElement, value, PartialDateDayUrl, true);
if (newDate != null)
{
Subject.BirthDateElement = newDate;
Expand All @@ -234,18 +234,21 @@
/// </summary>
protected string GetBirthTime()
{
if (Subject == null || Subject.BirthDateElement == null)
{
return null;
}
// First check for a time in the patient.birthDate PatientBirthTime extension.
if (Subject.BirthDateElement.Extension.Any(ext => ext.Url == VR.ExtensionURL.PatientBirthTime))
{
FhirDateTime dateTime = (FhirDateTime)Subject.BirthDateElement.GetExtension(VR.ExtensionURL.PatientBirthTime).Value;
return GetTimeFragment(dateTime);
if (Subject == null || Subject.BirthDateElement == null)
{
return null;
}
// First check for a time in the patient.birthDate PatientBirthTime extension.
if (Subject.BirthDateElement.Extension.Any(ext => ext.Url == VR.ExtensionURL.PatientBirthTime))
{
FhirDateTime dateTime = (FhirDateTime)Subject.BirthDateElement.GetExtension(VR.ExtensionURL.PatientBirthTime).Value;
string time = GetTimeFragment(dateTime);
if (time != null) {
return time;
}
// If it's not there, check for a PartialDateTime.
return this.GetPartialTime(this.Subject.BirthDateElement.GetExtension(PartialDateTimeUrl));
}
// If it's not there, check for a PartialDateTime.
return this.GetPartialTime(this.Subject.BirthDateElement.GetExtension(PartialDateTimeUrl));
}

/// <summary>
Expand All @@ -262,7 +265,11 @@
{
AddBirthDateToPatient(Subject, true);
}
AddTimeToDate(Subject.BirthDateElement, GetBirthYear(), GetBirthMonth(), GetBirthDay(), value, true);
Date newDate = UpdateFhirDateTimeElement(Subject.BirthDateElement, value, true);
if (newDate != null)
{
Subject.BirthDateElement = newDate;
}
}

/// <summary>
Expand Down Expand Up @@ -2469,7 +2476,7 @@
{
AddBirthDateToPatient(Mother, false);
}
Date newDate = UpdateFhirDate(Mother.BirthDateElement, value, PartialDateDayUrl);
Date newDate = UpdateFhirDateElement(Mother.BirthDateElement, value, PartialDateDayUrl);
if (newDate != null)
{
Mother.BirthDateElement = newDate;
Expand Down Expand Up @@ -2499,7 +2506,7 @@
{
AddBirthDateToPatient(Mother, false);
}
Date newDate = UpdateFhirDate(Mother.BirthDateElement, value, PartialDateMonthUrl);
Date newDate = UpdateFhirDateElement(Mother.BirthDateElement, value, PartialDateMonthUrl);
if (newDate != null)
{
Mother.BirthDateElement = newDate;
Expand Down Expand Up @@ -2529,7 +2536,7 @@
{
AddBirthDateToPatient(Mother, false);
}
Date newDate = UpdateFhirDate(Mother.BirthDateElement, value, PartialDateYearUrl);
Date newDate = UpdateFhirDateElement(Mother.BirthDateElement, value, PartialDateYearUrl);
if (newDate != null)
{
Mother.BirthDateElement = newDate;
Expand Down Expand Up @@ -2779,7 +2786,7 @@
Father.BirthDateElement = new Date();
Father.BirthDateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
Date newDate = UpdateFhirDate(Father.BirthDateElement, value, PartialDateDayUrl);
Date newDate = UpdateFhirDateElement(Father.BirthDateElement, value, PartialDateDayUrl);
if (newDate != null)
{
Father.BirthDateElement = newDate;
Expand Down Expand Up @@ -2810,7 +2817,7 @@
Father.BirthDateElement = new Date();
Father.BirthDateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
Date newDate = UpdateFhirDate(Father.BirthDateElement, value, PartialDateMonthUrl);
Date newDate = UpdateFhirDateElement(Father.BirthDateElement, value, PartialDateMonthUrl);
if (newDate != null)
{
Father.BirthDateElement = newDate;
Expand Down Expand Up @@ -2841,7 +2848,7 @@
Father.BirthDateElement = new Date();
Father.BirthDateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
Date newDate = UpdateFhirDate(Father.BirthDateElement, value, PartialDateYearUrl);
Date newDate = UpdateFhirDateElement(Father.BirthDateElement, value, PartialDateYearUrl);
if (newDate != null)
{
Father.BirthDateElement = newDate;
Expand Down Expand Up @@ -6066,7 +6073,7 @@
obs.Value = new FhirDateTime();
obs.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateDayUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateDayUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6105,7 +6112,7 @@
obs.Value = new FhirDateTime();
obs.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateMonthUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateMonthUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6144,7 +6151,7 @@
obs.Value = new FhirDateTime();
obs.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateYearUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateYearUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6213,7 +6220,7 @@
obs.Value = new FhirDateTime();
obs.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateDayUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateDayUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6252,7 +6259,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateMonthUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateMonthUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6291,7 +6298,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateYearUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateYearUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -6715,7 +6722,7 @@
}
}

protected int? GetWeight(string code)

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Missing XML comment for publicly visible type or member 'NatalityRecord.GetWeight(string)'

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Missing XML comment for publicly visible type or member 'NatalityRecord.GetWeight(string)'

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Missing XML comment for publicly visible type or member 'NatalityRecord.GetWeight(string)'

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Missing XML comment for publicly visible type or member 'NatalityRecord.GetWeight(string)'
{
var entry = Bundle.Entry.Where(e => e.Resource is Observation obs && CodeableConceptToDict(obs.Code)["code"] == code).FirstOrDefault();
if (entry != null)
Expand All @@ -6726,7 +6733,7 @@
return null;
}

protected Observation SetWeight(string code, int? value, string unit, string section, string subjectId)

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Missing XML comment for publicly visible type or member 'NatalityRecord.SetWeight(string, int?, string, string, string)'

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Missing XML comment for publicly visible type or member 'NatalityRecord.SetWeight(string, int?, string, string, string)'
{
var entry = Bundle.Entry.Where(e => e.Resource is Observation o && CodeableConceptToDict(o.Code)["code"] == code).FirstOrDefault();
if (!(entry?.Resource is Observation obs))
Expand Down Expand Up @@ -8029,7 +8036,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateYearUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateYearUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8062,7 +8069,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateMonthUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateMonthUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8096,7 +8103,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateDayUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateDayUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8204,7 +8211,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateYearUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateYearUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8237,7 +8244,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateMonthUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateMonthUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8270,7 +8277,7 @@
obs.Value = new FhirDateTime();
obs.Value.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(obs.Value as FhirDateTime), value, PartialDateDayUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(obs.Value as FhirDateTime, value, PartialDateDayUrl);
if (newDate != null)
{
obs.Value = newDate;
Expand Down Expand Up @@ -8328,7 +8335,7 @@
this.Composition.DateElement = new FhirDateTime();
this.Composition.DateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate =ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(this.Composition.DateElement), value, PartialDateYearUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(this.Composition.DateElement, value, PartialDateYearUrl);
if (newDate != null)
{
this.Composition.DateElement = newDate;
Expand Down Expand Up @@ -8364,7 +8371,7 @@
this.Composition.DateElement = new FhirDateTime();
this.Composition.DateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(this.Composition.DateElement), value, PartialDateMonthUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(this.Composition.DateElement, value, PartialDateMonthUrl);
if (newDate != null)
{
this.Composition.DateElement = newDate;
Expand Down Expand Up @@ -8400,7 +8407,7 @@
this.Composition.DateElement = new FhirDateTime();
this.Composition.DateElement.Extension.Add(NewBlankPartialDateTimeExtension(false));
}
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(this.Composition.DateElement), value, PartialDateDayUrl));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(this.Composition.DateElement, value, PartialDateDayUrl);
if (newDate != null)
{
this.Composition.DateElement = newDate;
Expand Down Expand Up @@ -9336,7 +9343,7 @@
}
}

protected int? GetCertifiedDateElement(Encounter encounter, string dateUrl)

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{
if (encounter == null)
{
Expand Down Expand Up @@ -9364,7 +9371,7 @@
return GetDateFragmentOrPartialDate(certifier.Period.StartElement, dateUrl);
}

protected void SetCertifiedDateElement(Encounter encounter, string dateUrl, int? value)

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{
if (value == null)
{
Expand All @@ -9391,7 +9398,7 @@
stateComp.Period = p;
}
// TODO create new helper function specific to FHIRDateTimes so we don't drop time information
FhirDateTime newDate = ConvertDateToFhirDateTime(UpdateFhirDate(ConvertFhirDateTimeToDate(stateComp.Period.StartElement), value, dateUrl, true));
FhirDateTime newDate = UpdateFhirDateTimeDateElement(stateComp.Period.StartElement, value, dateUrl);
if (newDate != null)
{
stateComp.Period.StartElement = newDate;
Expand All @@ -9417,12 +9424,12 @@
// }
}

protected string GetCertificationDate(Encounter encounter)

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Missing XML comment for publicly visible type or member 'NatalityRecord.GetCertificationDate(Encounter)'
{
Encounter.ParticipantComponent certifier = encounter?.Participant?.FirstOrDefault(entry => ((Encounter.ParticipantComponent)entry).Type.Any(t => t.Coding.Any(c => c.Code == "87287-9")));
return certifier?.Period?.Start;
}
protected void SetCertificationDate(Encounter encounter, string value)

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Missing XML comment for publicly visible type or member 'NatalityRecord.SetCertificationDate(Encounter, string)'
{
Encounter.ParticipantComponent certifier = encounter.Participant.FirstOrDefault(entry => ((Encounter.ParticipantComponent)entry).Type.Any(t => t.Coding.Any(c => c.Code == "87287-9")));
if (certifier != null)
Expand Down
20 changes: 1 addition & 19 deletions projects/VitalRecord/VitalRecord.xml
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