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Feature/diagnosis not checked in specimen #311

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f740db3
removed Specimen from DiagnosisCode function
enola-dkfz Dec 12, 2025
b31abde
Merge branch 'develop' of https://github.com/samply/focus into featur…
enola-dkfz Dec 16, 2025
d8938f4
removed specimen diagnosis from search condition
enola-dkfz Dec 17, 2025
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8 changes: 2 additions & 6 deletions resources/test/result_age_at_diagnosis_30_to_70.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((exists from [Condition] C
Expand Down
8 changes: 2 additions & 6 deletions resources/test/result_age_at_diagnosis_lower_than_70.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((exists from [Condition] C
Expand Down
10 changes: 3 additions & 7 deletions resources/test/result_all_gbn.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -76,18 +76,14 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((Patient.gender = 'male') or (Patient.gender = 'other'))) and ((((((exists[Condition: Code 'C25' from icd10]) or (exists[Condition: Code 'C25' from icd10gm]) or (exists[Condition: Code 'C25' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C25'))))) or (((((exists[Condition: Code 'C56' from icd10]) or (exists[Condition: Code 'C56' from icd10gm]) or (exists[Condition: Code 'C56' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C56')))))) and (exists from [Condition] C
((((Patient.gender = 'male') or (Patient.gender = 'other'))) and ((((((exists[Condition: Code 'C25' from icd10]) or (exists[Condition: Code 'C25' from icd10gm]) or (exists[Condition: Code 'C25' from icd10gmnew])))))) or (((((exists[Condition: Code 'C56' from icd10]) or (exists[Condition: Code 'C56' from icd10gm]) or (exists[Condition: Code 'C56' from icd10gmnew]))))))) and (exists from [Condition] C
where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling(10) and Ceiling(100)) and (exists from [Condition] C
where FHIRHelpers.ToDateTime(C.onset) between @2023-09-30 and @2023-10-29) and (exists from [Observation: Code '39156-5' from loinc] O
where ((O.value as Quantity) < 10 'kg/m2' and (O.value as Quantity) > 100 'kg/m2')) and (exists from [Observation: Code '29463-7' from loinc] O
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10 changes: 3 additions & 7 deletions resources/test/result_c61_and_male.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C61')))))) and ((((Patient.gender = 'male'))))))
((((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew]))))))) and ((((Patient.gender = 'male'))))))
10 changes: 3 additions & 7 deletions resources/test/result_current.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -74,16 +74,12 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C61')))))) and (( AgeInYears() between Ceiling(10) and Ceiling(90)))) or (((exists from [Specimen] S
((((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew]))))))) and (( AgeInYears() between Ceiling(10) and Ceiling(90)))) or (((exists from [Specimen] S
where FHIRHelpers.ToDateTime(S.collection.collected) between @1900-01-01 and @2024-10-25 )) and ((((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'temperature2to10' from StorageTemperature) ))))))
8 changes: 2 additions & 6 deletions resources/test/result_empty.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
true
10 changes: 3 additions & 7 deletions resources/test/result_lens2.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -74,15 +74,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((((Patient.gender = 'male'))) or (((Patient.gender = 'female')))) and ((((((exists[Condition: Code 'C41' from icd10]) or (exists[Condition: Code 'C41' from icd10gm]) or (exists[Condition: Code 'C41' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C41'))))) or (((((exists[Condition: Code 'C50' from icd10]) or (exists[Condition: Code 'C50' from icd10gm]) or (exists[Condition: Code 'C50' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C50')))))) and (((( exists [Specimen: Code 'tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'tumor-tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'normal-tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'other-tissue-frozen' from SampleMaterialType]))) or ((( exists [Specimen: Code 'blood-serum' from SampleMaterialType]) or ( exists [Specimen: Code 'serum' from SampleMaterialType]))))) or (((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C41' from icd10]) or (exists[Condition: Code 'C41' from icd10gm]) or (exists[Condition: Code 'C41' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C41'))))) or (((((exists[Condition: Code 'C50' from icd10]) or (exists[Condition: Code 'C50' from icd10gm]) or (exists[Condition: Code 'C50' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C50')))))) and (((( exists [Specimen: Code 'liquid-other' from SampleMaterialType]) or ( exists [Specimen: Code 'liquid' from SampleMaterialType]))) or ((( exists [Specimen: Code 'rna' from SampleMaterialType]))) or ((( exists [Specimen: Code 'urine' from SampleMaterialType])))) and ((((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'temperatureRoom' from StorageTemperature) ))) or (((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'four_degrees' from StorageTemperature) ))))))
((((((Patient.gender = 'male'))) or (((Patient.gender = 'female')))) and ((((((exists[Condition: Code 'C41' from icd10]) or (exists[Condition: Code 'C41' from icd10gm]) or (exists[Condition: Code 'C41' from icd10gmnew])))))) or (((((exists[Condition: Code 'C50' from icd10]) or (exists[Condition: Code 'C50' from icd10gm]) or (exists[Condition: Code 'C50' from icd10gmnew]))))))) and (((( exists [Specimen: Code 'tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'tumor-tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'normal-tissue-frozen' from SampleMaterialType]) or ( exists [Specimen: Code 'other-tissue-frozen' from SampleMaterialType]))) or ((( exists [Specimen: Code 'blood-serum' from SampleMaterialType]) or ( exists [Specimen: Code 'serum' from SampleMaterialType]))))) or (((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C41' from icd10]) or (exists[Condition: Code 'C41' from icd10gm]) or (exists[Condition: Code 'C41' from icd10gmnew])))))) or (((((exists[Condition: Code 'C50' from icd10]) or (exists[Condition: Code 'C50' from icd10gm]) or (exists[Condition: Code 'C50' from icd10gmnew]))))))) and (((( exists [Specimen: Code 'liquid-other' from SampleMaterialType]) or ( exists [Specimen: Code 'liquid' from SampleMaterialType]))) or ((( exists [Specimen: Code 'rna' from SampleMaterialType]))) or ((( exists [Specimen: Code 'urine' from SampleMaterialType])))) and ((((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'temperatureRoom' from StorageTemperature) ))) or (((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'four_degrees' from StorageTemperature) ))))))
8 changes: 2 additions & 6 deletions resources/test/result_male_or_female.cql
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Expand Up @@ -71,15 +71,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((((Patient.gender = 'male'))) or (((Patient.gender = 'female'))))))
10 changes: 3 additions & 7 deletions resources/test/result_quote.cql
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Expand Up @@ -73,15 +73,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((((((exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10]) or (exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10gm]) or (exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C61\"\'\\\n\r\t')))))) and ((((Patient.gender = 'male'))))))
((((((((exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10]) or (exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10gm]) or (exists[Condition: Code 'C61\"\'\\\n\r\t' from icd10gmnew]))))))) and ((((Patient.gender = 'male'))))))
10 changes: 3 additions & 7 deletions resources/test/result_some_gbn.cql
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Expand Up @@ -76,18 +76,14 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
((((Patient.gender = 'other') or (Patient.gender = 'male'))) and (((((exists[Condition: Code 'C24' from icd10]) or (exists[Condition: Code 'C24' from icd10gm]) or (exists[Condition: Code 'C24' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C24'))))) and (exists from [Condition] C
((((Patient.gender = 'other') or (Patient.gender = 'male'))) and (((((exists[Condition: Code 'C24' from icd10]) or (exists[Condition: Code 'C24' from icd10gm]) or (exists[Condition: Code 'C24' from icd10gmnew])))))) and (exists from [Condition] C
where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling(1) and Ceiling(11)) and (exists from [Condition] C
where FHIRHelpers.ToDateTime(C.onset) between @2023-10-29 and @2023-10-30) and (exists from [Observation: Code '39156-5' from loinc] O
where ((O.value as Quantity) < 1 'kg/m2' and (O.value as Quantity) > 111 'kg/m2')) and (exists from [Observation: Code '29463-7' from loinc] O
Expand Down
2 changes: 1 addition & 1 deletion src/projects/bbmri/mod.rs
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Expand Up @@ -57,7 +57,7 @@ pub static CQL_SNIPPETS: LazyLock<HashMap<(&'static str, CriterionRole), &'stati
(("gender", CriterionRole::Query), "Patient.gender = '{{C}}'"),
(
("diagnosis", CriterionRole::Query),
"((exists[Condition: Code '{{C}}' from {{A1}}]) or (exists[Condition: Code '{{C}}' from {{A2}}]) or (exists[Condition: Code '{{C}}' from {{A3}}])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains '{{C}}'))",
"((exists[Condition: Code '{{C}}' from {{A1}}]) or (exists[Condition: Code '{{C}}' from {{A2}}]) or (exists[Condition: Code '{{C}}' from {{A3}}])))",
),
(("diagnosis_old", CriterionRole::Query), " exists [Condition: Code '{{C}}' from {{A1}}]"),
(
Expand Down
8 changes: 2 additions & 6 deletions src/projects/bbmri/template.cql
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Expand Up @@ -69,15 +69,11 @@ define Diagnosis:
if InInitialPopulation then [Condition] else {} as List<Condition>

define function DiagnosisCode(condition FHIR.Condition):
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()

define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
Coalesce(
condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
)
condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
)

define InInitialPopulation:
{{retrieval_criteria}}
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