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fixed cql generation filter string #177

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merged 1 commit into from
Oct 30, 2024
Merged

fixed cql generation filter string #177

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89 changes: 89 additions & 0 deletions resources/test/result_current.cql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,89 @@
library Retrieve
using FHIR version '4.0.0'
include FHIRHelpers version '4.0.0'

codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
codesystem icd10gm: 'http://fhir.de/CodeSystem/dimdi/icd-10-gm'
codesystem icd10gmnew: 'http://fhir.de/CodeSystem/bfarm/icd-10-gm'
codesystem StorageTemperature: 'https://fhir.bbmri.de/CodeSystem/StorageTemperature'


context Patient

define AgeClass:
if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)

define Gender:
if (Patient.gender is null) then 'unknown' else Patient.gender

define Custodian:
First(from Specimen.extension E
where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
return (E.value as Reference).identifier.value)

define function SampleType(specimen FHIR.Specimen):
case FHIRHelpers.ToCode(specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').first())
when Code 'plasma-edta' from SampleMaterialType then 'blood-plasma'
when Code 'plasma-citrat' from SampleMaterialType then 'blood-plasma'
when Code 'plasma-heparin' from SampleMaterialType then 'blood-plasma'
when Code 'plasma-cell-free' from SampleMaterialType then 'blood-plasma'
when Code 'plasma-other' from SampleMaterialType then 'blood-plasma'
when Code 'plasma' from SampleMaterialType then 'blood-plasma'
when Code 'tissue-formalin' from SampleMaterialType then 'tissue-ffpe'
when Code 'tumor-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
when Code 'normal-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
when Code 'other-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
when Code 'tumor-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
when Code 'normal-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
when Code 'other-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
when Code 'tissue-paxgene-or-else' from SampleMaterialType then 'tissue-other'
when Code 'derivative' from SampleMaterialType then 'derivative-other'
when Code 'liquid' from SampleMaterialType then 'liquid-other'
when Code 'tissue' from SampleMaterialType then 'tissue-other'
when Code 'serum' from SampleMaterialType then 'blood-serum'
when Code 'cf-dna' from SampleMaterialType then 'dna'
when Code 'g-dna' from SampleMaterialType then 'dna'
when Code 'blood-plasma' from SampleMaterialType then 'blood-plasma'
when Code 'tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
when Code 'tissue-frozen' from SampleMaterialType then 'tissue-frozen'
when Code 'tissue-other' from SampleMaterialType then 'tissue-other'
when Code 'derivative-other' from SampleMaterialType then 'derivative-other'
when Code 'liquid-other' from SampleMaterialType then 'liquid-other'
when Code 'blood-serum' from SampleMaterialType then 'blood-serum'
when Code 'dna' from SampleMaterialType then 'dna'
when Code 'buffy-coat' from SampleMaterialType then 'buffy-coat'
when Code 'urine' from SampleMaterialType then 'urine'
when Code 'ascites' from SampleMaterialType then 'ascites'
when Code 'saliva' from SampleMaterialType then 'saliva'
when Code 'csf-liquor' from SampleMaterialType then 'csf-liquor'
when Code 'bone-marrow' from SampleMaterialType then 'bone-marrow'
when Code 'peripheral-blood-cells-vital' from SampleMaterialType then 'peripheral-blood-cells-vital'
when Code 'stool-faeces' from SampleMaterialType then 'stool-faeces'
when Code 'rna' from SampleMaterialType then 'rna'
when Code 'whole-blood' from SampleMaterialType then 'whole-blood'
when Code 'swab' from SampleMaterialType then 'swab'
when Code 'dried-whole-blood' from SampleMaterialType then 'dried-whole-blood'
when null then 'Unknown'
else 'Unknown'
end
define Specimen:
if InInitialPopulation then [Specimen] S where (((((FHIRHelpers.ToDateTime(S.collection.collected) between @1900-01-01 and @2024-10-25) )) and (((((S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding.code contains 'temperature2to10'))))))) else {} as List<Specimen>

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()
)

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
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) ))))))
16 changes: 7 additions & 9 deletions src/cql.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -346,13 +346,9 @@ pub fn process(
}
}
}
let position = filter_cond.rfind(')');
match position{
None => {}
Some(pos) => {
_ = filter_cond.split_off(pos);
}
};
if let Some(pos) = filter_cond.rfind(')') {
_ = filter_cond.split_off(pos + 1);
}
}
}

Expand Down Expand Up @@ -404,7 +400,6 @@ mod test {
}

#[test]
#[ignore]
#[cfg(feature = "bbmri")]
fn test_bbmri() {
use crate::projects::{self, bbmri::Bbmri};
Expand Down Expand Up @@ -449,7 +444,10 @@ mod test {
include_str!("../resources/test/result_empty.cql").to_string()
);

println!("{}",generate_cql(serde_json::from_str(CURRENT).unwrap()).unwrap());
pretty_assertions::assert_eq!(
generate_cql(serde_json::from_str(CURRENT).unwrap()).unwrap(),
include_str!("../resources/test/result_current.cql").to_string()
);

}

Expand Down
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