Merge pull request #177 from samply/fix/cql

fixed cql generation filter string
samply · Oct 30, 2024 · 8c3f1e9 · 8c3f1e9
2 parents 78b1d62 + c8fc9d6
commit 8c3f1e9
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Showing 2 changed files with 96 additions and 9 deletions.
diff --git a/resources/test/result_current.cql b/resources/test/result_current.cql
@@ -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) ))))))
diff --git a/src/cql.rs b/src/cql.rs
@@ -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);
+            }
         }
     }
 
@@ -404,7 +400,6 @@ mod test {
     }
 
     #[test]
-    #[ignore]
     #[cfg(feature = "bbmri")]
     fn test_bbmri() {
         use crate::projects::{self, bbmri::Bbmri};
@@ -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()
+        );
 
     }