Merge pull request #79 from samply/develop

added replacements into CQL replacement map

src/util.rs

@@ -102,6 +102,8 @@ pub(crate) fn replace_cql(decoded_library: impl Into<String>) -> String {
             ("EXLIQUID_ALIQUOTS_CQL_SPECIMEN", "define Specimen:\nif InInitialPopulation then [Specimen] else {} as List<Specimen>\n define Aliquot:\n [Specimen] S\n where exists S.collection.quantity.value and exists S.parent.reference and S.container.specimenQuantity.value > 0 define AliquotGroupReferences: flatten Aliquot S return S.parent.reference define AliquotGroupWithAliquot: [Specimen] S where not (S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen') and not exists S.collection.quantity.value and not exists S.container.specimenQuantity.value and AliquotGroupReferences contains 'Specimen/' + S.id define PrimarySampleReferences: flatten AliquotGroupWithAliquot S return S.parent.reference define ExliquidSpecimenWithAliquot: from [Specimen] PrimarySample where PrimarySample.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'   and PrimarySampleReferences contains 'Specimen/' + PrimarySample.id \n define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
             ("DKTK_STRAT_GENDER_STRATIFIER", "define Gender:\nif (Patient.gender is null) then 'unknown' else Patient.gender"),
             ("DKTK_STRAT_AGE_STRATIFIER", "define PrimaryDiagnosis:\nFirst(\nfrom [Condition] C\nwhere C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()\nsort by date from onset asc)\n\ndefine AgeClass:\nif (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)"),
+            ("DKTK_STRAT_PRIMARY_DIAGNOSIS_STRATIFIER", "define PrimaryDiagnosis:\nFirst(\nfrom [Condition] C\nwhere C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()\nsort by date from onset asc)\n"),
+            ("DKTK_STRAT_AGE_CLASS_STRATIFIER", "define AgeClass:\nif (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)"),
             ("DKTK_STRAT_DECEASED_STRATIFIER", "define PatientDeceased:\nFirst (from [Observation: Code '75186-7' from loinc] O return O.value.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/VitalstatusCS').code.first())\ndefine Deceased:\nif (PatientDeceased is null) then 'unbekannt' else PatientDeceased"),
             ("DKTK_STRAT_DIAGNOSIS_STRATIFIER", "define Diagnosis:\nif InInitialPopulation then [Condition] else {} as List<Condition>\n\ndefine function DiagnosisCode(condition FHIR.Condition):\ncondition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()"),
             ("DKTK_STRAT_SPECIMEN_STRATIFIER", "define Specimen:\nif InInitialPopulation then [Specimen] else {} as List<Specimen>\n\ndefine function SampleType(specimen FHIR.Specimen):\nspecimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()"),
@@ -111,7 +113,8 @@ pub(crate) fn replace_cql(decoded_library: impl Into<String>) -> String {
             ("DKTK_STRAT_ENCOUNTER_STRATIFIER", "define Encounter:\nif InInitialPopulation then [Encounter] else {} as List<Encounter>\n\ndefine function Departments(encounter FHIR.Encounter):\nencounter.identifier.where(system = 'http://dktk.dkfz.de/fhir/sid/hki-department').value.first()"),
             ("DKTK_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:"),
             ("EXLIQUID_STRAT_DEF_IN_INITIAL_POPULATION", "define InInitialPopulation:\n   exists ExliquidSpecimen and\n"),        
-            ("EXLIQUID_STRAT_W_ALIQUOTS", "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n")
+            ("EXLIQUID_STRAT_W_ALIQUOTS", "define InInitialPopulation: exists ExliquidSpecimenWithAliquot and \n"),
+            ("MTBA_STRAT_GENETIC_VARIANT", "define GeneticVariantCode:\nFirst (from [Observation: Code '69548-6' from loinc] O return O.component.where(code.coding contains Code '48018-6' from loinc).value.coding.code.first())")
         ].into();
 
     let mut decoded_library = decoded_library.into();
@@ -464,6 +467,14 @@ mod test {
         let expected_result = "define InInitialPopulation:\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
 
+        let decoded_library = "DKTK_STRAT_PRIMARY_DIAGNOSIS_STRATIFIER";
+        let expected_result = "define PrimaryDiagnosis:\nFirst(\nfrom [Condition] C\nwhere C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()\nsort by date from onset asc)\n\n";
+        assert_eq!(replace_cql(decoded_library), expected_result);
+
+        let decoded_library = "DKTK_STRAT_AGE_CLASS_STRATIFIER";
+        let expected_result = "define AgeClass:\nif (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)\n";
+        assert_eq!(replace_cql(decoded_library), expected_result);
+
         let decoded_library = "EXLIQUID_CQL_DIAGNOSIS";
         let expected_result = "define retrieveCondition: First(from [Condition] C return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())\ndefine Diagnosis: if (retrieveCondition is null) then 'unknown' else retrieveCondition\n\n";
         assert_eq!(replace_cql(decoded_library), expected_result);
@@ -489,6 +500,11 @@ mod test {
 
         assert_eq!(replace_cql(decoded_library), expected_result);
 
+        let decoded_library = "MTBA_STRAT_GENETIC_VARIANT";
+        let expected_result = "define GeneticVariantCode:\nFirst (from [Observation: Code '69548-6' from loinc] O return O.component.where(code.coding contains Code '48018-6' from loinc).value.coding.code.first())\n";
+
+        assert_eq!(replace_cql(decoded_library), expected_result);
+
         let decoded_library = "INVALID_KEY";
         let expected_result = "INVALID_KEY";
         assert_eq!(replace_cql(decoded_library), expected_result);