Merge develop into main for 0.20.1

CHANGELOG.md

@@ -1,3 +1,9 @@
+# Samply.Focus v0.20.1 2026-01-15
+
+## Minor changes
+
+* BETWEEN operator supported with only one boundary defined in the date range
+
 # Samply.Focus v0.20.0 2026-01-13
 
 ## Major changes

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.20.0"
+version = "0.20.1"
 edition = "2021"
 license = "Apache-2.0"
 

resources/test/result_after.cql

@@ -0,0 +1,86 @@
+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'
+
+
+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)  >= @2015-01-01) )))) 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:
+((((exists from [Specimen] S
+where FHIRHelpers.ToDateTime(S.collection.collected)  >= @2015-01-01 ))))

resources/test/result_before.cql

@@ -0,0 +1,86 @@
+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'
+
+
+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)  <= @2015-01-01) )))) 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:
+((((exists from [Specimen] S
+where FHIRHelpers.ToDateTime(S.collection.collected)  <= @2015-01-01 ))))

src/ast.rs

@@ -44,8 +44,8 @@ pub struct NumRange {
 
 #[derive(Serialize, Deserialize, Debug, Clone)]
 pub struct DateRange {
-    pub min: String, // we don't parse dates yet
-    pub max: String,
+    pub min: Option<String>, // we don't parse dates yet
+    pub max: Option<String>,
 }
 
 #[derive(Serialize, Deserialize, Debug, Clone)]