Merge pull request #99 from samply/develop

exporter bugs fixed, pulchrification of CQL replacements

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.3.0"
+version = "0.4.0"
 edition = "2021"
 license = "Apache-2.0"
 

build.rs

@@ -1,3 +1,5 @@
+use std::{path::Path, env, io::{BufWriter, Write}, fs::File};
+
 use build_data::get_git_dirty;
 
 /// Outputs a readable version number such as
@@ -15,11 +17,37 @@ fn version() -> String {
     }
 }
 
+fn build_cqlmap() {
+    let path = Path::new(&env::var("OUT_DIR").unwrap()).join("replace_map.rs");
+    let mut file = BufWriter::new(File::create(path).unwrap());
+
+    write!(&mut file, r#"
+        static REPLACE_MAP: once_cell::sync::Lazy<HashMap<&'static str, &'static str>> = once_cell::sync::Lazy::new(|| {{
+        let mut map = HashMap::new();
+    "#).unwrap();
+
+    for cqlfile in std::fs::read_dir(Path::new("resources/cql")).unwrap() {
+        let cqlfile = cqlfile.unwrap();
+        let cqlfilename = cqlfile.file_name().to_str().unwrap().to_owned();
+        let cqlcontent = std::fs::read_to_string(cqlfile.path()).unwrap();
+        write!(&mut file, r####"
+            map.insert(r###"{cqlfilename}"###, r###"{cqlcontent}"###);
+        "####).unwrap();
+    }
+
+    writeln!(&mut file, "
+        map
+    }});"
+    ).unwrap();
+}
+
 fn main() {
     build_data::set_GIT_COMMIT_SHORT();
     build_data::set_GIT_DIRTY();
     build_data::set_BUILD_DATE();
     build_data::set_BUILD_TIME();
     build_data::no_debug_rebuilds();
     println!("cargo:rustc-env=SAMPLY_USER_AGENT=Samply.Focus.{}/{}", env!("CARGO_PKG_NAME"), version());
+
+    build_cqlmap();
 }

resources/cql/BBMRI_STRAT_AGE_STRATIFIER

@@ -0,0 +1,2 @@
+define AgeClass:
+     (AgeInYears() div 10) * 10

resources/cql/BBMRI_STRAT_CUSTODIAN_STRATIFIER

@@ -0,0 +1,4 @@
+define Custodian:
+ First(from Specimen.extension E
+ where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
+ return (E.value as Reference).identifier.value)

resources/cql/BBMRI_STRAT_DEF_IN_INITIAL_POPULATION

@@ -0,0 +1 @@
+define InInitialPopulation:

resources/cql/BBMRI_STRAT_DEF_SPECIMEN

@@ -0,0 +1 @@
+define Specimen:

resources/cql/BBMRI_STRAT_DIAGNOSIS_STRATIFIER

@@ -0,0 +1,5 @@
+define Diagnosis:
+ if InInitialPopulation then [Condition] else {} as List<Condition> 
+ 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(), 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())
+

resources/cql/BBMRI_STRAT_GENDER_STRATIFIER

@@ -0,0 +1,2 @@
+define Gender:
+  if (Patient.gender is null) then 'unknown' else Patient.gender

resources/cql/BBMRI_STRAT_SAMPLE_TYPE_STRATIFIER

@@ -0,0 +1,45 @@
+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

resources/cql/DKTK_STRAT_AGE_CLASS_STRATIFIER

@@ -0,0 +1,2 @@
+define AgeClass:
+if (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)

resources/cql/DKTK_STRAT_AGE_STRATIFIER

@@ -0,0 +1,8 @@
+define PrimaryDiagnosis:
+First(
+from [Condition] C
+where C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()
+sort by date from onset asc)
+
+define AgeClass:
+if (PrimaryDiagnosis.onset is null) then 'unknown' else ToString((AgeInYearsAt(FHIRHelpers.ToDateTime(PrimaryDiagnosis.onset)) div 10) * 10)

resources/cql/DKTK_STRAT_DECEASED_STRATIFIER

@@ -0,0 +1,4 @@
+define PatientDeceased:
+First (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())
+define Deceased:
+if (PatientDeceased is null) then 'unbekannt' else PatientDeceased

resources/cql/DKTK_STRAT_DEF_IN_INITIAL_POPULATION

@@ -0,0 +1 @@
+define InInitialPopulation:

resources/cql/DKTK_STRAT_DIAGNOSIS_STRATIFIER

@@ -0,0 +1,5 @@
+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()

resources/cql/DKTK_STRAT_ENCOUNTER_STRATIFIER

@@ -0,0 +1,5 @@
+define Encounter:
+if InInitialPopulation then [Encounter] else {} as List<Encounter>
+
+define function Departments(encounter FHIR.Encounter):
+encounter.identifier.where(system = 'http://dktk.dkfz.de/fhir/sid/hki-department').value.first()

resources/cql/DKTK_STRAT_GENDER_STRATIFIER

@@ -0,0 +1,2 @@
+define Gender:
+if (Patient.gender is null) then 'unknown' else Patient.gender

resources/cql/DKTK_STRAT_HISTOLOGY_STRATIFIER

@@ -0,0 +1,5 @@
+define Histo:
+if InInitialPopulation then [Observation] else {} as List <Observation>
+
+define function Histlogoy(histo FHIR.Observation):
+ if histo.code.coding.where(code = '59847-4').code.first() is null then 0 else 1

resources/cql/DKTK_STRAT_MEDICATION_STRATIFIER

@@ -0,0 +1,2 @@
+define MedicationStatement:
+if InInitialPopulation then [MedicationStatement] else {} as List <MedicationStatement>

resources/cql/DKTK_STRAT_PRIMARY_DIAGNOSIS_STRATIFIER

@@ -0,0 +1,6 @@
+define PrimaryDiagnosis:
+First(
+from [Condition] C
+where C.extension.where(url='http://hl7.org/fhir/StructureDefinition/condition-related').empty()
+sort by date from onset asc)
+

resources/cql/DKTK_STRAT_PROCEDURE_STRATIFIER

@@ -0,0 +1,5 @@
+define Procedure:
+if InInitialPopulation then [Procedure] else {} as List <Procedure>
+
+define function ProcedureType(procedure FHIR.Procedure):
+procedure.category.coding.where(system = 'http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SYSTTherapieartCS').code.first()

resources/cql/DKTK_STRAT_SPECIMEN_STRATIFIER

@@ -0,0 +1,5 @@
+define Specimen:
+if InInitialPopulation then [Specimen] else {} as List<Specimen>
+
+define function SampleType(specimen FHIR.Specimen):
+specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()

resources/cql/EXLIQUID_ALIQUOTS_CQL_DIAGNOSIS

@@ -0,0 +1,3 @@
+define retrieveCondition: First(from [Condition] C return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())
+define Diagnosis: if (retrieveCondition is null) then 'unknown' else retrieveCondition
+

resources/cql/EXLIQUID_ALIQUOTS_CQL_SPECIMEN

@@ -0,0 +1,6 @@
+define Specimen:
+if InInitialPopulation then [Specimen] else {} as List<Specimen>
+ define Aliquot:
+ [Specimen] S
+ 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 
+ define function SampleType(specimen FHIR.Specimen): specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()

resources/cql/EXLIQUID_CQL_DIAGNOSIS

@@ -0,0 +1,3 @@
+define retrieveCondition: First(from [Condition] C return C.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first())
+define Diagnosis: if (retrieveCondition is null) then 'unknown' else retrieveCondition
+

resources/cql/EXLIQUID_CQL_SPECIMEN

@@ -0,0 +1,7 @@
+define Specimen:
+if InInitialPopulation then [Specimen] else {} as List<Specimen>
+define ExliquidSpecimen:
+  from [Specimen] S
+  where S.identifier.system contains 'http://dktk.dkfz.de/fhir/sid/exliquid-specimen'
+define function SampleType(specimen FHIR.Specimen):
+  specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()

resources/cql/EXLIQUID_STRAT_DEF_IN_INITIAL_POPULATION

@@ -0,0 +1,3 @@
+define InInitialPopulation:
+   exists ExliquidSpecimen and
+

resources/cql/EXLIQUID_STRAT_W_ALIQUOTS

@@ -0,0 +1,2 @@
+define InInitialPopulation: exists ExliquidSpecimenWithAliquot and 
+

resources/cql/MTBA_STRAT_GENETIC_VARIANT

@@ -0,0 +1,2 @@
+define GeneticVariantCode:
+First (from [Observation: Code '69548-6' from loinc] O return O.component.where(code.coding contains Code '48018-6' from loinc).value.coding.code.first())

resources/cql/UCT_STRAT_SPECIMEN_STRATIFIER

@@ -0,0 +1,12 @@
+define Specimen:
+if InInitialPopulation then [Specimen] else {} as List<Specimen>
+
+define function SampleType(specimen FHIR.Specimen):
+specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first()
+
+define function Lagerort(specimen FHIR.Specimen):
+specimen.extension.where(url = 'http://uct-locator/specimen/storage').value.coding.code.first()
+
+define function annotations(specimen FHIR.Specimen):
+(if (specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').code.first() is null) then 1 else 0) +
+(if (specimen.collection.collected is null) then 1 else 0)

resources/test/query_bbmri.cql

@@ -0,0 +1,87 @@
+library Retrieve
+using FHIR version '4.0.0'
+include FHIRHelpers version '4.0.0'
+
+codesystem loinc: 'http://loinc.org'
+
+codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
+
+codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
+
+context Patient
+
+define AgeClass:
+     (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] else {} as List<Specimen>
+
+define Diagnosis:
+ if InInitialPopulation then [Condition] else {} as List<Condition> 
+ 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(), 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

resources/test/query_bbmri_placeholders.cql

@@ -0,0 +1,27 @@
+library Retrieve
+using FHIR version '4.0.0'
+include FHIRHelpers version '4.0.0'
+
+codesystem loinc: 'http://loinc.org'
+
+codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
+
+codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
+
+context Patient
+
+BBMRI_STRAT_AGE_STRATIFIER
+
+BBMRI_STRAT_GENDER_STRATIFIER
+
+BBMRI_STRAT_CUSTODIAN_STRATIFIER
+
+BBMRI_STRAT_SAMPLE_TYPE_STRATIFIER
+
+BBMRI_STRAT_DEF_SPECIMEN
+    if InInitialPopulation then [Specimen] else {} as List<Specimen>
+
+BBMRI_STRAT_DIAGNOSIS_STRATIFIER
+
+BBMRI_STRAT_DEF_IN_INITIAL_POPULATION
+true

src/exporter.rs

@@ -36,13 +36,13 @@ pub async fn post_exporter_query(body: &String, execute: bool) -> Result<String,
     let mut headers = HeaderMap::new();
 
     headers.insert(
-        header::CONTENT_TYPE, //TODO discard the result, just return OK
-        HeaderValue::from_static("text/html; charset=UTF-8"),
+        header::CONTENT_TYPE, 
+        HeaderValue::from_static("application/json"),
     );
 
     if let Some(auth_header_value) = CONFIG.auth_header.clone() {
         headers.insert(
-            header::AUTHORIZATION,
+            "x-api-key",
             HeaderValue::from_str(auth_header_value.as_str())
                 .map_err(FocusError::InvalidHeaderValue)?,
         );