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Merge pull request #317 from samply/develop
v0.20.0
2 parents 2463fef + 344978f commit a41cc6f

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‎CHANGELOG.md‎

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# Samply.Focus v0.20.0 2026-01-13
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## Major changes
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* Optional obfuscation using limited Laplace distribution and rounding to the floor(number of digits /2) significant digits
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* Exporter uses DKTK CQL generation
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## Minor changes
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* Workaround for multiple ORed empty criteria fields
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* BETWEEN operator suported with only one boundary defined in the numeric range
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* Fixed double serialization in EUCAIM SQL
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# Samply.Focus v0.19.0 2025-11-03
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## Major changes

‎Cargo.toml‎

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[package]
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name = "focus"
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version = "0.19.0"
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version = "0.20.0"
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edition = "2021"
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license = "Apache-2.0"
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@@ -25,7 +25,7 @@ tokio = { version = "1.25.0", default-features = false, features = [
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beam-lib = { git = "https://github.com/samply/beam", branch = "develop", features = [
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"http-util",
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] }
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laplace_rs = { git = "https://github.com/samply/laplace-rs.git", tag = "v0.5.0" }
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laplace_rs = { git = "https://github.com/samply/laplace-rs.git", tag = "v0.6.0" }
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uuid = "1.8.0"
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rand = { default-features = false, version = "0.8.5" }
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futures-util = { version = "0.3", default-features = false, features = ["std"] }

‎README.md‎

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@@ -67,6 +67,8 @@ MAX_DB_ATTEMPTS = "8" # Max number of attempts to connect to the database; defau
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Obfuscating zero counts is by default switched off. To enable obfuscating zero counts, set the env. variable `OBFUSCATE_ZERO`.
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To obfuscate BBMRI-ERIC way (using a limited Laplace distribution and rounding to the floor(number of digits)/2 significant digits), set the env. variable `OBFUSCATE_BBMRI_ERIC_WAY`.
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Optionally, you can provide the `TLS_CA_CERTIFICATES_DIR` environment variable to add additional trusted certificates, e.g., if you have a TLS-terminating proxy server in place. The application respects the `HTTP_PROXY`, `HTTPS_PROXY`, `ALL_PROXY`, `NO_PROXY`, and their respective lowercase equivalents.
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Log level can be set using the `RUST_LOG` environment variable.

‎resources/cql/NNGM_STRAT_DIAGNOSIS_STRATIFIER‎

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define Diagnosis:
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if InInitialPopulation then [Condition] else {} as List<Condition>
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define function DiagnosisCode(condition FHIR.Condition):
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condition.bodySite.coding.where(system = 'http://terminology.hl7.org/CodeSystem/icd-o-3').code.first()

‎resources/test/result_greater.cql‎

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library Retrieve
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using FHIR version '4.0.0'
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include FHIRHelpers version '4.0.0'
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codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
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codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
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context Patient
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define AgeClass:
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if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)
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define Gender:
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if (Patient.gender is null) then 'unknown' else Patient.gender
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define Custodian:
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First(from Specimen.extension E
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where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
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return (E.value as Reference).identifier.value)
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define function SampleType(specimen FHIR.Specimen):
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case FHIRHelpers.ToCode(specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').first())
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when Code 'plasma-edta' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-citrat' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-heparin' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-cell-free' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-other' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-formalin' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'normal-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'other-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'normal-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'other-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-paxgene-or-else' from SampleMaterialType then 'tissue-other'
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when Code 'derivative' from SampleMaterialType then 'derivative-other'
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when Code 'liquid' from SampleMaterialType then 'liquid-other'
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when Code 'tissue' from SampleMaterialType then 'tissue-other'
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when Code 'serum' from SampleMaterialType then 'blood-serum'
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when Code 'cf-dna' from SampleMaterialType then 'dna'
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when Code 'g-dna' from SampleMaterialType then 'dna'
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when Code 'blood-plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-other' from SampleMaterialType then 'tissue-other'
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when Code 'derivative-other' from SampleMaterialType then 'derivative-other'
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when Code 'liquid-other' from SampleMaterialType then 'liquid-other'
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when Code 'blood-serum' from SampleMaterialType then 'blood-serum'
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when Code 'dna' from SampleMaterialType then 'dna'
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when Code 'buffy-coat' from SampleMaterialType then 'buffy-coat'
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when Code 'urine' from SampleMaterialType then 'urine'
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when Code 'ascites' from SampleMaterialType then 'ascites'
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when Code 'saliva' from SampleMaterialType then 'saliva'
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when Code 'csf-liquor' from SampleMaterialType then 'csf-liquor'
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when Code 'bone-marrow' from SampleMaterialType then 'bone-marrow'
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when Code 'peripheral-blood-cells-vital' from SampleMaterialType then 'peripheral-blood-cells-vital'
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when Code 'stool-faeces' from SampleMaterialType then 'stool-faeces'
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when Code 'rna' from SampleMaterialType then 'rna'
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when Code 'whole-blood' from SampleMaterialType then 'whole-blood'
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when Code 'swab' from SampleMaterialType then 'swab'
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when Code 'dried-whole-blood' from SampleMaterialType then 'dried-whole-blood'
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when null then 'Unknown'
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else 'Unknown'
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end
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define Specimen:
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if InInitialPopulation then [Specimen] S else {} as List<Specimen>
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define Diagnosis:
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if InInitialPopulation then [Condition] else {} as List<Condition>
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define function DiagnosisCode(condition FHIR.Condition):
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
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define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
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Coalesce(
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condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
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specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
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)
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define InInitialPopulation:
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((((exists from [Condition] C
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where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) >= Ceiling(60)))))

‎resources/test/result_less.cql‎

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library Retrieve
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using FHIR version '4.0.0'
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include FHIRHelpers version '4.0.0'
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codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
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codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
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context Patient
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define AgeClass:
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if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)
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define Gender:
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if (Patient.gender is null) then 'unknown' else Patient.gender
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define Custodian:
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First(from Specimen.extension E
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where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
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return (E.value as Reference).identifier.value)
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define function SampleType(specimen FHIR.Specimen):
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case FHIRHelpers.ToCode(specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').first())
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when Code 'plasma-edta' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-citrat' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-heparin' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-cell-free' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-other' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-formalin' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'normal-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'other-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'normal-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'other-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-paxgene-or-else' from SampleMaterialType then 'tissue-other'
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when Code 'derivative' from SampleMaterialType then 'derivative-other'
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when Code 'liquid' from SampleMaterialType then 'liquid-other'
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when Code 'tissue' from SampleMaterialType then 'tissue-other'
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when Code 'serum' from SampleMaterialType then 'blood-serum'
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when Code 'cf-dna' from SampleMaterialType then 'dna'
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when Code 'g-dna' from SampleMaterialType then 'dna'
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when Code 'blood-plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-other' from SampleMaterialType then 'tissue-other'
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when Code 'derivative-other' from SampleMaterialType then 'derivative-other'
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when Code 'liquid-other' from SampleMaterialType then 'liquid-other'
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when Code 'blood-serum' from SampleMaterialType then 'blood-serum'
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when Code 'dna' from SampleMaterialType then 'dna'
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when Code 'buffy-coat' from SampleMaterialType then 'buffy-coat'
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when Code 'urine' from SampleMaterialType then 'urine'
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when Code 'ascites' from SampleMaterialType then 'ascites'
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when Code 'saliva' from SampleMaterialType then 'saliva'
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when Code 'csf-liquor' from SampleMaterialType then 'csf-liquor'
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when Code 'bone-marrow' from SampleMaterialType then 'bone-marrow'
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when Code 'peripheral-blood-cells-vital' from SampleMaterialType then 'peripheral-blood-cells-vital'
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when Code 'stool-faeces' from SampleMaterialType then 'stool-faeces'
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when Code 'rna' from SampleMaterialType then 'rna'
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when Code 'whole-blood' from SampleMaterialType then 'whole-blood'
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when Code 'swab' from SampleMaterialType then 'swab'
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when Code 'dried-whole-blood' from SampleMaterialType then 'dried-whole-blood'
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when null then 'Unknown'
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else 'Unknown'
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end
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define Specimen:
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if InInitialPopulation then [Specimen] S else {} as List<Specimen>
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define Diagnosis:
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if InInitialPopulation then [Condition] else {} as List<Condition>
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define function DiagnosisCode(condition FHIR.Condition):
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
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define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
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Coalesce(
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condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
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specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
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)
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define InInitialPopulation:
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((((exists from [Condition] C
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where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) <= Ceiling(60)))))

‎src/ast.rs‎

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@@ -23,9 +23,6 @@ pub enum ConditionType {
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NotEquals,
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In,
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Between,
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LowerThan,
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GreaterThan,
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Contains,
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}
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#[derive(Serialize, Deserialize, Debug, Clone)]
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#[derive(Serialize, Deserialize, Debug, Clone)]
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pub struct NumRange {
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pub min: f64,
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pub max: f64,
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pub min: Option<f64>,
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pub max: Option<f64>,
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}
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#[derive(Serialize, Deserialize, Debug, Clone)]

‎src/blaze.rs‎

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use crate::util;
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use crate::util::get_json_field;
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#[derive(Deserialize, Debug)]
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#[serde(tag = "lang", rename_all = "lowercase")]
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pub enum Language {
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Cql(CqlQuery),
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Ast(AstQuery),
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}
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#[derive(Serialize, Deserialize, Debug, Default, Clone)]
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pub struct CqlQuery {
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pub lib: Value,

‎src/config.rs‎

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Blaze,
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Omop, // endpoint is URL of a query mediator translating AST to provider specific SQL
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EucaimApi, // endpoint is URL of custom API for querying EUCAIM provider
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EucaimBeacon,
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#[cfg(feature = "query-sql")]
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EucaimSql,
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#[cfg(feature = "query-sql")]
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EndpointType::Blaze => write!(f, "blaze"),
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EndpointType::Omop => write!(f, "omop"),
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EndpointType::EucaimApi => write!(f, "eucaim_api"),
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EndpointType::EucaimBeacon => write!(f, "eucaim_beacon"),
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#[cfg(feature = "query-sql")]
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EndpointType::EucaimSql => write!(f, "eucaim_sql"),
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#[cfg(feature = "query-sql")]
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#[clap(long, env, value_parser = clap::value_parser!(Obfuscate), default_value = "yes")]
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obfuscate: Obfuscate,
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/// Should the results be obfuscated the BBMRI ERIC way - default false
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#[clap(long, env, value_parser)]
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obfuscate_bbmri_eric_way: bool,
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/// Should zero values be obfuscated - default false
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#[clap(long, env, value_parser)]
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obfuscate_zero: bool,
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pub endpoint_type: EndpointType,
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pub cql_projects_enabled: Option<Vec<String>>,
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pub obfuscate: Obfuscate,
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pub obfuscate_bbmri_eric_way: bool,
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pub obfuscate_zero: bool,
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pub obfuscate_below_10_mode: usize,
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pub delta_patient: f64,
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endpoint_type: cli_args.endpoint_type,
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cql_projects_enabled: cli_args.cql_projects_enabled,
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obfuscate: cli_args.obfuscate,
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obfuscate_bbmri_eric_way: cli_args.obfuscate_bbmri_eric_way,
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obfuscate_zero: cli_args.obfuscate_zero,
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obfuscate_below_10_mode: cli_args.obfuscate_below_10_mode,
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delta_patient: cli_args.delta_patient,

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