Merge pull request #151 from samply/develop

CQL generation and some other stuff
samply · Jun 20, 2024 · 0f4dfe4 · 0f4dfe4
2 parents 072ffdd + 28ed3d3
commit 0f4dfe4
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Showing 32 changed files with 2,143 additions and 71 deletions.
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
@@ -17,7 +17,7 @@ jobs:
       #architectures: '[ "amd64", "arm64" ]'
       #profile: debug
       test-via-script: false
-      #features: '[ "" ]'
+      features: '[ "bbmri", "dktk", "" ]'
       push-to: ${{ (github.ref_protected == true || github.event_name == 'workflow_dispatch') && 'dockerhub' || 'ghcr' }}
     secrets:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}

diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,4 @@ dev/pki/*
 !dev/pki/pki
 Cargo.lock
 .vscode/*
+pkg/
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.5.2"
+version = "0.6.0"
 edition = "2021"
 license = "Apache-2.0"
 
@@ -13,9 +13,14 @@ reqwest = { version = "0.11", default_features = false, features = ["json", "def
 serde = { version = "1.0.152", features = ["serde_derive"] }
 serde_json = "1.0"
 thiserror = "1.0.38"
+chrono = "0.4.31"
+indexmap = "2.1.0"
 tokio = { version = "1.25.0", default_features = false, features = ["signal", "rt-multi-thread", "macros"] }
 beam-lib = { git = "https://github.com/samply/beam", branch = "develop", features = ["http-util"] }
 laplace_rs = {git = "https://github.com/samply/laplace-rs.git", tag = "v0.3.0" }
+uuid = "1.8.0"
+rand = { default-features = false, version = "0.8.5" }
+futures-util = { version = "0.3", default-features = false, features = ["std"] }
 
 # Logging
 tracing = { version = "0.1.37", default_features = false }
@@ -26,12 +31,15 @@ once_cell = "1.18"
 
 # Command Line Interface
 clap = { version = "4", default_features = false, features = ["std", "env", "derive", "help", "color"] }
-rand = { default-features = false, version = "0.8.5" }
-futures-util = { version = "0.3", default-features = false, features = ["std"] }
+
+[features]
+default = []
+bbmri = []
+dktk = []
 
 [dev-dependencies]
-tokio-test = "0.4.2"
 pretty_assertions = "1.4.0"
+tokio-test = "0.4.2"
 
 [build-dependencies]
 build-data = "0"

diff --git a/README.md b/README.md
diff --git a/resources/bbmri → ...ase64_encoded_queries_to_cache_results_of b/resources/bbmri → ...ase64_encoded_queries_to_cache_results_of
diff --git a/resources/cql/BBMRI_STRAT_DIAGNOSIS_STRATIFIER b/resources/cql/BBMRI_STRAT_DIAGNOSIS_STRATIFIER
@@ -4,5 +4,5 @@ define Diagnosis:
  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(), 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())
 
diff --git a/resources/measure.json → resources/measure_bbmri.json b/resources/measure.json → resources/measure_bbmri.json
diff --git a/resources/library.json → resources/test/library.json b/resources/library.json → resources/test/library.json
diff --git a/resources/test/query_bbmri.cql b/resources/test/query_bbmri.cql
@@ -82,7 +82,7 @@ define Diagnosis:
  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(), 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())
 
 
 

diff --git a/resources/test/result_age_at_diagnosis_30_to_70.cql b/resources/test/result_age_at_diagnosis_30_to_70.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  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 [Condition] C
+where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling(30) and Ceiling(70)))))
diff --git a/resources/test/result_age_at_diagnosis_lower_than_70.cql b/resources/test/result_age_at_diagnosis_lower_than_70.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  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 [Condition] C
+where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling(0) and Ceiling(70)))))