samply · enola-dkfz · May 29, 2026 · Dec 12, 2025 · Dec 16, 2025 · Dec 17, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# Samply.Focus v0.24.0 2026-05-29
+
+## Major changes
+
+* BBMRI: stop checking diagnosis in Specimen
+
 # Samply.Focus v0.23.0 2026-04-28
 
 ## Major changes

diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "focus"
-version = "0.23.0"
+version = "0.24.0"
 edition = "2021"
 license = "Apache-2.0"
 
@@ -31,6 +31,7 @@ rand = { default-features = false, version = "0.9.0" }
 futures-util = { version = "0.3", default-features = false, features = ["std"] }
 tryhard = "0.5"
 
+
 # Logging
 tracing = { version = "0.1.37", default-features = false }
 tracing-subscriber = { version = "0.3.11", default-features = false, features = [
@@ -58,17 +59,13 @@ sqlx = { version = "0.8.2", features = [
   "chrono",
   "rust_decimal",
   "uuid",
-], optional = true }
+]}
 kurtbuilds_sqlx_serde = { version = "0.3.2", features = [
   "json",
   "decimal",
   "chrono",
   "uuid",
-], optional = true }
-
-[features]
-default = ["query-sql"]
-query-sql = ["dep:sqlx", "dep:kurtbuilds_sqlx_serde"]
+]}
 
 [dev-dependencies]
 pretty_assertions = "1.4.0"

diff --git a/README.md b/README.md
@@ -56,7 +56,7 @@ AUTH_HEADER = "[Auth Type] XXXX" #Authorization header for accessing the store;
 EXPORTER_API_KEY = "XXXX" # Value of header x-api-key for accessing the Exporter application
 ```
 
-In order to use Postgres querying, a Docker image built with the feature "dktk" needs to be used and this optional variable set:
+In order to use Postgres querying this optional variable needs to be set:
 ```bash
 POSTGRES_CONNECTION_STRING = "postgresql://postgres:Test.123@localhost:5432/postgres" # Postgres connection string
 ```

diff --git a/resources/test/query_bbmri.cql b/resources/test/query_bbmri.cql
diff --git a/resources/test/query_bbmri_placeholders.cql b/resources/test/query_bbmri_placeholders.cql
diff --git a/resources/test/result_after.cql b/resources/test/result_after.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 ((((exists from [Specimen] S

diff --git a/resources/test/result_age_at_diagnosis_30_to_70.cql b/resources/test/result_age_at_diagnosis_30_to_70.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 ((((exists from [Condition] C

diff --git a/resources/test/result_age_at_diagnosis_lower_than_70.cql b/resources/test/result_age_at_diagnosis_lower_than_70.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 ((((exists from [Condition] C

diff --git a/resources/test/result_all_gbn.cql b/resources/test/result_all_gbn.cql
@@ -76,18 +76,14 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
-((((Patient.gender = 'male') or (Patient.gender = 'other'))) and ((((((exists[Condition: Code 'C25' from icd10]) or (exists[Condition: Code 'C25' from icd10gm]) or (exists[Condition: Code 'C25' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C25'))))) or (((((exists[Condition: Code 'C56' from icd10]) or (exists[Condition: Code 'C56' from icd10gm]) or (exists[Condition: Code 'C56' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C56')))))) and (exists from [Condition] C
+((((Patient.gender = 'male') or (Patient.gender = 'other'))) and ((((((exists[Condition: Code 'C25' from icd10]) or (exists[Condition: Code 'C25' from icd10gm]) or (exists[Condition: Code 'C25' from icd10gmnew]))))) or (((((exists[Condition: Code 'C56' from icd10]) or (exists[Condition: Code 'C56' from icd10gm]) or (exists[Condition: Code 'C56' from icd10gmnew])))))) and (exists from [Condition] C
 where AgeInYearsAt(FHIRHelpers.ToDateTime(C.onset)) between Ceiling(10) and Ceiling(100)) and (exists from [Condition] C
 where FHIRHelpers.ToDateTime(C.onset) between @2023-09-30 and @2023-10-29) and (exists from [Observation: Code '39156-5' from loinc] O
 where ((O.value as Quantity) < 10 'kg/m2' and (O.value as Quantity) > 100 'kg/m2')) and (exists from [Observation: Code '29463-7' from loinc] O

diff --git a/resources/test/result_before.cql b/resources/test/result_before.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 ((((exists from [Specimen] S

diff --git a/resources/test/result_c61_and_male.cql b/resources/test/result_c61_and_male.cql
@@ -73,15 +73,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
-((((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C61')))))) and ((((Patient.gender = 'male'))))))
+((((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])))))) and ((((Patient.gender = 'male'))))))
diff --git a/resources/test/result_current.cql b/resources/test/result_current.cql
@@ -74,16 +74,12 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
-((((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])) or (exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code contains 'C61')))))) and (( AgeInYears() between Ceiling(10) and Ceiling(90)))) or (((exists from [Specimen] S
+((((((Patient.gender = 'male')))) and ((((((exists[Condition: Code 'C61' from icd10]) or (exists[Condition: Code 'C61' from icd10gm]) or (exists[Condition: Code 'C61' from icd10gmnew])))))) and (( AgeInYears() between Ceiling(10) and Ceiling(90)))) or (((exists from [Specimen] S
 where FHIRHelpers.ToDateTime(S.collection.collected) between @1900-01-01 and @2024-10-25 )) and ((((exists from [Specimen] S where (S.extension.where(url='https://fhir.bbmri.de/StructureDefinition/StorageTemperature').value.coding contains Code 'temperature2to10' from StorageTemperature) ))))))
diff --git a/resources/test/result_empty.cql b/resources/test/result_empty.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 true
diff --git a/resources/test/result_greater.cql b/resources/test/result_greater.cql
@@ -71,15 +71,11 @@ 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()
-  )
+  condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
+)
 
 define InInitialPopulation:
 ((((exists from [Condition] C