From 9c05e7c9e33471a4511dca39c648e06973cbe485 Mon Sep 17 00:00:00 2001 From: Alexander Kiel Date: Mon, 24 Jun 2024 09:59:41 +0200 Subject: [PATCH 1/9] Set new Dev Version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 87b7d58..2326604 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.medizininformatik-initiative sq2cql - 0.3.0 + 0.4.0-SNAPSHOT sq2cql From 9bb4d1962f48f247853b5747f64a6d6963e1d8f1 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 10 Jul 2024 19:35:45 +0000 Subject: [PATCH 2/9] Update dependency org.apache.maven.plugins:maven-surefire-plugin to v3.3.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 2326604..c6974e1 100644 --- a/pom.xml +++ b/pom.xml @@ -128,7 +128,7 @@ org.apache.maven.plugins maven-surefire-plugin - 3.3.0 + 3.3.1 From 65ec176d8f2665773e7235d482bd670d474251fd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:30:17 +0000 Subject: [PATCH 3/9] Update dependency org.apache.maven.plugins:maven-failsafe-plugin to v3.3.1 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index c6974e1..cbcd8f8 100644 --- a/pom.xml +++ b/pom.xml @@ -134,7 +134,7 @@ org.apache.maven.plugins maven-failsafe-plugin - 3.3.0 + 3.3.1 From 8cf1754d8b2118cb16ed4bb257f15487a959771a Mon Sep 17 00:00:00 2001 From: Alexander Kiel Date: Fri, 12 Jul 2024 12:42:40 +0200 Subject: [PATCH 4/9] Fix Reference Comparison for Multi-Valued Paths I just use `contains` everywhere because FHIRPath expressions return a list anyway. Closes: 119 --- .../structured_query/ReferenceModifier.java | 2 +- .../de/numcodex/sq2cql/AcceptanceTest.java | 23 +++++- .../java/de/numcodex/sq2cql/EvaluationIT.java | 2 +- .../java/de/numcodex/sq2cql/SpecimenTest.java | 70 +++++++++---------- 4 files changed, 58 insertions(+), 39 deletions(-) diff --git a/src/main/java/de/numcodex/sq2cql/model/structured_query/ReferenceModifier.java b/src/main/java/de/numcodex/sq2cql/model/structured_query/ReferenceModifier.java index 4a1abb3..9b9d727 100644 --- a/src/main/java/de/numcodex/sq2cql/model/structured_query/ReferenceModifier.java +++ b/src/main/java/de/numcodex/sq2cql/model/structured_query/ReferenceModifier.java @@ -29,7 +29,7 @@ public Container updateQuery(MappingContext mappingContext, Con var referenceExpr = InvocationExpression.of(query.sourceAlias(), path); var alias = StandardIdentifierExpression.of(targetType.substring(0, 1)); var ref = AdditionExpressionTerm.of(StringLiteralExpression.of(targetType + "/"), InvocationExpression.of(alias, "id")); - var comparatorExpr = ComparatorExpression.equal(referenceExpr, ref); + var comparatorExpr = MembershipExpression.contains(referenceExpr, ref); return query.appendQueryInclusionClause(WithClause.of(AliasedQuerySource.of(referencesExprName, alias), comparatorExpr)); })); } diff --git a/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java b/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java index fe1a38e..98e143d 100644 --- a/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java +++ b/src/test/java/de/numcodex/sq2cql/AcceptanceTest.java @@ -13,6 +13,7 @@ import org.junit.jupiter.api.TestInstance; import org.junit.jupiter.api.TestInstance.Lifecycle; import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.CsvSource; import org.junit.jupiter.params.provider.MethodSource; import org.junit.jupiter.params.provider.ValueSource; import org.slf4j.Logger; @@ -49,7 +50,7 @@ public class AcceptanceTest { private static final Logger logger = LoggerFactory.getLogger(AcceptanceTest.class); private final GenericContainer blaze = new GenericContainer<>( - DockerImageName.parse("samply/blaze:0.27")) + DockerImageName.parse("samply/blaze:0.28")) .withImagePullPolicy(PullPolicy.alwaysPull()) .withEnv("LOG_LEVEL", "debug") .withExposedPorts(8080) @@ -158,7 +159,8 @@ public void consent() throws Exception { } @ParameterizedTest - @ValueSource(strings = {"large-query-worst-case-with-time-constraints.json", "test-large-query-more-crit-time-rest-1.json"}) + @ValueSource(strings = {"large-query-worst-case-with-time-constraints.json", + "test-large-query-more-crit-time-rest-1.json"}) public void largeQuery(String filename) throws Exception { var structuredQuery = new ObjectMapper().readValue(slurp(filename), StructuredQuery.class); var cql = translator.toCql(structuredQuery).print(); @@ -168,6 +170,23 @@ public void largeQuery(String filename) throws Exception { assertEquals(0, report.getGroupFirstRep().getPopulationFirstRep().getCount()); } + @ParameterizedTest + @CsvSource({ + "SpecimenSQ.json, 0", + "SpecimenSQExclusion.json, 159", + "SpecimenSQTwoInclusion.json, 0", + "SpecimenSQTwoReferenceCriteria.json, 0", + "SpecimenSQAndBodySite.json, 0" + }) + public void specimenQuery(String filename, int count) throws Exception { + var structuredQuery = new ObjectMapper().readValue(slurp(filename), StructuredQuery.class); + var cql = translator.toCql(structuredQuery).print(); + var measureUri = createMeasureAndLibrary(cql); + var report = evaluateMeasure(measureUri); + + assertEquals(count, report.getGroupFirstRep().getPopulationFirstRep().getCount()); + } + private String createMeasureAndLibrary(String cql) throws Exception { var libraryUri = "urn:uuid" + UUID.randomUUID(); var library = appendCql(parseResource(Library.class, slurp("Library.json")).setUrl(libraryUri), cql); diff --git a/src/test/java/de/numcodex/sq2cql/EvaluationIT.java b/src/test/java/de/numcodex/sq2cql/EvaluationIT.java index 46eede3..a607782 100644 --- a/src/test/java/de/numcodex/sq2cql/EvaluationIT.java +++ b/src/test/java/de/numcodex/sq2cql/EvaluationIT.java @@ -50,7 +50,7 @@ public class EvaluationIT { static final Map CODE_SYSTEM_ALIASES = Map.of("http://loinc.org", "loinc"); @Container - private final GenericContainer blaze = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.27")) + private final GenericContainer blaze = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.28")) .withImagePullPolicy(PullPolicy.alwaysPull()) .withExposedPorts(8080) .waitingFor(Wait.forHttp("/health").forStatusCode(200)) diff --git a/src/test/java/de/numcodex/sq2cql/SpecimenTest.java b/src/test/java/de/numcodex/sq2cql/SpecimenTest.java index f5456fe..11eaab2 100644 --- a/src/test/java/de/numcodex/sq2cql/SpecimenTest.java +++ b/src/test/java/de/numcodex/sq2cql/SpecimenTest.java @@ -52,25 +52,25 @@ public void translate() throws Exception { define Criterion: exists (from [Specimen: Code '119364003' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '258590006' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866034009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '2421000181104' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866035005' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '442427000' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '737089009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) define InInitialPopulation: Criterion @@ -108,25 +108,25 @@ public void translateExclusion() throws Exception { define "Criterion 2": exists (from [Specimen: Code '119364003' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '258590006' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866034009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '2421000181104' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866035005' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '442427000' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '737089009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) define Exclusion: "Criterion 2" @@ -165,25 +165,25 @@ public void translateTwoInclusion() throws Exception { define "Criterion 2": exists (from [Specimen: Code '119364003' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '258590006' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866034009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '2421000181104' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866035005' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '442427000' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '737089009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) define InInitialPopulation: "Criterion 1" and @@ -218,25 +218,25 @@ public void translateTwoReferenceCriteria() throws Exception { define Criterion: exists (from [Specimen: Code '119364003' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '258590006' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866034009' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '2421000181104' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '866035005' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '442427000' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) or + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) or exists (from [Specimen: Code '737089009' from snomed] S with "Diagnose E13.9 and Diagnose E13.1" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id) + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id) define InInitialPopulation: Criterion @@ -269,31 +269,31 @@ public void translateAndBodySite() throws Exception { define Criterion: exists (from [Specimen: Code '119364003' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '258590006' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '866034009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '2421000181104' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '866035005' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '442427000' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) or exists (from [Specimen: Code '737089009' from snomed] S with "Diagnose E13.9" C - such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference = 'Condition/' + C.id + such that S.extension.where(url='https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/StructureDefinition/Diagnose').first().value.as(Reference).reference contains 'Condition/' + C.id where S.collection.bodySite.coding contains Code 'C44.6' from icd_o_3) define InInitialPopulation: From 34b1af23a60a054dc44073762b1fa3cd217003fd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 12 Jul 2024 13:32:46 +0000 Subject: [PATCH 5/9] Update dependency org.assertj:assertj-core to v3.26.3 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index cbcd8f8..200418a 100644 --- a/pom.xml +++ b/pom.xml @@ -73,7 +73,7 @@ org.assertj assertj-core - 3.26.0 + 3.26.3 test From f471e8039c9bd58585031ec223c5ad365581fd89 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 12 Jul 2024 13:42:39 +0000 Subject: [PATCH 6/9] Update dependency com.fasterxml.jackson.core:jackson-databind to v2.17.2 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 200418a..5dde824 100644 --- a/pom.xml +++ b/pom.xml @@ -40,7 +40,7 @@ com.fasterxml.jackson.core jackson-databind - 2.17.1 + 2.17.2 From c4c432df4022a2a4bd4bcd25921abe38e6e2b37f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 12 Jul 2024 13:55:08 +0000 Subject: [PATCH 7/9] Update junit5 monorepo to v5.10.3 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 5dde824..34a1dd9 100644 --- a/pom.xml +++ b/pom.xml @@ -28,7 +28,7 @@ UTF-8 17 - 5.10.2 + 5.10.3 7.2.1 1.19.8 2.0.13 From 35f93ea2b26d7f6178979856e501c1fc5257d4e0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 17 Jul 2024 17:40:25 +0000 Subject: [PATCH 8/9] Update testcontainers-java monorepo to v1.20.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 34a1dd9..5f0acb5 100644 --- a/pom.xml +++ b/pom.xml @@ -30,7 +30,7 @@ 17 5.10.3 7.2.1 - 1.19.8 + 1.20.0 2.0.13 2.2.0 From fe9963b2afdadef99fd208a69894420f934441cc Mon Sep 17 00:00:00 2001 From: Alexander Kiel Date: Mon, 22 Jul 2024 11:57:11 +0200 Subject: [PATCH 9/9] Release v0.4.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 5f0acb5..d025222 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.medizininformatik-initiative sq2cql - 0.4.0-SNAPSHOT + 0.4.0 sq2cql