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Rev to CR 3.0.0-PRE13, HAPI 6.10.0, FHIR Core 6.1.2.2 (#390)
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* Rev to  CR 3.0.0-PRE13

* Fix formatting

* Update to CQL 3.5.1
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@JPercival
JPercival authored Dec 8, 2023
1 parent 3533fc4 commit 3354da7
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Showing 17 changed files with 97 additions and 89 deletions.
4 changes: 2 additions & 2 deletions cqf-fhir-api/pom.xml
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Expand Up @@ -5,14 +5,14 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-api</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (APIs)</name>
<description>FHIR Repository APIs used by this project. Implement these to incorporate clinical reasoning on your platform</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
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12 changes: 6 additions & 6 deletions cqf-fhir-benchmark/pom.xml
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Expand Up @@ -5,26 +5,26 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-benchmark</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (Benchmarks)</name>
<description>Tests validating performance of FHIR Clinical Reasoning operations</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-test</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.openjdk.jmh</groupId>
Expand All @@ -34,14 +34,14 @@
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<!--TODO: test-jars don't seem to work very well. Need to investigate some alternatives -->
<type>test-jar</type>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
<scope>test</scope>
</dependency>
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20 changes: 10 additions & 10 deletions cqf-fhir-bom/pom.xml
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Expand Up @@ -5,60 +5,60 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-bom</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<packaging>pom</packaging>
<name>FHIR Clinical Reasoning (Bill Of Materials)</name>
<description>This bom can be used to simplify dependency management when using this project</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-api</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-test</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-utility</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cql</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jaxb</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr-cli</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
</dependencies>
</dependencyManagement>
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12 changes: 6 additions & 6 deletions cqf-fhir-cql/pom.xml
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Expand Up @@ -5,26 +5,26 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cql</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (CQL)</name>
<description>Tools, utilities, code gen to support CQL in FHIR Clinical Reasoning operations</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-api</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-utility</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>info.cqframework</groupId>
Expand Down Expand Up @@ -53,13 +53,13 @@
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-test</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
<scope>test</scope>
</dependency>
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12 changes: 6 additions & 6 deletions cqf-fhir-cr-cli/pom.xml
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Expand Up @@ -5,36 +5,36 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr-cli</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (CLI)</name>
<description>CLI for running FHIR Clincial Reasoning operations</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-api</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-utility</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cql</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
</dependency>
<dependency>
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6 changes: 3 additions & 3 deletions cqf-fhir-cr-spring/pom.xml
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Expand Up @@ -6,21 +6,21 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr-spring</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (Spring)</name>
<description>Spring configurations for FHIR Clinical Reasoning</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
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14 changes: 7 additions & 7 deletions cqf-fhir-cr/pom.xml
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Expand Up @@ -5,45 +5,45 @@

<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cr</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<name>FHIR Clinical Reasoning (Operations)</name>
<description>Implementations of clinical reasoning operations</description>

<parent>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</parent>

<dependencies>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-api</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-cql</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-utility</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
</dependency>

<!-- test dependencies-->
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-jackson</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<type>pom</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencds.cqf.fhir</groupId>
<artifactId>cqf-fhir-test</artifactId>
<version>3.0.0-PRE13-SNAPSHOT</version>
<version>3.0.0-PRE13</version>
<scope>test</scope>
</dependency>
<dependency>
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11 changes: 6 additions & 5 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/dstu3/Dstu3MeasureProcessor.java
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Expand Up @@ -17,7 +17,6 @@
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.opencds.cqf.cql.engine.fhir.model.Dstu3FhirModelResolver;
import org.opencds.cqf.cql.engine.runtime.DateTime;
import org.opencds.cqf.cql.engine.runtime.Interval;
import org.opencds.cqf.fhir.api.Repository;
import org.opencds.cqf.fhir.cql.Engines;
Expand Down Expand Up @@ -59,7 +58,8 @@ public MeasureReport evaluateMeasure(
measure, periodStart, periodEnd, reportType, subjectIds, additionalData, parameters);
}

// NOTE: Do not make a top-level function that takes a Measure resource. This ensures that
// NOTE: Do not make a top-level function that takes a Measure resource. This
// ensures that
// the repositories are set up correctly.
protected MeasureReport evaluateMeasure(
Measure measure,
Expand Down Expand Up @@ -98,7 +98,8 @@ protected MeasureReport evaluateMeasure(
Map<String, Object> paramMap = resolveParameterMap(parameters);
context.getState().setParameters(lib.getLibrary(), paramMap);
// Set parameters for included libraries
// Note: this may not be the optimal method (e.g. libraries with the same parameter name, but different
// Note: this may not be the optimal method (e.g. libraries with the same
// parameter name, but different
// values)
if (lib.getLibrary().getIncludes() != null) {
lib.getLibrary()
Expand Down Expand Up @@ -147,9 +148,9 @@ protected MeasureReportType evalTypeToReportType(MeasureEvalType measureEvalType
private Interval buildMeasurementPeriod(String periodStart, String periodEnd) {
// resolve the measurement period
return new Interval(
DateTime.fromJavaDate(DateHelper.resolveRequestDate(periodStart, true)),
DateHelper.resolveRequestDate(periodStart, true),
true,
DateTime.fromJavaDate(DateHelper.resolveRequestDate(periodEnd, false)),
DateHelper.resolveRequestDate(periodEnd, false),
true);
}

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