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3153 update unknowncodesystemwarningvallidationsupport to have configurable severities (#3155) 

* 3153 updating the unknowncodesystemwarningvalidationsupport class

* 3153 updating version for smile

* 3153 update broken tests

* 3153 adding log

* 3153 cleanup

* 3153 cleanup

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM 2021-11-10 16:06:09 -05:00 committed by GitHub
parent 5de955c3c2
commit 25c025cdee
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GPG Key ID: 4AEE18F83AFDEB23
60 changed files with 165 additions and 81 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-android/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

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hapi-fhir-base/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-batch/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-bom/pom.xml
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@ -10,7 +10,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId> <artifactId>hapi-fhir-cli</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath> <relativePath>../../hapi-deployable-pom</relativePath>
</parent> </parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-client/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3153-updating-unknowncodesystem-to-allow-warnings-to-be-registered-as-warnings.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 3153
title: "Updated UnknownCodeSystemWarningValidationSupport to allow the throwing of warnings if
configured to do so."

2
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpa/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
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@ -120,7 +120,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
myValidationSettings.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.IGNORE); myValidationSettings.setLocalReferenceValidationDefaultPolicy(IResourceValidator.ReferenceValidationPolicy.IGNORE);
myFhirCtx.setParserErrorHandler(new StrictErrorHandler()); myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myUnknownCodeSystemWarningValidationSupport.setAllowNonExistentCodeSystem(UnknownCodeSystemWarningValidationSupport.ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT); myUnknownCodeSystemWarningValidationSupport.setNonExistentCodeSystemSeverity(UnknownCodeSystemWarningValidationSupport.DEFAULT_SEVERITY);
} }
/** /**
@ -162,11 +162,12 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
} }
/** /**
* By default an unknown code system should fail vaildation * By default, an unknown code system should fail validation
*/ */
@Test @Test
public void testValidateCodeInValueSetWithUnknownCodeSystem_Warning() { public void testValidateCodeInValueSetWithUnknownCodeSystem_Warning() {
myUnknownCodeSystemWarningValidationSupport.setAllowNonExistentCodeSystem(true); // set to warning
myUnknownCodeSystemWarningValidationSupport.setNonExistentCodeSystemSeverity(IValidationSupport.IssueSeverity.WARNING);
createStructureDefWithBindingToUnknownCs(); createStructureDefWithBindingToUnknownCs();
@ -189,14 +190,14 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
oo = validateAndReturnOutcome(obs); oo = validateAndReturnOutcome(obs);
encoded = encode(oo); encoded = encode(oo);
ourLog.info(encoded); ourLog.info(encoded);
assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encoded); assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
// Invalid code // Invalid code
obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123)); obs.setValue(new Quantity().setSystem("http://cs").setCode("code99").setValue(123));
oo = validateAndReturnOutcome(obs); oo = validateAndReturnOutcome(obs);
encoded = encode(oo); encoded = encode(oo);
ourLog.info(encoded); ourLog.info(encoded);
assertEquals("No issues detected during validation", oo.getIssueFirstRep().getDiagnostics(), encoded); assertTrue(oo.getIssueFirstRep().getDiagnostics().contains("No issues detected during validation"));
} }

2
hapi-fhir-jpaserver-cql/pom.xml
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@ -7,7 +7,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-model/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-searchparam/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-test-utilities/pom.xml
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@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-server-mdm/pom.xml
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@ -7,7 +7,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-server-openapi/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-server/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId> <artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId> <artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId> <artifactId>hapi-fhir-spring-boot</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId> <artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-spring-boot/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-storage/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-testpage-overlay/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation-resources-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation-resources-dstu3/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation-resources-r4/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation-resources-r5/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

2
hapi-fhir-validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

102
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/UnknownCodeSystemWarningValidationSupport.java
View File

@ -3,8 +3,9 @@ package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ConceptValidationOptions; import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.ValidationSupportContext; import ca.uhn.fhir.context.support.ValidationSupportContext;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull; import javax.annotation.Nonnull;
import javax.annotation.Nullable; import javax.annotation.Nullable;
@ -18,9 +19,11 @@ import javax.annotation.Nullable;
* in order to specify that unknown code systems should be allowed. * in order to specify that unknown code systems should be allowed.
*/ */
public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSupport { public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSupport {
public static final boolean ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT = false; private static final Logger ourLog = LoggerFactory.getLogger(UnknownCodeSystemWarningValidationSupport.class);
private boolean myAllowNonExistentCodeSystem = ALLOW_NON_EXISTENT_CODE_SYSTEM_DEFAULT; public static final IssueSeverity DEFAULT_SEVERITY = IssueSeverity.ERROR;
private IssueSeverity myNonExistentCodeSystemSeverity = DEFAULT_SEVERITY;
/** /**
* Constructor * Constructor
@ -34,17 +37,39 @@ public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSup
return true; return true;
} }
@Override
public boolean isCodeSystemSupported(ValidationSupportContext theValidationSupportContext, String theSystem) {
return canValidateCodeSystem(theValidationSupportContext, theSystem);
}
@Override
public CodeValidationResult validateCode(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, String theValueSetUrl) {
// filters out error/fatal
if (!canValidateCodeSystem(theValidationSupportContext, theCodeSystem)) {
return null;
}
CodeValidationResult result = new CodeValidationResult()
.setSeverity(myNonExistentCodeSystemSeverity); // will be warning or info
result.setMessage("No issues detected during validation");
switch (myNonExistentCodeSystemSeverity) {
case INFORMATION:
// for warnings, we don't set the code
// cause if we do, the severity is stripped out
// (see VersionSpecificWorkerContextWrapper.convertValidationResult)
result.setCode(theCode);
break;
}
return result;
}
@Nullable @Nullable
@Override @Override
public CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) { public CodeValidationResult validateCodeInValueSet(ValidationSupportContext theValidationSupportContext, ConceptValidationOptions theOptions, String theCodeSystem, String theCode, String theDisplay, @Nonnull IBaseResource theValueSet) {
if (!myAllowNonExistentCodeSystem) { if (!canValidateCodeSystem(theValidationSupportContext, theCodeSystem)) {
return null;
}
if (theCodeSystem == null) {
return null;
}
IBaseResource codeSystem = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystem);
if (codeSystem != null) {
return null; return null;
} }
@ -54,7 +79,60 @@ public class UnknownCodeSystemWarningValidationSupport extends BaseValidationSup
.setMessage("Code " + theCodeSystem + "#" + theCode + " was not checked because the CodeSystem is not available"); .setMessage("Code " + theCodeSystem + "#" + theCode + " was not checked because the CodeSystem is not available");
} }
/**
* Returns true if non existent code systems will still validate.
* False if they will throw errors.
* @return
*/
private boolean allowNonExistentCodeSystems() {
switch (myNonExistentCodeSystemSeverity) {
case ERROR:
case FATAL:
return false;
default:
ourLog.info("Unknown issue severity " + myNonExistentCodeSystemSeverity.name()
+ ". Treating as INFO/WARNING");
case WARNING:
case INFORMATION:
return true;
}
}
private boolean canValidateCodeSystem(ValidationSupportContext theValidationSupportContext,
String theCodeSystem) {
if (!allowNonExistentCodeSystems()) {
return false;
}
if (theCodeSystem == null) {
return false;
}
IBaseResource codeSystem = theValidationSupportContext.getRootValidationSupport().fetchCodeSystem(theCodeSystem);
if (codeSystem != null) {
return false;
}
return true;
}
/**
* If set to allow, code system violations will be flagged with Warning by default.
* Use setNonExistentCodeSystemSeverity instead.
*
* @param theAllowNonExistentCodeSystem
*/
@Deprecated
public void setAllowNonExistentCodeSystem(boolean theAllowNonExistentCodeSystem) { public void setAllowNonExistentCodeSystem(boolean theAllowNonExistentCodeSystem) {
myAllowNonExistentCodeSystem = theAllowNonExistentCodeSystem; if (theAllowNonExistentCodeSystem) {
setNonExistentCodeSystemSeverity(IssueSeverity.WARNING);
} else {
setNonExistentCodeSystemSeverity(IssueSeverity.ERROR);
}
}
/**
* Sets the non-existent code system severity.
* @param theSeverity
*/
public void setNonExistentCodeSystemSeverity(IssueSeverity theSeverity) {
myNonExistentCodeSystemSeverity = theSeverity;
} }
} }

16
hapi-tinder-plugin/pom.xml
View File

@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>
@ -58,37 +58,37 @@
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId> <artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId> <artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId> <artifactId>hapi-fhir-structures-r4</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId> <artifactId>hapi-fhir-structures-r5</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId> <artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId> <artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId> <artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.apache.velocity</groupId> <groupId>org.apache.velocity</groupId>

2
hapi-tinder-test/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath> <relativePath>../pom.xml</relativePath>
</parent> </parent>

2
pom.xml
View File

@ -6,7 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging> <packaging>pom</packaging>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<name>HAPI-FHIR</name> <name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description> <description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url> <url>https://hapifhir.io</url>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
View File

@ -6,7 +6,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
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@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
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@ -5,7 +5,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>5.7.0-PRE2-SNAPSHOT</version> <version>5.7.0-PRE3-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath> <relativePath>../../pom.xml</relativePath>
</parent> </parent>