Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core
This commit is contained in:
Grahame Grieve
commit
fc5a57c10b
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@ -0,0 +1 @@
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* fix bug for NullPointerException in Bundle convertors when resource is not available.
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@ -1,6 +1,15 @@
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# Resource Conversion
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##### Let's talk about converting resources between the various versions of FHIR...
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## IMPORTANT
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-----
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_The conversion code in this module is maintained as part of the development of the standard, but always under
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considerable time pressure. Only part of the code is rigorously tested [as detailed here](#reliable-conversion-code).
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Implementers should regard this code as a 'scaffold' for actual reliable conversions._
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**ALWAYS TEST ANY CONVERSION ROUTINES BEFORE USING THEM IN PRODUCTION!**
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_Ideally, this should be via unit tests in your code, or better yet [unit tests contributed to FHIR](#test-cases)._
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### A note regarding syntax
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@ -31,7 +40,7 @@ and [r4](http://hl7.org/fhir/R4/account.html)
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**N.B.** This information is only for code navigation purposes. It is important that when converting between versions
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you use the provided conversion factory classes as your entry point.
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### Using the conversion library
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## Using the conversion library
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-----
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The majority of use cases for conversion will involve using the provided VersionConvertorFactory_V1_V2 classes to convert
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@ -193,3 +202,31 @@ Once you've created your new advisor, they can be provided as an argument when c
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`public static (V1 Resource) convertResource((V2 Resource) src, <T extends BaseAdvisor> advisor)`
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`public static (V2 Resource) convertResource((V1 Resource) src, <T extends BaseAdvisor> advisor)`
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## Development notes
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-----
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### Reliable conversion code
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The FHIR project maintains and tests conversions on the following resources, from old versions to R5:
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- CodeSystem
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- ValueSet
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- ConceptMap
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- StructureDefinition
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- StructureMap
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- ImplementationGuide
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- CapabilityStatement
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- OperationDefinition
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- NamingSystem
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These can be relied on and are subject to extensive testing.
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### Test cases
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Some conversions have test cases for particular resources and particular version combinations. Where test cases exist,
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they will continue to be maintained and expected to pass.
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Contributing test cases is highly encouraged! To contribute, create a PRs to the
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[core library](https://github.com/hapifhir/org.hl7.fhir.core), or even better, to the
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[FHIR test cases library](https://github.com/FHIR/fhir-test-cases).
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@ -1,32 +0,0 @@
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About the version conversion routines
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The version conversion routines are maintained as part of
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the development of the standard, but always under considerable
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time pressure. Implementers should regard these as 'scaffolds' for
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an actual reliable conversion routine.
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The FHIR project maintains and tests conversions on the following
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resources, from old versions to R5:
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* CodeSystem
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* ValueSet
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* ConceptMap
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* StructureDefinition
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* StructureMap
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* ImplementationGuide
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* CapabilityStatement
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* OperationDefinition
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* NamingSystem
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These can be relied on and are subject to extensive testing.
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In addition to this, some of the conversions have test cases
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for particular resources and particular version combinations.
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Where test cases exist, they will continue to pass and be
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maintained.
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So:
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* test the conversion routines before using them in production
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* contribute test cases to ensure that your use cases continue to be reliable
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Test cases are welcome - make them as PRs to the core library, or even better,
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to the FHIR test cases library
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@ -60,8 +60,8 @@ public class Bundle10_30 {
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tgt.addLink(convertBundleLinkComponent(t));
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if (src.hasFullUrlElement())
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tgt.setFullUrlElement(Uri10_30.convertUri(src.getFullUrlElement()));
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org.hl7.fhir.dstu2.model.Resource res = ConversionContext10_30.INSTANCE.getVersionConvertor_10_30().convertResource(src.getResource());
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tgt.setResource(res);
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if (src.hasResource())
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tgt.setResource(ConversionContext10_30.INSTANCE.getVersionConvertor_10_30().convertResource(src.getResource()));
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if (src.hasSearch())
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tgt.setSearch(convertBundleEntrySearchComponent(src.getSearch()));
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if (src.hasRequest())
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@ -78,8 +78,8 @@ public class Bundle10_40 {
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for (org.hl7.fhir.r4.model.Bundle.BundleLinkComponent t : src.getLink()) tgt.addLink(convertBundleLinkComponent(t));
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if (src.hasFullUrlElement())
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tgt.setFullUrlElement(Uri10_40.convertUri(src.getFullUrlElement()));
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org.hl7.fhir.dstu2.model.Resource res = ConversionContext10_40.INSTANCE.getVersionConvertor_10_40().convertResource(src.getResource());
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tgt.setResource(res);
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if (src.hasResource())
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tgt.setResource(ConversionContext10_40.INSTANCE.getVersionConvertor_10_40().convertResource(src.getResource()));
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if (src.hasSearch())
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tgt.setSearch(convertBundleEntrySearchComponent(src.getSearch()));
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if (src.hasRequest())
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@ -78,8 +78,8 @@ public class Bundle10_50 {
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for (org.hl7.fhir.r5.model.Bundle.BundleLinkComponent t : src.getLink()) tgt.addLink(convertBundleLinkComponent(t));
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if (src.hasFullUrlElement())
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tgt.setFullUrlElement(Uri10_50.convertUri(src.getFullUrlElement()));
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org.hl7.fhir.dstu2.model.Resource res = ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().convertResource(src.getResource());
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tgt.setResource(res);
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if (src.hasResource())
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tgt.setResource(ConversionContext10_50.INSTANCE.getVersionConvertor_10_50().convertResource(src.getResource()));
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if (src.hasSearch())
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tgt.setSearch(convertBundleEntrySearchComponent(src.getSearch()));
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if (src.hasRequest())
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@ -0,0 +1,35 @@
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package org.hl7.fhir.convertors.conv10_30;
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import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.DisplayName;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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public class Bundle10_30Test {
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@Test
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@DisplayName("Test 10_30 bundle conversion when resource is null")
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public void testNoResourceBundleConversion() throws IOException {
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org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent bec = new org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent()
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.setRequest(
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new org.hl7.fhir.dstu3.model.Bundle.BundleEntryRequestComponent()
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.setMethod(org.hl7.fhir.dstu3.model.Bundle.HTTPVerb.DELETE)
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.setUrl("Patient?identifier=123456")
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);
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org.hl7.fhir.dstu3.model.Bundle stu3Bundle = new org.hl7.fhir.dstu3.model.Bundle()
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.addEntry(bec);
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org.hl7.fhir.dstu2.model.Resource dstu2Resource = VersionConvertorFactory_10_30.convertResource(stu3Bundle);
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Assertions.assertNotNull(dstu2Resource);
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Assertions.assertTrue(dstu2Resource instanceof org.hl7.fhir.dstu2.model.Bundle);
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org.hl7.fhir.dstu2.model.Bundle dstu2Bundle = (org.hl7.fhir.dstu2.model.Bundle) dstu2Resource;
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Assertions.assertEquals(1, dstu2Bundle.getEntry().size());
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Assertions.assertNull(dstu2Bundle.getEntry().get(0).getResource());
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}
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}
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@ -0,0 +1,34 @@
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package org.hl7.fhir.convertors.conv10_40;
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import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_40;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.DisplayName;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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public class Bundle10_40Test {
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@Test
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@DisplayName("Test 10_40 bundle conversion when resource is null")
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public void testNoResourceBundleConversion() throws IOException {
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org.hl7.fhir.r4.model.Bundle.BundleEntryComponent bec = new org.hl7.fhir.r4.model.Bundle.BundleEntryComponent()
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.setRequest(
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new org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent()
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.setMethod(org.hl7.fhir.r4.model.Bundle.HTTPVerb.DELETE)
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.setUrl("Patient?identifier=123456")
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);
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org.hl7.fhir.r4.model.Bundle r4Bundle = new org.hl7.fhir.r4.model.Bundle()
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.addEntry(bec);
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org.hl7.fhir.dstu2.model.Resource dstu2Resource = VersionConvertorFactory_10_40.convertResource(r4Bundle);
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Assertions.assertNotNull(dstu2Resource);
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Assertions.assertTrue(dstu2Resource instanceof org.hl7.fhir.dstu2.model.Bundle);
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org.hl7.fhir.dstu2.model.Bundle dstu2Bundle = (org.hl7.fhir.dstu2.model.Bundle) dstu2Resource;
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Assertions.assertEquals(1, dstu2Bundle.getEntry().size());
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Assertions.assertNull(dstu2Bundle.getEntry().get(0).getResource());
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}
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}
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@ -0,0 +1,34 @@
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package org.hl7.fhir.convertors.conv10_50;
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import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.DisplayName;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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public class Bundle10_50Test {
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@Test
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@DisplayName("Test 10_50 bundle conversion when resource is null")
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public void testNoResourceBundleConversion() throws IOException {
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org.hl7.fhir.r5.model.Bundle.BundleEntryComponent bec = new org.hl7.fhir.r5.model.Bundle.BundleEntryComponent()
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.setRequest(
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new org.hl7.fhir.r5.model.Bundle.BundleEntryRequestComponent()
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.setMethod(org.hl7.fhir.r5.model.Bundle.HTTPVerb.DELETE)
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.setUrl("Patient?identifier=123456")
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);
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org.hl7.fhir.r5.model.Bundle r5Bundle = new org.hl7.fhir.r5.model.Bundle()
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.addEntry(bec);
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org.hl7.fhir.dstu2.model.Resource dstu2Resource = VersionConvertorFactory_10_50.convertResource(r5Bundle);
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Assertions.assertNotNull(dstu2Resource);
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Assertions.assertTrue(dstu2Resource instanceof org.hl7.fhir.dstu2.model.Bundle);
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org.hl7.fhir.dstu2.model.Bundle dstu2Bundle = (org.hl7.fhir.dstu2.model.Bundle) dstu2Resource;
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Assertions.assertEquals(1, dstu2Bundle.getEntry().size());
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Assertions.assertNull(dstu2Bundle.getEntry().get(0).getResource());
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}
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}
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@ -1,33 +1,33 @@
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package org.hl7.fhir.r4.terminologies;
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/*
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Copyright (c) 2011+, HL7, Inc.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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|
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* Redistributions of source code must retain the above copyright notice, this
|
||||
list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
|
||||
this list of conditions and the following disclaimer in the documentation
|
||||
and/or other materials provided with the distribution.
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* Neither the name of HL7 nor the names of its contributors may be used to
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||||
endorse or promote products derived from this software without specific
|
||||
prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
||||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
|
||||
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
|
||||
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
|
||||
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
||||
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
*/
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/*
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Copyright (c) 2011+, HL7, Inc.
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All rights reserved.
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||||
|
||||
Redistribution and use in source and binary forms, with or without modification,
|
||||
are permitted provided that the following conditions are met:
|
||||
|
||||
* Redistributions of source code must retain the above copyright notice, this
|
||||
list of conditions and the following disclaimer.
|
||||
* Redistributions in binary form must reproduce the above copyright notice,
|
||||
this list of conditions and the following disclaimer in the documentation
|
||||
and/or other materials provided with the distribution.
|
||||
* Neither the name of HL7 nor the names of its contributors may be used to
|
||||
endorse or promote products derived from this software without specific
|
||||
prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
||||
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
||||
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
|
||||
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
|
||||
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
|
||||
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
||||
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
|
||||
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
||||
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
*/
|
||||
|
||||
|
||||
|
||||
|
|
@ -64,7 +64,7 @@ public class ConceptMapEngine {
|
|||
for (ConceptMapGroupComponent g : cm.getGroup()) {
|
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for (SourceElementComponent e : g.getElement()) {
|
||||
if (code.equals(e.getCode())) {
|
||||
if (e != null)
|
||||
if (ct != null)
|
||||
throw new FHIRException("Unable to process translate "+code+" because multiple candidate matches were found in concept map "+cm.getUrl());
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||||
ct = e;
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||||
cg = g;
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||||
|
|
@ -94,4 +94,4 @@ public class ConceptMapEngine {
|
|||
throw new Error("Not done yet");
|
||||
}
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||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,92 @@
|
|||
package org.hl7.fhir.r4.terminologies;
|
||||
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.r4.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
import org.hl7.fhir.r4.model.ConceptMap;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
import javax.annotation.Nonnull;
|
||||
import org.junit.jupiter.api.DisplayName;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collection;
|
||||
import java.util.Collections;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
class ConceptMapEngineTest {
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||||
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||||
private static final String CONCEPT_MAP_URL = "https://test-fhir.com/ConceptMap/fake";
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||||
public static final String SOURCE_CODE_STRING = "body-weight";
|
||||
public static final String TARGET_CODE_STRING = "vital-signs";
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||||
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||||
@Test
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||||
@DisplayName("Coding is translated according to ConceptMap")
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||||
void codingTranslate() throws IOException {
|
||||
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||||
final ConceptMap.SourceElementComponent sourceElementComponent = getSourceElementComponent();
|
||||
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||||
final ConceptMapEngine conceptMapEngine = getConceptMapEngine(Arrays.asList(sourceElementComponent));
|
||||
Coding coding = new Coding(null, SOURCE_CODE_STRING, "Body Weight");
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||||
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||||
Coding actual = conceptMapEngine.translate(coding, CONCEPT_MAP_URL);
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||||
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||||
assertEquals(TARGET_CODE_STRING, actual.getCode());
|
||||
}
|
||||
|
||||
@Test
|
||||
@DisplayName("Coding fails to translate due to multiple candidate matches in ConceptMap")
|
||||
void codingTranslateFailsForMultipleCandidateMatches() throws IOException {
|
||||
|
||||
final ConceptMap.SourceElementComponent sourceElementComponent = getSourceElementComponent();
|
||||
|
||||
final ConceptMapEngine conceptMapEngine = getConceptMapEngine(Arrays.asList(sourceElementComponent,
|
||||
sourceElementComponent
|
||||
));
|
||||
Coding coding = new Coding(null, SOURCE_CODE_STRING, "Body Weight");
|
||||
|
||||
assertThrows(FHIRException.class, () -> {
|
||||
conceptMapEngine.translate(coding, CONCEPT_MAP_URL);
|
||||
});
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private ConceptMapEngine getConceptMapEngine(Collection<ConceptMap.SourceElementComponent> elements) throws IOException {
|
||||
ConceptMap conceptMap = getConceptMap(elements);
|
||||
|
||||
SimpleWorkerContext simpleWorkerContext = mock(SimpleWorkerContext.class);
|
||||
when(simpleWorkerContext.fetchResource(ConceptMap.class, CONCEPT_MAP_URL)).thenReturn(conceptMap);
|
||||
|
||||
return new ConceptMapEngine(simpleWorkerContext);
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private ConceptMap.SourceElementComponent getSourceElementComponent() {
|
||||
ConceptMap.TargetElementComponent targetElementComponent = new ConceptMap.TargetElementComponent();
|
||||
targetElementComponent.setCode(TARGET_CODE_STRING);
|
||||
targetElementComponent.setEquivalence(Enumerations.ConceptMapEquivalence.EQUIVALENT);
|
||||
|
||||
ConceptMap.SourceElementComponent sourceElementComponent = new ConceptMap.SourceElementComponent();
|
||||
sourceElementComponent.setCode(SOURCE_CODE_STRING);
|
||||
sourceElementComponent.setTarget(Collections.singletonList(targetElementComponent));
|
||||
|
||||
return sourceElementComponent;
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private ConceptMap getConceptMap(Collection<ConceptMap.SourceElementComponent> elements) {
|
||||
|
||||
ConceptMap.ConceptMapGroupComponent conceptMapGroupComponent = new ConceptMap.ConceptMapGroupComponent();
|
||||
for (ConceptMap.SourceElementComponent element : elements) {
|
||||
conceptMapGroupComponent.addElement(element);
|
||||
}
|
||||
return new ConceptMap()
|
||||
.addGroup(conceptMapGroupComponent)
|
||||
.setUrl(CONCEPT_MAP_URL);
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue