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initial work Supporting FML transforms between different FHIR versions …
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -53,6 +53,7 @@ | |
| import org.hl7.fhir.r5.model.Narrative.NarrativeStatus; | ||
| import org.hl7.fhir.r5.model.StructureDefinition; | ||
| import org.hl7.fhir.r5.model.StructureMap; | ||
| import org.hl7.fhir.r5.model.UriType; | ||
| import org.hl7.fhir.r5.renderers.RendererFactory; | ||
| import org.hl7.fhir.r5.renderers.utils.RenderingContext; | ||
| import org.hl7.fhir.r5.utils.EOperationOutcome; | ||
|
|
@@ -63,6 +64,7 @@ | |
| import org.hl7.fhir.r5.fhirpath.FHIRPathEngine; | ||
| import org.hl7.fhir.utilities.ByteProvider; | ||
| import org.hl7.fhir.utilities.FhirPublication; | ||
| import org.hl7.fhir.utilities.Utilities; | ||
| import org.hl7.fhir.utilities.VersionUtilities; | ||
| import org.hl7.fhir.utilities.json.model.JsonObject; | ||
| import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager; | ||
|
|
@@ -74,6 +76,7 @@ | |
| import org.hl7.fhir.validation.ValidationEngine; | ||
| import org.hl7.fhir.validation.instance.InstanceValidator; | ||
|
|
||
| import ch.ahdis.matchbox.engine.MatchboxEngine.FilesystemPackageCacheMode; | ||
| import ch.ahdis.matchbox.engine.cli.VersionUtil; | ||
| import ch.ahdis.matchbox.mappinglanguage.MatchboxStructureMapUtilities; | ||
| import ch.ahdis.matchbox.mappinglanguage.TransformSupportServices; | ||
|
|
@@ -187,6 +190,8 @@ public MatchboxEngine getEngineR4() throws MatchboxEngineCreationException { | |
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.r4.core.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.terminology#5.4.0.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.extensions.r4#1.0.0.tgz")); | ||
| removeStructureMaps(engine); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.xver#[email protected]")); | ||
| } catch (final IOException e) { | ||
| throw new IgLoadException(e); | ||
| } | ||
|
|
@@ -209,6 +214,16 @@ public MatchboxEngine getEngineR4() throws MatchboxEngineCreationException { | |
| return engine; | ||
| } | ||
|
|
||
| /** | ||
| * remove old StructureMaps from the context, especially from hl7.fhir.uv.extensions.r4#1.0.0 which are replaced by newer versions | ||
| * @param engine | ||
| */ | ||
| public void removeStructureMaps(MatchboxEngine engine) { | ||
| for (StructureMap map : engine.getContext().fetchResourcesByType(StructureMap.class)) { | ||
| engine.getContext().dropResource(map); | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Returns a FHIR R5 engine configured with hl7 terminology | ||
| * | ||
|
|
@@ -226,6 +241,8 @@ public MatchboxEngine getEngineR5() throws MatchboxEngineCreationException { | |
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.r5.core.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.terminology#5.4.0.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.extensions#1.0.0.tgz")); | ||
| removeStructureMaps(engine); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.xver#[email protected]")); | ||
| } catch (final IOException e) { | ||
| throw new IgLoadException(e); | ||
| } | ||
|
|
@@ -357,15 +374,25 @@ public Resource transformToFhir(String input, boolean inputJson, String mapUri) | |
| public String transform(String input, boolean inputJson, String mapUri, boolean outputJson) | ||
| throws FHIRException, IOException { | ||
| log.info("Start transform: " + mapUri); | ||
|
|
||
| SimpleWorkerContext context = this.getContext(); | ||
| StructureMap map = context.fetchResource(StructureMap.class, mapUri); | ||
|
|
||
| String fhirVersionTarget = getFhirVersion(getCanonicalFromStructureMap(map, StructureMap.StructureMapModelMode.TARGET)); | ||
| if (fhirVersionTarget !=null && !fhirVersionTarget.equals(this.getVersion())) { | ||
| log.info("Loading additional FHIR version for Target into context" + fhirVersionTarget); | ||
| context = getContextForFhirVersion(fhirVersionTarget); | ||
| } | ||
|
|
||
| Element transformed = transform(ByteProvider.forBytes(input.getBytes("UTF-8")), (inputJson ? FhirFormat.JSON : FhirFormat.XML), | ||
| mapUri); | ||
| mapUri, context); | ||
| ByteArrayOutputStream boas = new ByteArrayOutputStream(); | ||
| if (outputJson) | ||
| new org.hl7.fhir.r5.elementmodel.JsonParser(getContext()).compose(transformed, boas, | ||
| new org.hl7.fhir.r5.elementmodel.JsonParser(context).compose(transformed, boas, | ||
| IParser.OutputStyle.PRETTY, | ||
| null); | ||
| else | ||
| new org.hl7.fhir.r5.elementmodel.XmlParser(getContext()).compose(transformed, boas, | ||
| new org.hl7.fhir.r5.elementmodel.XmlParser(context).compose(transformed, boas, | ||
| IParser.OutputStyle.PRETTY, | ||
| null); | ||
| String result = new String(boas.toByteArray()); | ||
|
|
@@ -378,22 +405,54 @@ public String transform(String input, boolean inputJson, String mapUri, boolean | |
| * Adapted transform operation from Validation Engine to use patched | ||
| * MatchboxStructureMapUtilities | ||
| */ | ||
| public org.hl7.fhir.r5.elementmodel.Element transform(ByteProvider source, FhirFormat cntType, String mapUri) | ||
| public org.hl7.fhir.r5.elementmodel.Element transform(ByteProvider source, FhirFormat cntType, String mapUri, SimpleWorkerContext targetContext) | ||
| throws FHIRException, IOException { | ||
| SimpleWorkerContext context = this.getContext(); | ||
|
|
||
| // usual case is that source and target are in the same FHIR version as in the context, however it could be that either source or target are in a different FHIR version | ||
| // if this is the case we do lazy loading of the additional FHIR version into the context | ||
|
|
||
| StructureMap map = context.fetchResource(StructureMap.class, mapUri); | ||
| String fhirVersion = getFhirVersion(getCanonicalFromStructureMap(map, StructureMap.StructureMapModelMode.SOURCE)); | ||
| if (!fhirVersion.equals(this.getVersion())) { | ||
| log.info("Loading additional FHIR version for Source into context" + fhirVersion); | ||
| context.loadFromPackage("hl7.fhir.r5.core", fhirVersion); | ||
| String fhirVersionSource = getFhirVersion(getCanonicalFromStructureMap(map, StructureMap.StructureMapModelMode.SOURCE)); | ||
| if (fhirVersionSource !=null && !fhirVersionSource.equals(this.getVersion())) { | ||
| log.info("Loading additional FHIR version for Source into context" + fhirVersionSource); | ||
| context = getContextForFhirVersion(fhirVersionSource); | ||
| } | ||
| org.hl7.fhir.r5.elementmodel.Element src = Manager.parseSingle(context, new ByteArrayInputStream(source.getBytes()), | ||
| cntType); | ||
| return transform(src, mapUri); | ||
| return transform(src, mapUri, targetContext); | ||
| } | ||
|
|
||
| /** | ||
| * Adapted transform operation from Validation Engine to use patched | ||
| * MatchboxStructureMapUtilities | ||
| */ | ||
| public SimpleWorkerContext getContextForFhirVersion(String fhirVersion) | ||
| throws FHIRException, IOException { | ||
| SimpleWorkerContext contextForFhirVersion = null; | ||
| if (fhirVersion.startsWith("4.0")) { | ||
| MatchboxEngine engine = new MatchboxEngineBuilder().getEngineR4(); | ||
| contextForFhirVersion = engine.getContext(); | ||
| } | ||
| if (fhirVersion.startsWith("5.0")) { | ||
| MatchboxEngine engine = new MatchboxEngineBuilder().getEngineR5(); | ||
| contextForFhirVersion = engine.getContext(); | ||
| } | ||
| if (contextForFhirVersion != null ) { | ||
| // we need to copy now all StructureDefinitions from this Version to the new context | ||
| for (StructureDefinition sd : contextForFhirVersion.listStructures()) { | ||
| StructureDefinition sdn = sd.copy(); | ||
| if (sdn.getKind()!=null && sdn.getKind() != StructureDefinition.StructureDefinitionKind.LOGICAL && !"Extensions".equals(sdn.getType())) { | ||
| sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/"+fhirVersion+"/")); | ||
| sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace") | ||
| .setValue(new UriType("http://hl7.org/fhir")); | ||
| this.getContext().cacheResource(sdn); | ||
| } | ||
| contextForFhirVersion.cacheResource(sd); | ||
| } | ||
| } | ||
|
|
||
| return contextForFhirVersion; | ||
| } | ||
|
|
||
| /** | ||
|
|
@@ -405,12 +464,12 @@ public org.hl7.fhir.r5.elementmodel.Element transform(ByteProvider source, FhirF | |
| * @throws FHIRException | ||
| * @throws IOException | ||
| */ | ||
| public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.r5.elementmodel.Element src, String mapUri) | ||
| public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.r5.elementmodel.Element src, String mapUri, SimpleWorkerContext targetContext) | ||
| throws FHIRException, IOException { | ||
| SimpleWorkerContext context = this.getContext(); | ||
| List<Base> outputs = new ArrayList<>(); | ||
| StructureMapUtilities scu = new MatchboxStructureMapUtilities(context, | ||
| new TransformSupportServices(context, outputs), this); | ||
| new TransformSupportServices(targetContext!=null ? targetContext : context, outputs), this); | ||
| StructureMap map = context.fetchResource(StructureMap.class, mapUri); | ||
| if (map == null) { | ||
| log.error("Unable to find map " + mapUri + " (Known Maps = " + context.listMapUrls() + ")"); | ||
|
|
@@ -420,6 +479,7 @@ public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.r5.elementmod | |
| + (map.getDateElement() != null && !map.getDateElement().isEmpty() ? "(" + map.getDateElement().asStringValue() + ")" : "")); | ||
|
|
||
| org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map); | ||
|
|
||
| scu.transform(null, src, map, resource); | ||
| resource.populatePaths(null); | ||
| return resource; | ||
|
|
@@ -468,6 +528,13 @@ private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(S | |
| throw new FHIRException("Unable to determine resource URL for target type"); | ||
| } | ||
|
|
||
| if (Utilities.isAbsoluteUrl(targetTypeUrl)) { | ||
| int index = targetTypeUrl.indexOf("/"+this.getVersion().substring(0,3)+"/"); | ||
| if (index >= 0) { | ||
| targetTypeUrl = targetTypeUrl.substring(0, index)+targetTypeUrl.substring(index+4); | ||
| } | ||
| } | ||
|
|
||
| StructureDefinition structureDefinition = null; | ||
| for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) { | ||
| if (sd.getUrl().equalsIgnoreCase(targetTypeUrl)) { | ||
|
|
||
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matchbox-engine/src/main/resources/hl7.fhir.uv.xver#[email protected]
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96 changes: 96 additions & 0 deletions
96
matchbox-engine/src/test/java/ch/ahdis/matchbox/engine/tests/FhirXVersTests.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| package ch.ahdis.matchbox.engine.tests; | ||
|
|
||
| /* | ||
| * #%L | ||
| * Matchbox Engine | ||
| * %% | ||
| * Copyright (C) 2022 ahdis | ||
| * %% | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * #L% | ||
| */ | ||
|
|
||
| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.nio.charset.StandardCharsets; | ||
|
|
||
| import org.apache.commons.io.IOUtils; | ||
| import org.hl7.fhir.exceptions.FHIRException; | ||
| import org.hl7.fhir.r4.formats.XmlParser; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.ExplanationOfBenefit; | ||
| import org.hl7.fhir.r4.model.Observation; | ||
| import org.hl7.fhir.r4.model.Patient; | ||
| import org.hl7.fhir.r4.model.Questionnaire; | ||
| import org.hl7.fhir.r4.model.Resource; | ||
| import org.hl7.fhir.r4.model.StructureDefinition; | ||
| import org.hl7.fhir.r4.model.StructureMap; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.api.BeforeEach; | ||
| import org.junit.jupiter.api.Disabled; | ||
| import org.junit.jupiter.api.Test; | ||
|
|
||
| import ch.ahdis.matchbox.engine.MatchboxEngine; | ||
| import ch.ahdis.matchbox.engine.MatchboxEngine.MatchboxEngineBuilder; | ||
|
|
||
| /** | ||
| * https://build.fhir.org/ig/HL7/fhir-cross-version/package.tgz | ||
| */ | ||
| class FhirXVersTests { | ||
|
|
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| static private MatchboxEngine engine; | ||
|
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| private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(FhirMappingLanguageTests.class); | ||
|
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| @BeforeAll | ||
| static void setUpBeforeClass() throws Exception { | ||
| engine = new MatchboxEngineBuilder().getEngineR4(); | ||
| } | ||
|
|
||
| @BeforeEach | ||
| void setUp() throws Exception { | ||
| } | ||
|
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| public String getFileAsStringFromResources(String file) throws IOException { | ||
| InputStream in = FhirXVersTests.class.getResourceAsStream("/xvers" + file); | ||
| return IOUtils.toString(in, StandardCharsets.UTF_8); | ||
| } | ||
|
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| public StructureDefinition getStructureDefinitionFromFile(String file) throws IOException { | ||
| return (StructureDefinition) new org.hl7.fhir.r4.formats.XmlParser() | ||
| .parse(FhirMappingLanguageTests.class.getResourceAsStream(file)); | ||
| } | ||
|
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| @Test | ||
| void testMedication5to4inR4() throws FHIRException, IOException { | ||
| MatchboxEngine engine = new MatchboxEngine(FhirXVersTests.engine); | ||
| String result = engine.transform(getFileAsStringFromResources("/medication-r5-med0301.json"), true, | ||
| "http://hl7.org/fhir/uv/xver/StructureMap/Medication5to4", true); | ||
| log.info(result); | ||
| CompareUtil.compare(getFileAsStringFromResources("/medication-r4-med0301.json"), result, false); | ||
| } | ||
|
|
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| @Test | ||
| void testMedication4to5inR4() throws FHIRException, IOException { | ||
| MatchboxEngine engine = new MatchboxEngine(FhirXVersTests.engine); | ||
| String result = engine.transform(getFileAsStringFromResources("/medication-r4-med0301.json"), true, | ||
| "http://hl7.org/fhir/uv/xver/StructureMap/Medication4to5", true); | ||
| log.info(result); | ||
| CompareUtil.compare(getFileAsStringFromResources("/medication-r5-med0301.json"), result, false); | ||
| } | ||
|
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||
|
|
||
| } |
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