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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -24,6 +24,7 @@ | |
| import java.io.FileNotFoundException; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.net.URISyntaxException; | ||
| import java.nio.charset.StandardCharsets; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
@@ -41,7 +42,6 @@ | |
| import org.hl7.fhir.r4.model.Resource; | ||
| import org.hl7.fhir.r5.context.ContextUtilities; | ||
| import org.hl7.fhir.r5.context.SimpleWorkerContext; | ||
| import org.hl7.fhir.r5.context.SimpleWorkerContext.SimpleWorkerContextBuilder; | ||
| import org.hl7.fhir.r5.elementmodel.Element; | ||
| import org.hl7.fhir.r5.elementmodel.Manager; | ||
| import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat; | ||
|
|
@@ -72,6 +72,7 @@ | |
| import org.hl7.fhir.utilities.xhtml.XhtmlNode; | ||
| import org.hl7.fhir.validation.IgLoader; | ||
| import org.hl7.fhir.validation.ValidationEngine; | ||
| import org.hl7.fhir.validation.cli.services.PassiveExpiringSessionCache; | ||
| import org.hl7.fhir.validation.instance.InstanceValidator; | ||
|
|
||
| import ch.ahdis.matchbox.engine.cli.VersionUtil; | ||
|
|
@@ -91,10 +92,16 @@ public class MatchboxEngine extends ValidationEngine { | |
|
|
||
| protected static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(MatchboxEngine.class); | ||
|
|
||
| protected final List<String> suppressedWarnInfoPatterns = new ArrayList<>(); | ||
| protected List<String> suppressedWarnInfoPatterns = new ArrayList<>(); | ||
| protected PassiveExpiringSessionCache sessionCache = new PassiveExpiringSessionCache(); | ||
|
|
||
| public MatchboxEngine(final @NonNull ValidationEngine other) throws FHIRException, IOException { | ||
| super(other); | ||
| if (other instanceof MatchboxEngine) { | ||
| MatchboxEngine otherMatchboxEgine = (MatchboxEngine) other; | ||
| this.sessionCache = otherMatchboxEgine.sessionCache; | ||
| this.suppressedWarnInfoPatterns = otherMatchboxEgine.suppressedWarnInfoPatterns; | ||
| } | ||
| // Create a new IgLoader, otherwise the context is desynchronized between the loader and the engine | ||
| this.setIgLoader(new IgLoader(this.getPcm(), this.getContext(), this.getVersion(), this.isDebug())); | ||
| try { | ||
|
|
@@ -103,6 +110,10 @@ public MatchboxEngine(final @NonNull ValidationEngine other) throws FHIRExceptio | |
| throw new MatchboxEngineCreationException(e); | ||
| } | ||
| } | ||
|
|
||
| public void cacheXVersionEngine(MatchboxEngine engine) { | ||
| sessionCache.cacheSession(engine.getVersion().substring(0,3), engine); | ||
| } | ||
|
|
||
| /** | ||
| * Builder class to instantiate a MappingEngine | ||
|
|
@@ -182,16 +193,15 @@ public void setPackageCachePath(final String packageCachePath) { | |
| public MatchboxEngine getEngineR4() throws MatchboxEngineCreationException { | ||
| log.info("Initializing Matchbox Engine (FHIR R4 with terminology provided in classpath)"); | ||
| log.info(VersionUtil.getPoweredBy()); | ||
| final MatchboxEngine engine; | ||
| try { engine = new MatchboxEngine(this.fromNothing()); } | ||
| catch (final IOException e) { throw new MatchboxEngineCreationException(e); } | ||
| final MatchboxEngine engine ; | ||
| try { engine = new MatchboxEngine(this.fromSource("hl7.fhir.r4.core#4.0.1")); } | ||
| catch (final Exception e) { throw new MatchboxEngineCreationException(e); } | ||
| engine.setVersion(FhirPublication.R4.toCode()); | ||
| try { | ||
| 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#0.1.0@bp.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.xver#0.1.0@mb.tgz")); | ||
| } catch (final IOException e) { | ||
| throw new IgLoadException(e); | ||
| } | ||
|
|
@@ -214,6 +224,46 @@ public MatchboxEngine getEngineR4() throws MatchboxEngineCreationException { | |
| return engine; | ||
| } | ||
|
|
||
| /** | ||
| * Returns a FHIR R4B engine configured with hl7 terminology | ||
| * | ||
| * @return | ||
| * @throws MatchboxEngineCreationException | ||
| */ | ||
| public MatchboxEngine getEngineR4B() throws MatchboxEngineCreationException { | ||
| log.info("Initializing Matchbox Engine (FHIR R4B with terminology provided in classpath)"); | ||
| log.info(VersionUtil.getPoweredBy()); | ||
| final MatchboxEngine engine ; | ||
| try { engine = new MatchboxEngine(this.fromSource("hl7.fhir.r4b.core#4.3.0")); } | ||
| catch (final Exception e) { throw new MatchboxEngineCreationException(e); } | ||
| engine.setVersion(FhirPublication.R4B.toCode()); | ||
| try { | ||
| 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); | ||
| } | ||
| if (this.txServer == null) { | ||
| engine.getContext().setCanRunWithoutTerminology(true); | ||
| engine.getContext().setNoTerminologyServer(true); | ||
| } else { | ||
| engine.getContext().setCanRunWithoutTerminology(false); | ||
| engine.getContext().setNoTerminologyServer(false); | ||
| try { | ||
| engine.setTerminologyServer(this.txServer, null, FhirPublication.R4, true); | ||
| } catch (final Exception e) { | ||
| throw new TerminologyServerException(e); | ||
| } | ||
| } | ||
| engine.getContext().setPackageTracker(engine); | ||
| engine.setPcm(this.getFilesystemPackageCacheManager()); | ||
| engine.setPolicyAdvisor(new ValidationPolicyAdvisor(ReferenceValidationPolicy.CHECK_VALID)); | ||
| engine.setAllowExampleUrls(true); | ||
| 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 | ||
|
|
@@ -234,15 +284,14 @@ public MatchboxEngine getEngineR5() throws MatchboxEngineCreationException { | |
| log.info("Initializing Matchbox Engine (FHIR R5 with terminology provided in classpath)"); | ||
| log.info(VersionUtil.getPoweredBy()); | ||
| final MatchboxEngine engine; | ||
| try { engine = new MatchboxEngine(this.fromNothing()); } | ||
| catch (final IOException e) { throw new MatchboxEngineCreationException(e); } | ||
| try { engine = new MatchboxEngine(this.fromSource("hl7.fhir.r5.core#5.0.0")); } | ||
| catch (final Exception e) { throw new MatchboxEngineCreationException(e); } | ||
| engine.setVersion(FhirPublication.R5.toCode()); | ||
| try { | ||
| 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#0.1.0@bp.tgz")); | ||
| engine.loadPackage(getClass().getResourceAsStream("/hl7.fhir.uv.xver#0.1.0@mb.tgz")); | ||
| } catch (final IOException e) { | ||
| throw new IgLoadException(e); | ||
| } | ||
|
|
@@ -303,12 +352,21 @@ public MatchboxEngine getEngine() throws MatchboxEngineCreationException { | |
| @Override | ||
| public ValidationEngine fromNothing() throws MatchboxEngineCreationException { | ||
| try { | ||
| return super.fromNothing(); | ||
| return super.fromNothing(); | ||
| } catch (final IOException e) { | ||
| throw new MatchboxEngineCreationException(e); | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public ValidationEngine fromSource(String src) throws IOException, URISyntaxException { | ||
| try { | ||
| return super.fromSource(src); | ||
| } catch (final IOException e) { | ||
| throw new MatchboxEngineCreationException(e); | ||
| } | ||
| } | ||
|
|
||
| public MatchboxEngineBuilder withVersion(final String version) { | ||
| super.withVersion(version); | ||
| this.fhirVersion = FhirPublication.fromCode(version); | ||
|
|
@@ -379,8 +437,8 @@ public String transform(String input, boolean inputJson, String mapUri, boolean | |
| StructureMap map = context.fetchResource(StructureMap.class, mapUri); | ||
|
|
||
| String fhirVersionTarget = getFhirVersion(getCanonicalFromStructureMap(map, StructureMap.StructureMapModelMode.TARGET)); | ||
| if (fhirVersionTarget !=null && !fhirVersionTarget.equals(this.getVersion().substring(0, 3))) { | ||
| log.info("Loading additional FHIR version for Target into context" + fhirVersionTarget); | ||
| if (fhirVersionTarget !=null && (fhirVersionTarget.startsWith("4.0") || fhirVersionTarget.startsWith("4.3") || fhirVersionTarget.startsWith("5.0")) && !fhirVersionTarget.equals(this.getVersion().substring(0, 3))) { | ||
| log.info("Loading additional FHIR version for Target into context " + fhirVersionTarget); | ||
| context = getContextForFhirVersion(fhirVersionTarget); | ||
| } | ||
|
|
||
|
|
@@ -414,8 +472,8 @@ public org.hl7.fhir.r5.elementmodel.Element transform(ByteProvider source, FhirF | |
|
|
||
| StructureMap map = context.fetchResource(StructureMap.class, mapUri); | ||
| String fhirVersionSource = getFhirVersion(getCanonicalFromStructureMap(map, StructureMap.StructureMapModelMode.SOURCE)); | ||
| if (fhirVersionSource !=null && !fhirVersionSource.equals(this.getVersion().substring(0,3))) { | ||
| log.info("Loading additional FHIR version for Source into context" + fhirVersionSource); | ||
| if (fhirVersionSource !=null && (fhirVersionSource.startsWith("4.0") || fhirVersionSource.startsWith("4.3") || fhirVersionSource.startsWith("5.0")) && !fhirVersionSource.equals(this.getVersion().substring(0,3))) { | ||
| 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()), | ||
|
|
@@ -431,24 +489,47 @@ public SimpleWorkerContext getContextForFhirVersion(String fhirVersion) | |
| throws FHIRException, IOException { | ||
| SimpleWorkerContext contextForFhirVersion = null; | ||
| if (fhirVersion.startsWith("4.0")) { | ||
| contextForFhirVersion = new SimpleWorkerContextBuilder().fromPackage(NpmPackage.fromPackage(getClass().getResourceAsStream("/hl7.fhir.r4.core.tgz"))); | ||
| ValidationEngine engine = sessionCache.fetchSessionValidatorEngine(fhirVersion.substring(0,3)); | ||
| if (engine == null) { | ||
| engine = new MatchboxEngineBuilder().getEngineR4(); | ||
| sessionCache.cacheSession(fhirVersion.substring(0,3), engine); | ||
| } | ||
| contextForFhirVersion = engine.getContext(); | ||
| } | ||
| if (fhirVersion.startsWith("4.3")) { | ||
| ValidationEngine engine = sessionCache.fetchSessionValidatorEngine(fhirVersion.substring(0,3)); | ||
| if (engine == null) { | ||
| engine = new MatchboxEngineBuilder().getEngineR4B(); | ||
| sessionCache.cacheSession(fhirVersion.substring(0,3), engine); | ||
| } | ||
| contextForFhirVersion = engine.getContext(); | ||
| } | ||
| if (fhirVersion.startsWith("5.0")) { | ||
| contextForFhirVersion = new SimpleWorkerContextBuilder().fromPackage(NpmPackage.fromPackage(getClass().getResourceAsStream("/hl7.fhir.r5.core.tgz"))); | ||
| } | ||
| ValidationEngine engine = sessionCache.fetchSessionValidatorEngine(fhirVersion.substring(0,3)); | ||
| if (engine == null) { | ||
| engine = new MatchboxEngineBuilder().getEngineR5(); | ||
| sessionCache.cacheSession(fhirVersion.substring(0,3), engine); | ||
| } | ||
| 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); | ||
| } | ||
| } | ||
| // check first if they are not already defined | ||
| if (this.getContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/"+fhirVersion.substring(0,3)+"/StructureDefinition/StructureDefinition") == null) { | ||
| int len = "http://hl7.org/fhir/".length(); | ||
| for (StructureDefinition sd : contextForFhirVersion.listStructures()) { | ||
| if (sd.getKind()!=null && sd.getKind() != StructureDefinition.StructureDefinitionKind.LOGICAL && !"Extensions".equals(sd.getType())) { | ||
| if (!Character.isDigit(sd.getUrl().charAt(len))) { | ||
| StructureDefinition sdn = sd.copy(); | ||
| sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/"+fhirVersion.substring(0,3)+"/")); | ||
| sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace") | ||
| .setValue(new UriType("http://hl7.org/fhir")); | ||
| this.getContext().cacheResource(sdn); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| return contextForFhirVersion; | ||
| } | ||
|
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|
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matchbox-engine/src/main/resources/hl7.fhir.uv.xver#[email protected]
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