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fix contexts
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@oliveregger
oliveregger committed Sep 10, 2024
1 parent 5e2bf4a commit 7f11889
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Showing 2 changed files with 19 additions and 22 deletions.
39 changes: 18 additions & 21 deletions matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/MatchboxEngine.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
package ch.ahdis.matchbox.engine;

import static org.apache.commons.lang3.StringUtils.substring;

/*
* #%L
* Matchbox Engine
Expand All @@ -27,13 +25,12 @@
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import ch.ahdis.matchbox.engine.exception.IgLoadException;
import ch.ahdis.matchbox.engine.exception.MatchboxEngineCreationException;
import ch.ahdis.matchbox.engine.exception.TerminologyServerException;
import org.checkerframework.checker.nullness.qual.NonNull;
import org.checkerframework.checker.nullness.qual.Nullable;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
Expand All @@ -44,9 +41,11 @@
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;
import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base;
Expand All @@ -61,7 +60,6 @@
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
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;
Expand All @@ -76,8 +74,10 @@
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.engine.exception.IgLoadException;
import ch.ahdis.matchbox.engine.exception.MatchboxEngineCreationException;
import ch.ahdis.matchbox.engine.exception.TerminologyServerException;
import ch.ahdis.matchbox.mappinglanguage.MatchboxStructureMapUtilities;
import ch.ahdis.matchbox.mappinglanguage.TransformSupportServices;

Expand Down Expand Up @@ -379,7 +379,7 @@ 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())) {
if (fhirVersionTarget !=null && !fhirVersionTarget.equals(this.getVersion().substring(0, 3))) {
log.info("Loading additional FHIR version for Target into context" + fhirVersionTarget);
context = getContextForFhirVersion(fhirVersionTarget);
}
Expand Down Expand Up @@ -414,7 +414,7 @@ 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())) {
if (fhirVersionSource !=null && !fhirVersionSource.equals(this.getVersion().substring(0,3))) {
log.info("Loading additional FHIR version for Source into context" + fhirVersionSource);
context = getContextForFhirVersion(fhirVersionSource);
}
Expand All @@ -431,14 +431,12 @@ public SimpleWorkerContext getContextForFhirVersion(String fhirVersion)
throws FHIRException, IOException {
SimpleWorkerContext contextForFhirVersion = null;
if (fhirVersion.startsWith("4.0")) {
MatchboxEngine engine = new MatchboxEngineBuilder().getEngineR4();
contextForFhirVersion = engine.getContext();
contextForFhirVersion = new SimpleWorkerContextBuilder().fromPackage(NpmPackage.fromPackage(getClass().getResourceAsStream("/hl7.fhir.r4.core.tgz")));
}
if (fhirVersion.startsWith("5.0")) {
MatchboxEngine engine = new MatchboxEngineBuilder().getEngineR5();
contextForFhirVersion = engine.getContext();
contextForFhirVersion = new SimpleWorkerContextBuilder().fromPackage(NpmPackage.fromPackage(getClass().getResourceAsStream("/hl7.fhir.r5.core.tgz")));
}
if (contextForFhirVersion != null ) {
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();
Expand All @@ -448,7 +446,6 @@ public SimpleWorkerContext getContextForFhirVersion(String fhirVersion)
.setValue(new UriType("http://hl7.org/fhir"));
this.getContext().cacheResource(sdn);
}
contextForFhirVersion.cacheResource(sd);
}
}

Expand Down Expand Up @@ -478,7 +475,7 @@ public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.r5.elementmod
log.info("Using map " + map.getUrl() + (map.getVersion()!=null ? "|" + map.getVersion() + " " : "" )
+ (map.getDateElement() != null && !map.getDateElement().isEmpty() ? "(" + map.getDateElement().asStringValue() + ")" : ""));

org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map);
org.hl7.fhir.r5.elementmodel.Element resource = getTargetResourceFromStructureMap(map, targetContext);

scu.transform(null, src, map, resource);
resource.populatePaths(null);
Expand Down Expand Up @@ -513,9 +510,9 @@ private String getCanonicalFromStructureMap(StructureMap map, StructureMap.Struc
return targetTypeUrl;
}

private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(StructureMap map) {
private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(StructureMap map, SimpleWorkerContext targetContext) {
String targetTypeUrl = null;
SimpleWorkerContext context = this.getContext();
SimpleWorkerContext context = (targetContext!=null ? targetContext : this.getContext());
for (StructureMap.StructureMapStructureComponent component : map.getStructure()) {
if (component.getMode() == StructureMap.StructureMapModelMode.TARGET) {
targetTypeUrl = component.getUrl();
Expand All @@ -529,7 +526,7 @@ private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(S
}

if (Utilities.isAbsoluteUrl(targetTypeUrl)) {
int index = targetTypeUrl.indexOf("/"+this.getVersion().substring(0,3)+"/");
int index = targetTypeUrl.indexOf("/"+context.getVersion().substring(0,3)+"/");
if (index >= 0) {
targetTypeUrl = targetTypeUrl.substring(0, index)+targetTypeUrl.substring(index+4);
}
Expand All @@ -548,7 +545,7 @@ private org.hl7.fhir.r5.elementmodel.Element getTargetResourceFromStructureMap(S
throw new FHIRException("Unable to find StructureDefinition for target type ('" + targetTypeUrl + "')");
}

return Manager.build(getContext(), structureDefinition);
return Manager.build(context, structureDefinition);
}

/**
Expand Down
2 changes: 1 addition & 1 deletion matchbox-engine/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ public void cacheResourceFromPackage(Resource r, PackageInformation packageInfo)
// matchbox patch for duplicate resources, see https://github.com/ahdis/matchbox/issues/227
// org.hl7.fhir.r5.conformance.R5ExtensionsLoader.loadR5SpecialTypes(R5ExtensionsLoader.java:141)
CanonicalResource ex = fetchResourceWithException(m.fhirType(), url);
if (laterVersion(m.getVersion(), ex.getVersion())) {
if (ex.getVersion()!=null && m.getVersion()!=null && laterVersion(m.getVersion(), ex.getVersion())) {
logger.logMessage("Note replacing old version: " + formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, m.getVersion(), ex.getVersion(), ex.fhirType()));
dropResource(ex);
} else {
Expand Down

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