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org.hl7.fhir.core
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don't load type definitions from example package

This commit is contained in:
Grahame Grieve 2023-09-20 16:58:56 +10:00
parent a6f43420d5
commit 483477c9c4
5 changed files with 37 additions and 11 deletions
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15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/CanonicalResourceManager.java
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@ -6,6 +6,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.PackageInformation;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -126,7 +127,7 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
}
}
private class CachedCanonicalResource<T1 extends CanonicalResource> {
public class CachedCanonicalResource<T1 extends CanonicalResource> {
private T1 resource;
private CanonicalResourceProxy proxy;
private PackageInformation packageInfo;
@ -186,6 +187,14 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
} else {
return resource instanceof CodeSystem ? ((CodeSystem) resource).getSupplements() : null;
}
}
public Object getDerivation() {
if (resource == null) {
return proxy.getDerivation();
} else {
return resource instanceof StructureDefinition ? ((StructureDefinition) resource).getDerivationElement().primitiveValue() : null;
}
}
}
@ -621,6 +630,10 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
}
public List<CachedCanonicalResource<T>> getCachedList() {
return list;
}
public List<T> getList() {
List<T> res = new ArrayList<>();
for (CachedCanonicalResource<T> t : list) {

20
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -97,11 +97,13 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private final String filename;
private final IContextResourceLoader loader;
private PackageInformation pi;
public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader) {
public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader, PackageInformation pi) {
super(pri.getResourceType(), pri.getId(), loader == null ? pri.getUrl() :loader.patchUrl(pri.getUrl(), pri.getResourceType()), pri.getVersion(), pri.getSupplements(), pri.getDerivation());
this.filename = pri.getFilename();
this.loader = loader;
this.pi = pi;
}
@Override
@ -110,9 +112,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
FileInputStream f = new FileInputStream(filename);
try {
if (loader != null) {
return R5Hacker.fixR5BrokenResource((CanonicalResource) loader.loadResource(f, true));
return setPi(R5Hacker.fixR5BrokenResource((CanonicalResource) loader.loadResource(f, true)));
} else {
return R5Hacker.fixR5BrokenResource((CanonicalResource) new JsonParser().parse(f));
return setPi(R5Hacker.fixR5BrokenResource((CanonicalResource) new JsonParser().parse(f)));
}
} finally {
f.close();
@ -121,6 +123,11 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
throw new FHIRException("Error loading "+filename+": "+e.getMessage(), e);
}
}
private CanonicalResource setPi(CanonicalResource cr) {
cr.setSourcePackage(pi);
return cr;
}
}
public interface ILoadFilter {
@ -478,6 +485,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
if ((types == null || types.size() == 0) && loader != null) {
types = loader.getTypes();
}
PackageInformation pii = new PackageInformation(pi);
if (VersionUtilities.isR2Ver(pi.fhirVersion()) || !pi.canLazyLoad() || !allowLazyLoading) {
// can't lazy load R2 because of valueset/codesystem implementation
if (types == null || types.size() == 0) {
@ -485,7 +493,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
for (String s : pi.listResources(types)) {
try {
loadDefinitionItem(s, pi.load("package", s), loader, null, new PackageInformation(pi));
loadDefinitionItem(s, pi.load("package", s), loader, null, pii);
t++;
} catch (Exception e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, s, pi.name(), pi.version(), e.getMessage()), e);
@ -499,9 +507,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
if (!pri.getFilename().contains("ig-r4") && (loader == null || loader.wantLoad(pi, pri))) {
try {
if (!pri.hasId()) {
loadDefinitionItem(pri.getFilename(), new FileInputStream(pri.getFilename()), loader, null, new PackageInformation(pi));
loadDefinitionItem(pri.getFilename(), new FileInputStream(pri.getFilename()), loader, null, pii);
} else {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageInformation(pi));
registerResourceFromPackage(new PackageResourceLoader(pri, loader, pii), pii);
}
t++;
} catch (FHIRException e) {

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TypeManager.java
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@ -33,8 +33,10 @@ public class TypeManager {
typeDefinitions.clear();
primitiveNames.clear();
dataTypeNames.clear();
for (StructureDefinition sd : structures.getList()) {
see(sd);
for (CanonicalResourceManager<StructureDefinition>.CachedCanonicalResource<StructureDefinition> cr : structures.getCachedList()) {
if (!"constraint".equals(cr.getDerivation())) {
see(cr.getResource());
}
}
}
@ -45,7 +47,7 @@ public class TypeManager {
}
public void see(StructureDefinition sd) {
if (sd.getDerivation() != TypeDerivationRule.CONSTRAINT) {
if (sd.getDerivation() != TypeDerivationRule.CONSTRAINT && (sd.getSourcePackage() == null || !sd.getSourcePackage().isExamplesPackage())) {
String type = sd.getType();
Set<StructureDefinition> types = typeDefinitions.get(type);
if (types == null) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
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@ -827,7 +827,7 @@ public class Element extends Base {
public boolean equalsDeep(Base other) {
if (!super.equalsDeep(other))
return false;
if (isPrimitive() && other.isPrimitive())
if (isPrimitive() && primitiveValue() != null && other.isPrimitive())
return primitiveValue().equals(other.primitiveValue());
if (isPrimitive() || other.isPrimitive())
return false;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/validation/IResourceValidator.java
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@ -102,6 +102,9 @@ public interface IResourceValidator {
boolean isForPublication();
IResourceValidator setForPublication(boolean forPublication);
boolean isExample();
IResourceValidator setExample(boolean example);
public boolean isWarnOnDraftOrExperimental();
public IResourceValidator setWarnOnDraftOrExperimental(boolean warnOnDraftOrExperimental);