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Add loading R5 extensions

This commit is contained in:
Grahame Grieve 2022-06-24 11:41:19 +02:00
parent 636c651d76
commit 2c46cfe690
2 changed files with 106 additions and 2 deletions
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106
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -56,13 +56,17 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.elementmodel.Property;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
@ -106,6 +110,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.renderers.TerminologyRenderer;
@ -125,6 +130,10 @@ import org.hl7.fhir.utilities.MarkDownProcessor;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@ -6838,4 +6847,99 @@ public class ProfileUtilities extends TranslatingUtilities {
this.masterSourceFileNames = masterSourceFileNames;
}
}
public static int loadR5Extensions(BasePackageCacheManager pcm, IWorkerContext context) throws FHIRException, IOException {
NpmPackage npm = pcm.loadPackage("hl7.fhir.r5.core", "current");
String[] types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem" };
Map<String, ValueSet> valueSets = new HashMap<>();
Map<String, CodeSystem> codeSystems = new HashMap<>();
List<StructureDefinition> extensions = new ArrayList<>();
JsonParser json = new JsonParser();
for (PackageResourceInformation pri : npm.listIndexedResources(types)) {
CanonicalResource r = (CanonicalResource) json.parse(npm.load(pri));
if (r instanceof CodeSystem) {
codeSystems.put(r.getUrl(), (CodeSystem) r);
} else if (r instanceof ValueSet) {
valueSets.put(r.getUrl(), (ValueSet) r);
} else if (r instanceof StructureDefinition) {
extensions.add((StructureDefinition) r);
}
}
PackageVersion pd = new PackageVersion(npm.name(), npm.version(), npm.dateAsDate());
int c = 0;
List<String> typeNames = context.getTypeNames();
for (StructureDefinition sd : extensions) {
if (sd.getType().equals("Extension") && sd.getDerivation() == TypeDerivationRule.CONSTRAINT &&
!context.hasResource(StructureDefinition.class, sd.getUrl())) {
if (survivesStrippingTypes(sd, context, typeNames)) {
c++;
sd.setUserData("path", Utilities.pathURL(npm.getWebLocation(), "extension-"+sd.getId()+".html"));
context.cacheResourceFromPackage(sd, pd);
registerTerminologies(sd, context, valueSets, codeSystems, pd);
}
}
}
return c;
}
private static void registerTerminologies(StructureDefinition sd, IWorkerContext context, Map<String, ValueSet> valueSets, Map<String, CodeSystem> codeSystems, PackageVersion pd) {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
String vs = ed.getBinding().getValueSet();
if (!context.hasResource(StructureDefinition.class, vs)) {
loadValueSet(vs, context, valueSets, codeSystems, pd);
}
}
}
}
private static void loadValueSet(String url, IWorkerContext context, Map<String, ValueSet> valueSets, Map<String, CodeSystem> codeSystems, PackageVersion pd) {
if (valueSets.containsKey(url)) {
ValueSet vs = valueSets.get(url);
context.cacheResourceFromPackage(vs, pd);
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
for (CanonicalType t : inc.getValueSet()) {
loadValueSet(t.asStringValue(), context, valueSets, codeSystems, pd);
}
if (inc.hasSystem()) {
if (!context.hasResource(CodeSystem.class, inc.getSystem()) && codeSystems.containsKey(inc.getSystem())) {
context.cacheResourceFromPackage(codeSystems.get(inc.getSystem()), pd);
}
}
}
}
}
private static boolean survivesStrippingTypes(StructureDefinition sd, IWorkerContext context, List<String> typeNames) {
for (ElementDefinition ed : sd.getDifferential().getElement()) {
stripTypes(ed, context, typeNames);
}
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
if (!stripTypes(ed, context, typeNames)) {
return false;
}
}
return true;
}
private static boolean stripTypes(ElementDefinition ed, IWorkerContext context, List<String> typeNames) {
if (!ed.getPath().contains(".") || !ed.hasType()) {
return true;
}
ed.getType().removeIf(tr -> !typeNames.contains(tr.getWorkingCode()));
if (!ed.hasType()) {
return false;
}
for (TypeRefComponent tr : ed.getType()) {
if (tr.hasTargetProfile()) {
tr.getTargetProfile().removeIf(n -> !context.hasResource(StructureDefinition.class, n.asStringValue()));
if (!tr.hasTargetProfile()) {
return false;
}
}
}
return true;
}
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -487,7 +487,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
t++;
} catch (Exception e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, s, pi.name(), pi.version(), e.getMessage()), e);
}
}
}
} else {
if (types.length == 0) {