mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-03-05 19:09:11 +00:00
work on loading speed for validator
This commit is contained in:
parent
68360cb110
commit
8136b00c86
@ -105,7 +105,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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private IContextResourceLoader loader;
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public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader) {
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super(pri.getType(), pri.getId(), pri.getUrl(),pri.getVersion());
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super(pri.getResourceType(), pri.getId(), pri.getUrl(),pri.getVersion());
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this.filename = pri.getFilename();
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this.loader = loader;
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}
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@ -1,12 +1,16 @@
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package org.hl7.fhir.r5.conformance;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.FHIRFormatError;
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import org.hl7.fhir.r5.conformance.R5ExtensionsLoader.Loadable;
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import org.hl7.fhir.r5.context.ContextUtilities;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
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@ -28,15 +32,40 @@ import org.hl7.fhir.utilities.npm.NpmPackage;
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import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
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public class R5ExtensionsLoader {
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public static class CanonicalResourceSortByUrl<T extends CanonicalResource> implements Comparator<Loadable<T>> {
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@Override
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public int compare(Loadable<T> arg0, Loadable<T> arg1) {
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return arg0.info.getUrl().compareTo(arg1.info.getUrl());
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}
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}
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public class Loadable<T extends CanonicalResource> {
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public Loadable(PackageResourceInformation info) {
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this.info = info;
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}
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private T resource;
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private PackageResourceInformation info;
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public T getResource() throws FHIRFormatError, FileNotFoundException, IOException {
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if (resource == null) {
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CanonicalResource r = (CanonicalResource) json.parse(pck.load(info));
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r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
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resource = (T) r;
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}
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return resource;
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}
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}
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private BasePackageCacheManager pcm;
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private int count;
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private byte[] map;
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private NpmPackage pck;
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private Map<String, ValueSet> valueSets;
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private Map<String, CodeSystem> codeSystems;
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private List<StructureDefinition> structures;
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private Map<String, Loadable<ValueSet>> valueSets;
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private Map<String, Loadable<CodeSystem>> codeSystems;
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private List<Loadable<StructureDefinition>> structures;
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private IWorkerContext context;
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private PackageVersion pd;
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private JsonParser json;
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public R5ExtensionsLoader(BasePackageCacheManager pcm, IWorkerContext context) {
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super();
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@ -51,45 +80,43 @@ public class R5ExtensionsLoader {
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public void load() throws FHIRException, IOException {
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pck = pcm.loadPackage("hl7.fhir.r5.core", "current");
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pd = new PackageVersion(pck.name(), pck.version(), pck.dateAsDate());
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map = pck.hasFile("other", "spec.internals") ? TextFile.streamToBytes(pck.load("other", "spec.internals")) : null;
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String[] types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem" };
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JsonParser json = new JsonParser();
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json = new JsonParser();
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for (PackageResourceInformation pri : pck.listIndexedResources(types)) {
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CanonicalResource r = (CanonicalResource) json.parse(pck.load(pri));
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r.setUserData("path", Utilities.pathURL(pck.getWebLocation(), r.fhirType().toLowerCase()+ "-"+r.getId().toLowerCase()+".html"));
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if (r instanceof CodeSystem) {
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codeSystems.put(r.getUrl(), (CodeSystem) r);
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codeSystems.put(r.getUrl()+"|"+r.getVersion(), (CodeSystem) r);
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} else if (r instanceof ValueSet) {
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valueSets.put(r.getUrl(), (ValueSet) r);
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valueSets.put(r.getUrl()+"|"+r.getVersion(), (ValueSet) r);
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} else if (r instanceof StructureDefinition) {
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structures.add((StructureDefinition) r);
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if (pri.getResourceType().equals("CodeSystem")) {
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codeSystems.put(pri.getUrl(), new Loadable<CodeSystem>(pri));
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codeSystems.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<CodeSystem>(pri));
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} else if (pri.getResourceType().equals("ValueSet")) {
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valueSets.put(pri.getUrl(), new Loadable<ValueSet>(pri));
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valueSets.put(pri.getUrl()+"|"+pri.getVersion(), new Loadable<ValueSet>(pri));
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} else if (pri.getResourceType().equals("StructureDefinition") && pri.getStatedType().equals("Extension")) {
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structures.add(new Loadable<StructureDefinition>(pri));
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}
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}
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structures.sort(new ResourceSorters.CanonicalResourceSortByUrl());
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}
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public void loadR5Extensions() throws FHIRException, IOException {
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count = 0;
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List<String> typeNames = new ContextUtilities(context).getTypeNames();
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for (StructureDefinition sd : structures) {
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if (sd.getType().equals("Extension") && sd.getDerivation() == TypeDerivationRule.CONSTRAINT &&
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!context.hasResource(StructureDefinition.class, sd.getUrl())) {
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if (survivesStrippingTypes(sd, context, typeNames)) {
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count++;
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sd.setUserData("path", Utilities.pathURL(pck.getWebLocation(), "extension-"+sd.getId().toLowerCase()+".html"));
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registerTerminologies(sd);
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context.cacheResourceFromPackage(sd, pd);
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for (Loadable<StructureDefinition> lsd : structures) {
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if (!context.hasResource(StructureDefinition.class, lsd.info.getUrl())) {
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StructureDefinition sd = lsd.getResource();
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if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
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if (survivesStrippingTypes(sd, context, typeNames)) {
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count++;
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sd.setUserData("path", Utilities.pathURL(pck.getWebLocation(), "extension-"+sd.getId().toLowerCase()+".html"));
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registerTerminologies(sd);
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context.cacheResourceFromPackage(sd, pd);
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}
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}
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}
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}
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}
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public void loadR5SpecialTypes(List<String> types) throws FHIRException, IOException {
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for (StructureDefinition sd : structures) {
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for (Loadable<StructureDefinition> lsd : structures) {
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StructureDefinition sd = lsd.getResource();
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if (Utilities.existsInList(sd.getType(), types)) {
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count++;
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sd.setUserData("path", Utilities.pathURL(pck.getWebLocation(), sd.getId().toLowerCase()+".html"));
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@ -99,7 +126,7 @@ public class R5ExtensionsLoader {
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}
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}
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private void registerTerminologies(StructureDefinition sd) {
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private void registerTerminologies(StructureDefinition sd) throws FHIRFormatError, FileNotFoundException, IOException {
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for (ElementDefinition ed : sd.getSnapshot().getElement()) {
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if (ed.hasBinding() && ed.getBinding().hasValueSet()) {
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String vsu = ed.getBinding().getValueSet();
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@ -113,9 +140,9 @@ public class R5ExtensionsLoader {
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}
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}
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private void loadValueSet(String url, IWorkerContext context, Map<String, ValueSet> valueSets, Map<String, CodeSystem> codeSystems, PackageVersion pd) {
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private void loadValueSet(String url, IWorkerContext context, Map<String, Loadable<ValueSet>> valueSets, Map<String, Loadable<CodeSystem>> codeSystems, PackageVersion pd) throws FHIRFormatError, FileNotFoundException, IOException {
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if (valueSets.containsKey(url)) {
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ValueSet vs = valueSets.get(url);
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ValueSet vs = valueSets.get(url).getResource();
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context.cacheResourceFromPackage(vs, pd);
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for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
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for (CanonicalType t : inc.getValueSet()) {
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@ -123,11 +150,11 @@ public class R5ExtensionsLoader {
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}
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if (inc.hasSystem() && !inc.hasVersion()) {
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if (codeSystems.containsKey(inc.getSystem())) {
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CodeSystem cs = codeSystems.get(inc.getSystem());
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CodeSystem cs = codeSystems.get(inc.getSystem()).getResource();
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inc.setVersion(cs.getVersion());
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context.cacheResourceFromPackage(cs, pd);
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} else if (!context.hasResource(CodeSystem.class, inc.getSystem()) && codeSystems.containsKey(inc.getSystem())) {
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context.cacheResourceFromPackage(codeSystems.get(inc.getSystem()), pd);
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context.cacheResourceFromPackage(codeSystems.get(inc.getSystem()).getResource(), pd);
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}
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}
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}
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@ -174,8 +201,8 @@ public class R5ExtensionsLoader {
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return count;
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}
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public byte[] getMap() {
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return map;
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public byte[] getMap() throws IOException {
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return pck.hasFile("other", "spec.internals") ? TextFile.streamToBytes(pck.load("other", "spec.internals")) : null;
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}
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public NpmPackage getPck() {
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@ -2221,6 +2221,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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if (!hasResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Base")) {
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cacheResource(ProfileUtilities.makeBaseDefinition(version));
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}
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System.out.print(".");
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for (StructureDefinition sd : listStructures()) {
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try {
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if (sd.getSnapshot().isEmpty()) {
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@ -2231,6 +2232,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
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}
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}
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System.out.print(":");
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codeSystems.setVersion(version);
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valueSets.setVersion(version);
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maps.setVersion(version);
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@ -102,7 +102,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
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private final IContextResourceLoader loader;
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public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader) {
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super(pri.getType(), pri.getId(), pri.getUrl(),pri.getVersion());
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super(pri.getResourceType(), pri.getId(), pri.getUrl(),pri.getVersion());
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this.filename = pri.getFilename();
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this.loader = loader;
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}
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@ -98,7 +98,7 @@ import org.slf4j.LoggerFactory;
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public abstract class JsonParserBase extends ParserBase implements IParser {
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static {
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LoggerFactory.getLogger("org.hl7.fhir.r5.formats.JsonParserBase").debug("JSON Parser is being loaded");
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// LoggerFactory.getLogger("org.hl7.fhir.r5.formats.JsonParserBase").debug("JSON Parser is being loaded");
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ClassesLoadedFlags.ourJsonParserBaseLoaded = true;
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}
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@ -748,6 +748,8 @@ public class I18nConstants {
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public static final String SD_PATH_TYPE_MISMATCH = "SD_PATH_TYPE_MISMATCH";
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public static final String XHTML_XHTML_Image_Reference_Illegal = "XHTML_XHTML_Image_Reference_Illegal";
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public static final String XHTML_XHTML_Entity_Illegal = "XHTML_XHTML_Entity_Illegal";
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public static final String UNABLE_TO_RESOLVE_CONTENT_REFERENCE = "UNABLE_TO_RESOLVE_CONTENT_REFERENCE";
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public static final String UNABLE_TO_RESOLVE_CONTENT_REFERENCE_IN_THIS_CONTEXT = "UNABLE_TO_RESOLVE_CONTENT_REFERENCE_IN_THIS_CONTEXT";
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}
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@ -102,26 +102,31 @@ public class NpmPackage {
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public class PackageResourceInformation {
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private String id;
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private String type;
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private String resourceType;
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private String url;
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private String version;
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private String filename;
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private String supplements;
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private String stype;
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public PackageResourceInformation(String root, JsonObject fi) throws IOException {
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super();
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id = JsonUtilities.str(fi, "id");
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type = JsonUtilities.str(fi, "resourceType");
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resourceType = JsonUtilities.str(fi, "resourceType");
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url = JsonUtilities.str(fi, "url");
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version = JsonUtilities.str(fi, "version");
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filename = Utilities.path(root, JsonUtilities.str(fi, "filename"));
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supplements = JsonUtilities.str(fi, "supplements");
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stype = JsonUtilities.str(fi, "type");
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}
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public String getId() {
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return id;
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}
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public String getType() {
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return type;
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public String getResourceType() {
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return resourceType;
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}
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public String getStatedType() {
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return stype;
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}
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public String getUrl() {
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return url;
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@ -2,7 +2,7 @@
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Bad_file_path_error = \n********************\n* The file name you passed in, ''{0}'', doesn''t exist on the local filesystem.\n* Please verify that this is valid file location.\n********************\n\n
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Bundle_BUNDLE_Entry_Canonical = The canonical URL ({0}) cannot match the fullUrl ({1}) unless on the canonical server itself
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Bundle_BUNDLE_Entry_Document = The first entry in a document must be a composition
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Bundle_BUNDLE_Entry_IdUrlMismatch = Resource ID does not match the ID in the entry full URL (''{0}'' vs ''{1}'')
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Bundle_BUNDLE_Entry_IdUrlMismatch = Resource ID does not match the ID in the entry fullUrl (''{0}'' vs ''{1}'')
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Bundle_BUNDLE_Entry_MismatchIdUrl = The canonical URL ({0}) cannot match the fullUrl ({1}) unless the resource id ({2}) also matches
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Bundle_BUNDLE_Entry_NoFirst = Documents or Messages must contain at least one entry
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Bundle_BUNDLE_Entry_NoFirstResource = No resource on first entry
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@ -133,8 +133,8 @@ Resource_RES_ID_Missing = Resource requires an id, but none is present
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Resource_RES_ID_Prohibited = Resource has an id, but none is allowed
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Terminology_PassThrough_TX_Message = {0} for ''{1}#{2}''
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Terminology_TX_Binding_CantCheck = Binding by URI reference cannot be checked
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Terminology_TX_Binding_Missing = Binding for {0} missing (cc)
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Terminology_TX_Binding_Missing2 = Binding for {0} missing
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Terminology_TX_Binding_Missing = Binding for CodeableConcept {0} missing
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Terminology_TX_Binding_Missing2 = Binding for Coding {0} missing
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Terminology_TX_Binding_NoServer = The value provided could not be validated in the absence of a terminology server
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Terminology_TX_Binding_NoSource = Binding for path {0} has no source, so can''t be checked
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Terminology_TX_Binding_NoSource2 = Binding has no source, so can''t be checked
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@ -637,7 +637,7 @@ BUNDLE_BUNDLE_ENTRY_MULTIPLE_PROFILES_one =
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BUNDLE_BUNDLE_ENTRY_MULTIPLE_PROFILES_other = {0} profiles found for {1} resource. More than one is not supported at this time. (Type {2}: {3})
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RENDER_BUNDLE_HEADER_ROOT = Bundle {0} of type {1}
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RENDER_BUNDLE_HEADER_ENTRY = Entry {0}
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RENDER_BUNDLE_HEADER_ENTRY_URL = Entry {0} - Full URL = {1}
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RENDER_BUNDLE_HEADER_ENTRY_URL = Entry {0} - fullUrl = {1}
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RENDER_BUNDLE_RESOURCE = Resource {0}:
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RENDER_BUNDLE_SEARCH = Search:
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RENDER_BUNDLE_SEARCH_MODE = mode = {0}
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@ -798,3 +798,5 @@ SD_CONSTRAINED_TYPE_NO_MATCH = The type {0} must be the same as the type in the
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SD_SPECIALIZED_TYPE_MATCHES = The type {0} must not be the same as the type in the base structure {1} that is being specialised
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SD_CONSTRAINED_KIND_NO_MATCH = The kind {0} must be the same as the kind {1} in the base structure {3} (base type = {2})
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SD_PATH_TYPE_MISMATCH = The path {1} must start with the type of the structure {0}
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UNABLE_TO_RESOLVE_CONTENT_REFERENCE = Unable to resolve the content reference {0} on element {1} (path = {2})
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UNABLE_TO_RESOLVE_CONTENT_REFERENCE_IN_THIS_CONTEXT = Unable to resolve the content reference {0} on element {1} (path = {2}) in this context
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@ -313,6 +313,9 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
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@With
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private final IWorkerContext.ILoggingService loggingService;
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@With
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private boolean THO = true;
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public ValidationEngineBuilder() {
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terminologyCachePath = null;
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@ -326,7 +329,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
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loggingService = new SystemOutLoggingService();
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}
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public ValidationEngineBuilder(String terminologyCachePath, String userAgent, String version, String txServer, String txLog, FhirPublication txVersion, TimeTracker timeTracker, boolean canRunWithoutTerminologyServer, IWorkerContext.ILoggingService loggingService) {
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public ValidationEngineBuilder(String terminologyCachePath, String userAgent, String version, String txServer, String txLog, FhirPublication txVersion, TimeTracker timeTracker, boolean canRunWithoutTerminologyServer, IWorkerContext.ILoggingService loggingService, boolean THO) {
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this.terminologyCachePath = terminologyCachePath;
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this.userAgent = userAgent;
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this.version = version;
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@ -336,10 +339,11 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
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this.timeTracker = timeTracker;
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this.canRunWithoutTerminologyServer = canRunWithoutTerminologyServer;
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this.loggingService = loggingService;
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this.THO = THO;
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}
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public ValidationEngineBuilder withTxServer(String txServer, String txLog, FhirPublication txVersion) {
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return new ValidationEngineBuilder(terminologyCachePath, userAgent, version, txServer, txLog, txVersion,timeTracker, canRunWithoutTerminologyServer, loggingService);
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return new ValidationEngineBuilder(terminologyCachePath, userAgent, version, txServer, txLog, txVersion, timeTracker, canRunWithoutTerminologyServer, loggingService, THO);
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}
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public ValidationEngine fromNothing() throws IOException {
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@ -364,7 +368,9 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
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}
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engine.setVersion(version);
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engine.setIgLoader(new IgLoader(engine.getPcm(), engine.getContext(), engine.getVersion(), engine.isDebug()));
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loadTx(engine);
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if (THO) {
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loadTx(engine);
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}
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return engine;
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}
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@ -52,22 +52,22 @@ public class ValidatorUtils {
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return null;
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}
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if (VersionUtilities.isR2Ver(version)) {
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return new R2ToR5Loader(new String[]{"Conformance", "StructureDefinition", "ValueSet", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
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return new R2ToR5Loader(new String[]{"Conformance", "StructureDefinition", "ValueSet", /* "SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
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}
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if (VersionUtilities.isR2BVer(version)) {
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return new R2016MayToR5Loader(new String[]{"Conformance", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5()); // special case
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return new R2016MayToR5Loader(new String[]{"Conformance", "StructureDefinition", "ValueSet", "CodeSystem", /*"SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5()); // special case
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}
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if (VersionUtilities.isR3Ver(version)) {
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return new R3ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
|
||||
return new R3ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", /*"SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
|
||||
}
|
||||
if (VersionUtilities.isR4Ver(version)) {
|
||||
return new R4ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5(), version);
|
||||
return new R4ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", /*"SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5(), version);
|
||||
}
|
||||
if (VersionUtilities.isR4BVer(version)) {
|
||||
return new R4BToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5(), version);
|
||||
return new R4BToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", /*"SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5(), version);
|
||||
}
|
||||
if (VersionUtilities.isR5Ver(version)) {
|
||||
return new R5ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
|
||||
return new R5ToR5Loader(new String[]{"CapabilityStatement", "StructureDefinition", "ValueSet", "CodeSystem", /*"SearchParameter", "OperationDefinition",*/ "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem"}, new NullLoaderKnowledgeProviderR5());
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
@ -364,13 +364,13 @@ public class ValidationService {
|
||||
System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
|
||||
}
|
||||
System.out.print(" Load FHIR v" + cliContext.getSv() + " from " + definitions);
|
||||
ValidationEngine validator = new ValidationEngine.ValidationEngineBuilder().withVersion(cliContext.getSv()).withTimeTracker(tt).withUserAgent("fhir/validator").fromSource(definitions);
|
||||
ValidationEngine validator = new ValidationEngine.ValidationEngineBuilder().withTHO(false).withVersion(cliContext.getSv()).withTimeTracker(tt).withUserAgent("fhir/validator").fromSource(definitions);
|
||||
|
||||
sessionId = sessionCache.cacheSession(validator);
|
||||
|
||||
FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());
|
||||
IgLoader igLoader = new IgLoader(validator.getPcm(), validator.getContext(), validator.getVersion(), validator.isDebug());
|
||||
System.out.println(" - " + validator.getContext().countAllCaches() + " resources (" + tt.milestone() + ")");
|
||||
IgLoader igLoader = new IgLoader(validator.getPcm(), validator.getContext(), validator.getVersion(), validator.isDebug());
|
||||
igLoader.loadIg(validator.getIgs(), validator.getBinaries(), "hl7.terminology", false);
|
||||
System.out.print(" Load R5 Extensions");
|
||||
R5ExtensionsLoader r5e = new R5ExtensionsLoader(validator.getPcm(), validator.getContext());
|
||||
|
2
pom.xml
2
pom.xml
@ -19,7 +19,7 @@
|
||||
|
||||
<properties>
|
||||
<hapi_fhir_version>5.4.0</hapi_fhir_version>
|
||||
<validator_test_case_version>1.1.125</validator_test_case_version>
|
||||
<validator_test_case_version>1.1.126-SNAPSHOT</validator_test_case_version>
|
||||
<junit_jupiter_version>5.7.1</junit_jupiter_version>
|
||||
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
|
||||
<maven_surefire_version>3.0.0-M5</maven_surefire_version>
|
||||
|
Loading…
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Reference in New Issue
Block a user