Add support for CodeSystem supplements and correctly processing extensions when doing expansions
This commit is contained in:
Grahame Grieve
parent
548284fcda
commit
7d4cb4b5a2
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@ -657,6 +657,30 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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}
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return cs;
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}
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@Override
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public CodeSystem fetchSupplementedCodeSystem(String system) {
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CodeSystem cs = fetchCodeSystem(system);
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if (cs != null) {
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List<CodeSystem> supplements = codeSystems.getSupplements(cs);
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if (supplements.size() > 0) {
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cs = CodeSystemUtilities.mergeSupplements(cs, supplements);
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}
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}
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return cs;
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}
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@Override
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public CodeSystem fetchSupplementedCodeSystem(String system, String version) {
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CodeSystem cs = fetchCodeSystem(system, version);
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if (cs != null) {
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List<CodeSystem> supplements = codeSystems.getSupplements(cs);
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if (supplements.size() > 0) {
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cs = CodeSystemUtilities.mergeSupplements(cs, supplements);
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}
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}
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return cs;
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}
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@Override
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public boolean supportsSystem(String system) throws TerminologyServiceException {
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@ -846,7 +870,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
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return res;
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}
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if (res.getErrorClass() == TerminologyServiceErrorClass.INTERNAL_ERROR) { // this class is created specifically to say: don't consult the server
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if (res.getErrorClass() == TerminologyServiceErrorClass.INTERNAL_ERROR || isNoTerminologyServer()) { // this class is created specifically to say: don't consult the server
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return new ValueSetExpansionOutcome(res.getError(), res.getErrorClass());
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}
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@ -30,14 +30,16 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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private String id;
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private String url;
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private String version;
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private String supplements;
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private CanonicalResource resource;
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public CanonicalResourceProxy(String type, String id, String url, String version) {
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public CanonicalResourceProxy(String type, String id, String url, String version, String supplements) {
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super();
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this.type = type;
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this.id = id;
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this.url = url;
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this.version = version;
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this.supplements = supplements;
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}
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public String getType() {
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@ -68,6 +70,10 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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return version != null;
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}
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public String getSupplements() {
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return supplements;
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}
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public CanonicalResource getResource() throws FHIRException {
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if (resource == null) {
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resource = loadResource();
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@ -111,7 +117,7 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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private T1 resource;
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private CanonicalResourceProxy proxy;
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private PackageInformation packageInfo;
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public CachedCanonicalResource(T1 resource, PackageInformation packageInfo) {
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super();
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this.resource = resource;
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@ -159,6 +165,14 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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@Override
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public String toString() {
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return resource != null ? resource.fhirType()+"/"+resource.getId()+"["+resource.getUrl()+"|"+resource.getVersion()+"]" : proxy.toString();
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}
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public String supplements() {
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if (resource == null) {
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return proxy.getSupplements();
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} else {
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return resource instanceof CodeSystem ? ((CodeSystem) resource).getSupplements() : null;
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}
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}
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}
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@ -191,6 +205,7 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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private Map<String, List<CachedCanonicalResource<T>>> listForId = new HashMap<>();
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private Map<String, List<CachedCanonicalResource<T>>> listForUrl = new HashMap<>();
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private Map<String, CachedCanonicalResource<T>> map = new HashMap<>();
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private Map<String, List<CachedCanonicalResource<T>>> supplements = new HashMap<>(); // general index based on CodeSystem.supplements
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private String version; // for debugging purposes
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@ -288,6 +303,7 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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if (!listForUrl.containsKey(cr.getUrl())) {
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listForUrl.put(cr.getUrl(), new ArrayList<>());
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}
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addToSupplements(cr);
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List<CachedCanonicalResource<T>> set = listForUrl.get(cr.getUrl());
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set.add(cr);
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Collections.sort(set, new MetadataResourceVersionComparator<CachedCanonicalResource<T>>());
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@ -324,10 +340,27 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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}
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}
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private void addToSupplements(CanonicalResourceManager<T>.CachedCanonicalResource<T> cr) {
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String surl = cr.supplements();
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if (surl != null) {
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List<CanonicalResourceManager<T>.CachedCanonicalResource<T>> list = supplements.get(surl);
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if (list == null) {
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list = new ArrayList<>();
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supplements.put(surl, list);
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}
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list.add(cr);
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}
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}
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public void drop(CachedCanonicalResource<T> cr) {
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while (map.values().remove(cr));
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while (listForId.values().remove(cr));
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while (listForUrl.values().remove(cr));
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String surl = cr.supplements();
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if (surl != null) {
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supplements.get(surl).remove(cr);
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}
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list.remove(cr);
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List<CachedCanonicalResource<T>> set = listForUrl.get(cr.getUrl());
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if (set != null) { // it really should be
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@ -514,6 +547,54 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
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}
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}
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public List<T> getSupplements(T cr) {
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if (cr.hasSourcePackage()) {
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List<String> pvl = new ArrayList<>();
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pvl.add(cr.getSourcePackage().getVID());
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return getSupplements(cr.getUrl(), cr.getVersion(), pvl);
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} else {
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return getSupplements(cr.getUrl(), cr.getVersion(), null);
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}
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}
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public List<T> getSupplements(String url) {
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return getSupplements(url, null, null);
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}
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public List<T> getSupplements(String url, String version) {
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return getSupplements(url, version, null);
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}
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public List<T> getSupplements(String url, String version, List<String> pvlist) {
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boolean possibleMatches = false;
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List<T> res = new ArrayList<>();
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if (version != null) {
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List<CanonicalResourceManager<T>.CachedCanonicalResource<T>> list = supplements.get(url+"|"+version);
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if (list != null) {
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for (CanonicalResourceManager<T>.CachedCanonicalResource<T> t : list) {
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possibleMatches = true;
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if (pvlist == null || pvlist.contains(t.getPackageInfo().getVID())) {
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res.add(t.getResource());
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}
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}
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}
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}
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List<CanonicalResourceManager<T>.CachedCanonicalResource<T>> list = supplements.get(url);
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if (list != null) {
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for (CanonicalResourceManager<T>.CachedCanonicalResource<T> t : list) {
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possibleMatches = true;
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if (pvlist == null || pvlist.contains(t.getPackageInfo().getVID())) {
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res.add(t.getResource());
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}
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}
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}
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if (res.isEmpty() && pvlist != null && possibleMatches) {
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return getSupplements(url, version, null);
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} else {
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return res;
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}
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}
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public void clear() {
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list.clear();
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map.clear();
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@ -544,6 +544,14 @@ public interface IWorkerContext {
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public CodeSystem fetchCodeSystem(String system);
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public CodeSystem fetchCodeSystem(String system, String version);
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/**
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* Like fetchCodeSystem, except that the context will find any CodeSysetm supplements and merge them into the
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* @param system
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* @return
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*/
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public CodeSystem fetchSupplementedCodeSystem(String system);
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public CodeSystem fetchSupplementedCodeSystem(String system, String version);
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/**
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* True if the underlying terminology service provider will do
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* expansion and code validation for the terminology. Corresponds
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@ -97,7 +97,7 @@ 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.getResourceType(), pri.getId(), loader == null ? pri.getUrl() :loader.patchUrl(pri.getUrl(), pri.getResourceType()), pri.getVersion());
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super(pri.getResourceType(), pri.getId(), loader == null ? pri.getUrl() :loader.patchUrl(pri.getUrl(), pri.getResourceType()), pri.getVersion(), pri.getSupplements());
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this.filename = pri.getFilename();
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this.loader = loader;
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}
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@ -12,6 +12,9 @@ import org.hl7.fhir.r5.model.DataType;
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import org.hl7.fhir.r5.model.DomainResource;
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import org.hl7.fhir.r5.model.Element;
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import org.hl7.fhir.r5.model.Extension;
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import org.hl7.fhir.r5.model.Property;
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import org.hl7.fhir.r5.model.Resource;
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import org.hl7.fhir.utilities.Utilities;
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public class ExtensionsUtils {
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@ -275,4 +278,103 @@ public class ExtensionsUtils {
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return result;
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}
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public static boolean stripExtensions(Element element, String... exceptions) {
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return stripExtensions(element, Utilities.strings(exceptions));
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}
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public static boolean stripExtensions(Element element, List<String> exceptions) {
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boolean res = element.getExtension().removeIf(ex -> !exceptions.contains(ex.getUrl()));
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if (element instanceof BackboneElement) {
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res = ((BackboneElement) element).getModifierExtension().removeIf(ex -> !exceptions.contains(ex.getUrl())) || res;
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}
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if (element instanceof BackboneElement) {
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res = ((BackboneElement) element).getModifierExtension().removeIf(ex -> !exceptions.contains(ex.getUrl())) || res;
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}
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for (Property p : element.children()) {
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for (Base v : p.getValues()) {
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if (v instanceof Element) {
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res = stripExtensions((Element) v, exceptions) || res;
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} else if (v instanceof Element) {
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res = stripExtensions((Resource) v, exceptions) || res;
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}
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}
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}
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return res;
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}
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public static boolean stripExtensions(Resource resource, String... exceptions) {
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return stripExtensions(resource, Utilities.strings(exceptions));
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}
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public static boolean stripExtensions(Resource resource, List<String> exceptions) {
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boolean res = false;
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if (resource instanceof DomainResource) {
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res = ((DomainResource) resource).getExtension().removeIf(ex -> !exceptions.contains(ex.getUrl())) ||
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((DomainResource) resource).getModifierExtension().removeIf(ex -> !exceptions.contains(ex.getUrl()));
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}
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for (Property p : resource.children()) {
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for (Base v : p.getValues()) {
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if (v instanceof Element) {
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res = stripExtensions((Element) v, exceptions) || res;
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} else if (v instanceof Element) {
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res = stripExtensions((Resource) v, exceptions) || res;
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}
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}
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}
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return res;
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}
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public static void copyExtensions(List<Extension> source, List<Extension> dest, String... urls) {
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if (source != null && dest != null) {
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for (Extension ex : source) {
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if (Utilities.existsInList(ex.getUrl(), urls)) {
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dest.add(ex.copy());
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}
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}
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}
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}
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public static DataType getExtensionValue(List<Extension> extensions, String url) {
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for (Extension ex : extensions) {
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if (ex.getUrl().equals(url)) {
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return ex.getValue();
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}
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}
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return null;
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}
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public static String getExtensionString(List<Extension> extensions, String url) {
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for (Extension ex : extensions) {
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if (ex.getUrl().equals(url)) {
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return ex.getValue().primitiveValue();
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}
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}
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return null;
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}
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public static Integer getExtensionInteger(List<Extension> extensions, String url) {
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for (Extension ex : extensions) {
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if (ex.getUrl().equals(url) && ex.hasValueIntegerType()) {
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return ex.getValueIntegerType().getValue();
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}
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}
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return null;
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}
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public static boolean hasExtension(List<Extension> extensions, String url) {
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if (extensions == null) {
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return false;
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}
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for (Extension ex : extensions) {
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if (ex.getUrl().equals(url)) {
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return true;
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}
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}
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return false;
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}
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}
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@ -57,6 +57,7 @@ import org.hl7.fhir.r5.model.DataType;
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import org.hl7.fhir.r5.model.DateTimeType;
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import org.hl7.fhir.r5.model.DecimalType;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r5.model.Extension;
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import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptDefinitionComponentSorter;
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import org.hl7.fhir.r5.model.Identifier;
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import org.hl7.fhir.r5.model.IntegerType;
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@ -64,6 +65,7 @@ import org.hl7.fhir.r5.model.Meta;
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import org.hl7.fhir.r5.model.StringType;
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import org.hl7.fhir.r5.model.UriType;
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import org.hl7.fhir.r5.utils.ToolingExtensions;
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import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
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import org.hl7.fhir.utilities.StandardsStatus;
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import org.hl7.fhir.utilities.Utilities;
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@ -246,7 +248,7 @@ public class CodeSystemUtilities {
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throw new Error("Unknown property type "+value.getClass().getName());
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}
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private static void defineProperty(CodeSystem cs, String code, PropertyType pt) {
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private static String defineProperty(CodeSystem cs, String code, PropertyType pt) {
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String url = "http://hl7.org/fhir/concept-properties#"+code;
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for (PropertyComponent p : cs.getProperty()) {
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if (p.getCode().equals(code)) {
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@ -256,11 +258,11 @@ public class CodeSystemUtilities {
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if (!p.getType().equals(pt)) {
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throw new Error("Type mismatch for code "+code+" type = "+p.getType()+" vs "+pt);
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}
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return;
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return code;
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}
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}
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cs.addProperty().setCode(code).setUri(url).setType(pt).setUri(url);
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return code;
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}
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public static void defineNotSelectableProperty(CodeSystem cs) {
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@ -720,5 +722,101 @@ public class CodeSystemUtilities {
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}
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return t;
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}
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public static CodeSystem mergeSupplements(CodeSystem cs, List<CodeSystem> supplements) {
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CodeSystem ret = cs.copy();
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CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
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for (CodeSystem sup : supplements) {
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b.append(sup.getVersionedUrl());
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}
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ret.setUserData("supplements.installed", b.toString());
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for (ConceptDefinitionComponent t : ret.getConcept()) {
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mergeSupplements(ret, t, supplements);
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}
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return ret;
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}
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private static void mergeSupplements(CodeSystem ret, ConceptDefinitionComponent fdef, List<CodeSystem> supplements) {
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for (CodeSystem cs : supplements) {
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ConceptDefinitionComponent def = CodeSystemUtilities.findCode(cs.getConcept(), fdef.getCode());
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if (def != null) {
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for (Extension ext : def.getExtension()) {
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fdef.addExtension(ext.copy());
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}
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for (ConceptDefinitionDesignationComponent d : def.getDesignation()) {
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fdef.addDesignation(d.copy());
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}
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for (ConceptPropertyComponent p : def.getProperty()) {
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PropertyComponent pd = CodeSystemUtilities.getPropertyDefinition(cs, p);
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String code;
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if (pd != null) {
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code = defineProperty(ret, pd, propertyTypeForType(p.getValue()));
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} else {
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code = defineProperty(ret, p.getCode(), propertyTypeForType(p.getValue()));
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}
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fdef.addProperty().setCode(code).setValue(p.getValue());
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}
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}
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for (ConceptDefinitionComponent t : fdef.getConcept()) {
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mergeSupplements(ret, t, supplements);
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}
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}
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}
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private static PropertyType propertyTypeForType(DataType value) {
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if (value == null) {
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return PropertyType.NULL;
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}
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if (value instanceof CodeType) {
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return PropertyType.CODE;
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}
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if (value instanceof CodeType) {
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return PropertyType.CODING;
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}
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if (value instanceof CodeType) {
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return PropertyType.STRING;
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}
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if (value instanceof CodeType) {
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return PropertyType.INTEGER;
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}
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if (value instanceof CodeType) {
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return PropertyType.BOOLEAN;
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}
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if (value instanceof CodeType) {
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return PropertyType.DATETIME;
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}
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if (value instanceof CodeType) {
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return PropertyType.DECIMAL;
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}
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throw new FHIRException("Unsupported property value for a CodeSystem Property: "+value.fhirType());
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}
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private static String defineProperty(CodeSystem cs, PropertyComponent pd, PropertyType pt) {
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for (PropertyComponent p : cs.getProperty()) {
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if (p.getCode().equals(pd.getCode())) {
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if (!p.getUri().equals(pd.getUri())) {
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throw new Error("URI mismatch for code "+pd.getCode()+" url = "+p.getUri()+" vs "+pd.getUri());
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}
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if (!p.getType().equals(pt)) {
|
||||
throw new Error("Type mismatch for code "+pd.getCode()+" type = "+p.getType().toCode()+" vs "+pt.toCode());
|
||||
}
|
||||
return pd.getCode();
|
||||
}
|
||||
}
|
||||
cs.addProperty().setCode(pd.getCode()).setUri(pd.getUri()).setType(pt);
|
||||
return pd.getCode();
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static PropertyComponent getPropertyDefinition(CodeSystem cs, ConceptPropertyComponent p) {
|
||||
for (PropertyComponent t : cs.getProperty()) {
|
||||
if (t.getCode().equals(p.getCode())) {
|
||||
return t;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ import org.hl7.fhir.r5.model.ValueSet;
|
|||
|
||||
public interface ValueSetExpander {
|
||||
public enum TerminologyServiceErrorClass {
|
||||
UNKNOWN, NOSERVICE, SERVER_ERROR, VALUESET_UNSUPPORTED, CODESYSTEM_UNSUPPORTED, BLOCKED_BY_OPTIONS, INTERNAL_ERROR;
|
||||
UNKNOWN, NOSERVICE, SERVER_ERROR, VALUESET_UNSUPPORTED, CODESYSTEM_UNSUPPORTED, BLOCKED_BY_OPTIONS, INTERNAL_ERROR, BUSINESS_RULE;
|
||||
|
||||
public boolean isInfrastructure() {
|
||||
return this == NOSERVICE || this == SERVER_ERROR || this == VALUESET_UNSUPPORTED;
|
||||
|
|
|
|||
|
|
@ -82,7 +82,9 @@ import org.hl7.fhir.exceptions.NoTerminologyServiceException;
|
|||
import org.hl7.fhir.exceptions.TerminologyServiceException;
|
||||
import org.hl7.fhir.r5.context.IWorkerContext;
|
||||
import org.hl7.fhir.r5.elementmodel.LangaugeUtils;
|
||||
import org.hl7.fhir.r5.extensions.ExtensionConstants;
|
||||
import org.hl7.fhir.r5.extensions.Extensions;
|
||||
import org.hl7.fhir.r5.extensions.ExtensionsUtils;
|
||||
import org.hl7.fhir.r5.model.BooleanType;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
|
||||
|
|
@ -206,6 +208,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
private ValueSet focus;
|
||||
private int maxExpansionSize = 500;
|
||||
private List<String> allErrors = new ArrayList<>();
|
||||
private List<String> requiredSupplements = new ArrayList<>();
|
||||
|
||||
private int total;
|
||||
private boolean checkCodesWhenExpanding;
|
||||
|
|
@ -227,7 +230,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
|
||||
private ValueSetExpansionContainsComponent addCode(String system, String code, String display, String dispLang, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations, Parameters expParams,
|
||||
boolean isAbstract, boolean inactive, String definition, List<ValueSet> filters, boolean noInactive, boolean deprecated, List<ValueSetExpansionPropertyComponent> vsProp,
|
||||
List<ConceptPropertyComponent> csProps, List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> expProps) {
|
||||
List<ConceptPropertyComponent> csProps, List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> expProps, List<Extension> csExtList, List<Extension> vsExtList) {
|
||||
|
||||
if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
|
||||
return null;
|
||||
|
|
@ -248,6 +251,37 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
if (expParams.getParameterBool("includeDefinition") && definition != null) {
|
||||
n.addExtension(Extensions.makeVSConceptDefinition(definition));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-label"));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#label", "label", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-label"));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder"));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#order", "order", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder"));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(csExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight"));
|
||||
}
|
||||
if (ExtensionsUtils.hasExtension(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight")) {
|
||||
ValueSetUtilities.addProperty(focus, n, "http://hl7.org/fhir/concept-properties#itemWeight", "weight", ExtensionsUtils.getExtensionValue(vsExtList, "http://hl7.org/fhir/StructureDefinition/itemWeight"));
|
||||
}
|
||||
ExtensionsUtils.copyExtensions(csExtList, n.getExtension(),
|
||||
"http://hl7.org/fhir/StructureDefinition/coding-sctdescid",
|
||||
"http://hl7.org/fhir/StructureDefinition/rendering-style",
|
||||
"http://hl7.org/fhir/StructureDefinition/rendering-xhtml",
|
||||
"http://hl7.org/fhir/StructureDefinition/codesystem-alternate");
|
||||
|
||||
ExtensionsUtils.copyExtensions(vsExtList, n.getExtension(),
|
||||
"http://hl7.org/fhir/StructureDefinition/valueset-supplement",
|
||||
"http://hl7.org/fhir/StructureDefinition/valueset-deprecated",
|
||||
"http://hl7.org/fhir/StructureDefinition/valueset-concept-definition",
|
||||
"http://hl7.org/fhir/StructureDefinition/coding-sctdescid",
|
||||
"http://hl7.org/fhir/StructureDefinition/rendering-style",
|
||||
"http://hl7.org/fhir/StructureDefinition/rendering-xhtml");
|
||||
|
||||
// display and designations
|
||||
String srcLang = dispLang;
|
||||
|
|
@ -349,7 +383,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
private void addCodeAndDescendents(ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc) throws FHIRException {
|
||||
focus.checkNoModifiers("Expansion.contains", "expanding");
|
||||
ValueSetExpansionContainsComponent np = addCode(focus.getSystem(), focus.getCode(), focus.getDisplay(), vsSrc.getLanguage(), parent,
|
||||
convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), focus.getExtensionString(ToolingExtensions.EXT_DEFINITION), filters, noInactive, false, vsProps, null, focus.getProperty());
|
||||
convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), focus.getExtensionString(ToolingExtensions.EXT_DEFINITION), filters, noInactive, false, vsProps, null, focus.getProperty(), null, focus.getExtension());
|
||||
for (ValueSetExpansionContainsComponent c : focus.getContains())
|
||||
addCodeAndDescendents(focus, np, expParams, filters, noInactive, vsProps, vsSrc);
|
||||
}
|
||||
|
|
@ -378,7 +412,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
boolean inc = CodeSystemUtilities.isInactive(cs, def);
|
||||
boolean dep = CodeSystemUtilities.isDeprecated(cs, def, false);
|
||||
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def)) {
|
||||
np = addCode(system, def.getCode(), def.getDisplay(), cs.getLanguage(), parent, def.getDesignation(), expParams, abs, inc, def.getDefinition(), filters, noInactive, dep, vsProps, def.getProperty(), null);
|
||||
np = addCode(system, def.getCode(), def.getDisplay(), cs.getLanguage(), parent, def.getDesignation(), expParams, abs, inc, def.getDefinition(), filters, noInactive, dep, vsProps, def.getProperty(), null, def.getExtension(), null);
|
||||
}
|
||||
for (ConceptDefinitionComponent c : def.getConcept()) {
|
||||
addCodeAndDescendents(cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps);
|
||||
|
|
@ -422,7 +456,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
throw fail("Processing Value set references in exclude is not yet done in "+ctxt);
|
||||
// importValueSet(imp.getValue(), params, expParams);
|
||||
|
||||
CodeSystem cs = context.fetchCodeSystem(exc.getSystem());
|
||||
CodeSystem cs = context.fetchSupplementedCodeSystem(exc.getSystem());
|
||||
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(exc.getSystem())) {
|
||||
ValueSetExpansionOutcome vse = context.expandVS(exc, false, false);
|
||||
ValueSet valueset = vse.getValueset();
|
||||
|
|
@ -493,11 +527,15 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
focus.getExpansion().addParameter().setName(p.getName()).setValue(p.getValue());
|
||||
}
|
||||
}
|
||||
for (Extension s : focus.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) {
|
||||
requiredSupplements.add(s.getValue().primitiveValue());
|
||||
}
|
||||
if (expParams.hasLanguage()) {
|
||||
focus.setLanguage(expParams.getLanguage());
|
||||
}
|
||||
|
||||
if (source.hasCompose()) {
|
||||
ExtensionsUtils.stripExtensions(focus.getCompose());
|
||||
handleCompose(source.getCompose(), focus.getExpansion(), expParams, source.getUrl(), focus.getExpansion().getExtension(), source);
|
||||
}
|
||||
|
||||
|
|
@ -517,6 +555,9 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
if (total > 0) {
|
||||
focus.getExpansion().setTotal(total);
|
||||
}
|
||||
if (!requiredSupplements.isEmpty()) {
|
||||
return new ValueSetExpansionOutcome("Required supplements not found: "+requiredSupplements.toString(), TerminologyServiceErrorClass.BUSINESS_RULE, allErrors);
|
||||
}
|
||||
|
||||
return new ValueSetExpansionOutcome(focus);
|
||||
}
|
||||
|
|
@ -656,7 +697,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
for (ValueSetExpansionContainsComponent c : list) {
|
||||
c.checkNoModifiers("Imported Expansion in Code System", "expanding");
|
||||
ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), vsSrc.getLanguage(), parent, null, expParams, c.getAbstract(), c.getInactive(), c.getExtensionString(ToolingExtensions.EXT_DEFINITION),
|
||||
filter, noInactive, false, vsProps, null, c.getProperty());
|
||||
filter, noInactive, false, vsProps, null, c.getProperty(), null, c.getExtension());
|
||||
copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc);
|
||||
}
|
||||
}
|
||||
|
|
@ -676,10 +717,15 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
base.checkNoModifiers("Imported ValueSet", "expanding");
|
||||
copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base);
|
||||
} else {
|
||||
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
|
||||
CodeSystem cs = context.fetchSupplementedCodeSystem(inc.getSystem());
|
||||
if (isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
|
||||
doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions, noInactive, valueSet.getExpansion().getProperty());
|
||||
} else {
|
||||
if (cs.hasUserData("supplements.installed")) {
|
||||
for (String s : cs.getUserString("supplements.installed").split("\\,")) {
|
||||
requiredSupplements.remove(s);
|
||||
}
|
||||
}
|
||||
doInternalIncludeCodes(inc, exp, expParams, imports, cs, noInactive, valueSet);
|
||||
}
|
||||
}
|
||||
|
|
@ -709,7 +755,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
}
|
||||
for (Extension ex : vs.getExpansion().getExtension()) {
|
||||
if (Utilities.existsInList(ex.getUrl(), ToolingExtensions.EXT_EXP_TOOCOSTLY, "http://hl7.org/fhir/StructureDefinition/valueset-unclosed")) {
|
||||
if (!hasExtension(extensions, ex.getUrl())) {
|
||||
if (!ExtensionsUtils.hasExtension(extensions, ex.getUrl())) {
|
||||
extensions.add(ex);
|
||||
}
|
||||
}
|
||||
|
|
@ -719,14 +765,6 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
}
|
||||
}
|
||||
|
||||
private boolean hasExtension(List<Extension> extensions, String url) {
|
||||
for (Extension ex : extensions) {
|
||||
if (ex.getUrl().equals(url)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive, Resource vsSrc) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
|
||||
if (cs == null) {
|
||||
|
|
@ -758,10 +796,11 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
if (!inc.getConcept().isEmpty()) {
|
||||
canBeHeirarchy = false;
|
||||
for (ConceptReferenceComponent c : inc.getConcept()) {
|
||||
c.checkNoModifiers("Code in Code System", "expanding");
|
||||
c.checkNoModifiers("Code in Value Set", "expanding");
|
||||
ConceptDefinitionComponent def = CodeSystemUtilities.findCode(cs.getConcept(), c.getCode());
|
||||
Boolean inactive = false; // default is true if we're a fragment and
|
||||
if (def == null) {
|
||||
def.checkNoModifiers("Code in Code System", "expanding");
|
||||
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
|
||||
addFragmentWarning(exp, cs);
|
||||
} else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
|
||||
|
|
@ -775,7 +814,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
inactive = CodeSystemUtilities.isInactive(cs, def);
|
||||
}
|
||||
addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), c.hasDisplay() ? vsSrc.getLanguage() : cs.getLanguage(), null, mergeDesignations(def, convertDesignations(c.getDesignation())),
|
||||
expParams, false, inactive, def == null ? null : def.getDefinition(), imports, noInactive, false, exp.getProperty(), def != null ? def.getProperty() : null, null);
|
||||
expParams, false, inactive, def == null ? null : def.getDefinition(), imports, noInactive, false, exp.getProperty(), def != null ? def.getProperty() : null, null, def == null ? null : def.getExtension(), c.getExtension());
|
||||
}
|
||||
}
|
||||
if (inc.getFilter().size() > 1) {
|
||||
|
|
@ -822,7 +861,7 @@ public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetEx
|
|||
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
|
||||
if (def.getDisplay().contains(fc.getValue())) {
|
||||
addCode(inc.getSystem(), def.getCode(), def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
|
||||
def.getDefinition(), imports, noInactive, false, exp.getProperty(), def.getProperty(), null);
|
||||
def.getDefinition(), imports, noInactive, false, exp.getProperty(), def.getProperty(), null, def.getExtension(), null);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -42,6 +42,8 @@ import org.hl7.fhir.r5.model.BooleanType;
|
|||
import org.hl7.fhir.r5.model.CanonicalType;
|
||||
import org.hl7.fhir.r5.model.CodeSystem;
|
||||
import org.hl7.fhir.r5.model.DateTimeType;
|
||||
import org.hl7.fhir.r5.model.StringType;
|
||||
import org.hl7.fhir.r5.model.IntegerType;
|
||||
import org.hl7.fhir.r5.model.Enumerations.FilterOperator;
|
||||
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
|
||||
import org.hl7.fhir.r5.model.Identifier;
|
||||
|
|
@ -52,6 +54,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
|
|||
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
|
||||
import org.hl7.fhir.r5.model.CodeType;
|
||||
import org.hl7.fhir.r5.model.Coding;
|
||||
import org.hl7.fhir.r5.model.DataType;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
|
||||
|
|
@ -328,5 +331,54 @@ public class ValueSetUtilities {
|
|||
return false;
|
||||
}
|
||||
|
||||
public static void addProperty(ValueSet vs, ValueSetExpansionContainsComponent ctxt, String url, String code, String value) {
|
||||
if (value != null) {
|
||||
addProperty(vs, ctxt, url, code, new StringType(value));
|
||||
}
|
||||
}
|
||||
|
||||
public static void addProperty(ValueSet vs, ValueSetExpansionContainsComponent ctxt, String url, String code, Integer value) {
|
||||
if (value != null) {
|
||||
addProperty(vs, ctxt, url, code, new IntegerType(value));
|
||||
}
|
||||
}
|
||||
|
||||
public static void addProperty(ValueSet vs, ValueSetExpansionContainsComponent ctxt, String url, String code, DataType value) {
|
||||
code = defineProperty(vs, url, code);
|
||||
org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent p = getProperty(ctxt.getProperty(), code);
|
||||
if (p != null)
|
||||
p.setValue(value);
|
||||
else
|
||||
ctxt.addProperty().setCode(code).setValue(value);
|
||||
|
||||
}
|
||||
|
||||
private static org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent getProperty(List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> list, String code) {
|
||||
for (org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent t : list) {
|
||||
if (code.equals(t.getCode())) {
|
||||
return t;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private static String defineProperty(ValueSet vs, String url, String code) {
|
||||
for (ValueSetExpansionPropertyComponent p : vs.getExpansion().getProperty()) {
|
||||
if (p.hasUri() && p.getUri().equals(url)) {
|
||||
return p.getCode();
|
||||
}
|
||||
}
|
||||
for (ValueSetExpansionPropertyComponent p : vs.getExpansion().getProperty()) {
|
||||
if (p.hasCode() && p.getCode().equals(code)) {
|
||||
p.setUri(url);
|
||||
return code;
|
||||
}
|
||||
}
|
||||
ValueSetExpansionPropertyComponent p = vs.getExpansion().addProperty();
|
||||
p.setUri(url);
|
||||
p.setCode(code);
|
||||
return code;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -7,6 +7,7 @@ import java.util.List;
|
|||
import org.hl7.fhir.r5.context.CanonicalResourceManager;
|
||||
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
|
||||
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.ValueSet;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
|
|
@ -18,7 +19,7 @@ public class CanonicalResourceManagerTests {
|
|||
private CanonicalResource resource;
|
||||
|
||||
public DeferredLoadTestResource(CanonicalResource resource) {
|
||||
super(resource.fhirType(), resource.getId(), resource.getUrl(), resource.getVersion());
|
||||
super(resource.fhirType(), resource.getId(), resource.getUrl(), resource.getVersion(), resource instanceof CodeSystem ? ((CodeSystem) resource).getSupplements() : null);
|
||||
this.resource = resource;
|
||||
}
|
||||
|
||||
|
|
@ -853,4 +854,77 @@ public class CanonicalResourceManagerTests {
|
|||
Assertions.assertEquals("2", mrm.get("http://url/ValueSet/234", "4.0.2", pvl2).getName());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSupplements() {
|
||||
CanonicalResourceManager<CodeSystem> mrm = new CanonicalResourceManager<>(true);
|
||||
CodeSystem csb1 = new CodeSystem();
|
||||
csb1.setId("2345");
|
||||
csb1.setUrl("http://url/CodeSystem/234");
|
||||
csb1.setVersion("4.0.1");
|
||||
csb1.setName("1");
|
||||
mrm.see(csb1, new PackageInformation("pid.one", "1.0.0", new Date()));
|
||||
|
||||
CodeSystem csb2 = new CodeSystem();
|
||||
csb2.setId("2346");
|
||||
csb2.setUrl("http://url/CodeSystem/234");
|
||||
csb2.setVersion("4.0.1");
|
||||
csb2.setName("2");
|
||||
mrm.see(csb2, new PackageInformation("pid.two", "1.0.0", new Date()));
|
||||
|
||||
CodeSystem css1 = new CodeSystem();
|
||||
css1.setId("s2345");
|
||||
css1.setUrl("http://url/CodeSystem/s234");
|
||||
css1.setVersion("4.0.1");
|
||||
css1.setName("s1");
|
||||
css1.setSupplements("http://url/CodeSystem/234");
|
||||
mrm.see(css1, new PackageInformation("pid.one", "1.0.0", new Date()));
|
||||
|
||||
CodeSystem css2 = new CodeSystem();
|
||||
css2.setId("s2346");
|
||||
css2.setUrl("http://url/CodeSystem/s234");
|
||||
css2.setVersion("4.0.1");
|
||||
css2.setName("s2");
|
||||
css2.setSupplements("http://url/CodeSystem/234");
|
||||
mrm.see(css2, new PackageInformation("pid.two", "1.0.0", new Date()));
|
||||
|
||||
List<CodeSystem> sl = mrm.getSupplements("http://url/CodeSystem/234");
|
||||
Assertions.assertEquals(2, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1");
|
||||
Assertions.assertEquals(2, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/s234");
|
||||
Assertions.assertEquals(0, sl.size());
|
||||
|
||||
List<String> pvl = new ArrayList<>();
|
||||
pvl.add("pid.two#1.0.0");
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1", pvl);
|
||||
Assertions.assertEquals(1, sl.size());
|
||||
|
||||
mrm.drop("s2346");
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234");
|
||||
Assertions.assertEquals(1, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1");
|
||||
Assertions.assertEquals(1, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/s234");
|
||||
Assertions.assertEquals(0, sl.size());
|
||||
|
||||
pvl = new ArrayList<>();
|
||||
pvl.add("pid.two#1.0.0");
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1", pvl);
|
||||
Assertions.assertEquals(1, sl.size()); // cause we fall back to the other
|
||||
|
||||
pvl = new ArrayList<>();
|
||||
pvl.add("pid.one#1.0.0");
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1", pvl);
|
||||
Assertions.assertEquals(1, sl.size());
|
||||
|
||||
mrm.drop("s2345");
|
||||
|
||||
mrm.drop("s2346");
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234");
|
||||
Assertions.assertEquals(0, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/234", "1.0.1");
|
||||
Assertions.assertEquals(0, sl.size());
|
||||
sl = mrm.getSupplements("http://url/CodeSystem/s234");
|
||||
Assertions.assertEquals(0, sl.size());
|
||||
}
|
||||
}
|
||||
|
|
@ -22,6 +22,10 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
|||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.Constants;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.ValueSet;
|
||||
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
|
||||
|
|
@ -103,7 +107,7 @@ public class TerminologyServiceTests {
|
|||
@Test
|
||||
public void test() throws Exception {
|
||||
if (baseEngine == null) {
|
||||
baseEngine = TestUtilities.getValidationEngine("hl7.fhir.r5.core#5.0.0", ValidationEngineTests.DEF_TX, null, FhirPublication.R5, true, "5.0.0");
|
||||
baseEngine = TestUtilities.getValidationEngine("hl7.fhir.r5.core#5.0.0", null, null, FhirPublication.R5, true, "5.0.0");
|
||||
}
|
||||
ValidationEngine engine = new ValidationEngine(this.baseEngine);
|
||||
for (String s : setup.suite.forceArray("setup").asStrings()) {
|
||||
|
|
@ -149,7 +153,45 @@ public class TerminologyServiceTests {
|
|||
Assertions.assertTrue(diff == null, diff);
|
||||
}
|
||||
} else {
|
||||
Assertions.fail("expand error not done yet");
|
||||
OperationOutcome oo = new OperationOutcome();
|
||||
OperationOutcomeIssueComponent e = new OperationOutcomeIssueComponent();
|
||||
e.setSeverity(IssueSeverity.ERROR);
|
||||
switch (vse.getErrorClass()) {
|
||||
case BLOCKED_BY_OPTIONS:
|
||||
e.setCode(IssueType.FORBIDDEN);
|
||||
break;
|
||||
case BUSINESS_RULE:
|
||||
e.setCode(IssueType.BUSINESSRULE);
|
||||
break;
|
||||
case CODESYSTEM_UNSUPPORTED:
|
||||
e.setCode(IssueType.INVALID);
|
||||
break;
|
||||
case INTERNAL_ERROR:
|
||||
e.setCode(IssueType.EXCEPTION);
|
||||
break;
|
||||
case NOSERVICE:
|
||||
e.setCode(IssueType.CONFLICT);
|
||||
break;
|
||||
case SERVER_ERROR:
|
||||
e.setCode(IssueType.EXCEPTION);
|
||||
break;
|
||||
case UNKNOWN:
|
||||
e.setCode(IssueType.UNKNOWN);
|
||||
break;
|
||||
case VALUESET_UNSUPPORTED:
|
||||
e.setCode(IssueType.NOTSUPPORTED);
|
||||
break;
|
||||
}
|
||||
e.getDetails().setText(vse.getError());
|
||||
oo.addIssue(e);
|
||||
|
||||
String ooj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
|
||||
String diff = CompareUtilities.checkJsonSrcIsSame(resp, ooj);
|
||||
if (diff != null) {
|
||||
Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
|
||||
TextFile.stringToFile(ooj, fp);
|
||||
}
|
||||
Assertions.assertTrue(diff == null, diff);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue