Testing Part 1
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@ -666,6 +666,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return expandVS(vs, cacheOk, heirarchical);
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}
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@Override
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public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical) throws TerminologyServiceException {
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ValueSet vs = new ValueSet();
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@ -713,6 +714,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return res;
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}
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//TESTME
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@Override
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public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical) {
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if (expParameters == null)
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@ -721,6 +723,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return expandVS(vs, cacheOk, heirarchical, false, p);
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}
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//TESTME
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@Override
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public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk) {
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if (expParameters == null)
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@ -729,6 +732,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return expandVS(vs, cacheOk, heirarchical, incompleteOk, p);
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}
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//TESTME
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public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk, Parameters p) {
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if (p == null) {
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throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
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@ -947,11 +951,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return code.hasVersion() ? code.getSystem()+"|"+code.getVersion() : code.getSystem();
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}
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//TESTME
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@Override
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public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs, ValidationContextCarrier ctxt) {
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if (options == null) {
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options = ValidationOptions.defaults();
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}
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public ValidationResult validateCode(final ValidationOptions optionsArg, final Coding code, final ValueSet vs, final ValidationContextCarrier ctxt) {
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ValidationOptions options = optionsArg != null ? optionsArg : ValidationOptions.defaults();
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if (code.hasSystem()) {
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codeSystemsUsed.add(code.getSystem());
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@ -1036,6 +1040,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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}
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}
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//TESTME
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@Override
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public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
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CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
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@ -1084,7 +1089,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
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return res;
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}
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private ValidationResult validateOnServer(ValueSet vs, Parameters pin, ValidationOptions options) throws FHIRException {
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protected ValidationResult validateOnServer(ValueSet vs, Parameters pin, ValidationOptions options) throws FHIRException {
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boolean cache = false;
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if (vs != null) {
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for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
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@ -94,6 +94,7 @@ public class TerminologyCache {
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public class CacheToken {
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private String name;
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private String key;
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@Getter
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private String request;
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private boolean hasVersion;
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@ -124,7 +125,6 @@ public class TerminologyCache {
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private CapabilityStatement capabilityStatementCache = null;
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public boolean hasCapabilityStatement() {
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return capabilityStatementCache != null;
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}
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@ -183,6 +183,7 @@ public class TerminologyCache {
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public void clear() {
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caches.clear();
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}
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public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
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CacheToken ct = new CacheToken();
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if (code.hasSystem())
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@ -198,7 +199,7 @@ public class TerminologyCache {
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} catch (IOException e) {
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throw new Error(e);
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}
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ct.key = String.valueOf(hashNWS(ct.request));
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ct.key = String.valueOf(hashJson(ct.request));
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return ct;
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}
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@ -227,7 +228,7 @@ public class TerminologyCache {
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} catch (IOException e) {
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throw new Error(e);
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}
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ct.key = String.valueOf(hashNWS(ct.request));
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ct.key = String.valueOf(hashJson(ct.request));
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return ct;
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}
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@ -268,7 +269,7 @@ public class TerminologyCache {
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} catch (IOException e) {
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throw new Error(e);
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}
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ct.key = String.valueOf(hashNWS(ct.request));
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ct.key = String.valueOf(hashJson(ct.request));
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return ct;
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}
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@ -500,6 +501,35 @@ public class TerminologyCache {
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}
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}
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private CacheEntry getCacheEntry(String request, String resultString) throws IOException {
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CacheEntry ce = new CacheEntry();
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ce.persistent = true;
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ce.request = request;
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boolean e = resultString.charAt(0) == 'e';
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resultString = resultString.substring(3);
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JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(resultString);
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String error = loadJS(o.get("error"));
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if (e) {
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if (o.has("valueSet"))
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ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
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else
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ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
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} else {
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String t = loadJS(o.get("severity"));
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IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t);
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String display = loadJS(o.get("display"));
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String code = loadJS(o.get("code"));
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String system = loadJS(o.get("system"));
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String definition = loadJS(o.get("definition"));
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t = loadJS(o.get("class"));
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TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t);
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ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass);
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}
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return ce;
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}
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private void loadNamedCache(String fn) {
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int c = 0;
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try {
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@ -508,7 +538,7 @@ public class TerminologyCache {
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NamedCache nc = new NamedCache();
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nc.name = title;
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caches.put(title, nc);
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if (src.startsWith("?"))
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src = src.substring(1);
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int i = src.indexOf(ENTRY_MARKER);
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@ -519,34 +549,15 @@ public class TerminologyCache {
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i = src.indexOf(ENTRY_MARKER);
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if (!Utilities.noString(s)) {
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int j = s.indexOf(BREAK);
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String q = s.substring(0, j);
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String request = s.substring(0, j);
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String p = s.substring(j + BREAK.length() + 1).trim();
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CacheEntry ce = new CacheEntry();
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ce.persistent = true;
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ce.request = q;
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boolean e = p.charAt(0) == 'e';
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p = p.substring(3);
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JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p);
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String error = loadJS(o.get("error"));
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if (e) {
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if (o.has("valueSet"))
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ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
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else
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ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
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} else {
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String t = loadJS(o.get("severity"));
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IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t);
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String display = loadJS(o.get("display"));
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String code = loadJS(o.get("code"));
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String system = loadJS(o.get("system"));
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String definition = loadJS(o.get("definition"));
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t = loadJS(o.get("class"));
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TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t);
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ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass);
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}
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nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
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nc.list.add(ce);
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CacheEntry cacheEntry = getCacheEntry(request, p);
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nc.map.put(String.valueOf(hashJson(cacheEntry.request)), cacheEntry);
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nc.list.add(cacheEntry);
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}
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caches.put(nc.name, nc);
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}
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} catch (Exception e) {
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throw new FHIRException("Error loading " + fn + ": " + e.getMessage() + " entry " + c, e);
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@ -580,7 +591,7 @@ public class TerminologyCache {
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return s;
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}
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private String hashNWS(String s) {
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private String hashJson(String s) {
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s = StringUtils.remove(s, ' ');
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s = StringUtils.remove(s, '\n');
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s = StringUtils.remove(s, '\r');
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@ -0,0 +1,8 @@
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package org.hl7.fhir.r5.context;
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import org.hl7.fhir.utilities.validation.ValidationOptions;
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public class CacheTestUtils {
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public static final ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
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}
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@ -0,0 +1,52 @@
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package org.hl7.fhir.r5.context;
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import org.hl7.fhir.exceptions.DefinitionException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.formats.IParser;
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import org.hl7.fhir.r5.formats.ParserType;
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import org.hl7.fhir.r5.model.CodeableConcept;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.hl7.fhir.r5.utils.validation.IResourceValidator;
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import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
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import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
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import org.hl7.fhir.utilities.npm.NpmPackage;
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import org.hl7.fhir.r5.model.Coding;
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import org.hl7.fhir.utilities.validation.ValidationOptions;
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import org.junit.jupiter.api.Test;
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import org.mockito.ArgumentMatchers;
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import org.mockito.Mockito;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.util.List;
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import static org.mockito.Mockito.mock;
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public class SimpleWorkerContextTests {
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@Test
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public void testValidateCodingOnServer() throws IOException {
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SimpleWorkerContext context = Mockito.spy(new SimpleWorkerContext());
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IWorkerContext.ValidationResult result = mock(IWorkerContext.ValidationResult.class);
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Mockito.doReturn(result).when(context).validateOnServer(ArgumentMatchers.any(), ArgumentMatchers.any(), ArgumentMatchers.any());
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ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
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ValueSet valueSet = new ValueSet();
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ValidationContextCarrier ctxt = null;
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context.validateCode(validationOptions, new Coding(), valueSet, ctxt);
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}
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@Test
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public void testValidateCodableConceptOnServer() throws IOException {
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SimpleWorkerContext context = Mockito.spy(new SimpleWorkerContext());
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IWorkerContext.ValidationResult result = mock(IWorkerContext.ValidationResult.class);
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Mockito.doReturn(result).when(context).validateOnServer(ArgumentMatchers.any(), ArgumentMatchers.any(), ArgumentMatchers.any());
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ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
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ValueSet valueSet = new ValueSet();
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CodeableConcept codeableConcept = new CodeableConcept();
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context.validateCode(validationOptions, codeableConcept, valueSet);
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}
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}
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@ -0,0 +1,74 @@
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package org.hl7.fhir.r5.context;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import org.checkerframework.checker.units.qual.C;
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import org.hl7.fhir.r5.model.CodeableConcept;
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import org.hl7.fhir.r5.model.Coding;
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import org.hl7.fhir.r5.model.ValueSet;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import java.net.URISyntaxException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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public class TerminologyCacheTests {
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private JsonParser jsonParser = new JsonParser();
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private JsonElement getJsonFromFile(String filename) throws URISyntaxException, IOException {
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final Path path = Paths.get("src","test","resources", "context", filename);
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final String stringValue = new String ( Files.readAllBytes(path));
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return jsonParser.parse(stringValue);
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};
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@Test
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public void testCodingCacheTokenGeneration() throws IOException, URISyntaxException {
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Object lock = new Object();
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TerminologyCache terminologyCache = new TerminologyCache(lock, null);
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ValueSet valueSet = new ValueSet();
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Coding coding = new Coding();
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coding.setCode("dummyCode");
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TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
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coding, valueSet );
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JsonElement actual = jsonParser.parse(cacheToken.getRequest());
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JsonElement expected = getJsonFromFile("codingEmptyValueSet.json");
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assertEquals(expected, actual);
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}
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@Test
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public void testCodableConceptCacheTokenGeneration() throws IOException, URISyntaxException {
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Object lock = new Object();
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TerminologyCache terminologyCache = new TerminologyCache(lock, null);
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CodeableConcept concept = new CodeableConcept();
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concept.addCoding(new Coding().setCode("dummyCode"));
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ValueSet valueSet = new ValueSet();
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TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
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concept, valueSet );
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JsonElement actual = jsonParser.parse(cacheToken.getRequest());
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JsonElement expected = getJsonFromFile("codableConceptEmptyValueSet.json");
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assertEquals(expected, actual);
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}
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@Test
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public void testDummyCache() throws IOException {
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Object lock = new Object();
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Path path = Paths.get("src","test","resources", "context", "dummyCache");
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TerminologyCache cache = new TerminologyCache(lock, path.toString());
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assertTrue(cache.hasTerminologyCapabilities());
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assertTrue(cache.hasCapabilityStatement());
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}
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}
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@ -0,0 +1,18 @@
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{
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"code": {
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"coding": [
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{
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"code": "dummyCode"
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}
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]
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},
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"valueSet": {
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"resourceType": "ValueSet"
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},
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"lang": "null",
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"useServer": "true",
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"useClient": "true",
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"guessSystem": "true",
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"valueSetMode": "ALL_CHECKS",
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"versionFlexible": "false"
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}
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@ -0,0 +1,14 @@
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{
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"code": {
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"code": "dummyCode"
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},
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"valueSet": {
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"resourceType": "ValueSet"
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},
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"lang": "null",
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"useServer": "true",
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"useClient": "true",
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"guessSystem": "true",
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"valueSetMode": "ALL_CHECKS",
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"versionFlexible": "false"
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}
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@ -0,0 +1,62 @@
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{
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"resourceType" : "CapabilityStatement",
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"id" : "FhirServer",
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"meta" : {
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"tag" : [{
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"system" : "http://hl7.org/fhir/v3/ObservationValue",
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"code" : "SUBSETTED",
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"display" : "Subsetted"
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}]
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},
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"url" : "http://fhir.healthintersections.com.au/open/metadata",
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"version" : "4.0.1-2.0.12-SNAPSHOT",
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"name" : "FHIR Reference Server Conformance Statement",
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"status" : "active",
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"date" : "2022-01-10T11:07:19.254Z",
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"contact" : [{
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"telecom" : [{
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"system" : "other",
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"value" : "http://healthintersections.com.au/"
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}]
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}],
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"kind" : "instance",
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"instantiates" : ["http://hl7.org/fhir/CapabilityStatement/terminology-server"],
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"software" : {
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"name" : "Reference Server",
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"version" : "2.0.12-SNAPSHOT",
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"releaseDate" : "2021-12-20T02:28:03.769Z"
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},
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"fhirVersion" : "4.0.1",
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"format" : ["application/fhir+xml",
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"application/fhir+json"],
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"rest" : [{
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"mode" : "server",
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"security" : {
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"cors" : true
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},
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"operation" : [{
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"name" : "expand",
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"definition" : "http://hl7.org/fhir/OperationDefinition/ValueSet-expand"
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},
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{
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"name" : "lookup",
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"definition" : "http://hl7.org/fhir/OperationDefinition/ValueSet-lookup"
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},
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{
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"name" : "validate-code",
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"definition" : "http://hl7.org/fhir/OperationDefinition/Resource-validate"
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},
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{
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"name" : "translate",
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"definition" : "http://hl7.org/fhir/OperationDefinition/ConceptMap-translate"
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},
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{
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"name" : "closure",
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"definition" : "http://hl7.org/fhir/OperationDefinition/ConceptMap-closure"
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},
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{
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"name" : "versions",
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"definition" : "/OperationDefinition/fso-versions"
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}]
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}]
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}
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Load Diff
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|
@ -0,0 +1,11 @@
|
|||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://dummysite.org/fhir/CodeSystem/dummy",
|
||||
"code" : "Every 4 weeks"
|
||||
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
|
||||
v: {
|
||||
"severity" : "error",
|
||||
"error" : "The code system 'http://dummysite.org/fhir/CodeSystem/dummy' is not known (encountered paired with code = 'Every 4 weeks'); The code provided (http://dummysite.org/fhir/CodeSystem/dummy#Every 4 weeks) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4)",
|
||||
"class" : "CODESYSTEM_UNSUPPORTED"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
|
@ -0,0 +1,49 @@
|
|||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://unitsofmeasure.org",
|
||||
"code" : "L/min"
|
||||
}, "valueSet" :null, "lang":"fi", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
|
||||
v: {
|
||||
"display" : "L/min",
|
||||
"code" : "L/min",
|
||||
"system" : "http://unitsofmeasure.org"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://unitsofmeasure.org",
|
||||
"code" : "21612-7"
|
||||
}, "valueSet" :null, "lang":"fi", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
|
||||
v: {
|
||||
"severity" : "error",
|
||||
"error" : "Error processing Unit: '21612-7': Expected \"/\" or \".\" at character 6; The code \"21612-7\" is not valid in the system http://unitsofmeasure.org; The code provided (http://unitsofmeasure.org#21612-7) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r3)"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://unitsofmeasure.org",
|
||||
"code" : "tbl"
|
||||
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
|
||||
v: {
|
||||
"severity" : "error",
|
||||
"error" : "Error processing Unit: 'tbl': The unit \"tbl\" is unknown at character 1; The code \"tbl\" is not valid in the system http://unitsofmeasure.org; The code provided (http://unitsofmeasure.org#tbl) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r3)"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://unitsofmeasure.org",
|
||||
"code" : "mmol/L"
|
||||
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
|
||||
v: {
|
||||
"display" : "mmol/L",
|
||||
"code" : "mmol/L",
|
||||
"system" : "http://unitsofmeasure.org"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
||||
{"code" : {
|
||||
"system" : "http://unitsofmeasure.org",
|
||||
"code" : "[lb_av]"
|
||||
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
|
||||
v: {
|
||||
"display" : "[lb_av]",
|
||||
"code" : "[lb_av]",
|
||||
"system" : "http://unitsofmeasure.org"
|
||||
}
|
||||
-------------------------------------------------------------------------------------
|
|
@ -287,7 +287,7 @@ 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(definitions, cliContext.getSv(), cliContext.getTxCache(), tt, "fhir/validator");
|
||||
ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt, "fhir/validator");
|
||||
sessionId = sessionCache.cacheSession(validator);
|
||||
|
||||
FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());
|
||||
|
|
Loading…
Reference in New Issue