Merge branch 'master' of github.com:jamesagnew/hapi-fhir
This commit is contained in:
jamesagnew
commit
04764ed07e
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@ -24,6 +24,7 @@ import java.lang.reflect.Method;
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import java.lang.reflect.Modifier;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Date;
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import java.util.List;
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import java.util.Map;
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@ -47,6 +48,7 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
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import ca.uhn.fhir.rest.api.RequestTypeEnum;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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import ca.uhn.fhir.rest.param.CollectionBinder;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.param.ResourceParameter;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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@ -66,6 +68,7 @@ public class OperationParameter implements IParameter {
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private Class<?> myParameterType;
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private String myParamType;
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private FhirContext myContext;
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private boolean myAllowGet;
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public OperationParameter(FhirContext theCtx, String theOperationName, OperationParam theOperationParam) {
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this(theCtx, theOperationName, theOperationParam.name(), theOperationParam.min(), theOperationParam.max());
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@ -107,6 +110,8 @@ public class OperationParameter implements IParameter {
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myMax = 1;
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}
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myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
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/*
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* The parameter can be of type string for validation methods - This is a bit
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* weird. See ValidateDstu2Test. We should probably clean this up..
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@ -114,6 +119,10 @@ public class OperationParameter implements IParameter {
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if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
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if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
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myParamType = "Resource";
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} else if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
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myParamType = "date";
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myMax = 2;
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myAllowGet = true;
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} else if (!IBase.class.isAssignableFrom(myParameterType) || myParameterType.isInterface() || Modifier.isAbstract(myParameterType.getModifiers())) {
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throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
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} else if (myParameterType.equals(ValidationModeEnum.class)) {
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@ -153,13 +162,25 @@ public class OperationParameter implements IParameter {
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if (theRequest.getRequestType() == RequestTypeEnum.GET) {
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String[] paramValues = theRequest.getParameters().get(myName);
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if (paramValues != null && paramValues.length > 0) {
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if (IPrimitiveType.class.isAssignableFrom(myParameterType)) {
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for (String nextValue : paramValues) {
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FhirContext ctx = theRequest.getServer().getFhirContext();
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RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
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IPrimitiveType<?> instance = def.newInstance();
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instance.setValueAsString(nextValue);
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matchingParamValues.add(instance);
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if (myAllowGet) {
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if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
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List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
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parameters.add(QualifiedParamList.singleton(paramValues[0]));
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if (paramValues.length > 1) {
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parameters.add(QualifiedParamList.singleton(paramValues[1]));
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}
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DateRangeParam dateRangeParam = new DateRangeParam();
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dateRangeParam.setValuesAsQueryTokens(parameters);
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matchingParamValues.add(dateRangeParam);
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} else {
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for (String nextValue : paramValues) {
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FhirContext ctx = theRequest.getServer().getFhirContext();
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RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
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IPrimitiveType<?> instance = def.newInstance();
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instance.setValueAsString(nextValue);
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matchingParamValues.add(instance);
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}
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}
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} else {
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HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
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@ -11,7 +11,14 @@ a browser.
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<!--*/-->
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<div>
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<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>
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<th:block th:switch="${fhirVersion}">
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<th:block th:case="'DSTU1'">
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<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>
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</th:block>
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<th:block th:case="*">
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<div class="hapiHeaderText" th:if="${not resource.code.empty}" th:narrative="${resource.code}"></div>
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</th:block>
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</th:block>
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</div>
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<!--/*-->
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@ -1227,11 +1227,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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} else {
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theOrders.add(theBuilder.desc(theFrom.get("myUpdated")));
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}
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createSort(theBuilder, theFrom, theSort.getChain(), theOrders, thePredicates);
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return;
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}
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RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceType);
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RuntimeSearchParam param = resourceDef.getSearchParam(theSort.getParamName());
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if (param == null) {
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@ -1615,7 +1615,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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/**
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* THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
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*/
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private HashSet<Long> loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
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private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
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if (theMatches.size() == 0) {
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return new HashSet<Long>();
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}
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@ -1902,7 +1902,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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Long pid = translateForcedIdToPid(theId);
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BaseHasResource entity = myEntityManager.find(ResourceTable.class, pid);
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if (entity == null) {
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throw new ResourceNotFoundException(theId);
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}
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@ -2023,6 +2023,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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}
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}
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// Load _include and _revinclude before filter and sort in everything mode
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if (theParams.isEverythingMode() == true) {
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if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
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loadPids.addAll(loadReverseIncludes(loadPids, theParams.getRevIncludes(), true));
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loadPids.addAll(loadReverseIncludes(loadPids, theParams.getIncludes(), false));
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}
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}
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// Handle _lastUpdated
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DateRangeParam lu = theParams.getLastUpdated();
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if (lu != null && (lu.getLowerBoundAsInstant() != null || lu.getUpperBoundAsInstant() != null)) {
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@ -2047,59 +2055,22 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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for (Long next : query.getResultList()) {
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loadPids.add(next);
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}
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if (loadPids.isEmpty()) {
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return new SimpleBundleProvider();
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}
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}
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// Handle sorting if any was provided
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final List<Long> pids;
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if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
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List<Order> orders = new ArrayList<Order>();
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List<Predicate> predicates = new ArrayList<Predicate>();
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CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
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CriteriaQuery<Tuple> cq = builder.createTupleQuery();
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Root<ResourceTable> from = cq.from(ResourceTable.class);
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predicates.add(from.get("myId").in(loadPids));
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createSort(builder, from, theParams.getSort(), orders, predicates);
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if (orders.size() > 0) {
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Set<Long> originalPids = loadPids;
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loadPids = new LinkedHashSet<Long>();
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cq.multiselect(from.get("myId").as(Long.class));
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cq.where(predicates.toArray(new Predicate[0]));
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cq.orderBy(orders);
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TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
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for (Tuple next : query.getResultList()) {
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loadPids.add(next.get(0, Long.class));
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}
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ourLog.debug("Sort PID order is now: {}", loadPids);
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pids = new ArrayList<Long>(loadPids);
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// Any ressources which weren't matched by the sort get added to the bottom
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for (Long next : originalPids) {
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if (loadPids.contains(next) == false) {
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pids.add(next);
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}
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}
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} else {
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pids = new ArrayList<Long>(loadPids);
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}
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} else {
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pids = new ArrayList<Long>(loadPids);
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}
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final List<Long> pids = processSort(theParams, loadPids);
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// Load _revinclude resources
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final Set<Long> revIncludedPids;
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if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
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revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
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if (theParams.isEverythingMode()) {
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revIncludedPids.addAll(loadReverseIncludes(pids, theParams.getIncludes(), false));
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if (theParams.isEverythingMode() == false) {
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if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
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revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
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} else {
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revIncludedPids = new HashSet<Long>();
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}
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} else {
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revIncludedPids = new HashSet<Long>();
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@ -2155,6 +2126,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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return retVal;
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}
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private List<Long> processSort(final SearchParameterMap theParams, Set<Long> loadPids) {
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final List<Long> pids;
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if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
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List<Order> orders = new ArrayList<Order>();
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List<Predicate> predicates = new ArrayList<Predicate>();
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CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
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CriteriaQuery<Tuple> cq = builder.createTupleQuery();
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Root<ResourceTable> from = cq.from(ResourceTable.class);
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predicates.add(from.get("myId").in(loadPids));
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createSort(builder, from, theParams.getSort(), orders, predicates);
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if (orders.size() > 0) {
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Set<Long> originalPids = loadPids;
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loadPids = new LinkedHashSet<Long>();
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cq.multiselect(from.get("myId").as(Long.class));
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cq.where(predicates.toArray(new Predicate[0]));
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cq.orderBy(orders);
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TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
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for (Tuple next : query.getResultList()) {
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loadPids.add(next.get(0, Long.class));
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}
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ourLog.debug("Sort PID order is now: {}", loadPids);
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pids = new ArrayList<Long>(loadPids);
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// Any ressources which weren't matched by the sort get added to the bottom
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for (Long next : originalPids) {
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if (loadPids.contains(next) == false) {
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pids.add(next);
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}
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}
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} else {
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pids = new ArrayList<Long>(loadPids);
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}
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} else {
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pids = new ArrayList<Long>(loadPids);
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}
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return pids;
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}
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@Override
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public IBundleProvider search(String theParameterName, IQueryParameterType theValue) {
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return search(Collections.singletonMap(theParameterName, theValue));
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@ -8,13 +8,15 @@ import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.UnsignedIntDt;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.server.IBundleProvider;
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public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
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@Override
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public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount) {
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public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
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SearchParameterMap paramMap = new SearchParameterMap();
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if (theCount != null) {
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paramMap.setCount(theCount.getValue());
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@ -23,6 +25,8 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
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paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
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paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
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paramMap.setEverythingMode(true);
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paramMap.setSort(theSort);
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paramMap.setLastUpdated(theLastUpdated);
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paramMap.add("_id", new StringParam(theId.getIdPart()));
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ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
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return retVal;
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|
|
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@ -26,10 +26,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.UnsignedIntDt;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.param.DateRangeParam;
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import ca.uhn.fhir.rest.server.IBundleProvider;
|
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public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
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|
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IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount);
|
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IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdate, SortSpec theSort);
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}
|
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|
|
|
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|
|
@ -51,12 +51,12 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
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private FhirContext myDstu2Ctx;
|
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|
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@Override
|
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public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
|
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public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
|
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return null;
|
||||
}
|
||||
|
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@Override
|
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public ValueSet fetchCodeSystem(String theSystem) {
|
||||
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
|
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return null;
|
||||
}
|
||||
|
||||
|
|
@ -85,20 +85,19 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
|
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/*
|
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* Validator wants RI structures and not HAPI ones, so convert
|
||||
*
|
||||
* TODO: we really need a more efficient way of converting.. Or maybe this will
|
||||
* just go away when we move to RI structures
|
||||
* TODO: we really need a more efficient way of converting.. Or maybe this will just go away when we move to RI structures
|
||||
*/
|
||||
String encoded = myDstu2Ctx.newJsonParser().encodeResourceToString(res);
|
||||
return myRiCtx.newJsonParser().parseResource(theClass, encoded);
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isCodeSystemSupported(String theSystem) {
|
||||
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
|
||||
return false;
|
||||
}
|
||||
|
||||
@Override
|
||||
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
|
||||
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
|
||||
return null;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -6,6 +6,10 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
|
|||
import ca.uhn.fhir.rest.annotation.IdParam;
|
||||
import ca.uhn.fhir.rest.annotation.Operation;
|
||||
import ca.uhn.fhir.rest.annotation.OperationParam;
|
||||
import ca.uhn.fhir.rest.annotation.Sort;
|
||||
import ca.uhn.fhir.rest.api.SortSpec;
|
||||
import ca.uhn.fhir.rest.param.DateRangeParam;
|
||||
import ca.uhn.fhir.rest.server.Constants;
|
||||
|
||||
public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu2<Patient> {
|
||||
|
||||
|
|
@ -18,12 +22,21 @@ public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu
|
|||
ca.uhn.fhir.model.primitive.IdDt theId,
|
||||
|
||||
@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the size of those pages.")
|
||||
@OperationParam(name = "_count")
|
||||
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount) {
|
||||
@OperationParam(name = Constants.PARAM_COUNT)
|
||||
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount,
|
||||
|
||||
@Description(shortDefinition="Only return resources which were last updated as specified by the given range")
|
||||
@OperationParam(name = Constants.PARAM_LASTUPDATED, min=0, max=1)
|
||||
DateRangeParam theLastUpdated,
|
||||
|
||||
// @OperationParam(name = Constants.PARAM_SORT, min=0, max=1)
|
||||
@Sort
|
||||
SortSpec theSortSpec
|
||||
) {
|
||||
|
||||
startRequest(theServletRequest);
|
||||
try {
|
||||
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount);
|
||||
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount, theLastUpdated, theSortSpec);
|
||||
} finally {
|
||||
endRequest(theServletRequest);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@
|
|||
<context:annotation-config />
|
||||
|
||||
<websocket:handlers>
|
||||
<websocket:mapping path="/baseDstu2/websocket" handler="mySubscriptionWebsocketHandler" />
|
||||
<websocket:mapping path="/websocket/dstu2" handler="mySubscriptionWebsocketHandler" />
|
||||
</websocket:handlers>
|
||||
|
||||
<!--
|
||||
|
|
|
|||
|
|
@ -602,6 +602,96 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
|
|||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEverythingWithLastUpdatedAndSort() throws Exception {
|
||||
String methodName = "testEverythingWithLastUpdatedAndSort";
|
||||
|
||||
long time0 = System.currentTimeMillis();
|
||||
Thread.sleep(10);
|
||||
|
||||
Organization org = new Organization();
|
||||
org.setName(methodName);
|
||||
IIdType oId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
|
||||
|
||||
long time1 = System.currentTimeMillis();
|
||||
Thread.sleep(10);
|
||||
|
||||
Patient p = new Patient();
|
||||
p.addName().addFamily(methodName);
|
||||
p.getManagingOrganization().setReference(oId);
|
||||
IIdType pId = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
|
||||
|
||||
long time2 = System.currentTimeMillis();
|
||||
Thread.sleep(10);
|
||||
|
||||
Condition c = new Condition();
|
||||
c.getCode().setText(methodName);
|
||||
c.getPatient().setReference(pId);
|
||||
IIdType cId = ourClient.create().resource(c).execute().getId().toUnqualifiedVersionless();
|
||||
|
||||
Thread.sleep(10);
|
||||
long time3 = System.currentTimeMillis();
|
||||
|
||||
// %3E=> %3C=<
|
||||
|
||||
HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString());
|
||||
CloseableHttpResponse response = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(200, response.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(response.getEntity().getContent());
|
||||
IOUtils.closeQuietly(response.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
|
||||
ourLog.info(ids.toString());
|
||||
assertThat(ids, containsInAnyOrder(pId, cId));
|
||||
} finally {
|
||||
response.close();
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantDt(new Date(time3)).getValueAsString());
|
||||
response = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(200, response.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(response.getEntity().getContent());
|
||||
IOUtils.closeQuietly(response.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
|
||||
ourLog.info(ids.toString());
|
||||
assertThat(ids, containsInAnyOrder(cId));
|
||||
} finally {
|
||||
response.close();
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString() + "&_sort=_lastUpdated");
|
||||
response = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(200, response.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(response.getEntity().getContent());
|
||||
IOUtils.closeQuietly(response.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
|
||||
ourLog.info(ids.toString());
|
||||
assertThat(ids, contains(pId, cId));
|
||||
} finally {
|
||||
response.close();
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_sort:desc=_lastUpdated");
|
||||
response = ourHttpClient.execute(get);
|
||||
try {
|
||||
assertEquals(200, response.getStatusLine().getStatusCode());
|
||||
String output = IOUtils.toString(response.getEntity().getContent());
|
||||
IOUtils.closeQuietly(response.getEntity().getContent());
|
||||
ourLog.info(output);
|
||||
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
|
||||
ourLog.info(ids.toString());
|
||||
assertThat(ids, contains(cId, pId, oId));
|
||||
} finally {
|
||||
response.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #148
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -324,7 +324,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
|
|||
SimpleEchoSocket socket = new SimpleEchoSocket(subsId);
|
||||
try {
|
||||
client.start();
|
||||
URI echoUri = new URI("ws://localhost:" + ourPort + "/baseDstu2/websocket");
|
||||
URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
|
||||
ClientUpgradeRequest request = new ClientUpgradeRequest();
|
||||
client.connect(socket, echoUri, request);
|
||||
ourLog.info("Connecting to : {}", echoUri);
|
||||
|
|
|
|||
|
|
@ -1,5 +1,9 @@
|
|||
package ca.uhn.fhirtest;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.PrintWriter;
|
||||
import java.io.Writer;
|
||||
|
||||
import org.apache.derby.drda.NetworkServerControl;
|
||||
import org.springframework.beans.factory.DisposableBean;
|
||||
import org.springframework.beans.factory.InitializingBean;
|
||||
|
|
@ -22,7 +26,30 @@ public class DerbyNetworkServer implements InitializingBean, DisposableBean {
|
|||
@Override
|
||||
public void afterPropertiesSet() throws Exception {
|
||||
server = new NetworkServerControl();
|
||||
server.start (null);
|
||||
Writer w = new Writer() {
|
||||
|
||||
@Override
|
||||
public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
|
||||
ourLog.info("[DERBY] " + new String(theCbuf, theOff, theLen));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void flush() throws IOException {
|
||||
// nothing
|
||||
}
|
||||
|
||||
@Override
|
||||
public void close() throws IOException {
|
||||
// nothing
|
||||
}};
|
||||
server.start (new PrintWriter(w));
|
||||
}
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
DerbyNetworkServer s = new DerbyNetworkServer();
|
||||
s.afterPropertiesSet();
|
||||
s.destroy();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ import javax.servlet.ServletException;
|
|||
import javax.servlet.http.HttpServletRequest;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.support.ClassPathXmlApplicationContext;
|
||||
import org.springframework.web.context.ContextLoaderListener;
|
||||
import org.springframework.web.context.WebApplicationContext;
|
||||
|
|
@ -35,7 +36,7 @@ public class TestRestfulServer extends RestfulServer {
|
|||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestRestfulServer.class);
|
||||
|
||||
private ClassPathXmlApplicationContext myAppCtx;
|
||||
private ApplicationContext myAppCtx;
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
@Override
|
||||
|
|
@ -44,6 +45,7 @@ public class TestRestfulServer extends RestfulServer {
|
|||
|
||||
// Get the spring context from the web container (it's declared in web.xml)
|
||||
WebApplicationContext parentAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
|
||||
myAppCtx = (parentAppCtx);
|
||||
|
||||
// These two parmeters are also declared in web.xml
|
||||
String implDesc = getInitParameter("ImplementationDescription");
|
||||
|
|
@ -64,9 +66,6 @@ public class TestRestfulServer extends RestfulServer {
|
|||
String baseUrlProperty;
|
||||
switch (fhirVersionParam.trim().toUpperCase()) {
|
||||
case "DSTU1": {
|
||||
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
|
||||
"hapi-fhir-server-database-config-dstu1.xml",
|
||||
"hapi-fhir-server-resourceproviders-dstu1.xml"}, parentAppCtx);
|
||||
setFhirContext(FhirContext.forDstu1());
|
||||
beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
|
||||
systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
|
||||
|
|
@ -79,11 +78,6 @@ public class TestRestfulServer extends RestfulServer {
|
|||
break;
|
||||
}
|
||||
case "DSTU2": {
|
||||
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
|
||||
"hapi-fhir-server-database-config-dstu2.xml",
|
||||
"hapi-fhir-server-resourceproviders-dstu2.xml",
|
||||
"fhir-spring-subscription-config-dstu2.xml"
|
||||
}, parentAppCtx);
|
||||
setFhirContext(FhirContext.forDstu2());
|
||||
beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
|
||||
systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
|
||||
|
|
|
|||
|
|
@ -12,6 +12,11 @@
|
|||
/WEB-INF/hapi-fhir-server-config.xml
|
||||
/WEB-INF/hapi-fhir-tester-application-context.xml
|
||||
/WEB-INF/hapi-fhir-tester-config.xml
|
||||
classpath:/hapi-fhir-server-database-config-dstu1.xml
|
||||
classpath:/hapi-fhir-server-database-config-dstu2.xml
|
||||
classpath:hapi-fhir-server-resourceproviders-dstu1.xml
|
||||
classpath:hapi-fhir-server-resourceproviders-dstu2.xml
|
||||
classpath:fhir-spring-subscription-config-dstu2.xml
|
||||
</param-value>
|
||||
</context-param>
|
||||
|
||||
|
|
@ -25,6 +30,7 @@
|
|||
<param-value>
|
||||
/WEB-INF/hapi-fhir-tester-application-context.xml
|
||||
/WEB-INF/hapi-fhir-tester-config.xml
|
||||
classpath:fhir-spring-subscription-config-dstu2.xml
|
||||
</param-value>
|
||||
</init-param>
|
||||
<load-on-startup>2</load-on-startup>
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package ca.uhn.fhir.narrative;
|
||||
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.assertTrue;
|
||||
|
|
@ -53,7 +54,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
Patient value = new Patient();
|
||||
|
||||
value.addIdentifier().setSystem("urn:names").setValue("123456");
|
||||
value.addName().addFamily("blow").addGiven("joe").addGiven((String)null).addGiven("john");
|
||||
value.addName().addFamily("blow").addGiven("joe").addGiven((String) null).addGiven("john");
|
||||
value.getAddressFirstRep().addLine("123 Fake Street").addLine("Unit 1");
|
||||
value.getAddressFirstRep().setCity("Toronto").setState("ON").setCountry("Canada");
|
||||
|
||||
|
|
@ -67,12 +68,12 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
|
||||
String title = myGen.generateTitle(value);
|
||||
assertEquals("joe john BLOW (123456)", title);
|
||||
// ourLog.info(title);
|
||||
// ourLog.info(title);
|
||||
|
||||
value.getIdentifierFirstRep().setValue("FOO MRN 123");
|
||||
title = myGen.generateTitle(value);
|
||||
assertEquals("joe john BLOW (FOO MRN 123)", title);
|
||||
// ourLog.info(title);
|
||||
// ourLog.info(title);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -80,7 +81,7 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
public void testGenerateEncounter() throws DataFormatException {
|
||||
Encounter enc = new Encounter();
|
||||
|
||||
enc.addIdentifier().setSystem("urn:visits").setValue( "1234567");
|
||||
enc.addIdentifier().setSystem("urn:visits").setValue("1234567");
|
||||
enc.setClassElement(EncounterClassEnum.AMBULATORY);
|
||||
enc.setPeriod(new PeriodDt().setStart(new DateTimeDt("2001-01-02T11:11:00")));
|
||||
enc.setType(ca.uhn.fhir.model.dstu2.valueset.EncounterTypeEnum.ANNUAL_DIABETES_MELLITUS_SCREENING);
|
||||
|
|
@ -92,7 +93,6 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testGenerateDiagnosticReport() throws DataFormatException {
|
||||
DiagnosticReport value = new DiagnosticReport();
|
||||
|
|
@ -127,9 +127,9 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
|
||||
OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, parse);
|
||||
|
||||
// String output = gen.generateTitle(oo);
|
||||
// ourLog.info(output);
|
||||
// assertEquals("Operation Outcome (2 issues)", output);
|
||||
// String output = gen.generateTitle(oo);
|
||||
// ourLog.info(output);
|
||||
// assertEquals("Operation Outcome (2 issues)", output);
|
||||
|
||||
NarrativeDt narrative = new NarrativeDt();
|
||||
myGen.generateNarrative(null, oo, narrative);
|
||||
|
|
@ -137,11 +137,11 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
|
||||
ourLog.info(output);
|
||||
|
||||
// oo = new OperationOutcome();
|
||||
// oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
|
||||
// output = gen.generateTitle(oo);
|
||||
// ourLog.info(output);
|
||||
// assertEquals("Operation Outcome (fatal)", output);
|
||||
// oo = new OperationOutcome();
|
||||
// oo.addIssue().setSeverity(IssueSeverityEnum.FATAL).setDetails("AA");
|
||||
// output = gen.generateTitle(oo);
|
||||
// ourLog.info(output);
|
||||
// assertEquals("Operation Outcome (fatal)", output);
|
||||
|
||||
}
|
||||
|
||||
|
|
@ -193,27 +193,43 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
|
|||
assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some & Diagnostic Report </div>"));
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testGenerateMedicationPrescription(){
|
||||
public void testGenerateMedicationPrescription() {
|
||||
MedicationOrder mp = new MedicationOrder();
|
||||
mp.setId("12345");
|
||||
Medication med = new Medication();
|
||||
med.getCode().setText("ciproflaxin");
|
||||
ResourceReferenceDt medRef = new ResourceReferenceDt(med);
|
||||
mp.setMedication(medRef );
|
||||
mp.setMedication(medRef);
|
||||
mp.setStatus(MedicationOrderStatusEnum.ACTIVE);
|
||||
mp.setDateWritten(new DateTimeDt("2014-09-01"));
|
||||
|
||||
|
||||
NarrativeDt narrative = new NarrativeDt();
|
||||
myGen.generateNarrative(mp, narrative);
|
||||
|
||||
assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin")>-1);
|
||||
assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE")>-1);
|
||||
|
||||
|
||||
assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin") > -1);
|
||||
assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE") > -1);
|
||||
|
||||
String title = myGen.generateTitle(mp);
|
||||
assertEquals("ciprofloaxin", title);
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testGenerateMedication() {
|
||||
Medication med = new Medication();
|
||||
med.getCode().setText("ciproflaxin");
|
||||
|
||||
NarrativeDt narrative = new NarrativeDt();
|
||||
myGen.generateNarrative(med, narrative);
|
||||
|
||||
String string = narrative.getDiv().toString();
|
||||
assertThat(string, containsString("ciproflaxin"));
|
||||
|
||||
String title = myGen.generateTitle(med);
|
||||
assertEquals("ciproflaxin", title);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -92,63 +92,6 @@ public class XmlParserDstu2Test {
|
|||
private static final FhirContext ourCtx = FhirContext.forDstu2();
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
|
||||
|
||||
@Test
|
||||
public void testParseBundleWithResourceId() {
|
||||
//@formatter:off
|
||||
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "</Bundle>\n";
|
||||
//@formatter:on
|
||||
|
||||
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("phitcc_pat_normal");
|
||||
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
|
||||
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
|
||||
patient.setGender(AdministrativeGenderEnum.FEMALE);
|
||||
patient.setBirthDate(new DateDt("2001-10-13"));
|
||||
|
||||
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
|
||||
|
||||
Observation obsParent = new Observation();
|
||||
obsParent.setId("phitcc_obs_bp_parent");
|
||||
obsParent.getSubject().setResource(patient);
|
||||
obsParent.setStatus(ObservationStatusEnum.FINAL);
|
||||
obsParent.setEffective(obsEffectiveTime);
|
||||
|
||||
Observation obsSystolic = new Observation();
|
||||
obsSystolic.setId("phitcc_obs_bp_dia");
|
||||
obsSystolic.getSubject().setResource(patient);
|
||||
obsSystolic.setEffective(obsEffectiveTime);
|
||||
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
|
||||
|
||||
Observation obsDiastolic = new Observation();
|
||||
obsDiastolic.setId("phitcc_obs_bp_dia");
|
||||
obsDiastolic.getSubject().setResource(patient);
|
||||
obsDiastolic.setEffective(obsEffectiveTime);
|
||||
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
|
||||
|
||||
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
|
||||
ourLog.info(str);
|
||||
|
||||
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
|
||||
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void testBundleWithBinary() {
|
||||
//@formatter:off
|
||||
|
|
@ -231,86 +174,6 @@ public class XmlParserDstu2Test {
|
|||
assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
|
||||
*/
|
||||
@Test
|
||||
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
|
||||
IParser xmlParser = ourCtx.newXmlParser();
|
||||
|
||||
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
|
||||
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
|
||||
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
|
||||
assertEquals("1", q.getValueElement().getValueAsString());
|
||||
|
||||
String output = xmlParser.encodeResourceToString(ms);
|
||||
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216
|
||||
*/
|
||||
@Test
|
||||
public void testEncodeAndParseIdentifierDstu2() {
|
||||
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
|
||||
|
||||
String out = xmlParser.encodeResourceToString(patient);
|
||||
ourLog.info(out);
|
||||
|
||||
//@formatter:off
|
||||
assertThat(out, stringContainsInOrder("<identifier>",
|
||||
"<type>",
|
||||
"<coding>",
|
||||
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
|
||||
"<code value=\"MR\"/>",
|
||||
"</coding>",
|
||||
"</type>",
|
||||
"<system value=\"SYS\"/>",
|
||||
"<value value=\"VAL\"/>",
|
||||
"</identifier>"));
|
||||
//@formatter:on
|
||||
|
||||
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
|
||||
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
|
||||
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
|
||||
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216
|
||||
*/
|
||||
@Test
|
||||
public void testParseMalformedIdentifierDstu2() {
|
||||
|
||||
// This was changed from 0.5 to 1.0.0
|
||||
|
||||
//@formatter:off
|
||||
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
|
||||
" <identifier>\n" +
|
||||
" <type value=\"MRN\"/>\n" +
|
||||
" <system value=\"SYS\"/>\n" +
|
||||
" <value value=\"VAL\"/>\n" +
|
||||
" </identifier>\n" +
|
||||
"</Patient>";
|
||||
//@formatter:on
|
||||
|
||||
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
|
||||
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setParserErrorHandler(errorHandler);
|
||||
|
||||
Patient patient = p.parseResource(Patient.class, out);
|
||||
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
|
||||
|
||||
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
|
||||
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
|
||||
|
||||
assertEquals("value", capt.getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeAndParseContained() {
|
||||
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
|
||||
|
|
@ -448,9 +311,11 @@ public class XmlParserDstu2Test {
|
|||
String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
|
||||
assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
|
||||
assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
|
||||
assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
|
||||
assertThat(enc, containsString(
|
||||
"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
|
||||
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
|
||||
assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
|
||||
assertThat(enc, containsString(
|
||||
"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
|
||||
|
||||
/*
|
||||
* Now parse this back
|
||||
|
|
@ -490,6 +355,38 @@ public class XmlParserDstu2Test {
|
|||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216
|
||||
*/
|
||||
@Test
|
||||
public void testEncodeAndParseIdentifierDstu2() {
|
||||
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
|
||||
|
||||
String out = xmlParser.encodeResourceToString(patient);
|
||||
ourLog.info(out);
|
||||
|
||||
//@formatter:off
|
||||
assertThat(out, stringContainsInOrder("<identifier>",
|
||||
"<type>",
|
||||
"<coding>",
|
||||
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
|
||||
"<code value=\"MR\"/>",
|
||||
"</coding>",
|
||||
"</type>",
|
||||
"<system value=\"SYS\"/>",
|
||||
"<value value=\"VAL\"/>",
|
||||
"</identifier>"));
|
||||
//@formatter:on
|
||||
|
||||
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
|
||||
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
|
||||
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
|
||||
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeAndParseMetaProfileAndTags() {
|
||||
Patient p = new Patient();
|
||||
|
|
@ -595,6 +492,38 @@ public class XmlParserDstu2Test {
|
|||
assertEquals(new Tag("scheme2", "term2", "label2"), tagList.get(1));
|
||||
}
|
||||
|
||||
/**
|
||||
* Test for #233
|
||||
*/
|
||||
@Test
|
||||
public void testEncodeAndParseProfiledDatatype() {
|
||||
MedicationOrder mo = new MedicationOrder();
|
||||
mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
|
||||
String out = ourCtx.newXmlParser().encodeResourceToString(mo);
|
||||
ourLog.info(out);
|
||||
assertThat(out, containsString("</boundsQuantity>"));
|
||||
|
||||
mo = ourCtx.newXmlParser().parseResource(MedicationOrder.class, out);
|
||||
DurationDt duration = (DurationDt) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
|
||||
assertEquals("code", duration.getCode());
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
|
||||
*/
|
||||
@Test
|
||||
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
|
||||
IParser xmlParser = ourCtx.newXmlParser();
|
||||
|
||||
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
|
||||
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
|
||||
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
|
||||
assertEquals("1", q.getValueElement().getValueAsString());
|
||||
|
||||
String output = xmlParser.encodeResourceToString(ms);
|
||||
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeAndParseSecurityLabels() {
|
||||
Patient p = new Patient();
|
||||
|
|
@ -791,12 +720,14 @@ public class XmlParserDstu2Test {
|
|||
ourLog.info(encoded);
|
||||
|
||||
// @formatter:on
|
||||
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
|
||||
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
assertThat(encoded,
|
||||
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
|
||||
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
|
||||
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
//@formatter:off
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* See #113
|
||||
*/
|
||||
|
|
@ -824,12 +755,13 @@ public class XmlParserDstu2Test {
|
|||
ourLog.info(encoded);
|
||||
|
||||
//@formatter:on
|
||||
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
|
||||
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
assertThat(encoded,
|
||||
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
|
||||
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
|
||||
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
//@formatter:off
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* See #113
|
||||
*/
|
||||
|
|
@ -861,8 +793,10 @@ public class XmlParserDstu2Test {
|
|||
ourLog.info(encoded);
|
||||
|
||||
//@formatter:on
|
||||
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
|
||||
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
assertThat(encoded,
|
||||
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
|
||||
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
|
||||
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
|
||||
//@formatter:off
|
||||
|
||||
}
|
||||
|
|
@ -893,7 +827,6 @@ public class XmlParserDstu2Test {
|
|||
assertThat(encoded, (containsString("BARFOO")));
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* #158
|
||||
|
|
@ -911,6 +844,7 @@ public class XmlParserDstu2Test {
|
|||
assertThat(encoded, not(containsString("tag")));
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* #158
|
||||
*/
|
||||
|
|
@ -929,7 +863,6 @@ public class XmlParserDstu2Test {
|
|||
assertThat(encoded, not(containsString("Label")));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeExtensionWithResourceContent() {
|
||||
IParser parser = ourCtx.newXmlParser();
|
||||
|
|
@ -951,6 +884,7 @@ public class XmlParserDstu2Test {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeNarrativeSuppressed() {
|
||||
Patient patient = new Patient();
|
||||
|
|
@ -1010,7 +944,44 @@ public class XmlParserDstu2Test {
|
|||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.setId("phitcc_pat_normal");
|
||||
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
|
||||
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
|
||||
patient.setGender(AdministrativeGenderEnum.FEMALE);
|
||||
patient.setBirthDate(new DateDt("2001-10-13"));
|
||||
|
||||
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
|
||||
|
||||
Observation obsParent = new Observation();
|
||||
obsParent.setId("phitcc_obs_bp_parent");
|
||||
obsParent.getSubject().setResource(patient);
|
||||
obsParent.setStatus(ObservationStatusEnum.FINAL);
|
||||
obsParent.setEffective(obsEffectiveTime);
|
||||
|
||||
Observation obsSystolic = new Observation();
|
||||
obsSystolic.setId("phitcc_obs_bp_dia");
|
||||
obsSystolic.getSubject().setResource(patient);
|
||||
obsSystolic.setEffective(obsEffectiveTime);
|
||||
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
|
||||
|
||||
Observation obsDiastolic = new Observation();
|
||||
obsDiastolic.setId("phitcc_obs_bp_dia");
|
||||
obsDiastolic.getSubject().setResource(patient);
|
||||
obsDiastolic.setEffective(obsEffectiveTime);
|
||||
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
|
||||
|
||||
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
|
||||
ourLog.info(str);
|
||||
|
||||
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
|
||||
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeSummary() {
|
||||
Patient patient = new Patient();
|
||||
|
|
@ -1052,6 +1023,57 @@ public class XmlParserDstu2Test {
|
|||
assertThat(encoded, not(containsString("maritalStatus")));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testEncodeWithEncodeElements() throws Exception {
|
||||
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addFamily("FAMILY");
|
||||
patient.addAddress().addLine("LINE1");
|
||||
|
||||
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
|
||||
bundle.setTotal(100);
|
||||
bundle.addEntry().setResource(patient);
|
||||
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, not(containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, not(containsString("address")));
|
||||
}
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
|
||||
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, (containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, not(containsString("address")));
|
||||
}
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, (containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, (containsString("address")));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMoreExtensions() throws Exception {
|
||||
|
||||
|
|
@ -1105,7 +1127,7 @@ public class XmlParserDstu2Test {
|
|||
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
|
||||
assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testOmitResourceId() {
|
||||
Patient p = new Patient();
|
||||
|
|
@ -1116,57 +1138,6 @@ public class XmlParserDstu2Test {
|
|||
assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), containsString("ABC"));
|
||||
assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testEncodeWithEncodeElements() throws Exception {
|
||||
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addName().addFamily("FAMILY");
|
||||
patient.addAddress().addLine("LINE1");
|
||||
|
||||
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
|
||||
bundle.setTotal(100);
|
||||
bundle.addEntry().setResource(patient);
|
||||
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, not(containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, not(containsString("address")));
|
||||
}
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
|
||||
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, (containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, not(containsString("address")));
|
||||
}
|
||||
{
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
|
||||
p.setPrettyPrint(true);
|
||||
String out = p.encodeResourceToString(bundle);
|
||||
ourLog.info(out);
|
||||
assertThat(out, (containsString("total")));
|
||||
assertThat(out, (containsString("Patient")));
|
||||
assertThat(out, (containsString("name")));
|
||||
assertThat(out, (containsString("address")));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testParseAndEncodeBundle() throws Exception {
|
||||
|
|
@ -1202,7 +1173,7 @@ public class XmlParserDstu2Test {
|
|||
assertTrue(d.toString(), d.identical());
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testParseAndEncodeBundleNewStyle() throws Exception {
|
||||
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
|
||||
|
|
@ -1239,7 +1210,8 @@ public class XmlParserDstu2Test {
|
|||
assertTrue(d.toString(), d.identical());
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void testParseAndEncodeExtensionOnResourceReference() {
|
||||
//@formatter:off
|
||||
|
|
@ -1642,6 +1614,22 @@ public class XmlParserDstu2Test {
|
|||
assertEquals("Observation", link.getUrl());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParseBundleWithResourceId() {
|
||||
//@formatter:off
|
||||
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
|
||||
+ "</Bundle>\n";
|
||||
//@formatter:on
|
||||
|
||||
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
|
||||
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* see #144 and #146
|
||||
*/
|
||||
|
|
@ -1710,6 +1698,38 @@ public class XmlParserDstu2Test {
|
|||
|
||||
}
|
||||
|
||||
/**
|
||||
* See #216
|
||||
*/
|
||||
@Test
|
||||
public void testParseMalformedIdentifierDstu2() {
|
||||
|
||||
// This was changed from 0.5 to 1.0.0
|
||||
|
||||
//@formatter:off
|
||||
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
|
||||
" <identifier>\n" +
|
||||
" <type value=\"MRN\"/>\n" +
|
||||
" <system value=\"SYS\"/>\n" +
|
||||
" <value value=\"VAL\"/>\n" +
|
||||
" </identifier>\n" +
|
||||
"</Patient>";
|
||||
//@formatter:on
|
||||
|
||||
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
|
||||
|
||||
IParser p = ourCtx.newXmlParser();
|
||||
p.setParserErrorHandler(errorHandler);
|
||||
|
||||
Patient patient = p.parseResource(Patient.class, out);
|
||||
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
|
||||
|
||||
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
|
||||
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
|
||||
|
||||
assertEquals("value", capt.getValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParseMetadata() throws Exception {
|
||||
//@formatter:off
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
package ca.uhn.fhir.validation;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
import java.io.InputStream;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.UnsupportedEncodingException;
|
||||
|
|
@ -20,67 +22,102 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
|||
|
||||
public class DefaultProfileValidationSupport implements IValidationSupport {
|
||||
|
||||
private Map<String, ValueSet> myDefaultValueSets;
|
||||
|
||||
@Override
|
||||
public boolean isCodeSystemSupported(String theSystem) {
|
||||
return false;
|
||||
}
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
@Override
|
||||
public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
|
||||
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
|
||||
return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
|
||||
}
|
||||
if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
|
||||
Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
|
||||
if (defaultValueSets == null) {
|
||||
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
|
||||
if (valuesetText == null) {
|
||||
return null;
|
||||
}
|
||||
InputStreamReader reader;
|
||||
try {
|
||||
reader = new InputStreamReader(valuesetText, "UTF-8");
|
||||
} catch (UnsupportedEncodingException e) {
|
||||
// Shouldn't happen!
|
||||
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
|
||||
}
|
||||
|
||||
defaultValueSets = new HashMap<String, ValueSet>();
|
||||
|
||||
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
|
||||
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
|
||||
for (BundleEntryComponent next : bundle.getEntry()) {
|
||||
IdType nextId = new IdType(next.getFullUrl());
|
||||
if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
|
||||
continue;
|
||||
}
|
||||
defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
|
||||
}
|
||||
|
||||
myDefaultValueSets = defaultValueSets;
|
||||
}
|
||||
|
||||
return (T) defaultValueSets.get(theUri);
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
private Map<String, ValueSet> myDefaultValueSets;
|
||||
private Map<String, ValueSet> myCodeSystems;
|
||||
|
||||
@Override
|
||||
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
|
||||
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
|
||||
return false;
|
||||
}
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
@Override
|
||||
public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
|
||||
if (theUri.startsWith("http://hl7.org/fhir/StructureDefinition/")) {
|
||||
return (T) FhirInstanceValidator.loadProfileOrReturnNull(null, FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext), theUri.substring("http://hl7.org/fhir/StructureDefinition/".length()));
|
||||
}
|
||||
if (theUri.startsWith("http://hl7.org/fhir/ValueSet/")) {
|
||||
Map<String, ValueSet> defaultValueSets = myDefaultValueSets;
|
||||
if (defaultValueSets == null) {
|
||||
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream("/org/hl7/fhir/instance/model/valueset/valuesets.xml");
|
||||
if (valuesetText == null) {
|
||||
return null;
|
||||
}
|
||||
InputStreamReader reader;
|
||||
try {
|
||||
reader = new InputStreamReader(valuesetText, "UTF-8");
|
||||
} catch (UnsupportedEncodingException e) {
|
||||
// Shouldn't happen!
|
||||
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
|
||||
}
|
||||
|
||||
defaultValueSets = new HashMap<String, ValueSet>();
|
||||
|
||||
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
|
||||
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
|
||||
for (BundleEntryComponent next : bundle.getEntry()) {
|
||||
IdType nextId = new IdType(next.getFullUrl());
|
||||
if (nextId.isEmpty() || !nextId.getValue().startsWith("http://hl7.org/fhir/ValueSet/")) {
|
||||
continue;
|
||||
}
|
||||
defaultValueSets.put(nextId.toVersionless().getValue(), (ValueSet) next.getResource());
|
||||
}
|
||||
|
||||
myDefaultValueSets = defaultValueSets;
|
||||
}
|
||||
|
||||
return (T) defaultValueSets.get(theUri);
|
||||
}
|
||||
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
|
||||
return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSet fetchCodeSystem(String theSystem) {
|
||||
return null;
|
||||
public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
|
||||
Map<String, ValueSet> codeSystems = myCodeSystems;
|
||||
if (codeSystems == null) {
|
||||
codeSystems = new HashMap<String, ValueSet>();
|
||||
|
||||
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
|
||||
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
|
||||
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
|
||||
|
||||
myCodeSystems = codeSystems;
|
||||
}
|
||||
|
||||
return codeSystems.get(theSystem);
|
||||
}
|
||||
|
||||
private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
|
||||
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
|
||||
if (valuesetText != null) {
|
||||
InputStreamReader reader;
|
||||
try {
|
||||
reader = new InputStreamReader(valuesetText, "UTF-8");
|
||||
} catch (UnsupportedEncodingException e) {
|
||||
// Shouldn't happen!
|
||||
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
|
||||
}
|
||||
|
||||
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
|
||||
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
|
||||
for (BundleEntryComponent next : bundle.getEntry()) {
|
||||
ValueSet nextValueSet = (ValueSet) next.getResource();
|
||||
String system = nextValueSet.getCodeSystem().getSystem();
|
||||
if (isNotBlank(system)) {
|
||||
codeSystems.put(system, nextValueSet);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
|
||||
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
|
||||
return null;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -269,7 +269,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
|
||||
@Override
|
||||
public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
|
||||
return myValidationSupport.expandValueSet(theInc);
|
||||
return myValidationSupport.expandValueSet(myCtx, theInc);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -282,7 +282,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
if (myValidationSupport == null) {
|
||||
return null;
|
||||
} else {
|
||||
return myValidationSupport.fetchCodeSystem(theSystem);
|
||||
return myValidationSupport.fetchCodeSystem(myCtx, theSystem);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -335,13 +335,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
if (myValidationSupport == null) {
|
||||
return false;
|
||||
} else {
|
||||
return myValidationSupport.isCodeSystemSupported(theSystem);
|
||||
return myValidationSupport.isCodeSystemSupported(myCtx, theSystem);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValidationResult validateCode(String theSystem, String theCode, String theDisplay) {
|
||||
CodeValidationResult result = myValidationSupport.validateCode(theSystem, theCode, theDisplay);
|
||||
CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay);
|
||||
if (result == null) {
|
||||
return null;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@ public interface IValidationSupport {
|
|||
* The portion to include
|
||||
* @return The expansion
|
||||
*/
|
||||
ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude);
|
||||
ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude);
|
||||
|
||||
/**
|
||||
* Fetch a code system by ID
|
||||
|
|
@ -27,7 +27,7 @@ public interface IValidationSupport {
|
|||
* The code system
|
||||
* @return The valueset (must not be null, but can be an empty ValueSet)
|
||||
*/
|
||||
ValueSet fetchCodeSystem(String theSystem);
|
||||
ValueSet fetchCodeSystem(FhirContext theContext, String theSystem);
|
||||
|
||||
/**
|
||||
* Loads a resource needed by the validation (a StructureDefinition, or a
|
||||
|
|
@ -53,7 +53,7 @@ public interface IValidationSupport {
|
|||
* @return Returns <code>true</code> if codes in the given code system can be
|
||||
* validated
|
||||
*/
|
||||
boolean isCodeSystemSupported(String theSystem);
|
||||
boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
|
||||
|
||||
/**
|
||||
* Validates that the given code exists and if possible returns a display
|
||||
|
|
@ -68,7 +68,7 @@ public interface IValidationSupport {
|
|||
* The display name, if it should also be validated
|
||||
* @return Returns a validation result object
|
||||
*/
|
||||
CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay);
|
||||
CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
|
||||
|
||||
public class CodeValidationResult {
|
||||
private ConceptDefinitionComponent definition;
|
||||
|
|
|
|||
|
|
@ -24,19 +24,19 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
}
|
||||
|
||||
@Override
|
||||
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
|
||||
public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theInclude.getSystem())) {
|
||||
return next.expandValueSet(theInclude);
|
||||
if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
|
||||
return next.expandValueSet(theCtx, theInclude);
|
||||
}
|
||||
}
|
||||
return myChain.get(0).expandValueSet(theInclude);
|
||||
return myChain.get(0).expandValueSet(theCtx, theInclude);
|
||||
}
|
||||
|
||||
@Override
|
||||
public ValueSet fetchCodeSystem(String theSystem) {
|
||||
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
ValueSet retVal = next.fetchCodeSystem(theSystem);
|
||||
ValueSet retVal = next.fetchCodeSystem(theCtx, theSystem);
|
||||
if (retVal != null) {
|
||||
return retVal;
|
||||
}
|
||||
|
|
@ -56,9 +56,9 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
}
|
||||
|
||||
@Override
|
||||
public boolean isCodeSystemSupported(String theSystem) {
|
||||
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theSystem)) {
|
||||
if (next.isCodeSystemSupported(theCtx, theSystem)) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
|
@ -66,13 +66,13 @@ public class ValidationSupportChain implements IValidationSupport {
|
|||
}
|
||||
|
||||
@Override
|
||||
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
|
||||
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
|
||||
for (IValidationSupport next : myChain) {
|
||||
if (next.isCodeSystemSupported(theCodeSystem)) {
|
||||
return next.validateCode(theCodeSystem, theCode, theDisplay);
|
||||
if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
|
||||
return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
|
||||
}
|
||||
}
|
||||
return myChain.get(0).validateCode(theCodeSystem, theCode, theDisplay);
|
||||
return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,7 +2,9 @@ package ca.uhn.fhir.validation;
|
|||
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.greaterThan;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.fail;
|
||||
import static org.mockito.Matchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
|
@ -16,6 +18,7 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.hl7.fhir.instance.model.CodeType;
|
||||
import org.hl7.fhir.instance.model.Observation;
|
||||
import org.hl7.fhir.instance.model.Observation.ObservationStatus;
|
||||
import org.hl7.fhir.instance.model.Patient;
|
||||
import org.hl7.fhir.instance.model.StringType;
|
||||
import org.hl7.fhir.instance.model.ValueSet;
|
||||
import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
|
||||
|
|
@ -61,19 +64,19 @@ public class FhirInstanceValidatorTest {
|
|||
myValidConcepts = new ArrayList<String>();
|
||||
|
||||
myMockSupport = mock(IValidationSupport.class);
|
||||
when(myMockSupport.expandValueSet(any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
|
||||
when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
|
||||
@Override
|
||||
public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
|
||||
ConceptSetComponent arg = (ConceptSetComponent)theInvocation.getArguments()[0];
|
||||
ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
|
||||
if (retVal == null) {
|
||||
retVal = myDefaultValidationSupport.expandValueSet(arg);
|
||||
retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
|
||||
}
|
||||
ourLog.info("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
|
||||
return retVal;
|
||||
}
|
||||
});
|
||||
when(myMockSupport.isCodeSystemSupported(any(String.class))).thenAnswer(new Answer<Boolean>() {
|
||||
when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
|
||||
@Override
|
||||
public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
|
||||
boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
|
||||
|
|
@ -93,28 +96,29 @@ public class FhirInstanceValidatorTest {
|
|||
return retVal;
|
||||
}
|
||||
});
|
||||
when(myMockSupport.validateCode(any(String.class), any(String.class), any(String.class)))
|
||||
when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class)))
|
||||
.thenAnswer(new Answer<CodeValidationResult>() {
|
||||
@Override
|
||||
public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
|
||||
String system = (String) theInvocation.getArguments()[0];
|
||||
String code = (String) theInvocation.getArguments()[1];
|
||||
FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
|
||||
String system = (String) theInvocation.getArguments()[1];
|
||||
String code = (String) theInvocation.getArguments()[2];
|
||||
CodeValidationResult retVal;
|
||||
if (myValidConcepts.contains(system + "___" + code)) {
|
||||
retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
|
||||
} else {
|
||||
retVal = myDefaultValidationSupport.validateCode(system, code, (String) theInvocation.getArguments()[2]);
|
||||
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
|
||||
}
|
||||
ourLog.info("validateCode({}, {}, {}) : {}",
|
||||
new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
|
||||
return retVal;
|
||||
}
|
||||
});
|
||||
when(myMockSupport.fetchCodeSystem(any(String.class))).thenAnswer(new Answer<ValueSet>() {
|
||||
when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<ValueSet>() {
|
||||
@Override
|
||||
public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
|
||||
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((String) theInvocation.getArguments()[0]);
|
||||
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
|
||||
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
|
||||
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
|
||||
return retVal;
|
||||
}
|
||||
});
|
||||
|
|
@ -306,6 +310,29 @@ public class FhirInstanceValidatorTest {
|
|||
output.getMessages().get(0).getMessage());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testValidateResourceWithValuesetExpansion() {
|
||||
|
||||
Patient patient = new Patient();
|
||||
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("foo").setCode("bar");
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(patient);
|
||||
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
|
||||
assertEquals(1, all.size());
|
||||
assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
|
||||
assertEquals("None of the codes are in the expected value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type)", all.get(0).getMessage());
|
||||
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
|
||||
|
||||
patient = new Patient();
|
||||
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
|
||||
|
||||
output = myVal.validateWithResult(patient);
|
||||
all = logResultsAndReturnAll(output);
|
||||
assertEquals(0, all.size());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
|
||||
Observation input = new Observation();
|
||||
|
|
@ -353,7 +380,11 @@ public class FhirInstanceValidatorTest {
|
|||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
|
||||
assertEquals(errors.toString(), 0, errors.size());
|
||||
assertEquals(errors.toString(), 1, errors.size());
|
||||
assertEquals("Unable to validate code \"1234\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
|
||||
assertEquals(ResultSeverityEnum.WARNING, errors.get(0).getSeverity());
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -84,6 +84,17 @@
|
|||
a more appropriate 400/404 in the JPA server (vread on invalid version,
|
||||
delete with no ID, etc.)
|
||||
</action>
|
||||
<action type="fix">
|
||||
Fix narrative generation for DSTU2 Medication resource
|
||||
</action>
|
||||
<action type="fix">
|
||||
Profile validator now works for valuesets which use
|
||||
v2 tables
|
||||
</action>
|
||||
<action type="add">
|
||||
JPA server Patient/[id]/$everything operation now supports
|
||||
_lastUpdated filtering and _sort'ing of results.
|
||||
</action>
|
||||
</release>
|
||||
<release version="1.2" date="2015-09-18">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue