Issue 5004 make bundleutil also accept name prev for previous links (#5042)
* Add test * Fix * Changelog * Small details to reset build pipe * Reformat * Make definition animal-sniffer (check-android-26-compliance) compliant --------- Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
ce04e897cf
commit
ed04dd2498
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@ -27,18 +27,22 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.rest.api.PatchTypeEnum;
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import ca.uhn.fhir.rest.api.RequestTypeEnum;
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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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import ca.uhn.fhir.util.bundle.BundleEntryMutator;
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import ca.uhn.fhir.util.bundle.BundleEntryParts;
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import ca.uhn.fhir.util.bundle.EntryListAccumulator;
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import ca.uhn.fhir.util.bundle.ModifiableBundleEntry;
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import ca.uhn.fhir.util.bundle.SearchBundleEntryParts;
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import com.google.common.collect.Sets;
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import org.apache.commons.lang3.tuple.Pair;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.ArrayList;
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import java.util.HashMap;
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@ -51,29 +55,41 @@ import java.util.function.Consumer;
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import java.util.stream.Collectors;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import static org.hl7.fhir.instance.model.api.IBaseBundle.LINK_PREV;
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/**
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* Fetch resources from a bundle
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*/
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public class BundleUtil {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BundleUtil.class);
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private static final Logger ourLog = LoggerFactory.getLogger(BundleUtil.class);
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private static final String PREVIOUS = LINK_PREV;
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private static final String PREV = "prev";
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private static final Set<String> previousOrPrev = Sets.newHashSet(PREVIOUS, PREV);
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public static final String DIFFERENT_LINK_ERROR_MSG = "Mismatching 'previous' and 'prev' links exist. 'previous' " +
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"is: '$PREVIOUS' and 'prev' is: '$PREV'.";
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/**
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* @return Returns <code>null</code> if the link isn't found or has no value
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*/
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public static String getLinkUrlOfType(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation) {
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return getLinkUrlOfType(theContext, theBundle, theLinkRelation, true);
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}
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private static String getLinkUrlOfType(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation, boolean isPreviousCheck) {
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RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
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BaseRuntimeChildDefinition entryChild = def.getChildByName("link");
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List<IBase> links = entryChild.getAccessor().getValues(theBundle);
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for (IBase nextLink : links) {
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boolean isRightRel = false;
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BaseRuntimeElementCompositeDefinition relDef = (BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
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BaseRuntimeElementCompositeDefinition<?> relDef = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(nextLink.getClass());
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BaseRuntimeChildDefinition relChild = relDef.getChildByName("relation");
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List<IBase> relValues = relChild.getAccessor().getValues(nextLink);
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for (IBase next : relValues) {
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IPrimitiveType<?> nextValue = (IPrimitiveType<?>) next;
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if (theLinkRelation.equals(nextValue.getValueAsString())) {
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if (isRelationMatch(theContext, theBundle,theLinkRelation, nextValue.getValueAsString(), isPreviousCheck)) {
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isRightRel = true;
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}
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}
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@ -82,7 +98,7 @@ public class BundleUtil {
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continue;
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}
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BaseRuntimeElementCompositeDefinition linkDef = (BaseRuntimeElementCompositeDefinition) theContext.getElementDefinition(nextLink.getClass());
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BaseRuntimeElementCompositeDefinition<?> linkDef = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(nextLink.getClass());
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BaseRuntimeChildDefinition urlChild = linkDef.getChildByName("url");
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List<IBase> values = urlChild.getAccessor().getValues(nextLink);
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for (IBase nextUrl : values) {
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@ -91,12 +107,40 @@ public class BundleUtil {
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return nextValue.getValueAsString();
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}
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}
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}
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return null;
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}
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private static boolean isRelationMatch(FhirContext theContext, IBaseBundle theBundle, String value, String matching, boolean theIsPreviousCheck) {
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if ( ! theIsPreviousCheck) {
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return value.equals(matching);
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}
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if ( previousOrPrev.contains(value) ) {
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validateUniqueOrMatchingPreviousValues(theContext, theBundle);
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if ( previousOrPrev.contains(matching) ) {
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return true;
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}
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}
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return (value.equals(matching));
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}
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private static void validateUniqueOrMatchingPreviousValues(FhirContext theContext, IBaseBundle theBundle) {
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String previousLink = getLinkNoCheck(theContext, theBundle, PREVIOUS);
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String prevLink = getLinkNoCheck(theContext, theBundle, PREV);
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if (prevLink != null && previousLink != null) {
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if ( ! previousLink.equals(prevLink)) {
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String msg = DIFFERENT_LINK_ERROR_MSG.replace("$PREVIOUS", previousLink).replace("$PREV", prevLink);
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throw new InternalErrorException(Msg.code(2368) + msg);
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}
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}
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}
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private static String getLinkNoCheck(FhirContext theContext, IBaseBundle theBundle, String theLinkRelation) {
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return getLinkUrlOfType(theContext, theBundle, theLinkRelation, false);
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}
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@SuppressWarnings("unchecked")
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public static List<Pair<String, IBaseResource>> getBundleEntryUrlsAndResources(FhirContext theContext, IBaseBundle theBundle) {
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RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
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@ -160,6 +204,7 @@ public class BundleUtil {
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BaseRuntimeChildDefinition entryChild = def.getChildByName("total");
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List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
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if (entries.size() > 0) {
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@SuppressWarnings("unchecked")
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IPrimitiveType<Number> typeElement = (IPrimitiveType<Number>) entries.get(0);
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if (typeElement != null && typeElement.getValue() != null) {
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return typeElement.getValue().intValue();
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@ -171,6 +216,7 @@ public class BundleUtil {
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public static void setTotal(FhirContext theContext, IBaseBundle theBundle, Integer theTotal) {
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RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
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BaseRuntimeChildDefinition entryChild = def.getChildByName("total");
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@SuppressWarnings("unchecked")
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IPrimitiveType<Integer> value = (IPrimitiveType<Integer>) entryChild.getChildByName("total").newInstance();
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value.setValue(theTotal);
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entryChild.getMutator().setValue(theBundle, value);
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@ -194,11 +240,11 @@ public class BundleUtil {
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* 1. Deletes
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* 2. Creates
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* 3. Updates
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*
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* <p>
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* Furthermore, within these operation types, the entries will be sorted based on the order in which they should be processed
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* e.g. if you have 2 CREATEs, one for a Patient, and one for an Observation which has this Patient as its Subject,
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* the patient will come first, then the observation.
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*
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* <p>
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* In cases of there being a cyclic dependency (e.g. Organization/1 is partOf Organization/2 and Organization/2 is partOf Organization/1)
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* this function will throw an IllegalStateException.
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*
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@ -207,12 +253,11 @@ public class BundleUtil {
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*/
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public static void sortEntriesIntoProcessingOrder(FhirContext theContext, IBaseBundle theBundle) throws IllegalStateException {
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Map<BundleEntryParts, IBase> partsToIBaseMap = getPartsToIBaseMap(theContext, theBundle);
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LinkedHashSet<IBase> retVal = new LinkedHashSet<>();
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//Get all deletions.
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LinkedHashSet<IBase> deleteParts = sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.DELETE, partsToIBaseMap);
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validatePartsNotNull(deleteParts);
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retVal.addAll(deleteParts);
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LinkedHashSet<IBase> retVal = new LinkedHashSet<>(deleteParts);
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//Get all Creations
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LinkedHashSet<IBase> createParts= sortEntriesOfTypeIntoProcessingOrder(theContext, RequestTypeEnum.POST, partsToIBaseMap);
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@ -408,8 +453,7 @@ public class BundleUtil {
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}
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}
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SearchBundleEntryParts parts = new SearchBundleEntryParts(fullUrl, resource, matchMode);
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return parts;
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return new SearchBundleEntryParts(fullUrl, resource, matchMode);
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}
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/**
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@ -485,8 +529,7 @@ public class BundleUtil {
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}
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}
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}
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BundleEntryParts parts = new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl);
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return parts;
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return new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl);
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}
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/**
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@ -540,12 +583,12 @@ public class BundleUtil {
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boolean isPatch = false;
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if (thePayloadResource instanceof IBaseBinary) {
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String contentType = ((IBaseBinary) thePayloadResource).getContentType();
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try {
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PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(theContext, contentType);
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isPatch = true;
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} catch (InvalidRequestException e) {
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// ignore
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}
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try {
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PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(theContext, contentType);
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isPatch = true;
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} catch (InvalidRequestException e) {
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// ignore
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}
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}
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return isPatch;
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}
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@ -0,0 +1,6 @@
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---
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type: fix
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issue: 5004
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title: "Previously when requesting `previous` or `prev` link using `BundleUtil.getLinkUrlOfType`, only the literal requested
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link was returned. Now when requesting either `previous` or `prev` `previous` or `prev` link is returned.
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If both exist, equality is validated and exception is thrown on failure."
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@ -1,11 +1,14 @@
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package ca.uhn.fhir.util.bundle;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.util.BundleBuilder;
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import ca.uhn.fhir.util.BundleUtil;
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import ca.uhn.fhir.util.TestUtil;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.ExplanationOfBenefit;
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import org.hl7.fhir.r4.model.Medication;
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@ -16,12 +19,14 @@ import org.hl7.fhir.r4.model.Quantity;
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import org.hl7.fhir.r4.model.Reference;
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import org.hl7.fhir.r4.model.UriType;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import java.util.Collections;
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import java.util.List;
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import java.util.function.Consumer;
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import static ca.uhn.fhir.util.BundleUtil.DIFFERENT_LINK_ERROR_MSG;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.equalTo;
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@ -33,39 +38,135 @@ import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.GET;
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import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST;
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import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.PUT;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertNull;
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import static org.junit.jupiter.api.Assertions.assertThrows;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.junit.jupiter.api.Assertions.fail;
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public class BundleUtilTest {
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private static FhirContext ourCtx = FhirContext.forR4();
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private static final FhirContext ourCtx = FhirContext.forR4Cached();
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@Test
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public void testGetLink() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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b.getLinkOrCreate("next").setUrl("http://foo");
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assertEquals("http://foo", BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
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}
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@Test
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public void testGetLinkDoesntExist() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertEquals(null, BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
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@Nested
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public class TestGetLinkUrlOfType {
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@Test
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public void testGetNextExists() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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b.getLinkOrCreate("next").setUrl("http://foo");
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assertEquals("http://foo", BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
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}
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@Test
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public void testGetNextDoesntExist() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertNull(BundleUtil.getLinkUrlOfType(ourCtx, b, "next"));
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}
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@Nested
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public class TestGetPreviousLink {
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@Test
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public void testGetPrevious_exists_and_no_prev() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, IBaseBundle.LINK_PREV));
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}
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@Test
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public void testGetPrevious_exists_and_prev_also_and_equals() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, IBaseBundle.LINK_PREV));
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}
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@Test
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public void testGetPrevious_exists_and_prev_also_and_different_must_throw() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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b.getLinkOrCreate("prev").setUrl("http://foo");
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InternalErrorException thrown = assertThrows(InternalErrorException.class,
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() -> BundleUtil.getLinkUrlOfType(ourCtx, b, IBaseBundle.LINK_PREV));
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String expectedExceptionMsg = Msg.code(2368) + DIFFERENT_LINK_ERROR_MSG
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.replace("$PREVIOUS", "http://bar").replace("$PREV", "http://foo");
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assertEquals(expectedExceptionMsg, thrown.getMessage());
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}
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@Test
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public void testGetPrevious_doesnt_exist_neither_prev() {
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Bundle b = new Bundle();
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assertNull(BundleUtil.getLinkUrlOfType(ourCtx, b, IBaseBundle.LINK_PREV));
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}
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@Test
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public void testGetPrevious_doesnt_exist_but_prev_does() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, IBaseBundle.LINK_PREV));
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}
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@Test
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public void testGetPrev_exists_and_no_previous() {
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Bundle b = new Bundle();
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, "prev"));
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}
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@Test
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public void testGetPrev_exists_and_previous_also_and_equals() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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b.getLinkOrCreate("prev").setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, "prev"));
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}
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@Test
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public void testGetPrev_exists_and_previous_also_and_different_must_throw() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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b.getLinkOrCreate("prev").setUrl("http://foo");
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InternalErrorException thrown = assertThrows(InternalErrorException.class,
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() -> BundleUtil.getLinkUrlOfType(ourCtx, b, "prev"));
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String expectedExceptionMsg = Msg.code(2368) + DIFFERENT_LINK_ERROR_MSG
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.replace("$PREVIOUS", "http://bar").replace("$PREV", "http://foo");
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assertEquals(expectedExceptionMsg, thrown.getMessage());
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}
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@Test
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public void testGetPrev_doesnt_exist_neither_previous() {
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Bundle b = new Bundle();
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assertNull(BundleUtil.getLinkUrlOfType(ourCtx, b, "prev"));
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}
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@Test
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public void testGetPrev_doesnt_exist_but_previous_does() {
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Bundle b = new Bundle();
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b.getLinkOrCreate(IBaseBundle.LINK_PREV).setUrl("http://bar");
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assertEquals("http://bar", BundleUtil.getLinkUrlOfType(ourCtx, b, "prev"));
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}
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}
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}
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@Test
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public void testGetTotal() {
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Bundle b = new Bundle();
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b.setTotal(999);
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assertEquals(999, BundleUtil.getTotal(ourCtx, b).intValue());
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Integer total = BundleUtil.getTotal(ourCtx, b);
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assertNotNull(total);
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assertEquals(999, total.intValue());
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}
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@Test
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public void testGetTotalNull() {
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Bundle b = new Bundle();
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assertEquals(null, BundleUtil.getTotal(ourCtx, b));
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assertNull(BundleUtil.getTotal(ourCtx, b));
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}
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@Test
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@ -148,7 +249,6 @@ public class BundleUtilTest {
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assertThat(b.getEntry(), hasSize(4));
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List<Bundle.BundleEntryComponent> entry = b.getEntry();
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int observationIndex = getIndexOfEntryWithId("Observation/O1", b);
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int patientIndex = getIndexOfEntryWithId("Patient/P1", b);
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int organizationIndex = getIndexOfEntryWithId("Organization/Org1", b);
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@ -182,7 +282,7 @@ public class BundleUtilTest {
|
|||
try {
|
||||
BundleUtil.sortEntriesIntoProcessingOrder(ourCtx, b);
|
||||
fail();
|
||||
} catch (IllegalStateException e ) {
|
||||
} catch (IllegalStateException ignored) {
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -274,71 +374,72 @@ public class BundleUtilTest {
|
|||
@Test
|
||||
public void testBundleToSearchBundleEntryParts() {
|
||||
//Given
|
||||
String bundleString = "{\n" +
|
||||
" \"resourceType\": \"Bundle\",\n" +
|
||||
" \"id\": \"bd194b7f-ac1e-429a-a206-ee2c470f23b5\",\n" +
|
||||
" \"meta\": {\n" +
|
||||
" \"lastUpdated\": \"2021-10-18T16:25:55.330-07:00\"\n" +
|
||||
" },\n" +
|
||||
" \"type\": \"searchset\",\n" +
|
||||
" \"total\": 1,\n" +
|
||||
" \"link\": [\n" +
|
||||
" {\n" +
|
||||
" \"relation\": \"self\",\n" +
|
||||
" \"url\": \"http://localhost:8000/Patient?_count=1&_id=pata&_revinclude=Condition%3Asubject%3APatient\"\n" +
|
||||
" }\n" +
|
||||
" ],\n" +
|
||||
" \"entry\": [\n" +
|
||||
" {\n" +
|
||||
" \"fullUrl\": \"http://localhost:8000/Patient/pata\",\n" +
|
||||
" \"resource\": {\n" +
|
||||
" \"resourceType\": \"Patient\",\n" +
|
||||
" \"id\": \"pata\",\n" +
|
||||
" \"meta\": {\n" +
|
||||
" \"versionId\": \"1\",\n" +
|
||||
" \"lastUpdated\": \"2021-10-18T16:25:48.954-07:00\",\n" +
|
||||
" \"source\": \"#rnEjIucr8LR6Ze3x\"\n" +
|
||||
" },\n" +
|
||||
" \"name\": [\n" +
|
||||
" {\n" +
|
||||
" \"family\": \"Simpson\",\n" +
|
||||
" \"given\": [\n" +
|
||||
" \"Homer\",\n" +
|
||||
" \"J\"\n" +
|
||||
" ]\n" +
|
||||
" }\n" +
|
||||
" ]\n" +
|
||||
" },\n" +
|
||||
" \"search\": {\n" +
|
||||
" \"mode\": \"match\"\n" +
|
||||
" }\n" +
|
||||
" },\n" +
|
||||
" {\n" +
|
||||
" \"fullUrl\": \"http://localhost:8000/Condition/1626\",\n" +
|
||||
" \"resource\": {\n" +
|
||||
" \"resourceType\": \"Condition\",\n" +
|
||||
" \"id\": \"1626\",\n" +
|
||||
" \"meta\": {\n" +
|
||||
" \"versionId\": \"1\",\n" +
|
||||
" \"lastUpdated\": \"2021-10-18T16:25:51.672-07:00\",\n" +
|
||||
" \"source\": \"#gSOcGAdA3acaaNq1\"\n" +
|
||||
" },\n" +
|
||||
" \"identifier\": [\n" +
|
||||
" {\n" +
|
||||
" \"system\": \"urn:hssc:musc:conditionid\",\n" +
|
||||
" \"value\": \"1064115000.1.5\"\n" +
|
||||
" }\n" +
|
||||
" ],\n" +
|
||||
" \"subject\": {\n" +
|
||||
" \"reference\": \"Patient/pata\"\n" +
|
||||
" }\n" +
|
||||
" },\n" +
|
||||
" \"search\": {\n" +
|
||||
" \"mode\": \"include\"\n" +
|
||||
" }\n" +
|
||||
" }\n" +
|
||||
" ]\n" +
|
||||
"}";
|
||||
String bundleString = """
|
||||
{
|
||||
"resourceType": "Bundle",
|
||||
"id": "bd194b7f-ac1e-429a-a206-ee2c470f23b5",
|
||||
"meta": {
|
||||
"lastUpdated": "2021-10-18T16:25:55.330-07:00"
|
||||
},
|
||||
"type": "searchset",
|
||||
"total": 1,
|
||||
"link": [
|
||||
{
|
||||
"relation": "self",
|
||||
"url": "http://localhost:8000/Patient?_count=1&_id=pata&_revinclude=Condition%3Asubject%3APatient"
|
||||
}
|
||||
],
|
||||
"entry": [
|
||||
{
|
||||
"fullUrl": "http://localhost:8000/Patient/pata",
|
||||
"resource": {
|
||||
"resourceType": "Patient",
|
||||
"id": "pata",
|
||||
"meta": {
|
||||
"versionId": "1",
|
||||
"lastUpdated": "2021-10-18T16:25:48.954-07:00",
|
||||
"source": "#rnEjIucr8LR6Ze3x"
|
||||
},
|
||||
"name": [
|
||||
{
|
||||
"family": "Simpson",
|
||||
"given": [
|
||||
"Homer",
|
||||
"J"
|
||||
]
|
||||
}
|
||||
]
|
||||
},
|
||||
"search": {
|
||||
"mode": "match"
|
||||
}
|
||||
},
|
||||
{
|
||||
"fullUrl": "http://localhost:8000/Condition/1626",
|
||||
"resource": {
|
||||
"resourceType": "Condition",
|
||||
"id": "1626",
|
||||
"meta": {
|
||||
"versionId": "1",
|
||||
"lastUpdated": "2021-10-18T16:25:51.672-07:00",
|
||||
"source": "#gSOcGAdA3acaaNq1"
|
||||
},
|
||||
"identifier": [
|
||||
{
|
||||
"system": "urn:hssc:musc:conditionid",
|
||||
"value": "1064115000.1.5"
|
||||
}
|
||||
],
|
||||
"subject": {
|
||||
"reference": "Patient/pata"
|
||||
}
|
||||
},
|
||||
"search": {
|
||||
"mode": "include"
|
||||
}
|
||||
}
|
||||
]
|
||||
}""";
|
||||
|
||||
Bundle bundle = ourCtx.newJsonParser().parseResource(Bundle.class, bundleString);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue