issue-2397 implementing the mdm expansion on everything and searches (#3044)

* issue-2397 implementing the mdm expansion on everything and searches

* issue-2397 code cleanup and removal of test code

* issue-2397 some tests

* issue-2397 changelog added

* issue-2397 review fixes

* issue-2397 updated change log with example and fixed failing tests

* issue-2397 test fixing

* issue-2397 fixing test

* issue-2397 review fix

* issue 2397 fixing changelog file

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Tadgh <tadgh@cs.toronto.edu>
This commit is contained in:
TipzCM 2021-10-07 10:46:23 -04:00 committed by GitHub
parent 71e2b82128
commit a474e88ed4
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18 changed files with 601 additions and 93 deletions

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@ -38,6 +38,8 @@ public class StringParam extends BaseParam implements IQueryParameterType {
private boolean myExact; private boolean myExact;
private String myValue; private String myValue;
private Boolean myMdmExpand;
/** /**
* Constructor * Constructor
*/ */
@ -75,6 +77,15 @@ public class StringParam extends BaseParam implements IQueryParameterType {
return ParameterUtil.escape(myValue); return ParameterUtil.escape(myValue);
} }
public boolean isMdmExpand() {
return myMdmExpand != null && myMdmExpand;
}
public StringParam setMdmExpand(boolean theMdmExpand) {
myMdmExpand = theMdmExpand;
return this;
}
@Override @Override
public int hashCode() { public int hashCode() {
return new HashCodeBuilder(17, 37) return new HashCodeBuilder(17, 37)

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@ -40,6 +40,8 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
private String mySystem; private String mySystem;
private String myValue; private String myValue;
private Boolean myMdmExpand;
/** /**
* Constructor * Constructor
*/ */
@ -99,6 +101,15 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
this(null, theCode); this(null, theCode);
} }
public boolean isMdmExpand() {
return myMdmExpand != null && myMdmExpand;
}
public TokenParam setMdmExpand(boolean theMdmExpand) {
myMdmExpand = theMdmExpand;
return this;
}
@Override @Override
String doGetQueryParameterQualifier() { String doGetQueryParameterQualifier() {
if (getModifier() != null) { if (getModifier() != null) {

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@ -0,0 +1,5 @@
---
type: add
issue: 2397
title: "Added mdm support on $everything operation for patients by adding _mdm=true query parameter.
Eg: <baseURL>/Patient/123/$everything?_mdm=true."

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@ -311,7 +311,6 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
@Transactional @Transactional
@Override @Override
public JobInfo submitJob(BulkDataExportOptions theBulkDataExportOptions, Boolean useCache, RequestDetails theRequestDetails) { public JobInfo submitJob(BulkDataExportOptions theBulkDataExportOptions, Boolean useCache, RequestDetails theRequestDetails) {
String outputFormat = Constants.CT_FHIR_NDJSON; String outputFormat = Constants.CT_FHIR_NDJSON;
if (isNotBlank(theBulkDataExportOptions.getOutputFormat())) { if (isNotBlank(theBulkDataExportOptions.getOutputFormat())) {
outputFormat = theBulkDataExportOptions.getOutputFormat(); outputFormat = theBulkDataExportOptions.getOutputFormat();
@ -359,11 +358,8 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_MDM).append("=").append(theBulkDataExportOptions.isExpandMdm()); requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_MDM).append("=").append(theBulkDataExportOptions.isExpandMdm());
} }
String request = requestBuilder.toString(); String request = requestBuilder.toString();
//If we are using the cache, then attempt to retrieve a matching job based on the Request String, otherwise just make a new one. //If we are using the cache, then attempt to retrieve a matching job based on the Request String, otherwise just make a new one.
if (useCache) { if (useCache) {
Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis); Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis);

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@ -122,15 +122,16 @@ public class IdHelperService {
*/ */
@Nonnull @Nonnull
public IResourceLookup resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId) throws ResourceNotFoundException { public IResourceLookup resolveResourceIdentity(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId) throws ResourceNotFoundException {
// We only pass 1 input in so only 0..1 will come back
IdDt id = new IdDt(theResourceType, theResourceId); IdDt id = new IdDt(theResourceType, theResourceId);
Collection<IResourceLookup> matches = translateForcedIdToPids(theRequestPartitionId, Collections.singletonList(id)); Map<String, List<IResourceLookup>> matches = translateForcedIdToPids(theRequestPartitionId,
Collections.singletonList(id));
if (matches.isEmpty()) { // We only pass 1 input in so only 0..1 will come back
if (matches.isEmpty() || !matches.containsKey(theResourceId)) {
throw new ResourceNotFoundException(id); throw new ResourceNotFoundException(id);
} }
if (matches.size() > 1) { if (matches.size() > 1 || matches.get(theResourceId).size() > 1) {
/* /*
* This means that: * This means that:
* 1. There are two resources with the exact same resource type and forced id * 1. There are two resources with the exact same resource type and forced id
@ -140,7 +141,60 @@ public class IdHelperService {
throw new PreconditionFailedException(msg); throw new PreconditionFailedException(msg);
} }
return matches.iterator().next(); return matches.get(theResourceId).get(0);
}
/**
* Returns a mapping of Id -> ResourcePersistentId.
* If any resource is not found, it will throw ResourceNotFound exception
* (and no map will be returned)
*
* @param theRequestPartitionId
* @param theResourceType
* @param theIds
* @return
*/
@Nonnull
public Map<String, ResourcePersistentId> resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
List<String> theIds) {
Validate.notNull(theIds, "theIds cannot be null");
Validate.isTrue(!theIds.isEmpty(), "theIds must not be empty");
Map<String, ResourcePersistentId> retVals = new HashMap<>();
for (String id : theIds) {
ResourcePersistentId retVal;
if (!idRequiresForcedId(id)) {
// is already a PID
retVal = new ResourcePersistentId(Long.parseLong(id));
retVals.put(id, retVal);
}
else {
// is a forced id
// we must resolve!
if (myDaoConfig.isDeleteEnabled()) {
retVal = new ResourcePersistentId(resolveResourceIdentity(theRequestPartitionId, theResourceType, id).getResourceId());
retVals.put(id, retVal);
}
else {
// fetch from cache... adding to cache if not available
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, id);
retVal = myMemoryCacheService.getThenPutAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, t -> {
List<IIdType> ids = Collections.singletonList(new IdType(theResourceType, id));
// fetches from cache using a function that checks cache first...
List<ResourcePersistentId> resolvedIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
if (resolvedIds.isEmpty()) {
throw new ResourceNotFoundException(ids.get(0));
}
return resolvedIds.get(0);
});
retVals.put(id, retVal);
}
}
}
return retVals;
} }
/** /**
@ -152,27 +206,10 @@ public class IdHelperService {
public ResourcePersistentId resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) { public ResourcePersistentId resolveResourcePersistentIds(@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
Validate.notNull(theId, "theId must not be null"); Validate.notNull(theId, "theId must not be null");
ResourcePersistentId retVal; Map<String, ResourcePersistentId> retVal = resolveResourcePersistentIds(theRequestPartitionId,
if (idRequiresForcedId (theId)) { theResourceType,
if (myDaoConfig.isDeleteEnabled()) { Collections.singletonList(theId));
retVal = new ResourcePersistentId(resolveResourceIdentity(theRequestPartitionId, theResourceType, theId).getResourceId()); return retVal.get(theId); // should be only one
} else {
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theId);
retVal = myMemoryCacheService.getThenPutAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, t -> {
List<IIdType> ids = Collections.singletonList(new IdType(theResourceType, theId));
List<ResourcePersistentId> resolvedIds = resolveResourcePersistentIdsWithCache(theRequestPartitionId, ids);
if (resolvedIds.isEmpty()) {
throw new ResourceNotFoundException(ids.get(0));
}
return resolvedIds.get(0);
});
}
} else {
retVal = new ResourcePersistentId(Long.parseLong(theId));
}
return retVal;
} }
/** /**
@ -332,14 +369,14 @@ public class IdHelperService {
return typeToIds; return typeToIds;
} }
private Collection<IResourceLookup> translateForcedIdToPids(@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId) { private Map<String, List<IResourceLookup>> translateForcedIdToPids(@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId) {
theId.forEach(id -> Validate.isTrue(id.hasIdPart())); theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
if (theId.isEmpty()) { if (theId.isEmpty()) {
return Collections.emptyList(); return new HashMap<>();
} }
List<IResourceLookup> retVal = new ArrayList<>(); Map<String, List<IResourceLookup>> retVal = new HashMap<>();
RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId); RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) { if (myDaoConfig.getResourceClientIdStrategy() != DaoConfig.ClientIdStrategyEnum.ANY) {
@ -353,6 +390,7 @@ public class IdHelperService {
} }
} }
// returns a map of resourcetype->id
ListMultimap<String, String> typeToIds = organizeIdsByResourceType(theId); ListMultimap<String, String> typeToIds = organizeIdsByResourceType(theId);
for (Map.Entry<String, Collection<String>> nextEntry : typeToIds.asMap().entrySet()) { for (Map.Entry<String, Collection<String>> nextEntry : typeToIds.asMap().entrySet()) {
String nextResourceType = nextEntry.getKey(); String nextResourceType = nextEntry.getKey();
@ -365,7 +403,10 @@ public class IdHelperService {
IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey); IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) { if (cachedLookup != null) {
forcedIdIterator.remove(); forcedIdIterator.remove();
retVal.add(cachedLookup); if (!retVal.containsKey(nextForcedId)) {
retVal.put(nextForcedId, new ArrayList<>());
}
retVal.get(nextForcedId).add(cachedLookup);
} }
} }
} }
@ -392,7 +433,10 @@ public class IdHelperService {
String forcedId = (String) next[2]; String forcedId = (String) next[2];
Date deletedAt = (Date) next[3]; Date deletedAt = (Date) next[3];
ResourceLookup lookup = new ResourceLookup(resourceType, resourcePid, deletedAt); ResourceLookup lookup = new ResourceLookup(resourceType, resourcePid, deletedAt);
retVal.add(lookup); if (!retVal.containsKey(forcedId)) {
retVal.put(forcedId, new ArrayList<>());
}
retVal.get(forcedId).add(lookup);
if (!myDaoConfig.isDeleteEnabled()) { if (!myDaoConfig.isDeleteEnabled()) {
String key = resourceType + "/" + forcedId; String key = resourceType + "/" + forcedId;
@ -420,8 +464,7 @@ public class IdHelperService {
return theRequestPartitionId; return theRequestPartitionId;
} }
private void resolvePids(@Nonnull RequestPartitionId theRequestPartitionId, List<Long> thePidsToResolve, List<IResourceLookup> theTarget) { private void resolvePids(@Nonnull RequestPartitionId theRequestPartitionId, List<Long> thePidsToResolve, Map<String, List<IResourceLookup>> theTargets) {
if (!myDaoConfig.isDeleteEnabled()) { if (!myDaoConfig.isDeleteEnabled()) {
for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) { for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) {
Long nextPid = forcedIdIterator.next(); Long nextPid = forcedIdIterator.next();
@ -429,7 +472,10 @@ public class IdHelperService {
IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey); IResourceLookup cachedLookup = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) { if (cachedLookup != null) {
forcedIdIterator.remove(); forcedIdIterator.remove();
theTarget.add(cachedLookup); if (!theTargets.containsKey(nextKey)) {
theTargets.put(nextKey, new ArrayList<>());
}
theTargets.get(nextKey).add(cachedLookup);
} }
} }
} }
@ -451,7 +497,11 @@ public class IdHelperService {
.stream() .stream()
.map(t -> new ResourceLookup((String) t[0], (Long) t[1], (Date) t[2])) .map(t -> new ResourceLookup((String) t[0], (Long) t[1], (Date) t[2]))
.forEach(t -> { .forEach(t -> {
theTarget.add(t); String id = t.getResourceId().toString();
if (!theTargets.containsKey(id)) {
theTargets.put(id, new ArrayList<>());
}
theTargets.get(id).add(t);
if (!myDaoConfig.isDeleteEnabled()) { if (!myDaoConfig.isDeleteEnabled()) {
String nextKey = Long.toString(t.getResourceId()); String nextKey = Long.toString(t.getResourceId());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, t); myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, t);

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@ -112,6 +112,7 @@ public class MdmLinkExpandSvc {
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH); List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuples = myMdmLinkDao.expandPidsByGoldenResourcePidAndMatchResult(theGoldenResourcePid, MdmMatchResultEnum.MATCH);
return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples); return flattenPidTuplesToSet(theGoldenResourcePid, goldenPidSourcePidTuples);
} }
public Set<String> expandMdmByGoldenResourceId(IdDt theId) { public Set<String> expandMdmByGoldenResourceId(IdDt theId) {
ourLog.debug("About to expand golden resource with golden resource id {}", theId); ourLog.debug("About to expand golden resource with golden resource id {}", theId);
Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId); Long pidOrThrowException = myIdHelperService.getPidOrThrowException(theId);

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@ -41,6 +41,7 @@ import org.hl7.fhir.r4.model.Patient;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletRequest;
import java.util.Arrays;
import java.util.Collections; import java.util.Collections;
public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>implements IFhirResourceDaoPatient<Patient> { public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>implements IFhirResourceDaoPatient<Patient> {
@ -48,7 +49,15 @@ public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>im
@Autowired @Autowired
private IRequestPartitionHelperSvc myPartitionHelperSvc; private IRequestPartitionHelperSvc myPartitionHelperSvc;
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, RequestDetails theRequest) { private IBundleProvider doEverythingOperation(IIdType theId,
IPrimitiveType<Integer> theCount,
IPrimitiveType<Integer> theOffset,
DateRangeParam theLastUpdated,
SortSpec theSort,
StringAndListParam theContent,
StringAndListParam theNarrative,
StringAndListParam theFilter,
RequestDetails theRequest) {
SearchParameterMap paramMap = new SearchParameterMap(); SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) { if (theCount != null) {
paramMap.setCount(theCount.getValue()); paramMap.setCount(theCount.getValue());
@ -67,7 +76,14 @@ public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>im
paramMap.setSort(theSort); paramMap.setSort(theSort);
paramMap.setLastUpdated(theLastUpdated); paramMap.setLastUpdated(theLastUpdated);
if (theId != null) { if (theId != null) {
paramMap.add("_id", new StringParam(theId.getIdPart())); StringParam idParam = new StringParam(theId.getIdPart());
if (theRequest.getParameters().containsKey("_mdm")) {
String[] paramVal = theRequest.getParameters().get("_mdm");
if (Arrays.asList(paramVal).contains("true")) {
idParam.setMdmExpand(true);
}
}
paramMap.add("_id", idParam);
} }
if (!isPagingProviderDatabaseBacked(theRequest)) { if (!isPagingProviderDatabaseBacked(theRequest)) {
@ -75,7 +91,12 @@ public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>im
} }
RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequest, getResourceName(), paramMap, null); RequestPartitionId requestPartitionId = myPartitionHelperSvc.determineReadPartitionForRequestForSearchType(theRequest, getResourceName(), paramMap, null);
return mySearchCoordinatorSvc.registerSearch(this, paramMap, getResourceName(), new CacheControlDirective().parse(theRequest.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequest, requestPartitionId); return mySearchCoordinatorSvc.registerSearch(this,
paramMap,
getResourceName(),
new CacheControlDirective().parse(theRequest.getHeaders(Constants.HEADER_CACHE_CONTROL)),
theRequest,
requestPartitionId);
} }
@Override @Override

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@ -30,11 +30,16 @@ import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt; import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import java.lang.reflect.Constructor;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Map;
import java.util.Set; import java.util.Set;
/** /**
@ -43,6 +48,11 @@ import java.util.Set;
*/ */
@Interceptor @Interceptor
public class MdmSearchExpandingInterceptor { public class MdmSearchExpandingInterceptor {
// A simple interface to turn ids into some form of IQueryParameterTypes
private interface Creator<T extends IQueryParameterType> {
T create(String id);
}
private static final Logger ourLog = Logs.getMdmTroubleshootingLog(); private static final Logger ourLog = Logs.getMdmTroubleshootingLog();
@Autowired @Autowired
@ -54,9 +64,13 @@ public class MdmSearchExpandingInterceptor {
@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED) @Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
public void hook(SearchParameterMap theSearchParameterMap) { public void hook(SearchParameterMap theSearchParameterMap) {
if (myDaoConfig.isAllowMdmExpansion()) { if (myDaoConfig.isAllowMdmExpansion()) {
for (List<List<IQueryParameterType>> andList : theSearchParameterMap.values()) { for (Map.Entry<String, List<List<IQueryParameterType>>> set : theSearchParameterMap.entrySet()) {
String paramName = set.getKey();
List<List<IQueryParameterType>> andList = set.getValue();
for (List<IQueryParameterType> orList : andList) { for (List<IQueryParameterType> orList : andList) {
expandAnyReferenceParameters(orList); // here we will know if it's an _id param or not
// from theSearchParameterMap.keySet()
expandAnyReferenceParameters(paramName, orList);
} }
} }
} }
@ -65,7 +79,7 @@ public class MdmSearchExpandingInterceptor {
/** /**
* If a Parameter is a reference parameter, and it has been set to expand MDM, perform the expansion. * If a Parameter is a reference parameter, and it has been set to expand MDM, perform the expansion.
*/ */
private void expandAnyReferenceParameters(List<IQueryParameterType> orList) { private void expandAnyReferenceParameters(String theParamName, List<IQueryParameterType> orList) {
List<IQueryParameterType> toRemove = new ArrayList<>(); List<IQueryParameterType> toRemove = new ArrayList<>();
List<IQueryParameterType> toAdd = new ArrayList<>(); List<IQueryParameterType> toAdd = new ArrayList<>();
for (IQueryParameterType iQueryParameterType : orList) { for (IQueryParameterType iQueryParameterType : orList) {
@ -85,12 +99,81 @@ public class MdmSearchExpandingInterceptor {
if (!expandedResourceIds.isEmpty()) { if (!expandedResourceIds.isEmpty()) {
ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds)); ourLog.debug("Parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
toRemove.add(refParam); toRemove.add(refParam);
expandedResourceIds.stream().map(resourceId -> new ReferenceParam(refParam.getResourceType() + "/" + resourceId)).forEach(toAdd::add); expandedResourceIds.stream()
.map(resourceId -> new ReferenceParam(refParam.getResourceType() + "/" + resourceId))
.forEach(toAdd::add);
} }
} }
} }
else if (theParamName.equalsIgnoreCase("_id")) {
expandIdParameter(iQueryParameterType, toAdd, toRemove);
}
} }
orList.removeAll(toRemove); orList.removeAll(toRemove);
orList.addAll(toAdd); orList.addAll(toAdd);
} }
/**
* Expands out the provided _id parameter into all the various
* ids of linked resources.
* @param theIdParameter
* @param theAddList
* @param theRemoveList
*/
private void expandIdParameter(IQueryParameterType theIdParameter,
List<IQueryParameterType> theAddList,
List<IQueryParameterType> theRemoveList) {
// id parameters can either be StringParam (for $everything operation)
// or TokenParam (for searches)
// either case, we want to expand it out and grab all related resources
IIdType id;
Creator<? extends IQueryParameterType> creator;
boolean mdmExpand = false;
if (theIdParameter instanceof StringParam) {
StringParam param = (StringParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = StringParam::new;
}
else if (theIdParameter instanceof TokenParam) {
TokenParam param = (TokenParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = TokenParam::new;
}
else {
creator = null;
id = null;
}
if (id == null || creator == null) {
// in case the _id paramter type is different from the above
ourLog.warn("_id parameter of incorrect type. Expected StringParam or TokenParam, but got {}. No expansion will be done!",
theIdParameter.getClass().getSimpleName());
}
else if (mdmExpand) {
ourLog.debug("_id parameter must be expanded out from: {}", id.getValue());
Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(id);
if (expandedResourceIds.isEmpty()) {
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(id.getIdPartAsLong());
}
//Rebuild
if (!expandedResourceIds.isEmpty()) {
ourLog.debug("_id parameter has been expanded to: {}", String.join(", ", expandedResourceIds));
// remove the original
theRemoveList.add(theIdParameter);
// add in all the linked values
expandedResourceIds.stream()
.map(creator::create)
.forEach(theAddList::add);
}
}
// else - no expansion required
}
} }

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@ -356,7 +356,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString, theRequestPartitionId, search); PersistedJpaSearchFirstPageBundleProvider retVal = submitSearch(theCallingDao, theParams, theResourceType, theRequestDetails, searchUuid, sb, queryString, theRequestPartitionId, search);
retVal.setCacheStatus(cacheStatus); retVal.setCacheStatus(cacheStatus);
return retVal; return retVal;
} }
@Override @Override

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@ -1232,9 +1232,10 @@ public class QueryStack {
} }
public void addPredicateEverythingOperation(String theResourceName, Long theTargetPid) { // expand out the pids
public void addPredicateEverythingOperation(String theResourceName, Long... theTargetPids) {
ResourceLinkPredicateBuilder table = mySqlBuilder.addReferencePredicateBuilder(this, null); ResourceLinkPredicateBuilder table = mySqlBuilder.addReferencePredicateBuilder(this, null);
Condition predicate = table.createEverythingPredicate(theResourceName, theTargetPid); Condition predicate = table.createEverythingPredicate(theResourceName, theTargetPids);
mySqlBuilder.addPredicate(predicate); mySqlBuilder.addPredicate(predicate);
} }

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@ -375,6 +375,44 @@ public class SearchBuilder implements ISearchBuilder {
query.ifPresent(t -> theQueries.add(t)); query.ifPresent(t -> theQueries.add(t));
} }
/**
* Combs through the params for any _id parameters and extracts the PIDs for them
* @param theTargetPids
*/
private void extractTargetPidsFromIdParams(HashSet<Long> theTargetPids) {
// get all the IQueryParameterType objects
// for _id -> these should all be StringParam values
HashSet<String> ids = new HashSet<>();
List<List<IQueryParameterType>> params = myParams.get(IAnyResource.SP_RES_ID);
for (List<IQueryParameterType> paramList : params) {
for (IQueryParameterType param : paramList) {
if (param instanceof StringParam) {
// we expect all _id values to be StringParams
ids.add(((StringParam) param).getValue());
}
else {
// we do not expect the _id parameter to be a non-string value
throw new IllegalArgumentException("_id parameter must be a StringParam");
}
}
}
// fetch our target Pids
// this will throw if an id is not found
Map<String, ResourcePersistentId> idToPid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId,
myResourceName,
new ArrayList<>(ids));
if (myAlsoIncludePids == null) {
myAlsoIncludePids = new ArrayList<>();
}
// add the pids to targetPids
for (ResourcePersistentId pid : idToPid.values()) {
myAlsoIncludePids.add(pid);
theTargetPids.add(pid.getIdAsLong());
}
}
private Optional<SearchQueryExecutor> createChunkedQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCount, RequestDetails theRequest, List<Long> thePidList) { private Optional<SearchQueryExecutor> createChunkedQuery(SearchParameterMap theParams, SortSpec sort, Integer theOffset, Integer theMaximumResults, boolean theCount, RequestDetails theRequest, List<Long> thePidList) {
String sqlBuilderResourceName = myParams.getEverythingMode() == null ? myResourceName : null; String sqlBuilderResourceName = myParams.getEverythingMode() == null ? myResourceName : null;
SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCount); SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCount);
@ -394,17 +432,10 @@ public class SearchBuilder implements ISearchBuilder {
} }
if (myParams.getEverythingMode() != null) { if (myParams.getEverythingMode() != null) {
Long targetPid = null; HashSet<Long> targetPids = new HashSet<>();
if (myParams.get(IAnyResource.SP_RES_ID) != null) { if (myParams.get(IAnyResource.SP_RES_ID) != null) {
StringParam idParam = (StringParam) myParams.get(IAnyResource.SP_RES_ID).get(0).get(0); extractTargetPidsFromIdParams(targetPids);
ResourcePersistentId pid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId, myResourceName, idParam.getValue());
if (myAlsoIncludePids == null) {
myAlsoIncludePids = new ArrayList<>(1);
}
myAlsoIncludePids.add(pid);
targetPid = pid.getIdAsLong();
} else { } else {
// For Everything queries, we make the query root by the ResourceLink table, since this query // For Everything queries, we make the query root by the ResourceLink table, since this query
// is basically a reverse-include search. For type/Everything (as opposed to instance/Everything) // is basically a reverse-include search. For type/Everything (as opposed to instance/Everything)
// the one problem with this approach is that it doesn't catch Patients that have absolutely // the one problem with this approach is that it doesn't catch Patients that have absolutely
@ -420,10 +451,9 @@ public class SearchBuilder implements ISearchBuilder {
myAlsoIncludePids.addAll(ResourcePersistentId.fromLongList(output)); myAlsoIncludePids.addAll(ResourcePersistentId.fromLongList(output));
} }
queryStack3.addPredicateEverythingOperation(myResourceName, targetPid);
queryStack3.addPredicateEverythingOperation(myResourceName, targetPids.toArray(new Long[0]));
} else { } else {
/* /*
* If we're doing a filter, always use the resource table as the root - This avoids the possibility of * If we're doing a filter, always use the resource table as the root - This avoids the possibility of
* specific filters with ORs as their root from working around the natural resource type / deletion * specific filters with ORs as their root from working around the natural resource type / deletion
@ -438,7 +468,6 @@ public class SearchBuilder implements ISearchBuilder {
// Normal search // Normal search
searchForIdsWithAndOr(sqlBuilder, queryStack3, myParams, theRequest); searchForIdsWithAndOr(sqlBuilder, queryStack3, myParams, theRequest);
} }
// If we haven't added any predicates yet, we're doing a search for all resources. Make sure we add the // If we haven't added any predicates yet, we're doing a search for all resources. Make sure we add the
@ -463,8 +492,9 @@ public class SearchBuilder implements ISearchBuilder {
} }
//-- exclude the pids already in the previous iterator //-- exclude the pids already in the previous iterator
if (hasNextIteratorQuery) if (hasNextIteratorQuery) {
sqlBuilder.excludeResourceIdsPredicate(myPidSet); sqlBuilder.excludeResourceIdsPredicate(myPidSet);
}
/* /*
* Sort * Sort

View File

@ -80,6 +80,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull; import javax.annotation.Nonnull;
import javax.annotation.Nullable; import javax.annotation.Nullable;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;
import java.util.ListIterator; import java.util.ListIterator;
@ -622,10 +623,14 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
} }
@Nonnull @Nonnull
public Condition createEverythingPredicate(String theResourceName, Long theTargetPid) { public Condition createEverythingPredicate(String theResourceName, Long... theTargetPids) {
if (theTargetPid != null) { if (theTargetPids != null && theTargetPids.length >= 1) {
return BinaryCondition.equalTo(myColumnTargetResourceId, generatePlaceholder(theTargetPid)); // if resource ids are provided, we'll create the predicate
// with ids in or equal to this value
return toEqualToOrInPredicate(myColumnTargetResourceId,
generatePlaceholders(Arrays.stream(theTargetPids).map(Object::toString).collect(Collectors.toList())));
} else { } else {
// ... otherwise we look for resource types
return BinaryCondition.equalTo(myColumnTargetResourceType, generatePlaceholder(theResourceName)); return BinaryCondition.equalTo(myColumnTargetResourceType, generatePlaceholder(theResourceName));
} }
} }

View File

@ -3,14 +3,12 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.config.PartitionSettings; import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig; import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil; import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig; import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig; import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber; import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig; import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
import ca.uhn.fhir.test.utilities.BatchJobHelper; import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
import org.springframework.batch.core.explore.JobExplorer; import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@ -40,7 +38,8 @@ public class TestJPAConfig {
@Bean @Bean
public ModelConfig modelConfig() { public ModelConfig modelConfig() {
return daoConfig().getModelConfig(); ModelConfig config = daoConfig().getModelConfig();
return config;
} }
/* /*

View File

@ -0,0 +1,136 @@
package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.function.Function;
@ExtendWith(MockitoExtension.class)
public class IdHelperServiceTest {
@Mock
private DaoConfig myDaoConfig;
@Mock
private IForcedIdDao myForcedIdDao;
@Mock
private MemoryCacheService myMemoryCacheService;
@Mock
private PartitionSettings myPartitionSettings;
@InjectMocks
private IdHelperService myHelperService;
@Test
public void resolveResourcePersistentIds_withValidPids_returnsMap() {
RequestPartitionId partitionId = RequestPartitionId.allPartitions();
String resourceType = Patient.class.getSimpleName();
List<String> patientIdsToResolve = new ArrayList<>();
patientIdsToResolve.add("123");
patientIdsToResolve.add("456");
// test
Map<String, ResourcePersistentId> idToPid = myHelperService.resolveResourcePersistentIds(partitionId,
resourceType,
patientIdsToResolve);
Assertions.assertFalse(idToPid.isEmpty());
for (String pid : patientIdsToResolve) {
Assertions.assertTrue(idToPid.containsKey(pid));
}
}
@Test
public void resolveResourcePersistentIds_withForcedIdsAndDeleteEnabled_returnsMap() {
RequestPartitionId partitionId = RequestPartitionId.allPartitions();
String resourceType = Patient.class.getSimpleName();
List<String> patientIdsToResolve = new ArrayList<>();
patientIdsToResolve.add("RED");
patientIdsToResolve.add("BLUE");
Object[] redView = new Object[] {
"Patient",
new Long(123l),
"RED",
new Date()
};
Object[] blueView = new Object[] {
"Patient",
new Long(456l),
"BLUE",
new Date()
};
// when
Mockito.when(myDaoConfig.isDeleteEnabled())
.thenReturn(true);
Mockito.when(myForcedIdDao.findAndResolveByForcedIdWithNoType(Mockito.anyString(),
Mockito.anyList()))
.thenReturn(Collections.singletonList(redView))
.thenReturn(Collections.singletonList(blueView));
// test
Map<String, ResourcePersistentId> map = myHelperService.resolveResourcePersistentIds(
partitionId,
resourceType,
patientIdsToResolve
);
Assertions.assertFalse(map.isEmpty());
for (String id : patientIdsToResolve) {
Assertions.assertTrue(map.containsKey(id));
}
}
@Test
public void resolveResourcePersistenIds_withForcedIdAndDeleteDisabled_returnsMap() {
RequestPartitionId partitionId = RequestPartitionId.allPartitions();
String resourceType = Patient.class.getSimpleName();
List<String> patientIdsToResolve = new ArrayList<>();
patientIdsToResolve.add("RED");
patientIdsToResolve.add("BLUE");
ResourcePersistentId red = new ResourcePersistentId("Patient", new Long(123l));
ResourcePersistentId blue = new ResourcePersistentId("Patient", new Long(456l));
// we will pretend the lookup value is in the cache
Mockito.when(myMemoryCacheService.getThenPutAfterCommit(Mockito.any(MemoryCacheService.CacheEnum.class),
Mockito.anyString(),
Mockito.any(Function.class)))
.thenReturn(red)
.thenReturn(blue);
// test
Map<String, ResourcePersistentId> map = myHelperService.resolveResourcePersistentIds(
partitionId,
resourceType,
patientIdsToResolve
);
Assertions.assertFalse(map.isEmpty());
for (String id : patientIdsToResolve) {
Assertions.assertTrue(map.containsKey(id));
}
Assertions.assertEquals(red, map.get("RED"));
Assertions.assertEquals(blue, map.get("BLUE"));
}
}

View File

@ -10,7 +10,6 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceTable; import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag; import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum; import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test; import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum; import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -4361,8 +4360,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
id = myAllergyIntoleranceDao.read(ai.getIdElement().toUnqualifiedVersionless()).getIdElement(); id = myAllergyIntoleranceDao.read(ai.getIdElement().toUnqualifiedVersionless()).getIdElement();
assertEquals("3", id.getVersionIdPart()); assertEquals("3", id.getVersionIdPart());
} }
} }

View File

@ -0,0 +1,58 @@
package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import com.healthmarketscience.sqlbuilder.BinaryCondition;
import com.healthmarketscience.sqlbuilder.Condition;
import com.healthmarketscience.sqlbuilder.InCondition;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbSchema;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbSpec;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.Mockito;
public class ResourceLinkPredicateBuilderTest {
private ResourceLinkPredicateBuilder myResourceLinkPredicateBuilder;
@BeforeEach
public void init() {
DbSpec spec = new DbSpec();
DbSchema schema = new DbSchema(spec, "schema");
DbTable table = new DbTable(schema, "table");
SearchQueryBuilder sb = Mockito.mock(SearchQueryBuilder.class);
Mockito.when(sb.addTable(Mockito.anyString()))
.thenReturn(table);
myResourceLinkPredicateBuilder = new ResourceLinkPredicateBuilder(
null,
sb,
false
);
}
@Test
public void createEverythingPredicate_withListOfPids_returnsInPredicate() {
Condition condition = myResourceLinkPredicateBuilder.createEverythingPredicate("Patient",
1l, 2l);
Assertions.assertTrue(condition instanceof InCondition);
}
@Test
public void createEverythingPredicate_withSinglePid_returnsInCondition() {
Condition condition = myResourceLinkPredicateBuilder.createEverythingPredicate("Patient",
1l);
Assertions.assertTrue(condition instanceof InCondition);
}
@Test
public void createEverythingPredicate_withNoPids_returnsBinaryCondition() {
Condition condition = myResourceLinkPredicateBuilder.createEverythingPredicate("Patient",
new Long[0]);
Assertions.assertTrue(condition instanceof BinaryCondition);
}
}

View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.mdm.interceptor; package ca.uhn.fhir.jpa.mdm.interceptor;
import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome; import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.entity.MdmLink; import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test; import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
@ -8,23 +9,31 @@ import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4; import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.MdmConstants; import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.IBundleProvider; import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId; import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceOrListParam; import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.ReferenceParam;
import org.elasticsearch.common.collect.Set; import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeableConcept; import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Observation; import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference; import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension; import org.junit.jupiter.api.extension.RegisterExtension;
import org.mockito.Mockito;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext; import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.ContextConfiguration;
import javax.servlet.http.HttpServletRequest;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List; import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat; import static org.hamcrest.MatcherAssert.assertThat;
@ -44,26 +53,52 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
@Autowired @Autowired
private DaoConfig myDaoConfig; private DaoConfig myDaoConfig;
/**
* creates a GoldenPatient
* a number of patients,
* and Observations for each created patient.
*
* Returns a list of stringified ids for the various resources.
*
* Currently, order of returned resources is patientids first,
* observation ids next. But this can be refined as needed.
*
* @param theResourceCount - number of patients to create
* @return
*/
private List<String> createAndLinkNewResources(int theResourceCount) throws InterruptedException {
boolean expansion = myDaoConfig.isAllowMdmExpansion();
myDaoConfig.setAllowMdmExpansion(false);
List<String> createdResourceIds = new ArrayList<>();
List<String> observationIds = new ArrayList<>();
for (int i = 0; i < theResourceCount; i++) {
// create patient
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
createdResourceIds.add(withLatch.getDaoMethodOutcome().getId().getIdPart());
// create observation with patient
Observation observation = createObservationWithSubject(createdResourceIds.get(i));
// we put the observation ids in a separate list so we can
// ensure our returned list is
// patient ids, followed by observation ids
observationIds.add(observation.getIdElement().getIdPart());
}
assertLinkCount(theResourceCount);
// add in our observationIds
createdResourceIds.addAll(observationIds);
myDaoConfig.setAllowMdmExpansion(expansion);
return createdResourceIds;
}
@Test @Test
public void testReferenceExpansionWorks() throws InterruptedException { public void testReferenceExpansionWorks() throws InterruptedException {
myDaoConfig.setAllowMdmExpansion(false); int resourceCount = 4;
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123")); List<String> ids = createAndLinkNewResources(resourceCount);
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch1 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123")); String id = ids.get(0);
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch2 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
MdmHelperR4.OutcomeAndLogMessageWrapper withLatch3 = myMdmHelper.createWithLatch(addExternalEID(buildJanePatient(), "123"));
assertLinkCount(4);
String id = withLatch.getDaoMethodOutcome().getId().getIdPart();
String id1 = withLatch1.getDaoMethodOutcome().getId().getIdPart();
String id2 = withLatch2.getDaoMethodOutcome().getId().getIdPart();
String id3 = withLatch3.getDaoMethodOutcome().getId().getIdPart();
//Create an Observation for each Patient
createObservationWithSubject(id);
createObservationWithSubject(id1);
createObservationWithSubject(id2);
createObservationWithSubject(id3);
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
searchParameterMap.setLoadSynchronous(true); searchParameterMap.setLoadSynchronous(true);
@ -72,6 +107,7 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
searchParameterMap.add(Observation.SP_SUBJECT, referenceOrListParam); searchParameterMap.add(Observation.SP_SUBJECT, referenceOrListParam);
//With MDM Expansion disabled, this should return 1 result. //With MDM Expansion disabled, this should return 1 result.
myDaoConfig.setAllowMdmExpansion(false);
IBundleProvider search = myObservationDao.search(searchParameterMap); IBundleProvider search = myObservationDao.search(searchParameterMap);
assertThat(search.size(), is(equalTo(1))); assertThat(search.size(), is(equalTo(1)));
@ -91,7 +127,78 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
goldenSpMap.add(Observation.SP_SUBJECT, goldenReferenceOrListParam); goldenSpMap.add(Observation.SP_SUBJECT, goldenReferenceOrListParam);
search = myObservationDao.search(goldenSpMap); search = myObservationDao.search(goldenSpMap);
assertThat(search.size(), is(equalTo(4))); assertThat(search.size(), is(equalTo(resourceCount)));
}
@Test
public void testMdmExpansionExpands_idParameter() throws InterruptedException {
int resourceCount = 4;
List<String> expectedIds = createAndLinkNewResources(resourceCount);
String patientId = expectedIds.get(0);
myDaoConfig.setAllowMdmExpansion(true);
SearchParameterMap map = new SearchParameterMap();
TokenOrListParam orListParam = new TokenOrListParam();
TokenParam patientIdParam = new TokenParam();
patientIdParam.setValue(patientId);
patientIdParam.setMdmExpand(true);
orListParam.add(patientIdParam);
map.add("_id", orListParam);
IBundleProvider outcome = myPatientDao.search(map);
Assertions.assertNotNull(outcome);
// we know 4 cause that's how many patients are created
// plus one golden resource
Assertions.assertEquals(resourceCount + 1, outcome.size());
List<String> resourceIds = outcome.getAllResourceIds();
// check the patients - first 4 ids
for (int i = 0; i < resourceIds.size() - 1; i++) {
Assertions.assertTrue(resourceIds.contains(expectedIds.get(i)));
}
}
@Test
public void testMdmExpansionIsSupportedOnEverythingOperation() throws InterruptedException {
int resourceCount = 4;
List<String> expectedIds = createAndLinkNewResources(resourceCount);
String id = expectedIds.get(0);
HashMap<String, String[]> queryParameters = new HashMap<>();
queryParameters.put("_mdm", new String[] { "true" });
HttpServletRequest req = Mockito.mock(HttpServletRequest.class);
RequestDetails theDetails = Mockito.mock(RequestDetails.class);
Mockito.when(theDetails.getParameters())
.thenReturn(queryParameters);
// test
myDaoConfig.setAllowMdmExpansion(true);
IFhirResourceDaoPatient<Patient> dao = (IFhirResourceDaoPatient<Patient>) myPatientDao;
IBundleProvider outcome = dao.patientInstanceEverything(
req,
new IdDt(id),
null,
null,
null,
null,
null,
null,
null,
theDetails
);
// verify return results
// we expect all the linked ids to be returned too
Assertions.assertNotNull(outcome);
// plus 1 for the golden resource
Assertions.assertEquals(expectedIds.size() + 1, outcome.size());
List<String> returnedIds = outcome.getAllResourceIds();
for (String expected : expectedIds) {
Assertions.assertTrue(returnedIds.contains(expected));
}
} }
@Test @Test
@ -116,6 +223,5 @@ public class MdmSearchExpandingInterceptorIT extends BaseMdmR4Test {
observation.setCode(new CodeableConcept().setText("Made for Patient/" + thePatientId)); observation.setCode(new CodeableConcept().setText("Made for Patient/" + thePatientId));
DaoMethodOutcome daoMethodOutcome = myObservationDao.create(observation); DaoMethodOutcome daoMethodOutcome = myObservationDao.create(observation);
return (Observation) daoMethodOutcome.getResource(); return (Observation) daoMethodOutcome.getResource();
} }
} }

View File

@ -80,7 +80,6 @@ public class ResourceIndexedSearchParamsTest {
return retVal; return retVal;
} }
@Test @Test
public void testExtractCompositeStringUniquesValueChains() { public void testExtractCompositeStringUniquesValueChains() {
List<List<String>> partsChoices; List<List<String>> partsChoices;