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Optimize location hierarchy #87

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Optimize location hierarchy #87

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de7868b
Add extra checks on AdminLevel filters
lincmba Sep 24, 2024
ec06253
Optimize non identifier request
lincmba Sep 24, 2024
77363cf
Optimize further:
lincmba Sep 25, 2024
d5fd24f
Optimize further:
lincmba Sep 25, 2024
fd7909a
Add tests
lincmba Sep 25, 2024
f8a344a
Functions reverted to work as before
lincmba Oct 1, 2024
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7 changes: 7 additions & 0 deletions plugins/src/main/java/org/smartregister/fhir/gateway/plugins/CacheHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ public enum CacheHelper {

Cache<String, String> stringCache;

Cache<String, List<String>> listStringCache;

CacheHelper() {
cache =
Caffeine.newBuilder()
Expand All @@ -42,6 +44,11 @@ public enum CacheHelper {
.expireAfterWrite(getCacheExpiryDurationInSeconds(), TimeUnit.SECONDS)
.maximumSize(DEFAULT_CACHE_SIZE)
.build();
listStringCache =
Caffeine.newBuilder()
.expireAfterWrite(getCacheExpiryDurationInSeconds(), TimeUnit.SECONDS)
.maximumSize(DEFAULT_CACHE_SIZE)
.build();
}

private int getCacheExpiryDurationInSeconds() {
Expand Down
138 changes: 75 additions & 63 deletions ...src/main/java/org/smartregister/fhir/gateway/plugins/LocationHierarchyEndpointHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,12 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Set;
import java.util.stream.Collectors;

import javax.annotation.Nullable;
Expand All @@ -16,8 +20,6 @@
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r4.model.Binary;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.ListResource;
import org.hl7.fhir.r4.model.Location;
Expand Down Expand Up @@ -86,7 +88,9 @@ public List<LocationHierarchy> getLocationHierarchies(
List<String> preFetchAdminLevels,
List<String> postFetchAdminLevels,
Boolean filterInventory) {
return locationIds.parallelStream()
Set<String> uniqueLocationIds = new HashSet<>(locationIds);

return uniqueLocationIds.parallelStream()
.map(
locationId ->
getLocationHierarchy(
Expand All @@ -109,7 +113,7 @@ public LocationHierarchy getLocationHierarchyCore(
if (location != null) {
logger.info("Building Location Hierarchy of Location Id : {}", locationId);

List<Location> descendants = getDescendants(locationId, location, preFetchAdminLevels);
List<Location> descendants = getDescendants(locationId, preFetchAdminLevels, location);
if (filterInventory) {
descendants = filterLocationsByInventory(descendants);
}
Expand All @@ -136,12 +140,12 @@ public List<Location> getLocationHierarchyLocations(
List<Location> descendants;

if (CacheHelper.INSTANCE.skipCache()) {
descendants = getDescendants(locationId, parentLocation, preFetchAdminLevels);
descendants = getDescendants(locationId, preFetchAdminLevels, parentLocation);
} else {
descendants =
CacheHelper.INSTANCE.locationListCache.get(
locationId,
key -> getDescendants(locationId, parentLocation, preFetchAdminLevels));
key -> getDescendants(locationId, preFetchAdminLevels, parentLocation));
}
if (filterInventory) {
descendants = filterLocationsByInventory(descendants);
Expand All @@ -150,7 +154,7 @@ public List<Location> getLocationHierarchyLocations(
}

public List<Location> getDescendants(
String locationId, Location parentLocation, List<String> adminLevels) {
String locationId, List<String> adminLevels, Location parentLocation) {
IQuery<IBaseBundle> query =
getFhirClientForR4()
.search()
Expand All @@ -172,28 +176,35 @@ public List<Location> getDescendants(
adminLevelArray));
}

Bundle childLocationBundle =
query.usingStyle(SearchStyleEnum.POST).returnBundle(Bundle.class).execute();
Queue<String> locationQueue = new LinkedList<>();
locationQueue.add(locationId);

List<Location> allLocations = Collections.synchronizedList(new ArrayList<>());
if (parentLocation != null) {
allLocations.add(parentLocation);
}

if (childLocationBundle != null) {

childLocationBundle.getEntry().parallelStream()
.forEach(
childLocation -> {
Location childLocationEntity =
(Location) childLocation.getResource();
allLocations.add(childLocationEntity);
allLocations.addAll(
getDescendants(
childLocationEntity.getIdElement().getIdPart(),
null,
adminLevels));
});
while (!locationQueue.isEmpty()) {
String currentLocationId = locationQueue.poll();
Bundle childLocationBundle =
query.where(
new ReferenceClientParam(Location.SP_PARTOF)
.hasAnyOfIds(currentLocationId))
.usingStyle(SearchStyleEnum.POST)
.returnBundle(Bundle.class)
.execute();

if (childLocationBundle != null) {
childLocationBundle.getEntry().parallelStream()
.forEach(
childLocation -> {
Location childLocationEntity =
(Location) childLocation.getResource();
allLocations.add(childLocationEntity);
locationQueue.add(
childLocationEntity.getIdElement().getIdPart());
});
}
}

return allLocations;
Expand Down Expand Up @@ -259,15 +270,9 @@ public Bundle handleNonIdentifierRequest(
return getPaginatedLocations(request, selectedSyncLocations);

} else {
List<Location> locations =
practitionerDetailsEndpointHelper
.getPractitionerDetailsByKeycloakId(practitionerId)
.getFhirPractitionerDetails()
.getLocations();
List<String> locationIds = new ArrayList<>();
for (Location location : locations) {
locationIds.add(location.getIdElement().getIdPart());
}
List<String> locationIds =
practitionerDetailsEndpointHelper.getPractitionerLocationIdsByByKeycloakId(
practitionerId);
return getPaginatedLocations(request, locationIds);
}

Expand All @@ -287,11 +292,15 @@ public Bundle handleNonIdentifierRequest(
.collect(Collectors.toList());
return Utils.createBundle(resourceList);
} else {
List<String> locationIds =
practitionerDetailsEndpointHelper.getPractitionerLocationIdsByByKeycloakId(
practitionerId);
List<LocationHierarchy> locationHierarchies =
practitionerDetailsEndpointHelper
.getPractitionerDetailsByKeycloakId(practitionerId)
.getFhirPractitionerDetails()
.getLocationHierarchyList();
getLocationHierarchies(
locationIds,
preFetchAdminLevels,
postFetchAdminLevels,
filterInventory);
List<Resource> resourceList =
locationHierarchies.stream()
.map(locationHierarchy -> (Resource) locationHierarchy)
Expand Down Expand Up @@ -358,6 +367,7 @@ public Bundle getPaginatedLocations(HttpServletRequest request, List<String> loc
List<String> postFetchAdminLevels =
generateAdminLevels(administrativeLevelMin, administrativeLevelMax);
Map<String, String[]> parameters = new HashMap<>(request.getParameterMap());
Set<String> uniqueLocationIds = new HashSet<>(locationIds);

int count =
pageSize != null
Expand All @@ -370,18 +380,18 @@ public Bundle getPaginatedLocations(HttpServletRequest request, List<String> loc

int start = Math.max(0, (page - 1)) * count;

List<Resource> resourceLocations = new ArrayList<>();
for (String identifier : locationIds) {
Location parentLocation = getLocationById(identifier);
List<Location> locations =
getLocationHierarchyLocations(
identifier,
parentLocation,
preFetchAdminLevels,
postFetchAdminLevels,
filterInventory);
resourceLocations.addAll(locations);
}
List<Resource> resourceLocations =
uniqueLocationIds.parallelStream()
.flatMap(
identifier ->
getLocationHierarchyLocations(
identifier,
getLocationById(identifier),
preFetchAdminLevels,
postFetchAdminLevels,
filterInventory)
.stream())
.collect(Collectors.toList());
int totalEntries = resourceLocations.size();

int end = Math.min(start + count, resourceLocations.size());
Expand Down Expand Up @@ -443,23 +453,25 @@ public List<String> generateAdminLevels(

public List<Location> filterLocationsByAdminLevels(
List<Location> locations, List<String> postFetchAdminLevels) {
if (postFetchAdminLevels == null) {

if (postFetchAdminLevels == null || postFetchAdminLevels.isEmpty()) {
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Resolves bug of filtering out all locations when adminlevels is not provided/is empty

return locations;
}
List<Location> allLocations = new ArrayList<>();
for (Location location : locations) {
for (CodeableConcept codeableConcept : location.getType()) {
List<Coding> codings = codeableConcept.getCoding();
for (Coding coding : codings) {
if (coding.getSystem().equals(Constants.DEFAULT_ADMIN_LEVEL_TYPE_URL)) {
if (postFetchAdminLevels.contains(coding.getCode())) {
allLocations.add(location);
}
}
}
}
}
return allLocations;

return locations.stream()
.filter(
location ->
location.getType().stream()
.flatMap(
codeableConcept ->
codeableConcept.getCoding().stream())
.anyMatch(
coding ->
Constants.DEFAULT_ADMIN_LEVEL_TYPE_URL
.equals(coding.getSystem())
&& postFetchAdminLevels.contains(
coding.getCode())))
.collect(Collectors.toList());
}

public List<Location> filterLocationsByInventory(List<Location> locations) {
Expand Down
79 changes: 74 additions & 5 deletions ...c/main/java/org/smartregister/fhir/gateway/plugins/PractitionerDetailsEndpointHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -251,6 +251,70 @@ public PractitionerDetails getPractitionerDetailsByPractitioner(Practitioner pra
return practitionerDetails;
}

public List<String> getPractitionerLocationIdsByByKeycloakId(String keycloakUUID) {
logger.info("Searching for Practitioner with user id: " + keycloakUUID);
Practitioner practitioner = getPractitionerByIdentifier(keycloakUUID);
List<String> locationIds = new ArrayList<>();

if (practitioner != null) {
String practitionerId = getPractitionerIdentifier(practitioner);
if (CacheHelper.INSTANCE.skipCache()) {
locationIds = getPractitionerLocationIdsByByKeycloakIdCore(practitionerId);
} else {
locationIds =
CacheHelper.INSTANCE.listStringCache.get(
keycloakUUID,
key ->
getPractitionerLocationIdsByByKeycloakIdCore(
practitionerId));
}

} else {
logger.error("Practitioner with KC identifier : " + keycloakUUID + " not found");
}
return locationIds;
}

@VisibleForTesting
protected List<String> getPractitionerLocationIdsByByKeycloakIdCore(String practitionerId) {

logger.info("Searching for CareTeams with Practitioner Id: " + practitionerId);
Bundle careTeams = getCareTeams(practitionerId);
List<CareTeam> careTeamsList = mapBundleToCareTeams(careTeams);

logger.info(
"Searching for Organizations tied to CareTeams list of size : "
+ careTeamsList.size());
Set<String> careTeamManagingOrganizationIds =
getManagingOrganizationsOfCareTeamIds(careTeamsList);

List<PractitionerRole> practitionerRoleList =
getPractitionerRolesByPractitionerId(practitionerId);
logger.info("Practitioner Roles fetched: " + practitionerRoleList.size());

Set<String> practitionerOrganizationIds =
getOrganizationIdsByPractitionerRoles(practitionerRoleList);

Set<String> organizationIds =
Stream.concat(
careTeamManagingOrganizationIds.stream(),
practitionerOrganizationIds.stream())
.collect(Collectors.toSet());

logger.info("Searching for locations by organizations: " + organizationIds.size());

Bundle organizationAffiliationsBundle =
getOrganizationAffiliationsByOrganizationIdsBundle(organizationIds);

List<OrganizationAffiliation> organizationAffiliations =
mapBundleToOrganizationAffiliation(organizationAffiliationsBundle);

List<String> locationIds =
getLocationIdsByOrganizationAffiliations(organizationAffiliations);

return locationIds;
}

public PractitionerDetails getPractitionerDetailsByPractitionerCore(
String practitionerId, Practitioner practitioner) {

Expand Down Expand Up @@ -367,12 +431,14 @@ public static <T> Predicate<T> distinctByKey(Function<? super T, ?> uniqueKeyExt
return t -> seen.add(uniqueKeyExtractor.apply(t));
}

private List<PractitionerRole> getPractitionerRolesByPractitionerId(String practitionerId) {
@VisibleForTesting
protected List<PractitionerRole> getPractitionerRolesByPractitionerId(String practitionerId) {
Bundle practitionerRoles = getPractitionerRoles(practitionerId);
return mapBundleToPractitionerRolesWithOrganization(practitionerRoles);
}

private Set<String> getOrganizationIdsByPractitionerRoles(
@VisibleForTesting
protected Set<String> getOrganizationIdsByPractitionerRoles(
List<PractitionerRole> practitionerRoles) {
return practitionerRoles.stream()
.filter(PractitionerRole::hasOrganization)
Expand Down Expand Up @@ -427,7 +493,8 @@ protected List<CareTeam> getCareTeamsByOrganizationIds(List<String> organization
.collect(Collectors.toList());
}

private Bundle getCareTeams(String practitionerId) {
@VisibleForTesting
protected Bundle getCareTeams(String practitionerId) {
return getFhirClientForR4()
.search()
.forResource(CareTeam.class)
Expand Down Expand Up @@ -544,7 +611,8 @@ protected Set<String> getManagingOrganizationsOfCareTeamIds(List<CareTeam> careT
.collect(Collectors.toSet());
}

private List<CareTeam> mapBundleToCareTeams(Bundle careTeams) {
@VisibleForTesting
protected List<CareTeam> mapBundleToCareTeams(Bundle careTeams) {
return careTeams != null
? careTeams.getEntry().stream()
.map(bundleEntryComponent -> (CareTeam) bundleEntryComponent.getResource())
Expand All @@ -569,7 +637,8 @@ private List<Group> mapBundleToGroups(Bundle groupsBundle) {
: Collections.emptyList();
}

private List<OrganizationAffiliation> mapBundleToOrganizationAffiliation(
@VisibleForTesting
protected List<OrganizationAffiliation> mapBundleToOrganizationAffiliation(
Bundle organizationAffiliationBundle) {
return organizationAffiliationBundle != null
? organizationAffiliationBundle.getEntry().stream()
Expand Down
3 changes: 1 addition & 2 deletions ...test/java/org/smartregister/fhir/gateway/plugins/LocationHierarchyEndpointHelperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -279,12 +279,11 @@ public void testGetDescendantsWithAdminLevelFiltersReturnsLocationsWithinAdminLe
Mockito.doReturn(queryMock).when(queryMock).and(any(ICriterion.class));
Mockito.doReturn(queryMock).when(queryMock).usingStyle(SearchStyleEnum.POST);
Mockito.doReturn(queryMock).when(queryMock).returnBundle(Bundle.class);

Mockito.doReturn(firstBundleMock, secondBundleMock).when(queryMock).execute();

List<Location> descendants =
locationHierarchyEndpointHelper.getDescendants(
locationId, parentLocation, adminLevels);
locationId, adminLevels, parentLocation);

Assert.assertNotNull(descendants);
Assert.assertEquals(2, descendants.size());
Expand Down
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