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Helper class and function to update a location ancestry with lineage tags (#20)
* Add helper class and function to update a location ancestry with lineage tags * Proper variable names Use correct client Remove redundant tag update Update return type * Refactor into smaller functions for easier maintainability Format code * Add tests * Upgrade version * Rename method * Add test packages * Test LocationHelper.java
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4 files changed

+290
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‎pom.xml‎

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@@ -6,7 +6,7 @@
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<groupId>org.smartregister</groupId>
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<artifactId>fhir-common-utils</artifactId>
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<version>1.0.1-SNAPSHOT</version>
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<version>1.0.2-SNAPSHOT</version>
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<distributionManagement>
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<repository>
@@ -26,6 +26,8 @@
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<maven.compiler.target>11</maven.compiler.target>
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<hapi.fhir.base.version>5.5.0</hapi.fhir.base.version>
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<junit.version>4.13.1</junit.version>
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<hapifhir.version>7.4.3</hapifhir.version>
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<mockito.version>5.15.2</mockito.version>
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</properties>
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<dependencies>
@@ -39,6 +41,11 @@
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<artifactId>org.hl7.fhir.r4</artifactId>
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<version>5.4.10</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-client</artifactId>
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<version>7.4.3</version>
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</dependency>
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<!-- Test Dependencies-->
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<dependency>
@@ -47,6 +54,11 @@
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<scope>test</scope>
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<version>${junit.version}</version>
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</dependency>
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<dependency>
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<groupId>org.mockito</groupId>
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<artifactId>mockito-core</artifactId>
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<version>${mockito.version}</version>
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<scope>test</scope>
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</dependency>
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</dependencies>
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</project>

‎src/main/java/org/smartregister/helpers/LocationHelper.java‎

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@@ -0,0 +1,194 @@
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package org.smartregister.helpers;
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import java.util.ArrayList;
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import java.util.LinkedList;
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import java.util.List;
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import java.util.Queue;
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import java.util.stream.Collectors;
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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.Coding;
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import org.hl7.fhir.r4.model.Location;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.UriType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.smartregister.utils.Constants;
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import com.google.common.annotations.VisibleForTesting;
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import ca.uhn.fhir.rest.api.SearchStyleEnum;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.client.impl.GenericClient;
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import ca.uhn.fhir.rest.gclient.IQuery;
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import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
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public class LocationHelper {
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private static final Logger logger = LoggerFactory.getLogger(LocationHelper.class);
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// Custom class to pair a Location with its lineage ancestors
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static class LocationWithTags {
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Location location;
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List<String> ancestorIds;
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public LocationWithTags(Location location, List<String> ancestorIds) {
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this.location = location;
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this.ancestorIds = ancestorIds;
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}
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}
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public static Location updateLocationLineage(IGenericClient client, String locationId) {
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Queue<LocationWithTags> locationsQueue = new LinkedList<>();
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Location location = client.read().resource(Location.class).withId(locationId).execute();
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List<String> ancestorIds = getParentLocationLineage(client, location);
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locationsQueue.add(new LocationWithTags(location, ancestorIds));
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while (!locationsQueue.isEmpty()) {
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LocationWithTags currentLocationWithTags = locationsQueue.poll();
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Location currentLocation = currentLocationWithTags.location;
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String currentLocationId = currentLocation.getIdElement().getIdPart();
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updateLocationTags(client, currentLocation, currentLocationWithTags.ancestorIds);
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List<Location> childLocations = fetchChildLocations(client, currentLocationId);
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for (Location childLocation : childLocations) {
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locationsQueue.add(
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new LocationWithTags(
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childLocation,
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new ArrayList<>(currentLocationWithTags.ancestorIds)));
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}
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}
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return location;
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}
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@VisibleForTesting
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protected static List<String> getParentLocationLineage(
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IGenericClient client, Location location) {
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if (!location.hasPartOf() || !location.getPartOf().hasReference()) {
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return new ArrayList<>();
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}
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String parentLocationId = location.getPartOf().getReferenceElement().getIdPart();
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Location parentLocation =
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client.read().resource(Location.class).withId(parentLocationId).execute();
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List<String> ancestorIds =
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parentLocation.getMeta().getTag().stream()
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.filter(
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tag ->
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Constants.DEFAULT_LOCATION_LINEAGE_TAG_URL.equals(
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tag.getSystem()))
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.map(Coding::getCode)
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.collect(Collectors.toList());
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ancestorIds.add(parentLocationId);
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client.update().resource(location).execute();
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return ancestorIds;
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}
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@VisibleForTesting
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protected static void updateLocationTags(
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IGenericClient client, Location location, List<String> ancestorIds) {
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logger.info("Adding lineage tags to Location Id : {}", location.getIdElement().getIdPart());
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List<Coding> newTags =
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location.getMeta().getTag().stream()
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.filter(
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tag ->
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!Constants.DEFAULT_LOCATION_LINEAGE_TAG_URL.equals(
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tag.getSystem()))
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.collect(Collectors.toList());
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for (String tag : ancestorIds) {
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newTags.add(
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new Coding()
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.setSystem(Constants.DEFAULT_LOCATION_LINEAGE_TAG_URL)
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.setCode(tag));
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}
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location.getMeta().setTag(newTags);
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client.update().resource(location).execute();
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}
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private static List<Location> fetchChildLocations(IGenericClient client, String locationId) {
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IQuery<IBaseBundle> query =
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client.search()
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.forResource(Location.class)
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.where(
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new ReferenceClientParam(Location.SP_PARTOF)
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.hasAnyOfIds(locationId));
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Bundle childLocationBundle =
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query.usingStyle(SearchStyleEnum.POST)
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.count(100)
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.returnBundle(Bundle.class)
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.execute();
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if (childLocationBundle != null) {
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fetchAllBundlePagesAndInject(client, childLocationBundle);
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return childLocationBundle.getEntry().stream()
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.map(Bundle.BundleEntryComponent::getResource)
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.filter(resource -> resource instanceof Location)
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.map(resource -> (Location) resource)
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.collect(Collectors.toList());
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}
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return new ArrayList<>();
139+
}
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/**
142+
* This is a recursive function which updates the result bundle with results of all pages
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* whenever there's an entry for Bundle.LINK_NEXT
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*
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* @param fhirClient the Generic FHIR Client instance
146+
* @param resultBundle the result bundle from the first request
147+
*/
148+
public static void fetchAllBundlePagesAndInject(
149+
IGenericClient fhirClient, Bundle resultBundle) {
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if (resultBundle.getLink(Bundle.LINK_NEXT) != null) {
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153+
cleanUpBundlePaginationNextLinkServerBaseUrl((GenericClient) fhirClient, resultBundle);
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Bundle pageResultBundle = fhirClient.loadPage().next(resultBundle).execute();
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resultBundle.getEntry().addAll(pageResultBundle.getEntry());
158+
resultBundle.setLink(pageResultBundle.getLink());
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160+
fetchAllBundlePagesAndInject(fhirClient, resultBundle);
161+
}
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163+
resultBundle.setLink(
164+
resultBundle.getLink().stream()
165+
.filter(
166+
bundleLinkComponent ->
167+
!Bundle.LINK_NEXT.equals(bundleLinkComponent.getRelation()))
168+
.collect(Collectors.toList()));
169+
resultBundle.getMeta().setLastUpdated(resultBundle.getMeta().getLastUpdated());
170+
}
171+
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public static void cleanUpBundlePaginationNextLinkServerBaseUrl(
173+
GenericClient fhirClient, Bundle resultBundle) {
174+
String cleanUrl =
175+
cleanHapiPaginationLinkBaseUrl(
176+
resultBundle.getLink(Bundle.LINK_NEXT).getUrl(), fhirClient.getUrlBase());
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resultBundle
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.getLink()
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.replaceAll(
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bundleLinkComponent ->
181+
Bundle.LINK_NEXT.equals(bundleLinkComponent.getRelation())
182+
? new Bundle.BundleLinkComponent(
183+
new StringType(Bundle.LINK_NEXT),
184+
new UriType(cleanUrl))
185+
: bundleLinkComponent);
186+
}
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188+
public static String cleanHapiPaginationLinkBaseUrl(
189+
String originalUrl, String fhirServerBaseUrl) {
190+
return originalUrl.indexOf('?') > -1
191+
? fhirServerBaseUrl + originalUrl.substring(originalUrl.indexOf('?'))
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: fhirServerBaseUrl;
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}
194+
}

‎src/main/java/org/smartregister/utils/Constants.java‎

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Original file line numberDiff line numberDiff line change
@@ -49,4 +49,5 @@ public interface Constants {
4949
String CODE = "code";
5050
String MEMBER = "member";
5151
String GROUP = "Group";
52+
String DEFAULT_LOCATION_LINEAGE_TAG_URL = "http://smartregister.org/CodeSystem/location-lineage";
5253
}

‎src/test/java/org/smartregister/helpers/LocationHelperTest.java‎

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package org.smartregister.helpers;
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3+
import static org.junit.Assert.assertEquals;
4+
import static org.junit.Assert.assertNotNull;
5+
import static org.mockito.Mockito.mock;
6+
import static org.mockito.Mockito.times;
7+
import static org.mockito.Mockito.verify;
8+
9+
import java.util.Collections;
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11+
import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Location;
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import org.junit.Before;
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import org.junit.Test;
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import org.mockito.Mockito;
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import org.mockito.MockitoAnnotations;
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import org.mockito.internal.stubbing.defaultanswers.ReturnsDeepStubs;
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import ca.uhn.fhir.rest.api.SearchStyleEnum;
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import ca.uhn.fhir.rest.client.api.IGenericClient;
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import ca.uhn.fhir.rest.gclient.ICriterion;
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import ca.uhn.fhir.rest.gclient.IQuery;
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import ca.uhn.fhir.rest.gclient.IRead;
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import ca.uhn.fhir.rest.gclient.IReadExecutable;
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import ca.uhn.fhir.rest.gclient.IReadTyped;
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import ca.uhn.fhir.rest.gclient.IUntypedQuery;
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public class LocationHelperTest {
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IGenericClient client;
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@Before
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public void setUp() {
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MockitoAnnotations.initMocks(this);
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client = mock(IGenericClient.class, new ReturnsDeepStubs());
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}
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@Test
40+
public void testUpdateLocationLineage() {
41+
Location location = new Location();
42+
location.setId("location1");
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location.setPartOf(null);
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Location childLocation = new Location();
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childLocation.setId("location2");
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childLocation.setPartOf(new org.hl7.fhir.r4.model.Reference("Location/location1"));
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Bundle childLocationBundle = new Bundle();
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Bundle.BundleEntryComponent entry = new Bundle.BundleEntryComponent();
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entry.setResource(childLocation);
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childLocationBundle.setEntry(Collections.singletonList(entry));
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IRead iReadMock = mock(IRead.class);
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IReadTyped<IBaseResource> iReadTypedMock = mock(IReadTyped.class);
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IReadExecutable<Location> iReadExecutableMock = mock(IReadExecutable.class);
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IUntypedQuery<Location> iUntypedQueryMock = mock(IUntypedQuery.class);
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IQuery<Location> iQueryMock = mock(IQuery.class);
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Mockito.doReturn(iReadMock).when(client).read();
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Mockito.doReturn(iReadTypedMock).when(iReadMock).resource(Location.class);
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Mockito.doReturn(iReadExecutableMock).when(iReadTypedMock).withId("location1");
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Mockito.doReturn(location).when(iReadExecutableMock).execute();
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Mockito.doReturn(iUntypedQueryMock).when(client).search();
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Mockito.doReturn(iQueryMock).when(iUntypedQueryMock).forResource(Location.class);
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Mockito.doReturn(iQueryMock).when(iQueryMock).where(Mockito.any(ICriterion.class));
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Mockito.doReturn(iQueryMock).when(iQueryMock).usingStyle(SearchStyleEnum.POST);
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Mockito.doReturn(iQueryMock).when(iQueryMock).count(100);
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Mockito.doReturn(iQueryMock).when(iQueryMock).returnBundle(Bundle.class);
72+
Mockito.doReturn(childLocationBundle, (Bundle) null).when(iQueryMock).execute();
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Location result = LocationHelper.updateLocationLineage(client, "location1");
75+
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assertNotNull(result);
77+
assertEquals("location1", result.getIdElement().getIdPart());
78+
verify(client, times(1)).read();
79+
verify(client, times(2)).search();
80+
}
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}

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