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committedMay 10, 2024·
Refactor FENCE mapping methods to FenceMappingUtility class
This commit includes the extraction of FENCE mapping methods from FENCEAuthenticationService to a new singleton class named FenceMappingUtility. This is an attempt to reduce the overhead of the FENCEAuthenticationService upon a user's initial login.
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+98
-69
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4 files changed

+98
-69
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‎pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/rest/StudyAccessService.java

+5-1
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
import edu.harvard.hms.dbmi.avillach.auth.data.entity.Role;
44
import edu.harvard.hms.dbmi.avillach.auth.data.repository.RoleRepository;
55
import edu.harvard.hms.dbmi.avillach.auth.service.auth.FENCEAuthenticationService;
6+
import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
67
import io.swagger.annotations.Api;
78
import io.swagger.annotations.ApiOperation;
89
import io.swagger.annotations.ApiParam;
@@ -40,6 +41,9 @@ public class StudyAccessService {
4041
@Inject
4142
FENCEAuthenticationService fenceAuthenticationService;
4243

44+
@Inject
45+
private FenceMappingUtility fenceMappingUtility;
46+
4347
@ApiOperation(value = "POST a single study and it creates the role, privs, and rules for it, requires SUPER_ADMIN role")
4448
@Transactional
4549
@POST
@@ -55,7 +59,7 @@ public Response addStudyAccess(@ApiParam(value="The Study Identifier of the new
5559
Map fenceMappingForStudy = null;
5660

5761
try {
58-
Map<String, Map> fenceMapping = fenceAuthenticationService.getFENCEMapping();
62+
Map<String, Map> fenceMapping = fenceMappingUtility.getFENCEMapping();
5963
if (fenceMapping == null) {
6064
throw new Exception("Fence mapping is null");
6165
}

‎pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java

+6-66
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@
2020

2121
import com.fasterxml.jackson.core.JsonProcessingException;
2222
import com.fasterxml.jackson.databind.node.ObjectNode;
23+
import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
2324
import org.apache.commons.lang3.StringUtils;
2425
import org.apache.http.Header;
2526
import org.apache.http.entity.StringEntity;
@@ -66,6 +67,9 @@ public class FENCEAuthenticationService {
6667
@Inject
6768
AuthUtils authUtil;
6869

70+
@Inject
71+
private FenceMappingUtility fenceMappingUtility;
72+
6973
private Application picSureApp;
7074
private Connection fenceConnection;
7175

@@ -242,7 +246,7 @@ public Response getFENCEProfile(String callback_url, Map<String, String> authReq
242246

243247
private void createAndUpsertRole(String access_role_name, User current_user) throws IOException {
244248
logger.debug("createAndUpsertRole() starting...");
245-
Map projectMetadata = getFenceMappingByAuthZ().get(access_role_name);
249+
Map projectMetadata = fenceMappingUtility.getFenceMappingByAuthZ().get(access_role_name);
246250

247251
if (projectMetadata == null) {
248252
logger.error("getFENCEProfile() -> createAndUpsertRole could not find study in FENCE mapping SKIPPING: {}", access_role_name);
@@ -1127,77 +1131,13 @@ private Map getFENCEMappingforProjectAndConsent(String projectId, String consent
11271131
String consentVal = (consent_group != null && consent_group != "") ? projectId + "." + consent_group : projectId;
11281132
logger.info("getFENCEMappingforProjectAndConsent() looking up {}", consentVal);
11291133

1130-
Object projectMetadata = getFENCEMapping().get(consentVal);
1134+
Object projectMetadata = fenceMappingUtility.getFENCEMapping().get(consentVal);
11311135
if( projectMetadata instanceof Map) {
11321136
return (Map)projectMetadata;
11331137
} else if (projectMetadata != null) {
11341138
logger.info("getFENCEMappingforProjectAndConsent() Obj instance of " + projectMetadata.getClass().getCanonicalName());
11351139
}
11361140
return null;
11371141
}
1138-
1139-
public Map<String, Map> getFENCEMapping(){
1140-
if(_projectMap == null || _projectMap.isEmpty()) {
1141-
try {
1142-
List<Map> projects = loadBioDataCatalystFenceMappingData();
1143-
_projectMap = new HashMap<String, Map>(projects.size());
1144-
for(Map project : projects) {
1145-
String consentVal = (project.get("consent_group_code") != null && project.get("consent_group_code") != "") ?
1146-
"" + project.get("study_identifier") + "." + project.get("consent_group_code") :
1147-
"" + project.get("study_identifier");
1148-
logger.debug("adding study " + consentVal);
1149-
_projectMap.put(consentVal, project);
1150-
}
1151-
1152-
} catch (Exception e) {
1153-
logger.error("getFENCEMapping: Non-fatal error parsing fence_mapping.json: "+JAXRSConfiguration.templatePath, e);
1154-
return new HashMap<String,Map>();
1155-
}
1156-
}
1157-
1158-
return _projectMap;
1159-
}
1160-
1161-
1162-
/**
1163-
* This method is used to improve the performance for looking up the FENCE project metadata by the authZ value.
1164-
*
1165-
* @return Map<String, Map> - a map of FENCE project metadata by the authZ value
1166-
* @throws IOException - if there is an issue parsing or finding the fence_mapping.json file
1167-
*/
1168-
private Map<String, Map> getFenceMappingByAuthZ() throws IOException {
1169-
if (fenceMappingByAuthZ == null || fenceMappingByAuthZ.isEmpty()) {
1170-
List<Map> projects = loadBioDataCatalystFenceMappingData();
1171-
fenceMappingByAuthZ = new HashMap<>(projects.size());
1172-
if (projects.size() == 1 && projects.get(0).isEmpty()) {
1173-
logger.error("getFENCEMapping: FENCE mapping data is empty");
1174-
throw new IOException("FENCE mapping data is empty");
1175-
}
1176-
1177-
for (Map project : projects) {
1178-
fenceMappingByAuthZ.put(project.get("authZ").toString().replace("\\/", "/"), project);
1179-
}
1180-
}
1181-
1182-
return fenceMappingByAuthZ;
1183-
}
1184-
1185-
private List<Map> loadBioDataCatalystFenceMappingData() {
1186-
Map fenceMapping = null;
1187-
List<Map> projects = null;
1188-
try {
1189-
fenceMapping = JAXRSConfiguration.objectMapper.readValue(
1190-
new File(String.join(File.separator,
1191-
new String[] {JAXRSConfiguration.templatePath ,"fence_mapping.json"}))
1192-
, Map.class);
1193-
1194-
projects = (List<Map>) fenceMapping.get("bio_data_catalyst");
1195-
logger.debug("getFENCEMapping: found FENCE mapping with {} entries", projects.size());
1196-
} catch (Exception e) {
1197-
logger.error("loadFenceMappingData: Non-fatal error parsing fence_mapping.json: {}", JAXRSConfiguration.templatePath, e);
1198-
return Collections.singletonList(new HashMap());
1199-
}
1200-
return projects;
1201-
}
12021142

12031143
}

‎pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avillach/auth/utils/FenceMappingUtility.java

+81
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,81 @@
1+
package edu.harvard.hms.dbmi.avillach.auth.utils;
2+
3+
import edu.harvard.hms.dbmi.avillach.auth.JAXRSConfiguration;
4+
import org.slf4j.Logger;
5+
import org.slf4j.LoggerFactory;
6+
7+
import javax.annotation.PostConstruct;
8+
import javax.ejb.Singleton;
9+
import javax.ejb.Startup;
10+
import java.io.File;
11+
import java.io.IOException;
12+
import java.util.Collections;
13+
import java.util.HashMap;
14+
import java.util.List;
15+
import java.util.Map;
16+
17+
@Singleton
18+
@Startup
19+
public class FenceMappingUtility {
20+
21+
private final Logger logger = LoggerFactory.getLogger(this.getClass());
22+
private Map<String, Map> _projectMap;
23+
private Map<String, Map> fenceMappingByAuthZ;
24+
25+
@PostConstruct
26+
public void init() {
27+
try {
28+
initializeFENCEMapping();
29+
initializeFenceMappingByAuthZ();
30+
} catch (IOException e) {
31+
// Handle exceptions appropriately
32+
logger.error("Error initializing FENCE mappings", e);
33+
}
34+
}
35+
36+
private void initializeFENCEMapping() throws IOException {
37+
List<Map> projects = loadBioDataCatalystFenceMappingData();
38+
_projectMap = new HashMap<>(projects.size());
39+
for (Map project : projects) {
40+
String consentVal = (project.get("consent_group_code") != null && project.get("consent_group_code") != "") ?
41+
project.get("study_identifier") + "." + project.get("consent_group_code") :
42+
project.get("study_identifier").toString();
43+
_projectMap.put(consentVal, project);
44+
}
45+
}
46+
47+
private void initializeFenceMappingByAuthZ() throws IOException {
48+
List<Map> projects = loadBioDataCatalystFenceMappingData();
49+
fenceMappingByAuthZ = new HashMap<>(projects.size());
50+
for (Map project : projects) {
51+
fenceMappingByAuthZ.put(project.get("authZ").toString().replace("\\/", "/"), project);
52+
}
53+
}
54+
55+
public Map<String, Map> getFENCEMapping() {
56+
return _projectMap;
57+
}
58+
59+
public Map<String, Map> getFenceMappingByAuthZ() {
60+
return fenceMappingByAuthZ;
61+
}
62+
63+
private List<Map> loadBioDataCatalystFenceMappingData() {
64+
Map fenceMapping = null;
65+
List<Map> projects = null;
66+
try {
67+
fenceMapping = JAXRSConfiguration.objectMapper.readValue(
68+
new File(String.join(File.separator,
69+
new String[] {JAXRSConfiguration.templatePath ,"fence_mapping.json"}))
70+
, Map.class);
71+
72+
projects = (List<Map>) fenceMapping.get("bio_data_catalyst");
73+
logger.debug("getFENCEMapping: found FENCE mapping with {} entries", projects.size());
74+
} catch (Exception e) {
75+
logger.error("loadFenceMappingData: Non-fatal error parsing fence_mapping.json: {}", JAXRSConfiguration.templatePath, e);
76+
return Collections.singletonList(new HashMap());
77+
}
78+
return projects;
79+
}
80+
81+
}

‎pic-sure-auth-services/src/test/java/edu/harvard/hms/dbmi/avillach/StudyAccessServiceTest.java

+6-2
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
import edu.harvard.hms.dbmi.avillach.auth.data.repository.RoleRepository;
44
import edu.harvard.hms.dbmi.avillach.auth.rest.StudyAccessService;
55
import edu.harvard.hms.dbmi.avillach.auth.service.auth.FENCEAuthenticationService;
6+
import edu.harvard.hms.dbmi.avillach.auth.utils.FenceMappingUtility;
67
import org.junit.Before;
78
import org.junit.Test;
89
import org.mockito.InjectMocks;
@@ -25,6 +26,9 @@ public class StudyAccessServiceTest {
2526
@Mock
2627
private FENCEAuthenticationService fenceAuthenticationService;
2728

29+
@Mock
30+
private FenceMappingUtility fenceMappingUtility;
31+
2832
@Before
2933
public void init() {
3034
MockitoAnnotations.initMocks(this);
@@ -42,7 +46,7 @@ public void testAddStudyAccessWithBlankIdentifier() {
4246
@Test
4347
public void testAddStudyAccess() {
4448
String studyIdentifier = "testStudy";
45-
when(fenceAuthenticationService.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, Map.of(StudyAccessService.STUDY_IDENTIFIER, studyIdentifier,StudyAccessService.CONSENT_GROUP_CODE, "")));
49+
when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, Map.of(StudyAccessService.STUDY_IDENTIFIER, studyIdentifier,StudyAccessService.CONSENT_GROUP_CODE, "")));
4650
when(fenceAuthenticationService.upsertRole(null, "MANUAL_testStudy", "MANUAL_ role MANUAL_testStudy")).thenReturn(true);
4751

4852
Response response = studyAccessService.addStudyAccess(studyIdentifier);
@@ -53,7 +57,7 @@ public void testAddStudyAccess() {
5357
@Test
5458
public void testAddStudyAccessWithConsent() {
5559
String studyIdentifier = "testStudy2.c2";
56-
when(fenceAuthenticationService.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, Map.of(StudyAccessService.STUDY_IDENTIFIER, "testStudy2", StudyAccessService.CONSENT_GROUP_CODE, "c2")));
60+
when(fenceMappingUtility.getFENCEMapping()).thenReturn(Map.of(studyIdentifier, Map.of(StudyAccessService.STUDY_IDENTIFIER, "testStudy2", StudyAccessService.CONSENT_GROUP_CODE, "c2")));
5761
when(fenceAuthenticationService.upsertRole(null, "MANUAL_testStudy2_c2", "MANUAL_ role MANUAL_testStudy2_c2")).thenReturn(true);
5862
Response response = studyAccessService.addStudyAccess(studyIdentifier);
5963

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