Added code to handle test context reloads.

Fixed permission tests.

src/main/java/org/ohdsi/webapi/cache/CacheService.java

@@ -17,7 +17,6 @@
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Optional;
 import java.util.stream.StreamSupport;
 import javax.cache.Cache;
 import javax.cache.CacheManager;
@@ -54,6 +53,10 @@ public CacheService(CacheManager cacheManager) {
  this.cacheManager = cacheManager;
  }
 
+ public CacheService() {
+ }
+
+
  @GET
  @Path("/")
  @Produces(MediaType.APPLICATION_JSON)
@@ -88,5 +91,4 @@ public ClearCacheResult clearAll() {
  }
  return result;
  }
-
 }

src/main/java/org/ohdsi/webapi/service/CohortDefinitionService.java

@@ -163,10 +163,12 @@ public static class CachingSetup implements JCacheManagerCustomizer {
  @Override
  public void customize(CacheManager cacheManager) {
  // Evict when a cohort definition is created or updated, or permissions, or tags
- cacheManager.createCache(COHORT_DEFINITION_LIST_CACHE, new MutableConfiguration<String, List<CohortMetadataDTO>>()
- .setTypes(String.class, (Class<List<CohortMetadataDTO>>) (Class<?>) List.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
+ if (!CacheHelper.getCacheNames(cacheManager).contains(COHORT_DEFINITION_LIST_CACHE)) {
+ cacheManager.createCache(COHORT_DEFINITION_LIST_CACHE, new MutableConfiguration<String, List<CohortMetadataDTO>>()
+ .setTypes(String.class, (Class<List<CohortMetadataDTO>>) (Class<?>) List.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
  }
  }
 

src/main/java/org/ohdsi/webapi/service/ConceptSetService.java

@@ -41,6 +41,7 @@
 import org.ohdsi.webapi.conceptset.dto.ConceptSetVersionFullDTO;
 import org.ohdsi.webapi.exception.ConceptNotExistException;
 import org.ohdsi.webapi.security.PermissionService;
+import static org.ohdsi.webapi.service.CohortDefinitionService.CachingSetup.COHORT_DEFINITION_LIST_CACHE;
 import org.ohdsi.webapi.service.dto.ConceptSetDTO;
 import org.ohdsi.webapi.shiro.Entities.UserEntity;
 import org.ohdsi.webapi.shiro.Entities.UserRepository;
@@ -51,6 +52,7 @@
 import org.ohdsi.webapi.source.SourceService;
 import org.ohdsi.webapi.tag.domain.HasTags;
 import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
+import org.ohdsi.webapi.util.CacheHelper;
 import org.ohdsi.webapi.util.ExportUtil;
 import org.ohdsi.webapi.util.NameUtils;
 import org.ohdsi.webapi.util.ExceptionUtils;
@@ -88,14 +90,18 @@ public static class CachingSetup implements JCacheManagerCustomizer {
 
  @Override
  public void customize(CacheManager cacheManager) {
+ // due to unit tests causing application contexts to reload cache manager caches, we
+ // have to check for the existance of a cache before creating it
+ Set<String> cacheNames = CacheHelper.getCacheNames(cacheManager);
  // Evict when a cohort definition is created or updated, or permissions, or tags
- cacheManager.createCache(CONCEPT_SET_LIST_CACHE, new MutableConfiguration<String, Collection<ConceptSetDTO>>()
- .setTypes(String.class, (Class<Collection<ConceptSetDTO>>) (Class<?>) List.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
+ if (!cacheNames.contains(CONCEPT_SET_LIST_CACHE)) {
+ cacheManager.createCache(CONCEPT_SET_LIST_CACHE, new MutableConfiguration<String, Collection<ConceptSetDTO>>()
+ .setTypes(String.class, (Class<Collection<ConceptSetDTO>>) (Class<?>) List.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
  }
  }
-
  @Autowired
  private ConceptSetGenerationInfoRepository conceptSetGenerationInfoRepository;
 

src/main/java/org/ohdsi/webapi/service/VocabularyService.java

@@ -53,6 +53,7 @@
 import org.ohdsi.webapi.source.SourceService;
 import org.ohdsi.webapi.source.SourceDaimon;
 import org.ohdsi.webapi.source.SourceInfo;
+import org.ohdsi.webapi.util.CacheHelper;
 import org.ohdsi.webapi.util.PreparedSqlRender;
 import org.ohdsi.webapi.util.PreparedStatementRenderer;
 import org.ohdsi.webapi.vocabulary.ConceptRecommendedNotInstalledException;
@@ -98,19 +99,28 @@ public static class CachingSetup implements JCacheManagerCustomizer {
 
  @Override
  public void customize(CacheManager cacheManager) {
+ // due to unit tests causing application contexts to reload cache manager caches, we
+ // have to check for the existance of a cache before creating it
+ Set<String> cacheNames = CacheHelper.getCacheNames(cacheManager);
  // Evict when a cohort definition is created or updated, or permissions, or tags
- cacheManager.createCache(CONCEPT_DETAIL_CACHE, new MutableConfiguration<String, Concept>()
- .setTypes(String.class, Concept.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
- cacheManager.createCache(CONCEPT_RELATED_CACHE, new MutableConfiguration<String, Collection<RelatedConcept>>()
- .setTypes(String.class, (Class<Collection<RelatedConcept>>) (Class<?>) Collection.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
- cacheManager.createCache(CONCEPT_HIERARCHY_CACHE, new MutableConfiguration<String, Collection<RelatedConcept>>()
- .setTypes(String.class, (Class<Collection<RelatedConcept>>) (Class<?>) Collection.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
+ if (!cacheNames.contains(CONCEPT_DETAIL_CACHE)) {
+ cacheManager.createCache(CONCEPT_DETAIL_CACHE, new MutableConfiguration<String, Concept>()
+ .setTypes(String.class, Concept.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
+ if (!cacheNames.contains(CONCEPT_RELATED_CACHE)) {
+ cacheManager.createCache(CONCEPT_RELATED_CACHE, new MutableConfiguration<String, Collection<RelatedConcept>>()
+ .setTypes(String.class, (Class<Collection<RelatedConcept>>) (Class<?>) Collection.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
+ if (!cacheNames.contains(CONCEPT_HIERARCHY_CACHE)) {
+ cacheManager.createCache(CONCEPT_HIERARCHY_CACHE, new MutableConfiguration<String, Collection<RelatedConcept>>()
+ .setTypes(String.class, (Class<Collection<RelatedConcept>>) (Class<?>) Collection.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
  }
  }
 

src/main/java/org/ohdsi/webapi/shiro/PermissionManager.java

@@ -41,6 +41,7 @@
 import org.apache.shiro.authz.Permission;
 import org.apache.shiro.authz.permission.WildcardPermission;
 import org.ohdsi.circe.helper.ResourceHelper;
+import org.ohdsi.webapi.util.CacheHelper;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.autoconfigure.cache.JCacheManagerCustomizer;
 import org.springframework.cache.annotation.CacheEvict;
@@ -62,14 +63,18 @@ public static class CachingSetup implements JCacheManagerCustomizer {
 
  @Override
  public void customize(CacheManager cacheManager) {
+ // due to unit tests causing application contexts to reload cache manager caches, we
+ // have to check for the existance of a cache before creating it
+ Set<String> cacheNames = CacheHelper.getCacheNames(cacheManager);
  // Evict when a user, role or permission is modified/deleted.
- cacheManager.createCache(AUTH_INFO_CACHE, new MutableConfiguration<String, UserSimpleAuthorizationInfo>()
- .setTypes(String.class, UserSimpleAuthorizationInfo.class)
- .setStoreByValue(false)
- .setStatisticsEnabled(true));
+ if (!cacheNames.contains(AUTH_INFO_CACHE)) {
+ cacheManager.createCache(AUTH_INFO_CACHE, new MutableConfiguration<String, UserSimpleAuthorizationInfo>()
+ .setTypes(String.class, UserSimpleAuthorizationInfo.class)
+ .setStoreByValue(false)
+ .setStatisticsEnabled(true));
+ }
  }
  }
-
 
  @Value("${datasource.ohdsi.schema}")
  private String ohdsiSchema;
@@ -95,6 +100,8 @@ public void customize(CacheManager cacheManager) {
  @Autowired
  private JdbcTemplate jdbcTemplate;
 
+ private ThreadLocal<ConcurrentHashMap<String, UserSimpleAuthorizationInfo>> authorizationInfoCache = ThreadLocal.withInitial(ConcurrentHashMap::new);
+
  public static class PermissionsDTO {
 
  public Map<String, List<String>> permissions = null;
@@ -163,39 +170,42 @@ public Iterable<RoleEntity> getRoles(boolean includePersonalRoles) {
  @Cacheable(cacheNames = CachingSetup.AUTH_INFO_CACHE)
  public UserSimpleAuthorizationInfo getAuthorizationInfo(final String login) {
 
- final UserSimpleAuthorizationInfo info = new UserSimpleAuthorizationInfo();
-
- final UserEntity userEntity = userRepository.findByLogin(login);
- if(userEntity == null) {
- throw new UnknownAccountException("Account does not exist");
- }
-
- info.setUserId(userEntity.getId());
- info.setLogin(userEntity.getLogin());
-
- for (UserRoleEntity userRole: userEntity.getUserRoles()) {
- info.addRole(userRole.getRole().getName());
- }
-
- // convert permission index from queryUserPermissions() into a map of WildcardPermissions
- Map<String, List<String>> permsIdx = this.queryUserPermissions(login).permissions;
- Map permissionMap = new HashMap<String, List<Permission>>();
- Set<String> permissionNames = new HashSet<>();
-
- for(String permIdxKey : permsIdx.keySet()) {
- List<String> perms = permsIdx.get(permIdxKey);
- permissionNames.addAll(perms);
- // convert raw string permission into Wildcard perm for each element in this key's array.
- permissionMap.put(permIdxKey, perms.stream().map(perm -> new WildcardPermission(perm)).collect(Collectors.toList()));
- }
-
- info.setStringPermissions(permissionNames);
- info.setPermissionIdx(permissionMap);
- return info;
- }
+ return authorizationInfoCache.get().computeIfAbsent(login, newLogin -> {
+ final UserSimpleAuthorizationInfo info = new UserSimpleAuthorizationInfo();
+
+ final UserEntity userEntity = userRepository.findByLogin(login);
+ if(userEntity == null) {
+ throw new UnknownAccountException("Account does not exist");
+ }
+
+ info.setUserId(userEntity.getId());
+ info.setLogin(userEntity.getLogin());
+
+ for (UserRoleEntity userRole: userEntity.getUserRoles()) {
+ info.addRole(userRole.getRole().getName());
+ }
+
+ // convert permission index from queryUserPermissions() into a map of WildcardPermissions
+ Map<String, List<String>> permsIdx = this.queryUserPermissions(login).permissions;
+ Map permissionMap = new HashMap<String, List<Permission>>();
+ Set<String> permissionNames = new HashSet<>();
+
+ for(String permIdxKey : permsIdx.keySet()) {
+ List<String> perms = permsIdx.get(permIdxKey);
+ permissionNames.addAll(perms);
+ // convert raw string permission into Wildcard perm for each element in this key's array.
+ permissionMap.put(permIdxKey, perms.stream().map(perm -> new WildcardPermission(perm)).collect(Collectors.toList()));
+ }
+
+ info.setStringPermissions(permissionNames);
+ info.setPermissionIdx(permissionMap);
+ return info;
+ });
+ }
 
  @CacheEvict(cacheNames = CachingSetup.AUTH_INFO_CACHE, allEntries = true)
  public void clearAuthorizationInfoCache() {
+ authorizationInfoCache.remove();
  }
 
  @Transactional

src/main/java/org/ohdsi/webapi/util/CacheHelper.java

@@ -1,8 +1,10 @@
 package org.ohdsi.webapi.util;
 
 import java.lang.management.ManagementFactory;
+import java.util.HashSet;
 import java.util.Set;
 import javax.cache.CacheManager;
+import javax.cache.configuration.MutableConfiguration;
 import javax.cache.management.CacheStatisticsMXBean;
 import javax.management.MBeanServer;
 import javax.management.MBeanServerInvocationHandler;
@@ -33,4 +35,10 @@ public static CacheStatisticsMXBean getCacheStats(CacheManager cacheManager, Str
  throw new RuntimeException(e);
  }
  }
+
+ public static Set<String> getCacheNames(CacheManager cacheManager) {
+ Set<String> cacheNames = new HashSet<>();
+ cacheManager.getCacheNames().forEach((name) -> cacheNames.add(name));
+ return cacheNames;
+ }
 }

src/test/java/org/ohdsi/webapi/security/PermissionTest.java

@@ -65,7 +65,7 @@ public void setup() {
  ThreadContext.bind(subject); 
  }
 
- @Ignore
+// @Ignore
  @Test
  public void permsTest() throws Exception {
  // need to clear authorization cache before each test
@@ -88,7 +88,7 @@ public void permsTest() throws Exception {
 
  }
 
- @Ignore
+// @Ignore
  @Test
  public void wildcardTest() throws Exception {
  // need to clear authorization cache before each test

src/test/resources/permission/permsTest_PREP.json

@@ -1,64 +1,64 @@
 {
  "public.sec_user": [
  {
- "id":1001,
+ "id":100001,
  "login":"permsTest",
  "name":"Perms Test User",
  "origin":"SYSTEM"
  }
  ],
  "public.sec_role": [
  {
- "id": 1001,
+ "id": 100001,
  "name":"permsTest",
  "system_role":false
  }
  ],
  "public.sec_permission" : [
  {
- "id": 1001,
+ "id": 100001,
  "value":"printer:manage:printer1"
  },
  {
- "id": 1002,
+ "id": 100002,
  "value":"printer:manage:printer2"
  },
  {
- "id": 1003,
+ "id": 100003,
  "value":"printer:query:*"
  },
  {
- "id": 1004,
+ "id": 100004,
  "value":"printer:print"
  }
  ],
  "public.sec_role_permission" : [
  {
- "id":1001,
- "role_id":1001,
- "permission_id":1001
+ "id":100001,
+ "role_id":100001,
+ "permission_id":100001
  },
  {
- "id":1002,
- "role_id":1001,
- "permission_id":1002
+ "id":100002,
+ "role_id":100001,
+ "permission_id":100002
  },
  {
- "id":1003,
- "role_id":1001,
- "permission_id":1003
+ "id":103,
+ "role_id":100001,
+ "permission_id":100003
  },
  {
- "id":1004,
- "role_id":1001,
- "permission_id":1004
+ "id":100004,
+ "role_id":100001,
+ "permission_id":100004
  }
  ],
  "public.sec_user_role": [
  {
- "id": 1001,
- "user_id":1001,
- "role_id":1001,
+ "id": 100001,
+ "user_id":100001,
+ "role_id":100001,
  "origin":"SYSTEM"
  }
  ]