Re-introduce Caching (#2393)

* Implemented caching for cohort def list, concept set list, permissions, and data sources.
Implementation uses ehCache 3.9.
Changed editor config to tabs.
Made cache endpoints auth restricted.

.editorconfig

@@ -4,7 +4,7 @@
 root = true
 
 [*]
-indent_style = space
+indent_style = tab
 indent_size = 2
 end_of_line = crlf
 charset = utf-8

pom.xml

@@ -236,6 +236,10 @@
     <logging.level.org.hibernate>info</logging.level.org.hibernate>
     <logging.level.org.apache.shiro>warn</logging.level.org.apache.shiro>
 
+    <!-- Spring Cache properties -->
+    <spring.cache.type>jcache</spring.cache.type>
+
+    <!-- Spring Batch -->
     <spring.batch.taskExecutor.corePoolSize>10</spring.batch.taskExecutor.corePoolSize>
     <spring.batch.taskExecutor.maxPoolSize>20</spring.batch.taskExecutor.maxPoolSize>
     <spring.batch.taskExecutor.queueCapacity>2147483647</spring.batch.taskExecutor.queueCapacity>
@@ -272,6 +276,7 @@
     <cache.jobs.count>3</cache.jobs.count>
     <!-- Achilles cache -->
     <cache.achilles.usePersonCount>true</cache.achilles.usePersonCount>
+    <cache.webapi.enabled>true</cache.webapi.enabled>
 
     <!-- Build info -->
     <buildinfo.atlas.milestone.id>47</buildinfo.atlas.milestone.id>
@@ -744,6 +749,10 @@
       <scope>provided</scope>
     </dependency>
     <dependency>
+      <groupId>javax.cache</groupId>
+      <artifactId>cache-api</artifactId>
+      <version>1.1.1</version>
+    </dependency>    <dependency>
       <groupId>org.ohdsi.sql</groupId>
       <artifactId>SqlRender</artifactId>
       <version>${SqlRender.version}</version>
@@ -1202,6 +1211,10 @@
       <version>1.1.7</version>
     </dependency>
     <dependency>
+      <groupId>org.ehcache</groupId>
+      <artifactId>ehcache</artifactId>
+      <version>3.9.11</version>
+    </dependency>    <dependency>
       <groupId>com.opentable.components</groupId>
       <artifactId>otj-pg-embedded</artifactId>
       <version>0.13.1</version>

src/main/java/org/ohdsi/webapi/CacheConfig.java

@@ -0,0 +1,10 @@
+package org.ohdsi.webapi;
+
+import org.springframework.cache.annotation.EnableCaching;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@EnableCaching
+public class CacheConfig {
+
+}

src/main/java/org/ohdsi/webapi/JerseyConfig.java

@@ -37,6 +37,7 @@
 
 import javax.inject.Singleton;
 import javax.ws.rs.ext.RuntimeDelegate;
+import org.ohdsi.webapi.cache.CacheService;
 
 /**
  *
@@ -59,31 +60,32 @@ public JerseyConfig() {
     public void afterPropertiesSet() throws Exception {
         packages(this.rootPackage);
         register(ActivityService.class);
+        register(CacheService.class);
+        register(CcController.class);
         register(CDMResultsService.class);
         register(CohortAnalysisService.class);
         register(CohortDefinitionService.class);
         register(CohortResultsService.class);
         register(CohortService.class);
         register(ConceptSetService.class);
+        register(DDLService.class);
         register(EvidenceService.class);
         register(FeasibilityService.class);
+        register(FeatureExtractionService.class);
         register(InfoService.class);
         register(IRAnalysisResource.class);
         register(JobService.class);
+        register(MultiPartFeature.class);
+        register(PermissionController.class);
         register(PersonService.class);
+        register(ScriptExecutionController.class);
+        register(ScriptExecutionCallbackController.class);
         register(SourceController.class);
         register(SqlRenderService.class);
-        register(DDLService.class);
+        register(SSOController.class);
         register(TherapyPathResultsService.class);
         register(UserService.class);
         register(VocabularyService.class);
-        register(ScriptExecutionController.class);
-        register(ScriptExecutionCallbackController.class);
-        register(MultiPartFeature.class);
-        register(FeatureExtractionService.class);
-        register(CcController.class);
-        register(SSOController.class);
-        register(PermissionController.class);
         register(new AbstractBinder() {
             @Override
             protected void configure() {

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

@@ -0,0 +1,30 @@
+/*
+ * Copyright 2019 cknoll1.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ohdsi.webapi.cache;
+
+import java.io.Serializable;
+import java.util.Optional;
+import javax.cache.management.CacheStatisticsMXBean;
+
+/**
+ *
+ * @author cknoll1
+ */
+public class CacheInfo implements Serializable{
+	public String cacheName;
+	public Long entries;
+	public CacheStatisticsMXBean cacheStatistics;
+}

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

@@ -0,0 +1,94 @@
+/*
+ * Copyright 2019 cknoll1.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.ohdsi.webapi.cache;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.StreamSupport;
+import javax.cache.Cache;
+import javax.cache.CacheManager;
+import javax.ws.rs.GET;
+import javax.ws.rs.Path;
+import javax.ws.rs.Produces;
+import javax.ws.rs.core.MediaType;
+import org.ohdsi.webapi.util.CacheHelper;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ *
+ * @author cknoll1
+ */
+@Path("/cache")
+@Component
+public class CacheService {
+
+	public static class ClearCacheResult {
+
+		public List<CacheInfo> clearedCaches;
+
+		private ClearCacheResult() {
+			this.clearedCaches = new ArrayList<>();
+		}
+	}
+
+	private CacheManager cacheManager;
+
+	@Autowired(required = false)
+	public CacheService(CacheManager cacheManager) {
+
+		this.cacheManager = cacheManager;
+	}
+
+	public CacheService() {
+	}
+
+
+	@GET
+	@Path("/")
+	@Produces(MediaType.APPLICATION_JSON)
+	public List<CacheInfo> getCacheInfoList() {
+		List<CacheInfo> caches = new ArrayList<>();
+
+		if (cacheManager == null) return caches;  //caching is disabled
+
+		for (String cacheName : cacheManager.getCacheNames()) {
+			Cache cache = cacheManager.getCache(cacheName);
+			CacheInfo info = new CacheInfo();
+			info.cacheName = cacheName;
+			info.entries = StreamSupport.stream(cache.spliterator(), false).count();
+			info.cacheStatistics = CacheHelper.getCacheStats(cacheManager , cacheName);
+			caches.add(info);
+		}
+		return caches;
+	}
+	@GET
+	@Path("/clear")
+	@Produces(MediaType.APPLICATION_JSON)
+	public ClearCacheResult clearAll() {
+		ClearCacheResult result = new ClearCacheResult();
+
+		for (String cacheName : cacheManager.getCacheNames()) {
+			Cache cache = cacheManager.getCache(cacheName);
+			CacheInfo info = new CacheInfo();
+			info.cacheName = cacheName;
+			info.entries = StreamSupport.stream(cache.spliterator(), false).count();
+			result.clearedCaches.add(info);
+			cache.clear();
+		}
+		return result;
+	}
+}

src/main/java/org/ohdsi/webapi/security/PermissionService.java

@@ -62,6 +62,9 @@ public class PermissionService {
     @Value("#{!'${security.provider}'.equals('DisabledSecurity')}")
     private boolean securityEnabled;
 
+	@Value("${security.defaultGlobalReadPermissions}")
+	private boolean defaultGlobalReadPermissions;
+
     private final EntityGraph PERMISSION_ENTITY_GRAPH = EntityGraphUtils.fromAttributePaths("rolePermissions", "rolePermissions.role");
 
     public PermissionService(
@@ -227,4 +230,17 @@ public void fillReadAccess(CommonEntity entity, CommonEntityDTO entityDTO) {
     public boolean isSecurityEnabled() {
       return this.securityEnabled;
     }
+
+		// Use this key for cache (asset lists) that may be associated to a user or shared across users.
+		public String getAssetListCacheKey() {
+			if (this.isSecurityEnabled() && !defaultGlobalReadPermissions) 
+				return permissionManager.getSubjectName();
+			else
+				return "ALL_USERS";
+		}
+
+		// use this cache key when the cache is associated to a user
+		public String getSubjectCacheKey() {
+			return this.isSecurityEnabled() ? permissionManager.getSubjectName() : "ALL_USERS";
+		}
 }

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

@@ -131,13 +131,18 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
+import javax.cache.CacheManager;
+import javax.cache.configuration.MutableConfiguration;
 import javax.ws.rs.core.Response.ResponseBuilder;
 
 import static org.ohdsi.webapi.Constants.Params.COHORT_DEFINITION_ID;
 import static org.ohdsi.webapi.Constants.Params.JOB_NAME;
 import static org.ohdsi.webapi.Constants.Params.SOURCE_ID;
 import org.ohdsi.webapi.source.SourceService;
 import static org.ohdsi.webapi.util.SecurityUtils.whitelist;
+import org.springframework.boot.autoconfigure.cache.JCacheManagerCustomizer;
+import org.springframework.cache.annotation.CacheEvict;
+import org.springframework.cache.annotation.Cacheable;
 
 /**
  * Provides REST services for working with cohort definitions.
@@ -149,6 +154,24 @@
 @Component
 public class CohortDefinitionService extends AbstractDaoService implements HasTags<Integer> {
 
+	//create cache
+	@Component
+	public static class CachingSetup implements JCacheManagerCustomizer {
+
+		public static final String COHORT_DEFINITION_LIST_CACHE = "cohortDefinitionList";
+
+		@Override
+		public void customize(CacheManager cacheManager) {
+			// Evict when a cohort definition is created or updated, or permissions, or tags
+			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));
+			}
+		}
+	}
+
 	private static final CohortExpressionQueryBuilder queryBuilder = new CohortExpressionQueryBuilder();
 
 	@Autowired
@@ -205,7 +228,7 @@ public class CohortDefinitionService extends AbstractDaoService implements HasTa
 	@Autowired
 	private VersionService<CohortVersion> versionService;
 
-        @Value("${security.defaultGlobalReadPermissions}")
+	@Value("${security.defaultGlobalReadPermissions}")
 	private boolean defaultGlobalReadPermissions;
 
 	private final MarkdownRender markdownPF = new MarkdownRender();
@@ -408,6 +431,7 @@ public GenerateSqlResult generateSql(GenerateSqlRequest request) {
 	@Path("/")
 	@Produces(MediaType.APPLICATION_JSON)
 	@Transactional
+	@Cacheable(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, key = "@permissionService.getSubjectCacheKey()")
 	public List<CohortMetadataDTO> getCohortDefinitionList() {
 		List<CohortDefinition> definitions = cohortDefinitionRepository.list();
 		return definitions.stream()
@@ -436,6 +460,7 @@ public List<CohortMetadataDTO> getCohortDefinitionList() {
 	@Transactional
 	@Produces(MediaType.APPLICATION_JSON)
 	@Consumes(MediaType.APPLICATION_JSON)
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	public CohortDTO createCohortDefinition(CohortDTO dto) {
 
 		Date currentTime = Calendar.getInstance().getTime();
@@ -538,6 +563,7 @@ public int getCountCDefWithSameName(@PathParam("id") @DefaultValue("0") final in
 	@Produces(MediaType.APPLICATION_JSON)
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Transactional
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	public CohortDTO saveCohortDefinition(@PathParam("id") final int id, CohortDTO def) {
 		Date currentTime = Calendar.getInstance().getTime();
 
@@ -670,6 +696,7 @@ public List<CohortGenerationInfoDTO> getInfo(@PathParam("id") final int id) {
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/{id}/copy")
 	@Transactional
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	public CohortDTO copy(@PathParam("id") final int id) {
 		CohortDTO sourceDef = getCohortDefinition(id);
 		sourceDef.setId(null); // clear the ID
@@ -954,6 +981,7 @@ private Response printFrindly(String markdown, String format) {
 	@POST
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/{id}/tag/")
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	@Transactional
 	public void assignTag(@PathParam("id") final Integer id, final int tagId) {
 		CohortDefinition entity = cohortDefinitionRepository.findOne(id);
@@ -971,6 +999,7 @@ public void assignTag(@PathParam("id") final Integer id, final int tagId) {
 	@DELETE
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/{id}/tag/{tagId}")
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	@Transactional
 	public void unassignTag(@PathParam("id") final Integer id, @PathParam("tagId") final int tagId) {
 		CohortDefinition entity = cohortDefinitionRepository.findOne(id);
@@ -1106,6 +1135,7 @@ public void deleteVersion(@PathParam("id") final int id, @PathParam("version") f
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/{id}/version/{version}/createAsset")
 	@Transactional
+	@CacheEvict(cacheNames = CachingSetup.COHORT_DEFINITION_LIST_CACHE, allEntries = true)
 	public CohortDTO copyAssetFromVersion(@PathParam("id") final int id, @PathParam("version") final int version) {
 		checkVersion(id, version, false);
 		CohortVersion cohortVersion = versionService.getById(VersionType.COHORT, id, version);