merging dev, recreating elasticsearch client in case it gets stuck

pom.xml

@@ -10,7 +10,7 @@
 
   <groupId>org.gbif.literature</groupId>
   <artifactId>literature-ws</artifactId>
-  <version>1.26-SNAPSHOT</version>
+  <version>1.27-SNAPSHOT</version>
   <name>GBIF Literature WS</name>
 
   <scm>

src/main/java/org/gbif/literature/config/EsClientConfigProperties.java

@@ -18,62 +18,16 @@
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.stereotype.Component;
 
+import lombok.Data;
+
 @Component
 @ConfigurationProperties(prefix = "elasticsearch")
+@Data
 public class EsClientConfigProperties {
-
   private Set<String> hosts;
   private String index;
   private int connectionTimeOut;
   private int socketTimeOut;
   private int connectionRequestTimeOut;
   private int maxResultWindow;
-
-  public Set<String> getHosts() {
-    return hosts;
-  }
-
-  public void setHosts(Set<String> hosts) {
-    this.hosts = hosts;
-  }
-
-  public String getIndex() {
-    return index;
-  }
-
-  public void setIndex(String index) {
-    this.index = index;
-  }
-
-  public int getConnectionTimeOut() {
-    return connectionTimeOut;
-  }
-
-  public void setConnectionTimeOut(int connectionTimeOut) {
-    this.connectionTimeOut = connectionTimeOut;
-  }
-
-  public int getSocketTimeOut() {
-    return socketTimeOut;
-  }
-
-  public void setSocketTimeOut(int socketTimeOut) {
-    this.socketTimeOut = socketTimeOut;
-  }
-
-  public int getConnectionRequestTimeOut() {
-    return connectionRequestTimeOut;
-  }
-
-  public void setConnectionRequestTimeOut(int connectionRequestTimeOut) {
-    this.connectionRequestTimeOut = connectionRequestTimeOut;
-  }
-
-  public int getMaxResultWindow() {
-    return maxResultWindow;
-  }
-
-  public void setMaxResultWindow(int maxResultWindow) {
-    this.maxResultWindow = maxResultWindow;
-  }
 }

src/main/java/org/gbif/literature/config/EsConfig.java

@@ -20,14 +20,37 @@
 import org.elasticsearch.client.NodeSelector;
 import org.elasticsearch.client.RestClient;
 import org.elasticsearch.client.RestHighLevelClient;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.support.DefaultSingletonBeanRegistry;
+import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
 
+import lombok.extern.slf4j.Slf4j;
+
 @Configuration
+@Slf4j
 public class EsConfig {
 
-  @Bean
+  @Autowired
+  private ApplicationContext applicationContext;
+
+  /**
+   * Re-creates the instance of the RestHighLevelClient.
+   */
+  public RestHighLevelClient reCreateRestHighLevelClient() {
+    RestHighLevelClient restHighLevelClient = applicationContext.getBean("restHighLevelClient", RestHighLevelClient.class);
+    if (!restHighLevelClient.getLowLevelClient().isRunning()) {
+      log.warn("Recreating Elasticsearch RestHighLevelClient");
+      DefaultSingletonBeanRegistry registry = (DefaultSingletonBeanRegistry) applicationContext.getAutowireCapableBeanFactory();
+      registry.destroySingleton("restHighLevelClient");
+      registry.registerSingleton("restHighLevelClient", restHighLevelClient(applicationContext.getBean(EsClientConfigProperties.class)));
+    }
+    return restHighLevelClient;
+  }
+
+  @Bean("restHighLevelClient")
   @Primary
   public RestHighLevelClient restHighLevelClient(EsClientConfigProperties esProperties) {
     return provideEsClient(esProperties);

src/main/java/org/gbif/literature/config/WebMvcConfig.java

@@ -47,4 +47,5 @@ public HttpFirewall allowUrlEncodedPercentHttpFirewall() {
   public ObjectMapper registryObjectMapper() {
     return JacksonJsonObjectMapperProvider.getObjectMapper();
   }
+
 }

src/main/java/org/gbif/literature/resource/LiteratureResource.java

@@ -245,11 +245,11 @@ public LiteratureResource(LiteratureSearchService searchService) {
             in = ParameterIn.QUERY,
             explode = Explode.TRUE),
         @Parameter(
-            name = "websites",
-            description = "Website of publication" + REPEATED,
-            array = @ArraySchema(schema = @Schema(implementation = String.class)),
-            in = ParameterIn.QUERY,
-            explode = Explode.TRUE),
+          name = "websites",
+          description = "Website of publication" + REPEATED,
+          array = @ArraySchema(schema = @Schema(implementation = String.class)),
+          in = ParameterIn.QUERY,
+          explode = Explode.TRUE),
         @Parameter(
             name = "year",
             description =
@@ -268,33 +268,33 @@ public LiteratureResource(LiteratureSearchService searchService) {
             in = ParameterIn.QUERY,
             explode = Explode.TRUE),
         @Parameter(
-            name = "added",
-            description =
-                "Date or date range when the publication was added. Format is ISO 8601, e.g., '2024-07-14' or '2024-07-14,2024-08-14'.",
-            schema = @Schema(implementation = Date.class),
-            in = ParameterIn.QUERY,
-            explode = Explode.TRUE),
+          name = "added",
+          description =
+            "Date or date range when the publication was added. Format is ISO 8601, e.g., '2024-07-14' or '2024-07-14,2024-08-14'.",
+          schema = @Schema(implementation = Date.class),
+          in = ParameterIn.QUERY,
+          explode = Explode.TRUE),
         @Parameter(
-            name = "published",
-            description =
-                "Date or date range when the publication was published. Format is ISO 8601, e.g., '2024-02-22' or '2024-02-22,2024-03-22'.",
-            schema = @Schema(implementation = Date.class),
-            in = ParameterIn.QUERY,
-            explode = Explode.TRUE),
+          name = "published",
+          description =
+            "Date or date range when the publication was published. Format is ISO 8601, e.g., '2024-02-22' or '2024-02-22,2024-03-22'.",
+          schema = @Schema(implementation = Date.class),
+          in = ParameterIn.QUERY,
+          explode = Explode.TRUE),
         @Parameter(
-            name = "discovered",
-            description =
-                "Date or date range when the publication was discovered. Format is ISO 8601, e.g., '2024-02-26' or '2024-02-26,2024-03-26'.",
-            schema = @Schema(implementation = Date.class),
-            in = ParameterIn.QUERY,
-            explode = Explode.TRUE),
+          name = "discovered",
+          description =
+            "Date or date range when the publication was discovered. Format is ISO 8601, e.g., '2024-02-26' or '2024-02-26,2024-03-26'.",
+          schema = @Schema(implementation = Date.class),
+          in = ParameterIn.QUERY,
+          explode = Explode.TRUE),
         @Parameter(
-            name = "modified",
-            description =
-                "Date or date range when the publication was discovered. Format is ISO 8601, e.g., '2024-07-26' or '2024-07-26,2024-10-26'.",
-            schema = @Schema(implementation = Date.class),
-            in = ParameterIn.QUERY,
-            explode = Explode.TRUE)
+          name = "modified",
+          description =
+            "Date or date range when the publication was discovered. Format is ISO 8601, e.g., '2024-07-26' or '2024-07-26,2024-10-26'.",
+          schema = @Schema(implementation = Date.class),
+          in = ParameterIn.QUERY,
+          explode = Explode.TRUE)
       })
   @CommonParameters.QParameter
   @interface CommonSearchParameters {}

src/main/java/org/gbif/literature/search/LiteratureSearchServiceEs.java

@@ -18,6 +18,7 @@
 import org.gbif.api.model.literature.search.LiteratureSearchRequest;
 import org.gbif.api.model.literature.search.LiteratureSearchResult;
 import org.gbif.literature.config.EsClientConfigProperties;
+import org.gbif.literature.config.EsConfig;
 
 import java.io.IOException;
 import java.util.Optional;
@@ -35,22 +36,33 @@ public class LiteratureSearchServiceEs implements LiteratureSearchService {
   @Value("${literature.bufferLimitBytesExport}")
   private int bufferLimitBytesExport;
 
-  private final RestHighLevelClient restHighLevelClient;
+  private RestHighLevelClient restHighLevelClient;
   private final LiteratureEsResponseParser esResponseParser;
   private final EsSearchRequestBuilder<LiteratureSearchParameter> esSearchRequestBuilder;
   private final String index;
   private final int maxResultWindow;
 
+  private final EsConfig esConfig;
+
   public LiteratureSearchServiceEs(
       EsClientConfigProperties esClientConfigProperties,
       RestHighLevelClient restHighLevelClient,
       LiteratureEsResponseParser esResponseParser,
-      EsSearchRequestBuilder<LiteratureSearchParameter> esSearchRequestBuilder) {
+      EsSearchRequestBuilder<LiteratureSearchParameter> esSearchRequestBuilder,
+      EsConfig esConfig) {
     this.index = esClientConfigProperties.getIndex();
     this.maxResultWindow = esClientConfigProperties.getMaxResultWindow();
     this.restHighLevelClient = restHighLevelClient;
     this.esResponseParser = esResponseParser;
     this.esSearchRequestBuilder = esSearchRequestBuilder;
+    this.esConfig = esConfig;
+  }
+
+  public RestHighLevelClient restHighLevelClient() {
+    if(!restHighLevelClient.getLowLevelClient().isRunning()) {
+      restHighLevelClient = esConfig.reCreateRestHighLevelClient();
+    }
+    return restHighLevelClient;
   }
 
   @Override
@@ -74,8 +86,7 @@ private SearchResponse<LiteratureSearchResult, LiteratureSearchParameter> search
       SearchRequest searchRequest =
           esSearchRequestBuilder.buildSearchRequest(literatureSearchRequest, true, index);
       SearchResponse<LiteratureSearchResult, LiteratureSearchParameter> response =
-          esResponseParser.buildSearchResponse(
-              restHighLevelClient.search(searchRequest, requestOptions), literatureSearchRequest);
+          esResponseParser.buildSearchResponse(restHighLevelClient().search(searchRequest, requestOptions), literatureSearchRequest);
 
       if (offsetExceeded) {
         response.setOffset(offset);
@@ -91,8 +102,7 @@ private SearchResponse<LiteratureSearchResult, LiteratureSearchParameter> search
   public Optional<LiteratureSearchResult> get(Object identifier) {
     SearchRequest getByIdRequest = esSearchRequestBuilder.buildGetRequest(identifier, index);
     try {
-      return esResponseParser.buildGetResponse(
-          restHighLevelClient.search(getByIdRequest, RequestOptions.DEFAULT));
+      return esResponseParser.buildGetResponse(restHighLevelClient().search(getByIdRequest, RequestOptions.DEFAULT));
     } catch (IOException e) {
       throw new RuntimeException(e);
     }

src/test/java/org/gbif/literature/LiteratureApplicationTests.java

@@ -13,11 +13,35 @@
  */
 package org.gbif.literature;
 
+import org.gbif.ws.server.filter.AppIdentityFilter;
+import org.gbif.ws.server.filter.HttpServletRequestWrapperFilter;
+import org.gbif.ws.server.filter.IdentityFilter;
+import org.gbif.ws.server.filter.RequestHeaderParamUpdateFilter;
+
 import org.junit.jupiter.api.Test;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.security.core.userdetails.UserDetailsService;
+import org.springframework.security.crypto.password.PasswordEncoder;
 
 @SpringBootTest
 class LiteratureApplicationTests {
+  @MockBean
+  UserDetailsService  userDetailsService;
+  @MockBean
+  PasswordEncoder passwordEncoder;
+
+  @MockBean
+  IdentityFilter identityFilter;
+
+  @MockBean
+  AppIdentityFilter appIdentityFilter;
+
+  @MockBean
+  HttpServletRequestWrapperFilter httpServletRequestWrapperFilter;
+
+  @MockBean
+  RequestHeaderParamUpdateFilter requestHeaderParamUpdateFilter;
 
   @Test
   void contextLoads() {}

src/test/java/org/gbif/literature/resource/LiteratureDocumentationTests.java

@@ -33,14 +33,15 @@ public class LiteratureDocumentationTests {
   @Test
   public void searchParametersDocumented() {
 
-    Set<LiteratureSearchParameter> handledParams =
-        new HashSet<>(
-            Arrays.asList(
-                LiteratureSearchParameter.DOI,
-                LiteratureSearchParameter.ADDED,
-                LiteratureSearchParameter.PUBLISHED,
-                LiteratureSearchParameter.DISCOVERED,
-                LiteratureSearchParameter.MODIFIED));
+    Set<LiteratureSearchParameter> handledParams = new HashSet<>(
+      Arrays.asList(
+        LiteratureSearchParameter.DOI,
+        LiteratureSearchParameter.ADDED,
+        LiteratureSearchParameter.PUBLISHED,
+        LiteratureSearchParameter.DISCOVERED,
+        LiteratureSearchParameter.MODIFIED
+      )
+    );
 
     Set<String> documentedParameters =
         Arrays.stream(