Better response to accession upsert

- Catch more exceptions
- Log failed ES documents
- Increased transaction timeout in AccessionUploader

src/main/java/org/genesys2/server/service/impl/ElasticsearchSearchServiceImpl.java

@@ -58,6 +58,7 @@ import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.elasticsearch.ElasticsearchException;
 import org.springframework.data.elasticsearch.core.ElasticsearchTemplate;
 import org.springframework.data.elasticsearch.core.FacetedPage;
 import org.springframework.data.elasticsearch.core.facet.FacetRequest;
@@ -386,7 +387,14 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 		if (!queries.isEmpty()) {
 			LOG.debug("Indexing {} count={} of provided objects count={}", className, queries.size(), ids.size());
-			elasticsearchTemplate.bulkIndex(queries);
+			try {
+				elasticsearchTemplate.bulkIndex(queries);
+			} catch (ElasticsearchException e) {
+				LOG.warn("Elasticsearch bulkIndex failed", e.getMessage());
+				if (e.getFailedDocuments() != null) {
+					e.getFailedDocuments().forEach((a, b) -> LOG.warn("Failed document {} {}", a, b));
+				}
+			}
 		}
 	}
 

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -112,7 +112,7 @@ public class AccessionUploader implements InitializingBean {
 	 * @param updates the updates
 	 * @throws IOException
 	 */
-	@Transactional(timeout = 200, isolation = Isolation.READ_UNCOMMITTED, rollbackFor = Throwable.class)
+	@Transactional(timeout = 250, isolation = Isolation.READ_UNCOMMITTED, rollbackFor = Throwable.class)
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE')")
 	public List<AccessionOpResponse> upsertAccessions(FaoInstitute institute, ArrayNode updates) {
 		assert (updates.isArray());
@@ -420,6 +420,7 @@ public class AccessionUploader implements InitializingBean {
 		}
 	}
 
+	@Transactional(timeout = 250, isolation = Isolation.READ_UNCOMMITTED, rollbackFor = Throwable.class)
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE')")
 	public List<AccessionOpResponse> deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> identifiers) {
 		// Security check

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java

@@ -21,6 +21,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
+import javax.persistence.PersistenceException;
 import javax.persistence.RollbackException;
 
 import org.apache.commons.lang3.RandomUtils;
@@ -49,6 +50,7 @@ import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.dao.CannotAcquireLockException;
+import org.springframework.dao.DataAccessException;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
@@ -211,7 +213,7 @@ public class AccessionController extends RestController {
 		for (int tryCount = 0; tryCount < UPLOAD_RETRIES; tryCount++) {
 			try {
 				return uploader.upsertAccessions(institute, updates);
-			} catch (TransactionException | RollbackException | CannotAcquireLockException | DataIntegrityViolationException e) {
+			} catch (DataAccessException | TransactionException | PersistenceException e) {
 				return upsert1By1(institute, updates);
 			} catch (PleaseRetryException e) {
 				LOG.error("Retry {} of {} tries due to: {}", tryCount, UPLOAD_RETRIES, e.getMessage());
@@ -287,7 +289,7 @@ public class AccessionController extends RestController {
 			try {
 				response = uploader.deleteAccessions(institute, batch);
 				LOG.info("Deleted {} accessions from {}", response.size(), instCode);
-			} catch (TransactionException | RollbackException | CannotAcquireLockException | DataIntegrityViolationException e) {
+			} catch (DataAccessException | TransactionException | PersistenceException e) {
 				LOG.info("Retrying delete one by one due to {}", e.getMessage());
 				response = deleteAccessions1by1(institute, batch);
 			}