updateAccessionCount called from outside transaction (causes too many locks)

src/main/java/org/genesys2/server/model/genesys/SelfCopy.java

@@ -2,15 +2,18 @@ package org.genesys2.server.model.genesys;
 
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 public class SelfCopy {
 	private static Log LOG = LogFactory.getLog(SelfCopy.class);
+	private static Map<Method, Method> gettersSetters = new HashMap<Method, Method>();
 
-	public static void copy(AccessionData source, AccessionData target) {
-		Method[] allMethods = source.getClass().getMethods();
+	static {
+		Method[] allMethods = AccessionData.class.getMethods();
 		for (Method getter : allMethods) {
 			String name = getter.getName();
 			boolean isGet = false;
@@ -23,33 +26,27 @@ public class SelfCopy {
 				name = name.substring(2);
 			}
 
-			LOG.debug("Getter coreName=" + name);
-
 			if (isGet) {
-				LOG.info("Using getter " + name);
+				LOG.info("Using getter " + getter);
 				try {
-					Object val = getter.invoke(source);
-					set(target, name, getter.getReturnType(), val);
-				} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException | SecurityException e) {
-					LOG.warn(e.getMessage(), e);
+					Method setter = AccessionData.class.getMethod("set" + name, getter.getReturnType());
+					gettersSetters.put(getter, setter);
+					LOG.info("Using setter " + setter);
+				} catch (NoSuchMethodException | SecurityException e) {
+					LOG.error("No setter for " + name);
 				}
 			}
 		}
 	}
 
-	private static void set(AccessionData target, String name, Class<?> type, Object val) throws NoSuchMethodException, SecurityException,
-			IllegalAccessException, IllegalArgumentException, InvocationTargetException {
-		LOG.info("Using setter 'get" + name + "' to apply type " + type + " val=" + val);
-		try {
-			Method setter = target.getClass().getMethod("set" + name, type);
-			if (setter == null) {
-				LOG.error("No setter for " + name);
-				return;
+	public static void copy(AccessionData source, AccessionData target) {
+		for (Method getter : gettersSetters.keySet()) {
+			try {
+				Object val = getter.invoke(source);
+				gettersSetters.get(getter).invoke(target, val);
+			} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+				LOG.error(e.getMessage(), e);
 			}
-			LOG.info("Setting property " + name);
-			setter.invoke(target, val);
-		} catch (NoSuchMethodException e) {
-			LOG.debug("No setter for " + name);
 		}
 	}
 

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

@@ -689,7 +689,6 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		} else {
 			res = accessionRepository.save((Accession) accession);
 		}
-		updateAccessionCount(accession.getInstitute());
 		return res;
 	}
 
@@ -735,8 +734,6 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			for (Accession a : toDelete) {
 				accessionRepository.deleteActive(a.getId());
 			}
-
-			updateAccessionCount(institute);
 		}
 
 		return deleted;

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

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.service.impl;
 
+import org.springframework.dao.CannotAcquireLockException;
+
 public class RESTApiException extends Exception {
 
 	/**
@@ -27,4 +29,8 @@ public class RESTApiException extends Exception {
 		super(message);
 	}
 
+	public RESTApiException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
 }

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

@@ -50,6 +50,7 @@ import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.CannotAcquireLockException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Sort;
@@ -224,10 +225,9 @@ public class AccessionController extends RestController {
 			}
 			batch.put(dataJson, (ObjectNode) json);
 		}
-		
+
 		// Step 1: Ensure all taxonomic data provided by client is persisted
 		batchRESTService.ensureTaxonomies(institute, batch);
-		
 
 		for (int i = 0; i < 10; i++) {
 			try {
@@ -292,9 +292,14 @@ public class AccessionController extends RestController {
 			throw new ResourceNotFoundException();
 		}
 
-		final int deleted = batchRESTService.deleteAccessions(institute, batch);
-		LOG.info("Deleted " + deleted + " accessions from " + instCode);
-		return new JsonDeleteResult(deleted);
+		try {
+			final int deleted = batchRESTService.deleteAccessions(institute, batch);
+			LOG.info("Deleted " + deleted + " accessions from " + instCode);
+			genesysService.updateAccessionCount(institute);
+			return new JsonDeleteResult(deleted);
+		} catch (CannotAcquireLockException e) {
+			throw new PleaseRetryException("Operation failed, please retry.", e);
+		}
 	}
 
 	/**
@@ -317,6 +322,7 @@ public class AccessionController extends RestController {
 
 		final int deleted = batchRESTService.deleteAccessionsById(institute, batch);
 		LOG.info("Deleted " + deleted + " accessions from " + instCode);
+		genesysService.updateAccessionCount(institute);
 		return new JsonDeleteResult(deleted);
 	}
 

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

+package org.genesys2.server.servlet.controller.rest;
+
+import org.genesys2.server.service.impl.RESTApiException;
+import org.springframework.dao.CannotAcquireLockException;
+
+public class PleaseRetryException extends RESTApiException {
+
+	public PleaseRetryException(String message, Throwable cause) {
+		super(message, cause);
+	}
+
+}

src/main/resources/spring/spring.properties

@@ -25,7 +25,7 @@ db.url=jdbc:mysql://localhost/genesys?useUnicode=true&characterEncoding=UTF-8&us
 db.driverClassName=com.mysql.jdbc.Driver
 db.username=root
 db.password=
-db.showSql=true
+db.showSql=false
 db.hbm2ddl=false
 hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect