Merge branch '372-fix-glis-integration' into 'master'

Resolve "Fix GLIS integration"

Closes #372

See merge request genesys-pgr/genesys-server!287

src/main/java/org/genesys2/server/mvc/admin/BeanshellController.java

@@ -29,8 +29,11 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
 
 import org.genesys.glis.v1.api.GenesysApi;
+import org.genesys2.server.service.AccessionService;
 import org.genesys2.server.service.GenesysFilterService;
 import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.worker.AccessionModifiedAspect;
+import org.genesys2.server.service.worker.AccessionProcessor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -71,6 +74,15 @@ public class BeanshellController implements InitializingBean {
 	@Autowired
 	private GenesysApi glisGenesys;
 
+	@Autowired
+	private AccessionProcessor accessionProcessor;
+	
+	@Autowired
+	private AccessionModifiedAspect accessionsModifiedAspect;
+
+	@Autowired
+	private AccessionService accessionService;
+
 	@PersistenceContext
 	private EntityManager entityManager;
 
@@ -91,6 +103,9 @@ public class BeanshellController implements InitializingBean {
 		this.exposedBeans.put("genesysService", genesysService);
 		this.exposedBeans.put("filterService", filterService);
 		this.exposedBeans.put("glisGenesys", glisGenesys);
+		this.exposedBeans.put("accessionService", accessionService);
+		this.exposedBeans.put("accessionsModifiedAspect", accessionsModifiedAspect);
+		this.exposedBeans.put("accessionProcessor", accessionProcessor);
 		this.exposedBeans.put("entityManager", entityManager);
 		this.exposedBeans.put("jdbc", jdbcTemplate);
 	}

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

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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.genesys2.server.service.worker;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.time.StopWatch;
+import org.aspectj.lang.JoinPoint;
+import org.aspectj.lang.annotation.After;
+import org.aspectj.lang.annotation.Aspect;
+import org.aspectj.lang.annotation.Before;
+import org.genesys2.server.model.genesys.Accession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+import org.springframework.stereotype.Component;
+
+import com.google.common.collect.Lists;
+
+/**
+ * Trigger out-of-bound actions when accessions are added, updated or removed from
+ * Genesys.
+ * 
+ * @author Matija Obreza
+ */
+@Aspect
+@Component
+public class AccessionModifiedAspect implements InitializingBean {
+	
+	/**
+	 * A processor that wishes to receive notifications about changes to Accession
+	 * records in Genesys.
+	 * 
+	 * The code will be executed as a task in a common thread pool and no security
+	 * context will be available to the implementing class.
+	 */
+	public static interface AccessionModifiedListener {
+
+		/**
+		 * Execute an action when {@link Accession} records are removed from Genesys.
+		 *
+		 * @param accessions the accessions that were removed. Never null, never blank.
+		 */
+		void onRemove(Collection<Accession> accessions);
+
+		/**
+		 * Execute an action when {@link Accession} records are updated in Genesys.
+		 *
+		 * @param accessions the accessions that were updated. Never null, never blank.
+		 */
+		void onUpdate(Collection<Accession> accessions);
+	}
+	
+	@Autowired(required = false)
+	private List<AccessionModifiedListener> accessionModifiedListeners;
+	
+	@Autowired
+	private ThreadPoolTaskExecutor taskExecutor;
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+		if (accessionModifiedListeners == null) {
+			LOG.error("List of Listeners must not be null. Check your configuration.");
+		}
+		assert(accessionModifiedListeners != null);
+	}
+
+	/** The Constant LOG. */
+	private static final Logger LOG = LoggerFactory.getLogger(AccessionModifiedAspect.class);
+
+	@After(value = "execution(* org.genesys2.server.persistence.AccessionRepository.save(*)) && args(arg)")
+	protected void afterPersistAccession(JoinPoint joinPoint, Object arg) throws Throwable {
+
+		StopWatch stopWatch=StopWatch.createStarted();
+		LOG.trace("After persist accession(s): {}", arg);
+		if (arg == null) {
+			return;
+		}
+		if (arg instanceof Collection<?>) {
+			handlePersist((Collection<Accession>) arg);
+			LOG.debug("Persist notification for {} accession took {}ms", ((Collection<?>) arg).size(), stopWatch.getTime(TimeUnit.MILLISECONDS));
+		} else if (arg instanceof Accession) {
+			handlePersist(Lists.newArrayList((Accession) arg));
+			LOG.debug("Persist notification for 1 accession took {}ms", stopWatch.getTime(TimeUnit.MILLISECONDS));
+		}
+	}
+	
+	/**
+	 * Fake persist accession records to trigger listeners.
+	 *
+	 * @param accessions the accessions
+	 */
+	public void fakePersist(Collection<Accession> accessions) {
+		LOG.info("Fake-persisting {} accessions", accessions.size());
+		handlePersist(accessions);
+	}
+
+	private void handlePersist(Collection<Accession> accessions) {
+		if (CollectionUtils.isEmpty(accessions)) {
+			return;
+		}
+		LOG.info("{} accessions were updated", accessions.size());
+		accessionModifiedListeners.forEach(listener -> taskExecutor.submit(() -> listener.onUpdate(accessions)));
+	}
+
+	@Before(value = "execution(* org.genesys2.server.persistence.AccessionRepository.delete(*)) && args(arg)")
+	protected void beforeDeleteAccession(JoinPoint joinPoint, Object arg) throws Throwable {
+
+		StopWatch stopWatch=StopWatch.createStarted();
+		LOG.trace("Before delete accession(s): {}", arg);
+		if (arg == null) {
+			return;
+		}
+		if (arg instanceof Collection<?>) {
+			handleDelete((Collection<Accession>) arg);
+			LOG.debug("Delete notification for {} accession took {}ms", ((Collection<?>) arg).size(), stopWatch.getTime(TimeUnit.MILLISECONDS));
+		} else if (arg instanceof Accession) {
+			handleDelete(Lists.newArrayList((Accession) arg));
+			LOG.debug("Delete notification for 1 accession took {}ms", stopWatch.getTime(TimeUnit.MILLISECONDS));
+		}
+	}
+	
+	private void handleDelete(Collection<Accession> accessions) {
+		if (CollectionUtils.isEmpty(accessions)) {
+			return;
+		}
+		LOG.info("{} accessions were deleted", accessions.size());
+		accessionModifiedListeners.forEach(listener -> taskExecutor.submit(() -> listener.onRemove(accessions)));
+	}
+
+}

src/main/java/org/genesys2/spring/config/AccessionListenersConfig.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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.genesys2.spring.config;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.genesys.glis.v1.TermConstants;
+import org.genesys.glis.v1.api.GenesysApi;
+import org.genesys.glis.v1.model.UpdateTargets;
+import org.genesys.glis.v1.model.UpdatedTarget;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.service.worker.AccessionModifiedAspect.AccessionModifiedListener;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import com.google.common.collect.Lists;
+
+/**
+ * The AccessionListenersConfig configures hard-wired listeners to accession
+ * modifications in Genesys.
+ * 
+ * @author Matija Obreza
+ */
+@Configuration
+public class AccessionListenersConfig {
+
+	@Bean
+	public List<AccessionModifiedListener> accessionModifiedListeners(GenesysApi glisGenesysApi) {
+		ArrayList<AccessionModifiedListener> listeners = Lists.newArrayList(glisUpdater(glisGenesysApi));
+		System.err.println("Declared AccessionModifiedListeners " + listeners.size());
+		List<AccessionModifiedListener> active = listeners.stream().filter(listener -> listener != null).collect(Collectors.toList());
+		System.err.println("Active AccessionModifiedListeners " + listeners.size());
+		return active;
+	}
+
+	
+	/**
+	 * An in-line implementation of the Genesys updater to GLIS.
+	 *
+	 * @param glisGenesysApi the glis genesys api
+	 * @return the listener
+	 */
+	private AccessionModifiedListener glisUpdater(GenesysApi glisGenesysApi) {
+		if (glisGenesysApi == null) {
+			System.err.println("GLIS Client not available. Not initializing GLIS Updater.");
+			return null;
+		}
+
+		return new AccessionModifiedListener() {
+			private final Logger LOG = LoggerFactory.getLogger(AccessionListenersConfig.class + ".glisUpdater");
+
+			@Override
+			public void onUpdate(Collection<Accession> accessions) {
+				UpdateTargets targets = new UpdateTargets();
+				targets.addKwsItem(TermConstants.PASSPORT_DATA);
+				accessions.stream().map(a -> a.getDoi()).filter(doi -> doi != null).forEach(doi -> targets.addDoisItem(doi));
+
+				if (CollectionUtils.isEmpty(targets.getDois())) {
+					try {
+						LOG.info("Updating GLIS for {} accessions with DOIs", targets.getDois().size());
+						List<UpdatedTarget> glisResponse = glisGenesysApi.registerGenesysAsTarget(targets);
+						glisResponse.forEach(updatedTarget -> {
+							if (StringUtils.equals("OK", updatedTarget.getResult())) {
+								LOG.trace("GLIS for {} result={}", updatedTarget.getDoi(), updatedTarget.getResult());
+							} else if (StringUtils.equals("KO", updatedTarget.getResult())) {
+								LOG.info("GLIS for {} result={} msg={}", updatedTarget.getDoi(), updatedTarget.getResult());
+							}
+						});
+					} catch (Throwable e) {
+						LOG.error("Error updating GLIS targets: {}", e.getMessage(), e);
+					}
+				}
+			}
+
+			@Override
+			public void onRemove(Collection<Accession> accessions) {
+				// No operation
+			}
+		};
+	}
+
+}

src/main/java/org/genesys2/spring/config/ApplicationConfig.java

@@ -45,7 +45,7 @@ import org.springframework.security.config.annotation.web.configuration.EnableWe
 
 @Configuration
 @Import({ HazelcastConfig.class, CommonConfig.class, SchedulerConfig.class, DatabaseConfig.class, TemplatingConfig.class, MailConfig.class, OAuth2ServerConfig.class, SecurityConfig.class, CacheConfig.class,
-		ElasticsearchConfig.class, FileRepositoryConfig.class, WebSecurityConfig.class, WebConfiguration.class, AuditConfig.class, GLISConfig.class, SwaggerConfig.class })
+		ElasticsearchConfig.class, FileRepositoryConfig.class, WebSecurityConfig.class, WebConfiguration.class, AuditConfig.class, GLISConfig.class, SwaggerConfig.class, AccessionListenersConfig.class })
 
 @EnableAspectJAutoProxy
 @EnableWebSecurity

src/test/java/org/genesys/test/config/ApplicationConfig.java

@@ -64,7 +64,7 @@ public final class ApplicationConfig {
 	 */
 	@Configuration
 	@Import({ NoHazelcastConfig.class, SchedulerConfig.class, DatabaseConfig.class, TestElasticsearchConfig.class, TemplatingConfig.class, MailConfig.class, SecurityConfig.class, CacheConfig.class,
-			FileRepositoryTestConfig.class, AuditConfig.class })
+			FileRepositoryTestConfig.class, AuditConfig.class, TestAccessionListenersConfig.class })
 	@ComponentScan(basePackages = { "org.genesys.catalog.service.impl", "org.genesys2.brapi.service", "org.genesys2.server.service.impl", "org.genesys2.server.service.worker" } )
 	@EnableAspectJAutoProxy
 	public static class BaseConfig {

src/test/java/org/genesys/test/config/TestAccessionListenersConfig.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * 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.genesys.test.config;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.genesys2.server.service.worker.AccessionModifiedAspect.AccessionModifiedListener;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+/**
+ * Accession listeners config for tests (no listeners)
+ */
+@Configuration
+public class TestAccessionListenersConfig {
+
+	@Bean
+	public List<AccessionModifiedListener> accessionModifiedListeners() {
+		return new ArrayList<>();
+	}
+
+}