Register Genesys as target for passport data for accessions with DOI

- when upserted through the API

pom.xml

@@ -532,6 +532,11 @@
 			<artifactId>liquibase-core</artifactId>
 			<version>${liquibase.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.genesys-pgr</groupId>
+			<artifactId>glis-client-resttemplate</artifactId>
+			<version>1.0-SNAPSHOT</version>
+		</dependency>
 	</dependencies>
 
 	<build>

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

@@ -33,6 +33,10 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang.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.model.genesys.AccessionAlias;
 import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
@@ -99,6 +103,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Autowired
 	private TaxonomyManager taxonomyManager;
 
+	@Autowired
+	private GenesysApi glisGenesysApi;
+
 	@Override
 	// Read-only, everything happens in manager
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
@@ -264,7 +271,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			}
 
 			updateDoi(accession, accnJson.get(Api1Constants.Accession.DOI));
-			if (accession.getDoi()!=null) {
+			if (accession.getDoi() != null) {
 				// Update ACCENUMB if DOI is provided
 				accession.setAccessionName(dataJson.acceNumb);
 			}
@@ -586,6 +593,26 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		// Update PDCI
 		genesysService.updatePDCI(savedData.stream().map(a -> a.getId()).collect(Collectors.toSet()));
 
+		// Update GLIS
+		UpdateTargets targets = new UpdateTargets();
+		targets.addKwsItem(TermConstants.PASSPORT_DATA);
+		savedData.stream().map(a -> a.getDoi()).filter(doi -> doi != null).forEach(doi -> targets.addDoisItem(doi));
+		if (targets.getDois().size() > 0) {
+			try {
+				LOG.debug("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);
+			}
+		}
+
 		return upsertResponses;
 	}
 

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

@@ -40,10 +40,10 @@ import org.springframework.core.io.Resource;
 
 @Configuration
 @Import({ CommonConfig.class, SchedulerConfig.class, DatabaseConfig.class, MailConfig.class, OAuth2ServerConfig.class, SecurityConfig.class, CacheConfig.class,
-		ElasticsearchConfig.class, FileRepositoryConfig.class, WebConfiguration.class, AuditConfig.class })
+		ElasticsearchConfig.class, FileRepositoryConfig.class, WebConfiguration.class, AuditConfig.class, GLISConfig.class })
 public class ApplicationConfig {
 	public static final Logger LOG = LoggerFactory.getLogger(ApplicationConfig.class);
-
+	
 	@Bean
 	public TransifexService transifexService() {
 		return new TransifexServiceImpl();

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

+/*
+ * Copyright 2017 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 org.genesys.glis.v1.GlisRateLimiter;
+import org.genesys.glis.v1.invoker.ApiClient;
+import org.genesys.glis.v1.invoker.auth.HttpBasicAuth;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+// Get the beans!
+@ComponentScan(basePackages = { "org.genesys.glis.v1.api" })
+public class GLISConfig {
+
+	@Value("${itpgrfa.glis.basepath}")
+	private String basePath;
+
+	@Value("${itpgrfa.glis.username}")
+	private String username;
+
+	@Value("${itpgrfa.glis.password}")
+	private String password;
+
+	@Value("${itpgrfa.glis.ratelimit}")
+	private double glisRateLimit;
+
+	@Bean
+	public GlisRateLimiter glisRateLimiter() {
+		return new GlisRateLimiter(glisRateLimit);
+	}
+
+	@Bean
+	public ApiClient glisClient() {
+		ApiClient client = new ApiClient();
+		client.setDebugging("true".equals(System.getenv("GLIS_DEBUG")));
+		client.setBasePath(basePath);
+
+		// Configure HTTP basic authorization: glis_auth
+		HttpBasicAuth easySmtaAuth = (HttpBasicAuth) client.getAuthentication("easySmta");
+		easySmtaAuth.setUsername(username);
+		easySmtaAuth.setPassword(password);
+		
+		System.err.println("GLIS at " + client.getBasePath() + " with username=" + username);
+		return client;
+	}
+}

src/main/resources/application.properties

@@ -191,3 +191,9 @@ repository.ftp.keystore.password=changeit!
 repository.ftp.port=8021
 repository.ftp.passivePorts=2300-2350
 repository.ftp.externalAddress=
+
+# GLIS 
+itpgrfa.glis.basepath=https://glistest.planttreaty.org
+itpgrfa.glis.username=
+itpgrfa.glis.password=
+itpgrfa.glis.ratelimit=20

src/test/java/org/genesys2/tests/resttests/AbstractRestTest.java

@@ -50,6 +50,7 @@ import org.genesys.filerepository.service.impl.FilesystemStorageServiceImpl;
 import org.genesys.filerepository.service.impl.ImageGalleryServiceImpl;
 import org.genesys.filerepository.service.impl.RepositoryServiceImpl;
 import org.genesys.filerepository.service.impl.ThumbnailGenerator1;
+import org.genesys.glis.v1.api.GenesysApi;
 import org.genesys2.brapi.service.impl.BrAPIServiceImpl;
 import org.genesys2.server.aspect.AsAdminAspect;
 import org.genesys2.server.aspect.GenesysImageGalleryAspects;
@@ -396,6 +397,11 @@ public abstract class AbstractRestTest extends BaseSpringTest {
 		public BatchRESTService batchRESTService() {
 			return new BatchRESTServiceImpl();
 		}
+		
+		@Bean
+		public GenesysApi glisGenesysApi() {
+			return new GenesysApi();
+		}
 
 		@Bean
 		public TaxonomyManager taxonomyManager() {