Update accession-country references, accession-faoinstitute references

src/main/java/org/crophub/rest/common/persistence/domain/GenesysLowlevelRepository.java

+/**
+ * Copyright 2013 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.crophub.rest.common.persistence.domain;
+
+public interface GenesysLowlevelRepository {
+
+	void updateCountryRefs();
+
+	void updateFaoInstituteRefs();
+
+}

src/main/java/org/crophub/rest/common/persistence/domain/GenesysLowlevelRepositoryImpl.java

+/**
+ * Copyright 2013 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.crophub.rest.common.persistence.domain;
+
+import javax.sql.DataSource;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.stereotype.Repository;
+import org.springframework.transaction.annotation.Transactional;
+
+@Repository
+@Transactional(readOnly = true)
+public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository {
+	public static final Log LOG = LogFactory.getLog(GenesysLowlevelRepositoryImpl.class);
+
+	private JdbcTemplate jdbcTemplate;
+
+	@Autowired
+	public void setDataSource(final DataSource dataSource) {
+		this.jdbcTemplate = new JdbcTemplate(dataSource);
+	}
+
+	@Override
+	@Transactional(readOnly = false)
+	public void updateFaoInstituteRefs() {
+		LOG.info("Updating institute references");
+		int count = jdbcTemplate.update("UPDATE `accession` A inner join `faoinstitute` FI on FI.code=A.Institute set A.instituteId=FI.id;");
+		LOG.info("Institute references updated: " + count);
+
+		
+		LOG.info("Updating institute accession count");
+		count = jdbcTemplate
+				.update("UPDATE faoinstitute FI inner join (select instituteId, count(*) X from accession group by instituteId) A on A.instituteId=FI.id set FI.accessionCount=A.X;");
+		LOG.info("Institute accession counts updated: " + count);
+	}
+
+	@Override
+	@Transactional(readOnly = false)
+	public void updateCountryRefs() {
+		LOG.info("Updating country references");
+		int count = jdbcTemplate.update("UPDATE `accession` A inner join `country` C on C.code3=A.Origin set A.originId=C.id WHERE A.Origin IS NOT NULL;");
+		LOG.info("Country references updated: " + count);
+	}
+}

src/main/java/org/crophub/rest/common/service/GenesysService.java

@@ -96,4 +96,8 @@ public interface GenesysService {
 
 	Page<Accession> listAccessionsByOrganization(Organization organization, Pageable pageable);
 
+	void updateAccessionCountryRefs();
+
+	void updateAccessionInstitueRefs();
+
 }

src/main/java/org/crophub/rest/common/service/impl/GenesysServiceImpl.java

@@ -45,6 +45,7 @@ import org.crophub.rest.common.persistence.domain.AccessionNameRepository;
 import org.crophub.rest.common.persistence.domain.AccessionRepository;
 import org.crophub.rest.common.persistence.domain.AccessionTraitRepository;
 import org.crophub.rest.common.persistence.domain.CropTaxonomyRepository;
+import org.crophub.rest.common.persistence.domain.GenesysLowlevelRepository;
 import org.crophub.rest.common.persistence.domain.MetadataMethodRepository;
 import org.crophub.rest.common.persistence.domain.MetadataRepository;
 import org.crophub.rest.common.persistence.domain.MethodRepository;
@@ -100,6 +101,9 @@ public class GenesysServiceImpl implements GenesysService, TraitService {
 	@Autowired
 	private OrganizationRepository organizationRepository;
 
+	@Autowired
+	private GenesysLowlevelRepository genesysLowlevelRepository;
+
 	@Override
 	public long countByInstitute(FaoInstitute institute) {
 		return accessionRepository.countByInstitute(institute);
@@ -275,4 +279,16 @@ public class GenesysServiceImpl implements GenesysService, TraitService {
 	public List<Metadata> listMetadataByMethod(Method method) {
 		return metadataMethodRepository.listMetadataByMethod(method);
 	}
+
+	@Override
+	@Transactional(readOnly = false)
+	public void updateAccessionCountryRefs() {
+		genesysLowlevelRepository.updateCountryRefs();
+	}
+
+	@Override
+	@Transactional(readOnly = false)
+	public void updateAccessionInstitueRefs() {
+		genesysLowlevelRepository.updateFaoInstituteRefs();
+	}
 }

src/main/java/org/crophub/rest/servlet/controller/AdminController.java

@@ -20,6 +20,7 @@ import java.io.IOException;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.crophub.rest.common.service.GenesysService;
 import org.crophub.rest.common.service.GeoService;
 import org.crophub.rest.common.service.LuceneIndexer;
 import org.crophub.rest.common.service.impl.InstituteUpdater;
@@ -40,6 +41,9 @@ public class AdminController {
 	@Autowired
 	LuceneIndexer luceneIndexer;
 
+	@Autowired
+	GenesysService genesysService;
+
 	@Autowired
 	GeoService geoService;
 
@@ -73,11 +77,22 @@ public class AdminController {
 		luceneIndexer.reindexEverything();
 		return "redirect:/admin/";
 	}
-	
+
 	@RequestMapping(method = RequestMethod.POST, value = "/reindexEntity")
 	public String reindexEntities(@RequestParam("entity") String entityName) {
 		luceneIndexer.reindexEntity(entityName);
 		return "redirect:/admin/";
 	}
 
+	@RequestMapping(method = RequestMethod.POST, value = "/updateAccessionCountryRefs")
+	public String updateAccessionCountryRefs() {
+		genesysService.updateAccessionCountryRefs();
+		return "redirect:/admin/";
+	}
+
+	@RequestMapping(method = RequestMethod.POST, value = "/updateAccessionInstituteRefs")
+	public String updateAccessionInstituteRefs() {
+		genesysService.updateAccessionInstitueRefs();
+		return "redirect:/admin/";
+	}
 }

src/main/webapp/WEB-INF/jsp/admin/index.jsp

@@ -22,6 +22,13 @@
 		<form method="post" action="<c:url value="/admin/reindexEverything" />">
 			<input type="submit" value="Reindex search indexes" />
 		</form>
+		<form method="post" action="<c:url value="/admin/updateAccessionCountryRefs" />">
+			<input type="submit" value="Update accession country info" />
+		</form>		
+		
+		<form method="post" action="<c:url value="/admin/updateAccessionInstituteRefs" />">
+			<input type="submit" value="Update accession institute info" />
+		</form>
 		
 		
 		<form method="post" action="<c:url value="/admin/reindexEntity" />">