/* * This is eMonocot, a global online biodiversity information resource. * * Copyright © 2011–2015 The Board of Trustees of the Royal Botanic Gardens, Kew and The University of Oxford * * eMonocot is free software: you can redistribute it and/or modify it under the terms of the * GNU Affero General Public License as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * eMonocot is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even * the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Affero General Public License for more details. * * The complete text of the GNU Affero General Public License is in the source repository as the file * ‘COPYING’. It is also available from <http://www.gnu.org/licenses/>. */ package org.emonocot.job.dwc.read; import java.util.HashMap; import java.util.Map; import org.joda.time.DateTime; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.springframework.batch.core.ExitStatus; import org.springframework.batch.core.StepContribution; import org.springframework.batch.core.scope.context.ChunkContext; import org.springframework.batch.core.step.tasklet.Tasklet; import org.springframework.batch.repeat.RepeatStatus; /** * * @author ben * */ public class OwnedRecordAnnotator extends AbstractRecordAnnotator implements Tasklet { private Logger logger = LoggerFactory.getLogger(OwnedRecordAnnotator.class); private String subtribe; private String tribe; private String subfamily; private String family; private String annotatedObjType; public void setSubtribe(String subtribe) { this.subtribe = subtribe; } public void setTribe(String tribe) { this.tribe = tribe; } public void setSubfamily(String subfamily) { this.subfamily = subfamily; } public void setFamily(String family) { this.family = family; } public void setAnnotatedObjType(String annotatedObjType) { this.annotatedObjType = annotatedObjType; } @Override public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception { String subsetRank = null; String subsetValue = null; if (subtribe != null) { subsetRank = "subtribe"; subsetValue = subtribe; } else if (tribe != null) { subsetRank = "tribe"; subsetValue = tribe; } else if (subfamily != null) { subsetRank = "subfamily"; subsetValue = subfamily; } else if (family != null) { subsetRank = "family"; subsetValue = family; } String queryString = null; Map<String, Object> queryParameters = new HashMap<String, Object>(); if (subsetValue != null) { queryString = "insert into Annotation (annotatedObjId, annotatedObjType, jobId, dateTime, authority_id, type, code, recordType) select o.id, :annotatedObjType, :jobId, now(), :authorityId, 'Warn', 'Absent', :annotatedObjType from #annotatedObjType o join taxon t on (o.taxon_id = t.id) left join taxon a on (t.acceptedNameUsage_id = a.id) where o.authority_id = :authorityId and (t.#subsetRank = :subsetValue or a.#subsetRank = :subsetValue)"; queryString = queryString.replaceAll("#subsetRank", subsetRank); queryParameters.put("subsetValue", subsetValue); } else { queryString = "insert into Annotation (annotatedObjId, annotatedObjType, jobId, dateTime, authority_id, type, code, recordType) select o.id, :annotatedObjType, :jobId, now(), :authorityId, 'Warn', 'Absent', :annotatedObjType from #annotatedObjType o where o.authority_id = :authorityId"; } queryString = queryString.replaceAll("#annotatedObjType", annotatedObjType); queryParameters.put("annotatedObjType", annotatedObjType); logger.debug(queryString); int numberUpdated = annotate(queryString, queryParameters); logger.debug(numberUpdated + " Annotation records inserted"); return RepeatStatus.FINISHED; } }