Java tutorial
/* * Copyright 2015 Observational Health Data Sciences and Informatics [OHDSI.org]. * * 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.ohdsi.webapi.ircalc; import com.fasterxml.jackson.databind.ObjectMapper; import java.util.Calendar; import java.util.Collection; import java.util.Date; import java.util.List; import java.util.Map; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.ohdsi.sql.SqlSplit; import org.ohdsi.sql.SqlTranslate; import org.ohdsi.webapi.GenerationStatus; import org.ohdsi.webapi.util.SessionUtils; 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; import org.springframework.jdbc.core.JdbcTemplate; import org.springframework.transaction.TransactionDefinition; import org.springframework.transaction.TransactionStatus; import org.springframework.transaction.support.DefaultTransactionDefinition; import org.springframework.transaction.support.TransactionCallback; import org.springframework.transaction.support.TransactionTemplate; /** * * @author Chris Knoll <cknoll@ohdsi.org> */ public class PerformAnalysisTasklet implements Tasklet { private static final Log log = LogFactory.getLog(PerformAnalysisTasklet.class); private static final int MAX_MESSAGE_LENGTH = 2000; private final static IRAnalysisQueryBuilder analysisQueryBuilder = new IRAnalysisQueryBuilder(); private final JdbcTemplate jdbcTemplate; private final TransactionTemplate transactionTemplate; private final IncidenceRateAnalysisRepository incidenceRateAnalysisRepository; public PerformAnalysisTasklet(final JdbcTemplate jdbcTemplate, final TransactionTemplate transactionTemplate, final IncidenceRateAnalysisRepository incidenceRateAnalysisRepository) { this.jdbcTemplate = jdbcTemplate; this.transactionTemplate = transactionTemplate; this.incidenceRateAnalysisRepository = incidenceRateAnalysisRepository; } private ExecutionInfo findExecutionInfoBySourceId(Collection<ExecutionInfo> infoList, Integer sourceId) { for (ExecutionInfo info : infoList) { if (sourceId.equals(info.getId().getSourceId())) return info; } return null; } private int[] doTask(ChunkContext chunkContext) { ObjectMapper mapper = new ObjectMapper(); Map<String, Object> jobParams = chunkContext.getStepContext().getJobParameters(); Integer analysisId = Integer.valueOf(jobParams.get("analysis_id").toString()); int[] result = null; try { String sessionId = SessionUtils.sessionId(); IncidenceRateAnalysis analysis = this.incidenceRateAnalysisRepository.findOne(analysisId); IncidenceRateAnalysisExpression expression = mapper.readValue(analysis.getDetails().getExpression(), IncidenceRateAnalysisExpression.class); IRAnalysisQueryBuilder.BuildExpressionQueryOptions options = new IRAnalysisQueryBuilder.BuildExpressionQueryOptions(); options.cdmSchema = jobParams.get("cdm_database_schema").toString(); options.resultsSchema = jobParams.get("results_database_schema").toString(); String deleteSql = String.format("DELETE FROM %s.ir_strata WHERE analysis_id = %d", options.resultsSchema, analysisId); this.jdbcTemplate.update(deleteSql); String insertSql = StringUtils.replace( "INSERT INTO @results_schema.ir_strata (analysis_id, strata_sequence, name, description) VALUES (?,?,?,?)", "@results_schema", options.resultsSchema); insertSql = SqlTranslate.translateSql(insertSql, "sql server", jobParams.get("target_dialect").toString(), sessionId, null); List<StratifyRule> strataRules = expression.strata; for (int i = 0; i < strataRules.size(); i++) { StratifyRule r = strataRules.get(i); this.jdbcTemplate.update(insertSql, new Object[] { analysisId, i, r.name, r.description }); } String expressionSql = analysisQueryBuilder.buildAnalysisQuery(analysis, options); String translatedSql = SqlTranslate.translateSql(expressionSql, "sql server", jobParams.get("target_dialect").toString(), sessionId, null); String[] sqlStatements = SqlSplit.splitSql(translatedSql); result = PerformAnalysisTasklet.this.jdbcTemplate.batchUpdate(sqlStatements); } catch (Exception e) { throw new RuntimeException(e); } return result; } @Override public RepeatStatus execute(final StepContribution contribution, final ChunkContext chunkContext) throws Exception { Date startTime = Calendar.getInstance().getTime(); Map<String, Object> jobParams = chunkContext.getStepContext().getJobParameters(); Integer analysisId = Integer.valueOf(jobParams.get("analysis_id").toString()); Integer sourceId = Integer.valueOf(jobParams.get("source_id").toString()); boolean isValid = false; String statusMessage = "OK"; DefaultTransactionDefinition requresNewTx = new DefaultTransactionDefinition(); requresNewTx.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW); TransactionStatus initStatus = this.transactionTemplate.getTransactionManager() .getTransaction(requresNewTx); IncidenceRateAnalysis analysis = this.incidenceRateAnalysisRepository.findOne(analysisId); ExecutionInfo analysisInfo = findExecutionInfoBySourceId(analysis.getExecutionInfoList(), sourceId); analysisInfo.setIsValid(false); analysisInfo.setStartTime(startTime); analysisInfo.setStatus(GenerationStatus.RUNNING); this.incidenceRateAnalysisRepository.save(analysis); this.transactionTemplate.getTransactionManager().commit(initStatus); try { final int[] ret = this.transactionTemplate.execute(new TransactionCallback<int[]>() { @Override public int[] doInTransaction(final TransactionStatus status) { return doTask(chunkContext); } }); log.debug("Update count: " + ret.length); isValid = true; } catch (final Exception e) { isValid = false; statusMessage = e.getMessage(); log.error(e.getMessage(), e); throw e;//FAIL job status } finally { TransactionStatus completeStatus = this.transactionTemplate.getTransactionManager() .getTransaction(requresNewTx); Date endTime = Calendar.getInstance().getTime(); analysis = this.incidenceRateAnalysisRepository.findOne(analysisId); analysisInfo = findExecutionInfoBySourceId(analysis.getExecutionInfoList(), sourceId); analysisInfo.setIsValid(isValid); analysisInfo.setExecutionDuration((int) (endTime.getTime() - startTime.getTime())); analysisInfo.setStatus(GenerationStatus.COMPLETE); analysisInfo .setMessage(statusMessage.substring(0, Math.min(MAX_MESSAGE_LENGTH, statusMessage.length()))); this.incidenceRateAnalysisRepository.save(analysis); this.transactionTemplate.getTransactionManager().commit(completeStatus); } return RepeatStatus.FINISHED; } }