package edu.harvard.i2b2.crc.loader.ejb;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.Date;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.crc.loader.dao.IConceptDAO;
import edu.harvard.i2b2.crc.loader.dao.IUploaderDAOFactory;
import edu.harvard.i2b2.crc.loader.dao.UploadStatusDAO;
import edu.harvard.i2b2.crc.loader.dao.UploadStatusDAOI;
import edu.harvard.i2b2.crc.loader.datavo.loader.UploadSetStatus;
/**
* This specific loader class for Visit dimension. This class performs three
* operations, namely. 1.Build PatientData xml file based, if input file is csv
* 2.Load PatientData xml information into staging area in database. 3.Run
* procedure which will merge staging area into Visit dimension.
*
* @author rk903
*
*/
public class ConceptLoader extends AbstractDimensionLoader {
private static Log log = LogFactory.getLog(ConceptLoader.class);
IConceptDAO conceptDAO = null;
boolean deleteOldDataFlag = false;
public ConceptLoader(IUploaderDAOFactory uploaderDaoFactory,
String inputLoadFile, String inputLoadFileFormat,
String encounterSource, String sourceSystemCd,
boolean deleteOldDataFlag, int uploadId) {
setUploaderDaoFactory(uploaderDaoFactory);
setInputLoadFile(inputLoadFile);
setInputLoadFileFormat(inputLoadFileFormat);
setEncounterSource(encounterSource);
setUploadId(uploadId);
setSourceSystemCd(sourceSystemCd);
this.deleteOldDataFlag = deleteOldDataFlag;
conceptDAO = uploaderDaoFactory.getConceptDAO();
}
public void load() throws I2B2Exception {
try {
// update the status table
UploadStatusDAOI uploadStatusDao = uploaderDaoFactory
.getUploadStatusDAO();
UploadSetStatus setStatus = new UploadSetStatus();
setStatus.setUploadId(getUploadId());
setStatus.setLoadStatus("STARTED");
setStatus.setSetTypeId(UploadStatusDAO.CONCEPT_SET);
setStatus.setInputFileName(this.getInputLoadFile());
setStatus.setSourceCd(getSourceSystemCd());
setStatus.setLoadDate(new Date(System.currentTimeMillis()));
uploadStatusDao.insertUploadSetStatus(setStatus);
// set pdo xml file
setOutputXmlFileName(getInputLoadFile());
String tempConceptTableName = "TEMP_CONCEPT_" + getUploadId();
setStagingTableName(tempConceptTableName);
IConceptDAO conceptDAO = uploaderDaoFactory.getConceptDAO();
conceptDAO.createTempTable(tempConceptTableName);
log.info("Created Visit staging table" + getStagingTableName());
ConceptXmlDbLoader conceptDbLoader = new ConceptXmlDbLoader(
uploaderDaoFactory, getOutputXmlFileName(),
getStagingTableName(), getUploadId());
conceptDbLoader.doUpload();
log.info("Uploaded " + getOutputXmlFileName() + "to staging table"
+ getStagingTableName());
conceptDAO.createConceptFromTempTable(getStagingTableName(),
getUploadId());
log.info("Completed Concept insert operation for staging table"
+ getStagingTableName());
setStatus = uploadStatusDao.getUploadSetStatus(getUploadId(),
UploadStatusDAO.CONCEPT_SET);
setStatus.setLoadStatus("COMPLETED");
setStatus.setEndDate(new Date(System.currentTimeMillis()));
setStatus.setLoadedRecord(conceptDAO
.getRecordCountByUploadId(getUploadId()));
// setStatus.setDeletedRecord(deletedRecord);
setStatus.setNoOfRecord(conceptDbLoader.getRowCount());
uploadStatusDao.updateUploadSetStatus(setStatus);
} catch (I2B2Exception i2b2Ex) {
// try to write error to set status table, if that fails then simply
// pass the exception to top level
UploadStatusDAOI uploadStatusDao = uploaderDaoFactory
.getUploadStatusDAO();
UploadSetStatus setStatus = uploadStatusDao.getUploadSetStatus(
getUploadId(), UploadStatusDAO.CONCEPT_SET);
setStatus.setLoadStatus("ERROR");
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
i2b2Ex.printStackTrace(pw);
setStatus.setMessage(sw.toString().substring(0, 500));
uploadStatusDao.updateUploadSetStatus(setStatus);
throw i2b2Ex;
}
}
@Override
public void createTempTable() throws I2B2Exception {
// set pdo xml file
setOutputXmlFileName(getInputLoadFile());
String tempConceptTableName = "TEMP_CONCEPT_" + getUploadId();
setStagingTableName(tempConceptTableName);
conceptDAO.createTempTable(tempConceptTableName);
log.info("Created Visit staging table" + getStagingTableName());
}
@Override
public int loadTempTable() throws I2B2Exception {
ConceptXmlDbLoader conceptDbLoader = new ConceptXmlDbLoader(
uploaderDaoFactory, getOutputXmlFileName(),
getStagingTableName(), getUploadId());
conceptDbLoader.doUpload();
log.info("Uploaded " + getOutputXmlFileName() + "to staging table"
+ getStagingTableName());
return conceptDbLoader.getRowCount();
}
@Override
public int mergeTempTable() throws I2B2Exception {
String backupConceptDimensionTableName = "cd_bkup_" + getUploadId();
if (deleteOldDataFlag) {
conceptDAO.backupAndSyncConceptDimensionTable(
getStagingTableName(), backupConceptDimensionTableName,
getUploadId());
} else {
conceptDAO.createConceptFromTempTable(getStagingTableName(),
getUploadId());
}
log.info("Completed Concept insert operation for staging table"
+ getStagingTableName());
UploadStatusDAOI uploadStatusDao = uploaderDaoFactory
.getUploadStatusDAO();
UploadSetStatus setStatus = uploadStatusDao.getUploadSetStatus(
getUploadId(), UploadStatusDAO.CONCEPT_SET);
setStatus.setLoadStatus("COMPLETED");
setStatus.setEndDate(new Date(System.currentTimeMillis()));
setStatus.setLoadedRecord(conceptDAO
.getRecordCountByUploadId(getUploadId()));
// setStatus.setDeletedRecord(deletedRecord);
// ssetStatus.setNoOfRecord(conceptDbLoader.getRowCount());
uploadStatusDao.updateUploadSetStatus(setStatus);
return conceptDAO.getRecordCountByUploadId(getUploadId());
}
@Override
public void setStartStatus() {
// update the status table
UploadStatusDAOI uploadStatusDao = uploaderDaoFactory
.getUploadStatusDAO();
UploadSetStatus setStatus = new UploadSetStatus();
setStatus.setUploadId(getUploadId());
setStatus.setLoadStatus("STARTED");
setStatus.setSetTypeId(UploadStatusDAO.CONCEPT_SET);
setStatus.setInputFileName(this.getInputLoadFile());
setStatus.setSourceCd(getSourceSystemCd());
setStatus.setLoadDate(new Date(System.currentTimeMillis()));
uploadStatusDao.insertUploadSetStatus(setStatus);
}
}