List of usage examples for org.hibernate.stat SessionStatistics getCollectionCount
int getCollectionCount();
From source file:org.inbio.neoportal.index.Importer.java
License:Open Source License
/** * //from w w w . j av a 2 s .com */ @Transactional public void indexOccurrences() { Session session = sessionFactory.getCurrentSession(); // FullTextSession fullTextSession = Search.getFullTextSession(session); // config session for bash job session.setFlushMode(FlushMode.MANUAL); // fullTextSession.setFlushMode(FlushMode.MANUAL); logger.log(org.apache.log4j.Level.DEBUG, "Starting importOccurrences process"); //get current date for dateLastModified field DateFormat dateFormat = new SimpleDateFormat("dd/MM/yyyy"); Date date = new Date(); String dateLastModified = dateFormat.format(date); DateFormat sourceDateFormat = new SimpleDateFormat("dd-MMM-yy", Locale.ENGLISH); int firstResult = 0; int setCounter = 0; //every 100 (the jdbc batch size) call flush DataProvider dp = dataProviderDAO.findAll().get(0); logger.log(org.apache.log4j.Level.DEBUG, "importOccurrences Begin Transaction"); ScrollableResults scroll = session.createCriteria(ImportDwc.class).setFetchSize(BATCH_SIZE) .setCacheMode(CacheMode.IGNORE).setReadOnly(true).scroll(ScrollMode.FORWARD_ONLY); boolean update; int batch = 0; int rowsCounter = 0; while (scroll.next()) { batch++; rowsCounter++; ImportDwc importDwc = (ImportDwc) scroll.get(0); logger.trace("ImportDwc after scroll.get"); try { //avoid repeated occurrenceId OccurrenceDwc occurrence = occurrenceDAO .findByCatalogNumberHql(importDwc.getCatalogNumber().replace("\"", "")); logger.trace("OccurrenceDwc after findByCatalogNumber " + importDwc.getCatalogNumber().replace("\"", "")); if (occurrence != null) { update = true; // continue; } else { update = false; occurrence = new OccurrenceDwc(); } Taxon taxon = null; //check if taxonId is empty (unidentify specimens) if (importDwc.getTaxonId().isEmpty()) { taxon = null; } else { // check if is the same taxon already associated with the occurrence if (update && occurrence.getTaxonId().equals(importDwc.getTaxonId().replace("\"", ""))) { taxon = occurrence.getTaxon(); logger.trace("Occurrence update with same taxon"); } else { // find taxon entity // taxon = taxonNewDAO.findById(new BigDecimal(importDwc.getTaxonId().replace("\"", ""))); List<Taxon> taxonList = taxonDAO.findByDefaultName(importDwc.getScientificName()); logger.trace("Taxon after findByDefaultName"); if (taxonList.size() == 1) taxon = taxonList.get(0); else if (taxonList.size() > 1) { for (Taxon taxon2 : taxonList) { if (taxon2.getKingdom().equals(importDwc.getKingdom())) { taxon = taxon2; break; } } } } } // TODO: fix, use specimenId instead occurrence.setOccurrenceId(importDwc.getCatalogNumber().replace("\"", "")); occurrence.setDataProvider(dp); occurrence.setTaxon(taxon); //find or create location Location location = locationDAO.findById(new BigDecimal(importDwc.getLocationId())); logger.trace("Location after findById"); if (location == null) { location = new Location(new BigDecimal(importDwc.getLocationId())); location.setHigherGeographyId(importDwc.getHigherGeographyId()); location.setHigherGeography(importDwc.getHigherGeography()); location.setContinent(importDwc.getContinent()); location.setWaterBody(importDwc.getWaterBody()); location.setIslandGroup(importDwc.getIslandGroup()); location.setIsland(importDwc.getIsland()); location.setCountry(importDwc.getCountry()); location.setCountryCode(importDwc.getCountryCode()); location.setStateProvince(importDwc.getStateProvince()); location.setCounty(importDwc.getCounty()); location.setMunicipality(importDwc.getMunicipality()); location.setLocality(importDwc.getLocality()); location.setVerbatimLocality(importDwc.getVerbatimLocality()); location.setVerbatimElevation(importDwc.getVerbatimElevation()); location.setMinimumElevationInMeters(importDwc.getMinimumElevationInMeters()); location.setMaximumElevationInMeters(importDwc.getMaximumElevationInMeters()); location.setVerbatimDepth(importDwc.getVerbatimDepth()); location.setMinimumDepthInMeters(importDwc.getMinimumDepthInMeters()); location.setMaximumDepthInMeters(importDwc.getMaximumDepthInMeters()); location.setMinimumDistanceAboveSurfaceInMeters( importDwc.getMinimumDistanceAboveSurfaceInMeters()); location.setMaximumDistanceAboveSurfaceInMeters( importDwc.getMaximumDistanceAboveSurfaceInMeters()); location.setLocationAccordingTo(importDwc.getLocationAccordingTo()); location.setLocationRemarks(importDwc.getLocationRemarks()); location.setVerbatimCoordinates(importDwc.getVerbatimCoordinates()); location.setVerbatimLatitude(importDwc.getVerbatimLatitude()); location.setVerbatimLongitude(importDwc.getVerbatimLongitude()); location.setVerbatimCoordinateSystem(importDwc.getVerbatimCoordinateSystem()); location.setVerbatimSRS(importDwc.getVerbatimSRS()); if (!importDwc.getDecimalLatitude().isEmpty()) location.setDecimalLatitude(Double.valueOf(importDwc.getDecimalLatitude())); if (!importDwc.getDecimalLongitude().isEmpty()) location.setDecimalLongitude(Double.valueOf(importDwc.getDecimalLongitude())); location.setGeodeticDatum(importDwc.getGeodeticDatum()); location.setCoordinateUncertaintyInMeters(importDwc.getCoordinateUncertaintyInMeters()); location.setCoordinatePrecision(importDwc.getCoordinatePrecision()); location.setPointRadiusSpatialFit(importDwc.getPointRadiusSpatialFit()); location.setFootprintWKT(importDwc.getFootprintWKT()); location.setFootprintSRS(importDwc.getFootprintSRS()); location.setFootprintSpatialFit(importDwc.getFootprintSpatialFit()); location.setGeoreferencedBy(importDwc.getGeoreferencedBy()); location.setGeoreferencedDate(importDwc.getGeoreferencedDate()); location.setGeoreferenceProtocol(importDwc.getGeoreferenceProtocol()); location.setGeoreferenceSources(importDwc.getGeoreferenceSources()); location.setGeoreferenceVerificationStatus(importDwc.getGeoreferenceVerificationStatus()); location.setGeoreferenceRemarks(importDwc.getGeoreferenceRemarks()); locationDAO.create(location); // increment batch because location should be inserted batch++; } occurrence.setLocation(location); occurrence.setType(importDwc.getType()); occurrence.setModified(importDwc.getModified()); occurrence.setLanguage(importDwc.getLanguage()); occurrence.setRights(importDwc.getRights()); occurrence.setRightsHolder(importDwc.getRightsHolder()); occurrence.setAccessRights(importDwc.getAccessRights()); occurrence.setBibliographicCitation(importDwc.getBibliographicCitation()); occurrence.setReferences(importDwc.getReferences()); occurrence.setInstitutionId(importDwc.getInstitutionId()); occurrence.setCollectionId(importDwc.getCollectionId()); occurrence.setDatasetId(importDwc.getDatasetId()); occurrence.setInstitutionCode(importDwc.getInstitutionCode()); occurrence.setCollectionCode(importDwc.getCollectionCode()); occurrence.setDatasetName(importDwc.getDatasetName()); occurrence.setOwnerInstitutionCode(importDwc.getOwnerInstitutionCode()); occurrence.setBasisOfRecord(importDwc.getBasisOfRecord()); occurrence.setInformationWithheld(importDwc.getInformationWithheld()); occurrence.setDataGeneralizations(importDwc.getDataGeneralizations()); occurrence.setDynamicProperties(importDwc.getDynamicProperties()); occurrence.setOccurrenceId(importDwc.getOccurrenceId().toString()); occurrence.setCatalogNumber(importDwc.getCatalogNumber()); occurrence.setOccurrenceRemarks(importDwc.getOccurrenceRemarks()); occurrence.setRecordNumber(importDwc.getRecordNumber()); occurrence.setRecordedBy(importDwc.getRecordedBy()); occurrence.setIndividualId(importDwc.getIndividualId()); occurrence.setIndividualCount(importDwc.getIndividualCount()); occurrence.setSex(importDwc.getSex()); occurrence.setLifeStage(importDwc.getLifeStage()); occurrence.setReproductiveCondition(importDwc.getReproductiveCondition()); occurrence.setBehavior(importDwc.getBehavior()); occurrence.setEstablishmentMeans(importDwc.getEstablishmentMeans()); occurrence.setOccurrenceStatus(importDwc.getOccurrenceStatus()); occurrence.setPreparations(importDwc.getPreparations()); occurrence.setDisposition(importDwc.getDisposition()); occurrence.setOtherCatalogNumbers(importDwc.getOtherCatalogNumbers()); occurrence.setPreviousIdentifications(importDwc.getPreviousIdentifications()); occurrence.setAssociatedMedia(importDwc.getAssociatedMedia()); occurrence.setAssociatedReferences(importDwc.getAssociatedReferences()); occurrence.setAssociatedOccurrences(importDwc.getAssociatedOccurrences()); occurrence.setAssociatedSequences(importDwc.getAssociatedSequences()); occurrence.setAssociatedTaxa(importDwc.getAssociatedTaxa()); occurrence.setEventId(importDwc.getEventId()); occurrence.setSamplingProtocol(importDwc.getSamplingProtocol()); occurrence.setSamplingEffort(importDwc.getSamplingEffort()); occurrence.setEventDate(importDwc.getEventDate()); occurrence.setEventTime(importDwc.getEventTime()); occurrence.setStartDayOfYear(importDwc.getStartDayOfYear()); occurrence.setEndDayOfYear(importDwc.getEndDayOfYear()); occurrence.setYear(importDwc.getYear()); occurrence.setMonth(importDwc.getMonth()); occurrence.setDay(importDwc.getDay()); occurrence.setVerbatimEventDate(importDwc.getVerbatimEventDate()); occurrence.setHabitat(importDwc.getHabitat()); occurrence.setFieldNotes(importDwc.getFieldNumber()); occurrence.setFieldNotes(importDwc.getFieldNotes()); occurrence.setEventRemarks(importDwc.getEventRemarks()); occurrence.setGeologicalContextId(importDwc.getGeologicalContextId()); occurrence.setEarliestEonOrLowestEonothem(importDwc.getEarliestEonOrLowestEonothem()); occurrence.setLatestEonOrHighestEonothem(importDwc.getLatestEonOrHighestEonothem()); occurrence.setEarliestEraOrLowestErathem(importDwc.getEarliestEraOrLowestErathem()); occurrence.setLatestEraOrHighestErathem(importDwc.getLatestEraOrHighestErathem()); occurrence.setEarliestPeriodOrLowestSystem(importDwc.getEarliestPeriodOrLowestSystem()); occurrence.setLatestPeriodOrHighestSystem(importDwc.getLatestPeriodOrHighestSystem()); occurrence.setEarliestEpochOrLowestSeries(importDwc.getEarliestEpochOrLowestSeries()); occurrence.setLatestEpochOrHighestSeries(importDwc.getLatestEpochOrHighestSeries()); occurrence.setEarliestAgeOrLowestStage(importDwc.getEarliestAgeOrLowestStage()); occurrence.setLatestAgeOrHighestStage(importDwc.getLatestAgeOrHighestStage()); occurrence.setLowestBiostratigraphicZone(importDwc.getLowestBiostratigraphicZone()); occurrence.setHighestBiostratigraphicZone(importDwc.getHighestBiostratigraphicZone()); occurrence.setLithostratigraphicTerms(importDwc.getLithostratigraphicTerms()); occurrence.setGroup(importDwc.getGroup()); occurrence.setFormation(importDwc.getFormation()); occurrence.setMember(importDwc.getMember()); occurrence.setBed(importDwc.getBed()); occurrence.setIdentificationId(importDwc.getIdentificationId()); occurrence.setIdentifiedBy(importDwc.getIdentifiedBy()); if (importDwc.getDateIdentified() != null && importDwc.getDateIdentified().length() > 0) occurrence.setDateIdentified(sourceDateFormat.parse(importDwc.getDateIdentified())); occurrence.setIdentificationReferences(importDwc.getIdentificationReferences()); occurrence.setIdentificationVerificationStatus(importDwc.getIdentificationVerificationStatus()); occurrence.setIdentificationRemarks(importDwc.getIdentificationRemarks()); occurrence.setIdentificationQualifier(importDwc.getIdentificationQualifier()); occurrence.setTypeStatus(importDwc.getTypeStatus()); occurrence.setTaxonId(importDwc.getTaxonId()); occurrence.setScientificNameId(importDwc.getScientificNameId()); occurrence.setAcceptedNameUsageId(importDwc.getAcceptedNameUsageId()); occurrence.setParentNameUsageId(importDwc.getParentNameUsageId()); occurrence.setOriginalNameUsageId(importDwc.getOriginalNameUsageId()); occurrence.setNameAccordingToId(importDwc.getNameAccordingToId()); occurrence.setNamePublishedInId(importDwc.getNamePublishedInId()); occurrence.setTaxonConceptId(importDwc.getTaxonConceptId()); occurrence.setScientificName(importDwc.getScientificName()); occurrence.setAcceptedNameUsage(importDwc.getAcceptedNameUsage()); occurrence.setParentNameUsage(importDwc.getParentNameUsage()); occurrence.setOriginalNameUsage(importDwc.getOriginalNameUsage()); occurrence.setNameAccordingTo(importDwc.getNameAccordingTo()); occurrence.setNamePublishedIn(importDwc.getNamePublishedIn()); occurrence.setNamePublishedInYear(importDwc.getNamePublishedInYear()); occurrence.setHigherClassification(importDwc.getHigherClassification()); occurrence.setKingdom(importDwc.getKingdom()); occurrence.setPhylum(importDwc.getPhylum()); occurrence.setClass_(importDwc.getClass_()); occurrence.setOrder(importDwc.getOrder()); occurrence.setFamily(importDwc.getFamily()); occurrence.setGenus(importDwc.getGenus()); occurrence.setSubgenus(importDwc.getSubgenus()); occurrence.setSpecificEpithet(importDwc.getSpecificEpithet()); occurrence.setInfraspecificEpithet(importDwc.getInfraspecificEpithet()); occurrence.setTaxonRank(importDwc.getTaxonRank()); occurrence.setVerbatimTaxonRank(importDwc.getVerbatimTaxonRank()); occurrence.setScientificNameAuthorship(importDwc.getScientificNameAuthorship()); occurrence.setVernacularName(importDwc.getVernacularName()); occurrence.setNomenclaturalCode(importDwc.getNomenclaturalCode()); occurrence.setTaxonomicStatus(importDwc.getTaxonomicStatus()); occurrence.setNomenclaturalStatus(importDwc.getNomenclaturalStatus()); occurrence.setTaxonRemarks(importDwc.getTaxonRemarks()); if (!update) occurrenceDAO.create(occurrence); else occurrenceDAO.update(occurrence); // clear objects occurrence.setImages(null); occurrence = null; taxon = null; location = null; } catch (NonUniqueResultException ex) { logger.warn("NonUniqueResultException occurrenceId " + importDwc.getCatalogNumber()); } catch (NumberFormatException ex) { logger.error("NumberFormatException occurrenceId " + importDwc.getCatalogNumber()); ex.printStackTrace(); System.exit(-1); } catch (ParseException e) { e.printStackTrace(); } // } // end for, 1000 importDwc rows session.evict(importDwc); if (batch >= BATCH_SIZE) { batch = 0; SessionStatistics statistics = session.getStatistics(); logger.trace("Entities before flush: " + String.valueOf(statistics.getEntityCount())); session.flush(); logger.trace("Entities before clear: " + String.valueOf(statistics.getEntityCount())); // fullTextSession.flushToIndexes(); session.clear(); logger.trace("Entities after clear: " + String.valueOf(statistics.getEntityCount())); // System.exit(1); } if (rowsCounter % maxResults == 0) { // fullTextSession.flushToIndexes(); logger.info("Occurrences added " + rowsCounter); SessionStatistics statistics = session.getStatistics(); logger.debug("Entities: " + String.valueOf(statistics.getEntityCount())); logger.debug("Collections: " + String.valueOf(statistics.getCollectionCount())); } // ******* for debug only *********** // if(rowsCounter == 1) { // session.getTransaction().rollback(); // scroll.close(); // System.exit(1); // } // firstResult += maxResults; // occurrencesDwcList = // importDwcDAO.scrollAll(ImportDwc.class, // maxResults, // firstResult); } // end while, no more importDwc rows scroll.close(); // transactionManager.commit(status); session.flush(); session.clear(); logger.info("Total occurrences processed " + rowsCounter); // session.getTransaction().commit(); // session.close(); }
From source file:org.openbravo.dal.service.OBDal.java
License:Open Source License
/** * Flushes the current state to the database. *//*from www . j av a 2 s . c o m*/ public void flush() { if (SessionHandler.isSessionHandlerPresent()) { long s1 = System.currentTimeMillis(); SessionHandler.getInstance().getSession().flush(); if (log.isDebugEnabled()) { long s2 = System.currentTimeMillis(); SessionStatistics sessStat = SessionHandler.getInstance().getSession().getStatistics(); dumpSessionEntities(); log.debug("Flush of " + sessStat.getEntityCount() + " entities and " + sessStat.getCollectionCount() + " collections took: " + (s2 - s1), new Throwable()); } } }