Java tutorial
// $HeadURL$ // $Id$ // // Copyright 2010 by the President and Fellows of Harvard College. // // Screensaver is an open-source project developed by the ICCB-L and NSRB labs // at Harvard Medical School. This software is distributed under the terms of // the GNU General Public License. package edu.harvard.med.screensaver.service.libraries; import java.math.BigDecimal; import java.math.RoundingMode; import java.util.Collection; import java.util.Collections; import java.util.Comparator; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Set; import org.apache.log4j.Logger; import org.joda.time.LocalDate; import org.springframework.transaction.annotation.Transactional; import com.google.common.base.Function; import com.google.common.base.Predicate; import com.google.common.base.Predicates; import com.google.common.collect.ImmutableMap; import com.google.common.collect.Iterables; import com.google.common.collect.Iterators; import com.google.common.collect.Lists; import com.google.common.collect.Maps; import com.google.common.collect.Multimaps; import com.google.common.collect.Sets; import edu.harvard.med.screensaver.ScreensaverConstants; import edu.harvard.med.screensaver.db.GenericEntityDAO; import edu.harvard.med.screensaver.db.Query; import edu.harvard.med.screensaver.model.BusinessRuleViolationException; import edu.harvard.med.screensaver.model.MolarConcentration; import edu.harvard.med.screensaver.model.Volume; import edu.harvard.med.screensaver.model.activities.AdministrativeActivity; import edu.harvard.med.screensaver.model.activities.AdministrativeActivityType; import edu.harvard.med.screensaver.model.libraries.ConcentrationStatistics; import edu.harvard.med.screensaver.model.libraries.Copy; import edu.harvard.med.screensaver.model.libraries.Library; import edu.harvard.med.screensaver.model.libraries.LibraryWellType; import edu.harvard.med.screensaver.model.libraries.Plate; import edu.harvard.med.screensaver.model.libraries.PlateLocation; import edu.harvard.med.screensaver.model.libraries.PlateStatus; import edu.harvard.med.screensaver.model.libraries.PlateType; import edu.harvard.med.screensaver.model.libraries.Well; import edu.harvard.med.screensaver.model.users.AdministratorUser; import edu.harvard.med.screensaver.util.NullSafeUtils; public class PlateUpdater { private static final Logger log = Logger.getLogger(PlateUpdater.class); public static final String NO_BIN = "<not specified>"; public static final String NO_SHELF = "<not specified>"; public static final String NO_FREEZER = "<not specified>"; public static final String NO_ROOM = "<not specified>"; private static final Function<Collection<?>, Integer> CollectionSize = new Function<Collection<?>, Integer>() { public Integer apply(Collection<?> c) { return c.size(); } }; private static final Predicate<PlateStatus> isStoredAtFacility = new Predicate<PlateStatus>() { @Override public boolean apply(PlateStatus input) { switch (input) { case AVAILABLE: case NOT_AVAILABLE: case NOT_SPECIFIED: case RETIRED: return true; case NOT_CREATED: case DISCARDED: case GIVEN_AWAY: case LOST: case VOLUME_TRANSFERRED_AND_DISCARDED: return false; } return false; } }; private GenericEntityDAO _dao; private PlateFacilityIdInitializer _plateFacilityIdInitializer; protected PlateUpdater() { } public PlateUpdater(GenericEntityDAO dao, PlateFacilityIdInitializer plateFacilityIdInitializer) { _dao = dao; _plateFacilityIdInitializer = plateFacilityIdInitializer; } @Transactional public boolean updatePlateStatus(Plate plate, PlateStatus newStatus, AdministratorUser recordedBy, AdministratorUser performedBy, LocalDate datePerformed) { if (plate.getStatus().equals(newStatus)) { return false; } // if (!!!plate.getStatus().canTransitionTo(newStatus)) { // throw new BusinessRuleViolationException("plate status cannot be changed from '" + plate.getStatus() + "' to '" + newStatus + // "'"); // } plate = _dao.reloadEntity(plate); recordedBy = _dao.reloadEntity(recordedBy); performedBy = _dao.reloadEntity(performedBy); StringBuilder comments = new StringBuilder().append("Status changed from '").append(plate.getStatus()) .append("' to '").append(newStatus).append("'"); AdministrativeActivity updateActivity = plate.createUpdateActivity( AdministrativeActivityType.PLATE_STATUS_UPDATE, recordedBy, comments.toString()); updateActivity.setPerformedBy(performedBy); updateActivity.setDateOfActivity(datePerformed); if (plate.getStatus() != newStatus) { plate.setStatus(newStatus); // TODO: if this method is being called repeatedly for multiple plates, it is inefficient to make the following call each time updatePrimaryPlateStatus(plate.getCopy()); } if (plate.getPlatedActivity() == null && (newStatus == PlateStatus.AVAILABLE || newStatus == PlateStatus.NOT_AVAILABLE)) { plateCreated(plate, updateActivity); } if (newStatus.compareTo(PlateStatus.RETIRED) >= 0) { if (plate.getRetiredActivity() == null) { plate.setRetiredActivity(updateActivity); } if (newStatus.compareTo(PlateStatus.RETIRED) > 0) { plateNoLongerMaintained(plate, newStatus, recordedBy, performedBy, datePerformed); } } return true; } private static Comparator<Map.Entry<PlateStatus, Integer>> plateStatusFrequencyComparator = new Comparator<Map.Entry<PlateStatus, Integer>>() { @Override public int compare(Entry<PlateStatus, Integer> o1, Entry<PlateStatus, Integer> o2) { int result = o1.getValue().compareTo(o2.getValue()); if (result == 0) { result = -1 * o1.getKey().compareTo(o2.getKey()); } return result; } }; private void updatePrimaryPlateStatus(Copy copy) { Map<PlateStatus, Integer> statusCounts = Maps.transformValues( Multimaps.index(copy.getPlates().values(), Plate.ToStatus).asMap(), CollectionSize); PlateStatus primaryPlateStatus = Collections.max(statusCounts.entrySet(), plateStatusFrequencyComparator) .getKey(); copy.setPrimaryPlateStatus(primaryPlateStatus); copy.setPlatesAvailable(statusCounts.get(PlateStatus.AVAILABLE)); } @Transactional public void updatePrimaryWellConcentrations(Library library) { library = _dao.reloadEntity(library, false, Library.copies); for (Copy c : library.getCopies()) { updatePrimaryPlateConcentrations(c); } } @Transactional public void updatePrimaryPlateConcentrations(Copy copy) { ConcentrationStatistics concentrationStatistics = new ConcentrationStatistics(); copy.setConcentrationStatistics(concentrationStatistics); // update the plates using values from the wells Collection<Plate> platesToConsider = Sets.newHashSet(copy.getPlates().values()); for (Iterator<Plate> iter = platesToConsider.iterator(); iter.hasNext();) { Plate p = iter.next(); p.setConcentrationStatistics(new ConcentrationStatistics()); updatePrimaryWellConcentration(p); // update the copy with the values from the plate if (p.getMaxMgMlConcentration() != null) { if (concentrationStatistics.getMaxMgMlConcentration() == null) concentrationStatistics.setMaxMgMlConcentration(p.getMaxMgMlConcentration()); else if (p.getMaxMgMlConcentration() .compareTo(concentrationStatistics.getMaxMgMlConcentration()) > 0) concentrationStatistics.setMaxMgMlConcentration(p.getMaxMgMlConcentration()); if (concentrationStatistics.getMinMgMlConcentration() == null) concentrationStatistics.setMinMgMlConcentration(p.getMinMgMlConcentration()); else if (p.getMinMgMlConcentration() .compareTo(concentrationStatistics.getMinMgMlConcentration()) < 0) concentrationStatistics.setMinMgMlConcentration(p.getMinMgMlConcentration()); } if (p.getMaxMolarConcentration() != null) { if (concentrationStatistics.getMaxMolarConcentration() == null) concentrationStatistics.setMaxMolarConcentration(p.getMaxMolarConcentration()); else if (p.getMaxMolarConcentration() .compareTo(concentrationStatistics.getMaxMolarConcentration()) > 0) concentrationStatistics.setMaxMolarConcentration(p.getMaxMolarConcentration()); if (concentrationStatistics.getMinMolarConcentration() == null) concentrationStatistics.setMinMolarConcentration(p.getMinMolarConcentration()); else if (p.getMinMolarConcentration() .compareTo(concentrationStatistics.getMinMolarConcentration()) < 0) concentrationStatistics.setMinMolarConcentration(p.getMinMolarConcentration()); } if (!isStoredAtFacility.apply(p.getStatus())) // consider only plates stored at this facility { iter.remove(); continue; } } Map<BigDecimal, Integer> mgMlCounts = Maps .transformValues( Multimaps.index( Lists.newArrayList(Iterators.filter(platesToConsider.iterator(), Predicates.compose(Predicates.notNull(), Plate.ToPrimaryWellMgMlConcentration))), Plate.ToPrimaryWellMgMlConcentration).asMap(), CollectionSize); if (!mgMlCounts.isEmpty()) concentrationStatistics.setPrimaryWellMgMlConcentration(findMaxByValueThenKey(mgMlCounts).getKey()); Map<MolarConcentration, Integer> molarCounts = Maps .transformValues( Multimaps.index( Lists.newArrayList(Iterators.filter(platesToConsider.iterator(), Predicates.compose(Predicates.notNull(), Plate.ToPrimaryWellMolarConcentration))), Plate.ToPrimaryWellMolarConcentration).asMap(), CollectionSize); if (!molarCounts.isEmpty()) concentrationStatistics.setPrimaryWellMolarConcentration(findMaxByValueThenKey(molarCounts).getKey()); } private void updatePrimaryWellConcentration(Plate plate) { Map<String, Object> properties = Maps.newHashMap(); properties.put("plateNumber", plate.getPlateNumber()); properties.put("libraryWellType", LibraryWellType.EXPERIMENTAL); List<Well> wells = _dao.findEntitiesByProperties(Well.class, properties); ConcentrationStatistics concentrationStatistics = plate.getConcentrationStatistics(); for (Well well : wells) { if (well.getMgMlConcentration() != null) { if (concentrationStatistics.getMaxMgMlConcentration() == null) concentrationStatistics.setMaxMgMlConcentration(well.getMgMlConcentration()); else if (well.getMgMlConcentration() .compareTo(concentrationStatistics.getMaxMgMlConcentration()) > 0) concentrationStatistics.setMaxMgMlConcentration(well.getMgMlConcentration()); if (concentrationStatistics.getMinMgMlConcentration() == null) concentrationStatistics.setMinMgMlConcentration(well.getMgMlConcentration()); else if (well.getMgMlConcentration() .compareTo(concentrationStatistics.getMinMgMlConcentration()) < 0) concentrationStatistics.setMinMgMlConcentration(well.getMgMlConcentration()); } if (well.getMolarConcentration() != null) { if (concentrationStatistics.getMaxMolarConcentration() == null) concentrationStatistics.setMaxMolarConcentration(well.getMolarConcentration()); else if (well.getMolarConcentration() .compareTo(concentrationStatistics.getMaxMolarConcentration()) > 0) concentrationStatistics.setMaxMolarConcentration(well.getMolarConcentration()); if (concentrationStatistics.getMinMolarConcentration() == null) concentrationStatistics.setMinMolarConcentration(well.getMolarConcentration()); else if (well.getMolarConcentration() .compareTo(concentrationStatistics.getMinMolarConcentration()) < 0) concentrationStatistics.setMinMolarConcentration(well.getMolarConcentration()); } } Map<BigDecimal, Integer> mgMlCounts = Maps.transformValues(Multimaps.index( Lists.newArrayList(Iterators.filter(wells.iterator(), Predicates.compose(Predicates.notNull(), Well.ToMgMlConcentration))), Well.ToMgMlConcentration).asMap(), CollectionSize); if (!mgMlCounts.isEmpty()) concentrationStatistics.setPrimaryWellMgMlConcentration(findMaxByValueThenKey(mgMlCounts).getKey()); Map<MolarConcentration, Integer> molarCounts = Maps.transformValues(Multimaps.index( Lists.newArrayList(Iterators.filter(wells.iterator(), Predicates.compose(Predicates.notNull(), Well.ToMolarConcentration))), Well.ToMolarConcentration).asMap(), CollectionSize); if (!molarCounts.isEmpty()) concentrationStatistics.setPrimaryWellMolarConcentration(findMaxByValueThenKey(molarCounts).getKey()); } private <T extends Comparable<? super T>, U extends Comparable<? super U>> Map.Entry<T, U> findMaxByValueThenKey( Map<T, U> map) { // This method avoids having to define a comparator for each type if (map.isEmpty()) return null; Map.Entry<T, U> max = null; for (Map.Entry<T, U> entry : map.entrySet()) { if (max == null || entry.getValue().compareTo(max.getValue()) > 0) max = entry; if (entry.getValue().compareTo(max.getValue()) == 0) { if (entry.getKey().compareTo(max.getKey()) > 0) max = entry; } } return max; } private void plateNoLongerMaintained(Plate plate, PlateStatus newStatus, AdministratorUser recordedBy, AdministratorUser performedBy, LocalDate datePerformed) { updatePlateLocation(plate, null, recordedBy, performedBy, datePerformed); AdministrativeActivity lastActivity = plate .getLastRecordedUpdateActivityOfType(AdministrativeActivityType.PLATE_LOCATION_TRANSFER); lastActivity.setComments(lastActivity.getComments() + " (plate no longer has a location due to change of status to " + newStatus + ")"); } private void plateCreated(Plate plate, AdministrativeActivity updateActivity) { plate.setPlatedActivity(updateActivity); LocalDate datePlated = updateActivity.getDateOfActivity(); plate.getCopy().setDatePlated(datePlated); LocalDate dateLibraryScreenable = plate.getCopy().getLibrary().getDateScreenable(); if (dateLibraryScreenable == null || datePlated.compareTo(dateLibraryScreenable) < 0) { plate.getCopy().getLibrary().setDateScreenable(datePlated); } } /* * Due to Hibernate issues with flush(), the caller should invoke this method in a transaction, and must call * validateLocations() before the end of the transaction. Any newly created locations must be flushed before calling * this method */ @Transactional public boolean updatePlateLocation(Plate plate, PlateLocation newLocationDto, AdministratorUser recordedByAdmin, AdministratorUser performedByAdmin, LocalDate datePerformed) { if (performedByAdmin == null) { throw new IllegalArgumentException("performedByAdmin required"); } if (!!!plate.getStatus().isInventoried() && newLocationDto != null) { throw new BusinessRuleViolationException( "plate location cannot be specified for non-inventoried plate status " + plate.getStatus()); } recordedByAdmin = _dao.reloadEntity(recordedByAdmin); performedByAdmin = _dao.reloadEntity(performedByAdmin); PlateLocation newLocation = null; if (newLocationDto != null) { newLocation = findLocation(newLocationDto); if (newLocation == null) { newLocation = createLocation(newLocationDto); } } plate = _dao.reloadEntity(plate); PlateLocation oldLocation = plate.getLocation(); if (NullSafeUtils.nullSafeEquals(oldLocation, newLocation)) { return false; } plate.setLocation(newLocation); // TODO: if this method is being called repeatedly for multiple plates, it is inefficient to make the following call each time updatePrimaryPlateLocation(plate.getCopy()); StringBuilder comments = new StringBuilder(); comments.append("Location changed from '") .append(oldLocation == null ? "<none>" : oldLocation.toDisplayString()).append("' to '") .append(newLocation == null ? "<none>" : newLocation.toDisplayString()).append("'"); AdministrativeActivity updateActivity = plate.createUpdateActivity( AdministrativeActivityType.PLATE_LOCATION_TRANSFER, recordedByAdmin, comments.toString()); updateActivity.setPerformedBy(performedByAdmin); updateActivity.setDateOfActivity(datePerformed); // TODO: we want to be able to call validateLocations() here, but the resultant flush() call is causing problems with Plate.updateActivities, where newly added elements are not being added to the collection, although the activity itself is being persisted //validateLocations(); return true; } private static Comparator<Map.Entry<PlateLocation, Integer>> plateLocationFrequencyComparator = new Comparator<Map.Entry<PlateLocation, Integer>>() { @Override public int compare(Entry<PlateLocation, Integer> o1, Entry<PlateLocation, Integer> o2) { int result = o1.getValue().compareTo(o2.getValue()); if (result == 0) { result = -1 * o1.getKey().toDisplayString().compareTo(o2.getKey().toDisplayString()); } return result; } }; private void updatePrimaryPlateLocation(Copy copy) { Set<Entry<PlateLocation, Integer>> plateLocationCounts = Maps .transformValues(Multimaps .index(Iterables.filter(copy.getPlates().values(), Predicates.compose(Predicates.notNull(), Plate.ToLocation)), Plate.ToLocation) .asMap(), CollectionSize) .entrySet(); if (plateLocationCounts.isEmpty()) { copy.setPrimaryPlateLocation(null); } else { PlateLocation primaryPlateLocation = Collections .max(plateLocationCounts, plateLocationFrequencyComparator).getKey(); copy.setPrimaryPlateLocation(primaryPlateLocation); copy.setPlateLocationsCount(plateLocationCounts.size()); } } private PlateLocation findLocation(PlateLocation locationDto) { if (locationDto.getRoom() == null || locationDto.getFreezer() == null || locationDto.getShelf() == null || locationDto.getBin() == null) { return null; } //_dao.flush(); TODO: reinstate, causing problems with Plate.updateActivities, where newly added elements are not being added to the collection, although the activity itself is being persisted PlateLocation plateLocation = _dao.findEntityByProperties(PlateLocation.class, ImmutableMap.<String, Object>of("room", locationDto.getRoom(), "freezer", locationDto.getFreezer(), "shelf", locationDto.getShelf(), "bin", locationDto.getBin())); return plateLocation; } private PlateLocation createLocation(PlateLocation locationDto) { PlateLocation newPlateLocation = new PlateLocation(locationDto); _dao.persistEntity(newPlateLocation); // TODO: report which location parts are new ("created new room", "created new freezer", etc.) return newPlateLocation; } // TODO: this should be a pluggable strategy/policy public void validateLocations() { _dao.flush(); // ICCB-L constraint: freezer implies room List<String> splitFreezers = _dao.runQuery(new Query<String>() { @SuppressWarnings("unchecked") public List<String> execute(org.hibernate.Session session) { org.hibernate.Query query = session.createQuery("select pl.freezer " + "from PlateLocation pl " + "where exists (select p from Plate p where p.location = pl) " + "and pl.freezer <> :noFreezer " + "group by pl.freezer having count(distinct pl.room) > 1"); query.setString("noFreezer", NO_FREEZER); return query.list(); } }); if (!!!splitFreezers.isEmpty()) { throw new BusinessRuleViolationException("attempted to assign freezer " + splitFreezers.get(0) + " to multiple rooms, but freezer name must be unique across all rooms (hint: to change a freezer's room, you must move all plates in freezer at once)"); } // ICCB-L constraint: bin number is unique for freezer List<Object> splitBins = _dao.runQuery(new Query<Object>() { @SuppressWarnings("unchecked") public List<Object> execute(org.hibernate.Session session) { org.hibernate.Query query = session.createQuery("select pl.bin, pl.freezer " + "from PlateLocation pl " + "where exists (select p from Plate p where p.location = pl) " + "and pl.bin <> :noBin " + "group by pl.freezer, pl.bin having count(distinct pl.shelf) > 1"); query.setString("noBin", NO_BIN); return query.list(); } }); if (!!!splitBins.isEmpty()) { Object[] row = (Object[]) splitBins.get(0); throw new BusinessRuleViolationException("attempted to assign bin " + row[0] + " to multiple shelves within freezer " + row[1] + ", but bin name must be unique within a freezer (hint: to change a bin's shelf you must move all plates in bin at once)"); } } @Transactional public boolean updateWellVolume(Plate plate, Volume newWellVolume, AdministratorUser recordedByAdmin) { if (!!!NullSafeUtils.nullSafeEquals(newWellVolume, plate.getWellVolume())) { plate = _dao.reloadEntity(plate); StringBuilder updateComments = new StringBuilder().append("Well Volume changed from '") .append(NullSafeUtils.toString(plate.getWellVolume(), "<not specified>")).append("' to '") .append(newWellVolume).append("'"); plate.createUpdateActivity(recordedByAdmin, updateComments.toString()); plate.setWellVolume(newWellVolume); return true; } return false; } @Transactional public boolean updatePlateType(Plate plate, PlateType newPlateType, AdministratorUser recordedByAdmin) { if (!!!newPlateType.equals(plate.getPlateType())) { plate = _dao.reloadEntity(plate); StringBuilder updateComments = new StringBuilder().append("Plate Type changed from '") .append(NullSafeUtils.toString(plate.getPlateType(), "<not specified>")).append("' to '") .append(newPlateType).append("'"); plate.createUpdateActivity(recordedByAdmin, updateComments.toString()); plate.setPlateType(newPlateType); return true; } return false; } @Transactional public boolean updateFacilityId(Plate plate, AdministratorUser recordedByAdmin) { plate = _dao.reloadEntity(plate); String oldFacilityId = plate.getFacilityId(); _plateFacilityIdInitializer.initializeFacilityId(plate); if (!!!NullSafeUtils.nullSafeEquals(oldFacilityId, plate.getFacilityId())) { plate.createUpdateActivity(recordedByAdmin, "Facility ID changed from '" + NullSafeUtils.toString(oldFacilityId, "<not specified>") + "' to '" + NullSafeUtils.toString(plate.getFacilityId(), "<not specified>") + "'"); return true; } return false; } @Transactional public void addComment(Plate plate, AdministratorUser recordedByAdmin, String comment) { plate = _dao.reloadEntity(plate); plate.createComment(recordedByAdmin, comment); } }