Java tutorial
// $HeadURL$ // $Id$ // // Copyright 2006, 2010, 2011, 2012 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.ui.cherrypickrequests; import java.util.Arrays; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; import javax.faces.model.SelectItem; import com.google.common.base.Joiner; import com.google.common.collect.Multimap; import com.google.common.collect.Sets; import com.google.common.collect.TreeMultimap; import org.apache.log4j.Logger; import org.springframework.transaction.annotation.Transactional; import edu.harvard.med.screensaver.db.CherryPickRequestDAO; import edu.harvard.med.screensaver.db.GenericEntityDAO; import edu.harvard.med.screensaver.model.BusinessRuleViolationException; import edu.harvard.med.screensaver.model.Volume; import edu.harvard.med.screensaver.model.VolumeUnit; import edu.harvard.med.screensaver.model.activities.AdministrativeActivity; import edu.harvard.med.screensaver.model.cherrypicks.CherryPickAssayProtocolsFollowed; import edu.harvard.med.screensaver.model.cherrypicks.CherryPickFollowupResultsStatus; import edu.harvard.med.screensaver.model.cherrypicks.CherryPickRequest; import edu.harvard.med.screensaver.model.cherrypicks.LabCherryPick; import edu.harvard.med.screensaver.model.cherrypicks.RNAiCherryPickRequest; import edu.harvard.med.screensaver.model.cherrypicks.ScreenerCherryPick; import edu.harvard.med.screensaver.model.cherrypicks.SmallMoleculeCherryPickRequest; import edu.harvard.med.screensaver.model.libraries.Library; import edu.harvard.med.screensaver.model.libraries.LibraryScreeningStatus; import edu.harvard.med.screensaver.model.libraries.PlateType; import edu.harvard.med.screensaver.model.libraries.Well; import edu.harvard.med.screensaver.model.libraries.WellKey; import edu.harvard.med.screensaver.model.libraries.WellName; import edu.harvard.med.screensaver.model.users.AdministratorUser; import edu.harvard.med.screensaver.model.users.ScreeningRoomUser; import edu.harvard.med.screensaver.model.users.ScreensaverUserComparator; import edu.harvard.med.screensaver.policy.CherryPickRequestAllowancePolicy; import edu.harvard.med.screensaver.ui.arch.util.JSFUtils; import edu.harvard.med.screensaver.ui.arch.util.UISelectOneBean; import edu.harvard.med.screensaver.ui.arch.util.UISelectOneEntityBean; import edu.harvard.med.screensaver.ui.arch.view.EditResult; import edu.harvard.med.screensaver.ui.arch.view.EditableEntityViewerBackingBean; import edu.harvard.med.screensaver.ui.arch.view.aspects.UICommand; import edu.harvard.med.screensaver.ui.screens.ScreenViewer; import edu.harvard.med.screensaver.util.DevelopmentException; /** * Backing bean for Cherry Pick Request Detail Viewer page. * * @author <a mailto="andrew_tolopko@hms.harvard.edu">Andrew Tolopko</a> */ public class CherryPickRequestDetailViewer extends EditableEntityViewerBackingBean<CherryPickRequest> { private static Logger log = Logger.getLogger(CherryPickRequestDetailViewer.class); private CherryPickRequestDAO _cherryPickRequestDao; private CherryPickRequestViewer _cherryPickRequestViewer; private ScreenViewer _screenViewer; private CherryPickRequestAllowancePolicy<SmallMoleculeCherryPickRequest> _smallMoleculeCherryPickRequestAllowancePolicy; private CherryPickRequestAllowancePolicy<RNAiCherryPickRequest> _rnaiCherryPickRequestAllowancePolicy; private UISelectOneBean<PlateType> _assayPlateType; private UISelectOneEntityBean<ScreeningRoomUser> _requestedBy; private UISelectOneEntityBean<AdministratorUser> _volumeApprovedBy; private UISelectOneBean<VolumeUnit> _transferVolumePerWellRequestedType; private String _transferVolumePerWellRequestedValue; private UISelectOneBean<VolumeUnit> _transferVolumePerWellApprovedType; private String _transferVolumePerWellApprovedValue; /** * @motivation for CGLIB2 */ protected CherryPickRequestDetailViewer() { } public CherryPickRequestDetailViewer(CherryPickRequestDetailViewer thisProxy, CherryPickRequestViewer cherryPickRequestViewer, GenericEntityDAO dao, CherryPickRequestDAO cherryPickRequestDao, ScreenViewer screenViewer, CherryPickRequestAllowancePolicy<SmallMoleculeCherryPickRequest> smallMoleculeCherryPickRequestAllowancePolicy, CherryPickRequestAllowancePolicy<RNAiCherryPickRequest> rnaiCherryPickRequestAllowancePolicy) { super(thisProxy, CherryPickRequest.class, EDIT_CHERRY_PICK_REQUEST, dao); _cherryPickRequestDao = cherryPickRequestDao; _cherryPickRequestViewer = cherryPickRequestViewer; _screenViewer = screenViewer; _smallMoleculeCherryPickRequestAllowancePolicy = smallMoleculeCherryPickRequestAllowancePolicy; _rnaiCherryPickRequestAllowancePolicy = rnaiCherryPickRequestAllowancePolicy; getIsPanelCollapsedMap().put("cherryPickRequestDetails", false); getIsPanelCollapsedMap().put("cherryPickFollowupAssays", true); } @Override public void initializeEntity(CherryPickRequest cherryPickRequest) { getDao().needReadOnly(cherryPickRequest, CherryPickRequest.requestedBy); getDao().needReadOnly(cherryPickRequest, CherryPickRequest.emptyWellsOnAssayPlate); getDao().needReadOnly(cherryPickRequest, CherryPickRequest.cherryPickScreenings); } @Override public void initializeViewer(final CherryPickRequest cherryPickRequest) { SortedSet<ScreeningRoomUser> requestedByCandidates = Sets.newTreeSet(); requestedByCandidates.addAll(cherryPickRequest.getScreen().getAssociatedScreeningRoomUsers()); // add the current requestedBy user, even if it's no longer a valid candidate, to avoid inadvertently changing it requestedByCandidates.add(cherryPickRequest.getRequestedBy()); _requestedBy = new UISelectOneEntityBean<ScreeningRoomUser>(requestedByCandidates, cherryPickRequest.getRequestedBy(), getDao()) { @Override protected String makeLabel(ScreeningRoomUser u) { return u.getFullNameLastFirst(); } }; SortedSet<AdministratorUser> candidateVolumeApprovers = new TreeSet<AdministratorUser>( ScreensaverUserComparator.getInstance()); candidateVolumeApprovers.addAll(getDao().findAllEntitiesOfType(AdministratorUser.class)); // TODO: filter out all but CherryPickAdmins _volumeApprovedBy = new UISelectOneEntityBean<AdministratorUser>(candidateVolumeApprovers, cherryPickRequest.getVolumeApprovedBy(), true, getDao()) { @Override protected String makeLabel(AdministratorUser a) { return a.getFullNameLastFirst(); } }; _assayPlateType = new UISelectOneBean<PlateType>(Arrays.asList(PlateType.values()), cherryPickRequest.getAssayPlateType()); _transferVolumePerWellRequestedType = null; _transferVolumePerWellRequestedValue = null; _transferVolumePerWellApprovedType = null; _transferVolumePerWellApprovedValue = null; } @Override protected void initializeNewEntity(CherryPickRequest entity) { entity.addEmptyWellsOnAssayPlate(entity.getAssayPlateType().getPlateSize().getEdgeWellNames(2)); } public UISelectOneBean<PlateType> getAssayPlateType() { return _assayPlateType; } public UISelectOneEntityBean<ScreeningRoomUser> getRequestedBy() { return _requestedBy; } public UISelectOneEntityBean<AdministratorUser> getVolumeApprovedBy() { return _volumeApprovedBy; } public int getActiveCherryPickPlatesCount() { return getEntity().getActiveCherryPickAssayPlates().size(); } public int getCompletedCherryPickPlatesCount() { return getEntity().getCompletedCherryPickAssayPlates().size(); } public UISelectOneBean<VolumeUnit> getTransferVolumePerWellRequestedType() { try { if (_transferVolumePerWellRequestedType == null) { Volume v = getEntity().getTransferVolumePerWellRequested(); VolumeUnit unit = (v == null ? VolumeUnit.MICROLITERS : v.getUnits()); _transferVolumePerWellRequestedType = new UISelectOneBean<VolumeUnit>(VolumeUnit.DISPLAY_VALUES, unit) { @Override protected String makeLabel(VolumeUnit t) { return t.getValue(); } }; } return _transferVolumePerWellRequestedType; } catch (Exception e) { log.error("err: " + e); return null; } } /** * This method exists to grab the value portion of the Quantity stored */ public String getTransferVolumePerWellRequestedValue() { if (_transferVolumePerWellRequestedValue == null) { if (getEntity().getTransferVolumePerWellRequested() != null) _transferVolumePerWellRequestedValue = getEntity().getTransferVolumePerWellRequested() .getDisplayValue().toString(); else _transferVolumePerWellRequestedValue = null; } return _transferVolumePerWellRequestedValue; } /** * This method exists to set the value portion of the Quantity stored * @see #save() */ public void setTransferVolumePerWellRequestedValue(String value) { _transferVolumePerWellRequestedValue = value; } public UISelectOneBean<VolumeUnit> getTransferVolumePerWellApprovedType() { try { if (_transferVolumePerWellApprovedType == null) { Volume v = getEntity().getTransferVolumePerWellApproved(); VolumeUnit unit = (v == null ? VolumeUnit.MICROLITERS : v.getUnits()); _transferVolumePerWellApprovedType = new UISelectOneBean<VolumeUnit>(VolumeUnit.DISPLAY_VALUES, unit) { @Override protected String makeLabel(VolumeUnit t) { return t.getValue(); } }; } return _transferVolumePerWellApprovedType; } catch (Exception e) { log.error("err: " + e); return null; } } /** * This method exists to grab the value portion of the Quantity stored */ public String getTransferVolumePerWellApprovedValue() { if (_transferVolumePerWellApprovedValue == null) { if (getEntity().getTransferVolumePerWellApproved() != null) _transferVolumePerWellApprovedValue = getEntity().getTransferVolumePerWellApproved() .getDisplayValue().toString(); else _transferVolumePerWellApprovedValue = null; } return _transferVolumePerWellApprovedValue; } /** * This method exists to set the value portion of the Quantity stored * @see #save() */ public void setTransferVolumePerWellApprovedValue(String value) { _transferVolumePerWellApprovedValue = value; } public List<SelectItem> getCherryPickAssayProtocolsFollowedSelectItems() { return JSFUtils.createUISelectItemsWithEmptySelection( Arrays.asList(CherryPickAssayProtocolsFollowed.values()), "<none>"); } public List<SelectItem> getCherryPickFollowupResultsStatusSelectItems() { return JSFUtils.createUISelectItemsWithEmptySelection( Arrays.asList(CherryPickFollowupResultsStatus.values()), "<none>"); } @Override public boolean isDeleteSupported() { return !!!getEntity().isAllocated() && !!!(getEntity() instanceof RNAiCherryPickRequest && ((RNAiCherryPickRequest) getEntity()).isScreened()); } @UICommand @Override public String delete() { if (!!!isDeleteSupported()) { throw new BusinessRuleViolationException( "cannot delete a cherry pick request that has been allocated or that has been screened"); } _cherryPickRequestDao.deleteCherryPickRequest(getEntity()); return _screenViewer.viewEntity(getEntity().getScreen()); } @UICommand public String deleteAllCherryPicks() { _cherryPickRequestDao.deleteAllCherryPicks(getEntity()); return _cherryPickRequestViewer.reload(); } @Override protected boolean validateEntity(CherryPickRequest entity) { boolean valid = true; try { Volume.makeVolume(_transferVolumePerWellRequestedValue, _transferVolumePerWellRequestedType.getSelection()); } catch (Exception e) { showFieldInputError("Requested Volume", e.getLocalizedMessage()); valid = false; } try { Volume.makeVolume(_transferVolumePerWellApprovedValue, _transferVolumePerWellApprovedType.getSelection()); } catch (Exception e) { showFieldInputError("Approved Volume", e.getLocalizedMessage()); valid = false; } return valid; } @Override protected void updateEntityProperties(CherryPickRequest entity) { getEntity().setTransferVolumePerWellRequested(Volume.makeVolume(_transferVolumePerWellRequestedValue, _transferVolumePerWellRequestedType.getSelection())); getEntity().setTransferVolumePerWellApproved(Volume.makeVolume(_transferVolumePerWellApprovedValue, _transferVolumePerWellApprovedType.getSelection())); entity.setAssayPlateType(_assayPlateType.getSelection()); entity.setRequestedBy(_requestedBy.getSelection()); entity.setVolumeApprovedBy(_volumeApprovedBy.getSelection()); } /** * Get the set of empty rows requested by the screener. * @return well names that must be left empty on each cherry pick assay plate */ public Set<WellName> getEmptyWellsOnAssayPlate() { return getEntity().getEmptyWellsOnAssayPlate(); } /** * Set the set of empty wells. * @param emptyWellsOnAssayPlate wells that screener has requested be * left empty on each cherry pick assay plate */ public void setEmptyWellsOnAssayPlate(Set<WellName> emptyWellsOnAssayPlate) { getEntity().clearEmptyWellsOnAssayPlate(); getEntity().addEmptyWellsOnAssayPlate(emptyWellsOnAssayPlate); } @UICommand @Transactional public void showAdminWarnings() { // eager fetch all data needed to calculate warnings CherryPickRequest cherryPickRequest = getDao().reloadEntity(getEntity(), true, CherryPickRequest.screen); getDao().needReadOnly(cherryPickRequest, CherryPickRequest.labCherryPicks.to(LabCherryPick.screenerCherryPick) .to(ScreenerCherryPick.screenedWell).to(Well.deprecationActivity)); getDao().needReadOnly(cherryPickRequest, CherryPickRequest.labCherryPicks.to(LabCherryPick.sourceWell).to(Well.deprecationActivity)); getDao().needReadOnly(cherryPickRequest, CherryPickRequest.screenerCherryPicks.to(ScreenerCherryPick.screenedWell).to(Well.library)); boolean warningIssued = false; warningIssued |= doWarnOnCherryPickAllowanceExceeded(cherryPickRequest); warningIssued |= doWarnOnInvalidSourceWell(cherryPickRequest); warningIssued |= doWarnOnDuplicateScreenerCherryPicks(cherryPickRequest); warningIssued |= doWarnOnDeprecatedWells(cherryPickRequest); warningIssued |= doWarnOnLibraryScreeningStatus(cherryPickRequest); if (!warningIssued) { showMessage("cherryPicks.allCherryPicksAreValid"); } } private <CPR extends CherryPickRequest> boolean doWarnOnCherryPickAllowanceExceeded(CPR cherryPickRequest) { CherryPickRequestAllowancePolicy<CPR> policy; if (cherryPickRequest instanceof SmallMoleculeCherryPickRequest) { policy = (CherryPickRequestAllowancePolicy<CPR>) _smallMoleculeCherryPickRequestAllowancePolicy; } else if (cherryPickRequest instanceof RNAiCherryPickRequest) { policy = (CherryPickRequestAllowancePolicy<CPR>) _rnaiCherryPickRequestAllowancePolicy; } else { throw new DevelopmentException( "unsupported cherry pick request type: " + cherryPickRequest.getClass().getName()); } if (policy.isCherryPickAllowanceExceeded(cherryPickRequest)) { showMessage("cherryPicks.cherryPickAllowanceExceeded", policy.getCherryPickAllowanceUsed(cherryPickRequest), policy.getCherryPickAllowance(cherryPickRequest)); return true; } return false; } private boolean doWarnOnInvalidSourceWell(CherryPickRequest cherryPickRequest) { Set<WellKey> invalidCherryPicks = Sets.newHashSet(); for (ScreenerCherryPick screenerCherryPick : cherryPickRequest.getScreenerCherryPicks()) { if (screenerCherryPick.getLabCherryPicks().size() == 0) { invalidCherryPicks.add(screenerCherryPick.getScreenedWell().getWellKey()); } } if (!!!invalidCherryPicks.isEmpty()) { showMessage("cherryPicks.invalidWells", Joiner.on(", ").join(invalidCherryPicks)); return true; } return false; } private boolean doWarnOnDuplicateScreenerCherryPicks(CherryPickRequest cherryPickRequest) { Map<WellKey, Number> duplicateScreenerCherryPickWellKeysMap = _cherryPickRequestDao .findDuplicateCherryPicksForScreen(cherryPickRequest.getScreen()); Set<WellKey> duplicateScreenerCherryPickWellKeys = duplicateScreenerCherryPickWellKeysMap.keySet(); Set<WellKey> ourScreenerCherryPickWellsKeys = new HashSet<WellKey>(); for (ScreenerCherryPick screenerCherryPick : cherryPickRequest.getScreenerCherryPicks()) { ourScreenerCherryPickWellsKeys.add(screenerCherryPick.getScreenedWell().getWellKey()); } duplicateScreenerCherryPickWellKeys.retainAll(ourScreenerCherryPickWellsKeys); if (duplicateScreenerCherryPickWellKeysMap.size() > 0) { String duplicateWellsList = Joiner.on(", ").join(duplicateScreenerCherryPickWellKeys); showMessage("cherryPicks.duplicateCherryPicksInScreen", cherryPickRequest.getScreen().getFacilityId(), duplicateWellsList); return true; } return false; } private boolean doWarnOnDeprecatedWells(CherryPickRequest cherryPickRequest) { Multimap<AdministrativeActivity, WellKey> wellDeprecations = TreeMultimap.create(); for (LabCherryPick labCherryPick : cherryPickRequest.getLabCherryPicks()) { Well well = labCherryPick.getSourceWell(); if (well.isDeprecated()) { wellDeprecations.put(well.getDeprecationActivity(), well.getWellKey()); } well = labCherryPick.getScreenerCherryPick().getScreenedWell(); if (well.isDeprecated()) { wellDeprecations.put(well.getDeprecationActivity(), well.getWellKey()); } } for (AdministrativeActivity deprecationActivity : wellDeprecations.keySet()) { showMessage("cherryPicks.deprecatedWells", deprecationActivity.getComments(), Joiner.on(", ").join(wellDeprecations.values())); return true; } return false; } private boolean doWarnOnLibraryScreeningStatus(CherryPickRequest cherryPickRequest) { Set<Library> libraries = new LinkedHashSet<Library>(); for (LabCherryPick labCherryPick : cherryPickRequest.getLabCherryPicks()) { libraries.add(labCherryPick.getSourceWell().getLibrary()); libraries.add(labCherryPick.getScreenerCherryPick().getScreenedWell().getLibrary()); } for (Library library : libraries) { if (library.getScreeningStatus() != LibraryScreeningStatus.ALLOWED) { if (!cherryPickRequest.getScreen().getLibrariesPermitted().contains(library)) { showMessage("libraries.libraryUsageConflict", library.getShortName(), library.getScreeningStatus().getValue()); return true; } } } return false; } @Override protected String postEditAction(EditResult editResult) { switch (editResult) { case CANCEL_EDIT: return _cherryPickRequestViewer.reload(); case SAVE_EDIT: return _cherryPickRequestViewer.reload(); case CANCEL_NEW: return _screenViewer.reload(); case SAVE_NEW: return _screenViewer.reload(); default: return null; } } }