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.libraries; import java.math.BigDecimal; import java.math.RoundingMode; import java.util.List; import org.apache.log4j.Logger; import org.joda.time.LocalDate; import com.google.common.base.Joiner; import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import edu.harvard.med.screensaver.db.GenericEntityDAO; import edu.harvard.med.screensaver.db.LibrariesDAO; import edu.harvard.med.screensaver.db.Criterion.Operator; import edu.harvard.med.screensaver.db.datafetcher.EntityDataFetcher; import edu.harvard.med.screensaver.db.hqlbuilder.HqlBuilder; import edu.harvard.med.screensaver.model.MolarConcentration; import edu.harvard.med.screensaver.model.Volume; import edu.harvard.med.screensaver.model.libraries.ConcentrationStatistics; import edu.harvard.med.screensaver.model.libraries.Copy; import edu.harvard.med.screensaver.model.libraries.CopyUsageType; import edu.harvard.med.screensaver.model.libraries.Library; import edu.harvard.med.screensaver.model.libraries.LibraryType; import edu.harvard.med.screensaver.model.libraries.PlateStatus; import edu.harvard.med.screensaver.model.libraries.VolumeStatistics; import edu.harvard.med.screensaver.model.meta.PropertyPath; import edu.harvard.med.screensaver.model.meta.RelationshipPath; import edu.harvard.med.screensaver.model.screens.ScreenType; import edu.harvard.med.screensaver.ui.activities.ActivitySearchResults; import edu.harvard.med.screensaver.ui.arch.datatable.column.DateColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.FixedDecimalColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.IntegerColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.TableColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.VolumeColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.entity.DateEntityColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.entity.EnumEntityColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.entity.FixedDecimalEntityColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.entity.IntegerEntityColumn; import edu.harvard.med.screensaver.ui.arch.datatable.column.entity.TextEntityColumn; import edu.harvard.med.screensaver.ui.arch.datatable.model.InMemoryEntityDataModel; import edu.harvard.med.screensaver.ui.arch.searchresults.EntityBasedEntitySearchResults; import edu.harvard.med.screensaver.ui.arch.searchresults.SearchResults; import edu.harvard.med.screensaver.util.StringUtils; /** * A {@link SearchResults} for {@link Copy Copies}. * * @author <a mailto="andrew_tolopko@hms.harvard.edu">Andrew Tolopko</a> */ public class LibraryCopySearchResults extends EntityBasedEntitySearchResults<Copy, Integer> { private static final Logger log = Logger.getLogger(LibraryCopySearchResults.class); protected static final int DECIMAL_SCALE = 1; // number of decimal digits (to the right of decimal point) for plate screening count average private static final String COLUMN_GROUP_CONCENTRATION = "Concentration"; private GenericEntityDAO _dao; private LibrariesDAO _librariesDao; private LibraryCopyViewer _libraryCopyViewer; private LibraryViewer _libraryViewer; private ActivitySearchResults _activitesBrowser; private LibraryCopyPlateSearchResults _libraryCopyPlateSearchResults; /** * @motivation for CGLIB2 */ protected LibraryCopySearchResults() { } public LibraryCopySearchResults(GenericEntityDAO dao, LibrariesDAO librariesDao, LibraryCopyViewer libraryCopyViewer, LibraryViewer libraryViewer, ActivitySearchResults activitiesBrowser, LibraryCopyPlateSearchResults libraryCopyPlateSearchResults) { super(libraryCopyViewer); _dao = dao; _librariesDao = librariesDao; _libraryCopyViewer = libraryCopyViewer; _libraryViewer = libraryViewer; _activitesBrowser = activitiesBrowser; _libraryCopyPlateSearchResults = libraryCopyPlateSearchResults; } /** * For command line usage only */ public LibraryCopySearchResults(GenericEntityDAO dao, LibrariesDAO librariesDao) { super(null); _dao = dao; _librariesDao = librariesDao; } @Override public void searchAll() { setTitle("Library Copies"); initialize(new EntityDataFetcher<Copy, Integer>(Copy.class, _dao)); } public void searchCopiesByLibrary(final Library library) { setTitle("Library Copies for library " + library.getLibraryName()); EntityDataFetcher<Copy, Integer> copyDataFetcher = new EntityDataFetcher<Copy, Integer>(Copy.class, _dao) { @Override public void addDomainRestrictions(HqlBuilder hql) { hql.where(getRootAlias(), Copy.library.getLeaf(), Operator.EQUAL, library); } }; initialize(copyDataFetcher); } private void initialize(EntityDataFetcher<Copy, Integer> copyDataFetcher) { initialize(new InMemoryEntityDataModel<Copy, Integer, Copy>(copyDataFetcher) { @Override public void fetch(List<? extends TableColumn<Copy, ?>> columns) { super.fetch(columns); _librariesDao.calculateCopyScreeningStatistics(_unfilteredData); _librariesDao.calculateCopyVolumeStatistics(_unfilteredData); } }); } @Override protected List<TableColumn<Copy, ?>> buildColumns() { List<TableColumn<Copy, ?>> columns = Lists.newArrayList(); columns.add(new TextEntityColumn<Copy>(Copy.library, "Library", "The library that this copy represents", TableColumn.UNGROUPED) { @Override public String getCellValue(Copy copy) { return copy.getLibrary().getLibraryName(); } @Override public boolean isCommandLink() { return true; } @Override public Object cellAction(Copy copy) { return _libraryViewer.viewEntity(copy.getLibrary()); } }); Iterables.getLast(columns).setVisible(!isNested()); columns.add(new EnumEntityColumn<Copy, ScreenType>(RelationshipPath.from(Copy.class).toProperty("library"), "Screen Type", "'RNAi' or 'Small Molecule'", TableColumn.UNGROUPED, ScreenType.values()) { @Override public ScreenType getCellValue(Copy copy) { return copy.getLibrary().getScreenType(); } }); Iterables.getLast(columns).setVisible(false); String names = Joiner.on("','").join(StringUtils.getVocabularyTerms(LibraryType.values())); columns.add(new EnumEntityColumn<Copy, LibraryType>(RelationshipPath.from(Copy.class).toProperty("library"), "Library Type", names, TableColumn.UNGROUPED, LibraryType.values()) { @Override public LibraryType getCellValue(Copy copy) { return copy.getLibrary().getLibraryType(); } }); Iterables.getLast(columns).setVisible(false); columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("name"), "Copy Name", "The name of the the copy", TableColumn.UNGROUPED) { @Override public String getCellValue(Copy copy) { return copy.getName(); } @Override public boolean isCommandLink() { return true; } @Override public Object cellAction(Copy copy) { if (isNested()) { LibraryCopySearchResults libraryCopySearchResults = (LibraryCopySearchResults) _libraryCopyViewer .getContextualSearchResults(); libraryCopySearchResults.searchCopiesByLibrary(copy.getLibrary()); libraryCopySearchResults.findEntity(copy); return BROWSE_LIBRARY_COPIES; } return viewSelectedEntity(); } }); ((TextEntityColumn<Copy>) Iterables.getLast(columns)).addRelationshipPath(Copy.library); columns.add(new EnumEntityColumn<Copy, CopyUsageType>(PropertyPath.from(Copy.class).toProperty("usageType"), "Usage Type", "The usage type of the copy", TableColumn.UNGROUPED, CopyUsageType.values()) { @Override public CopyUsageType getCellValue(Copy copy) { return copy.getUsageType(); } }); columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("primaryPlateLocation"), "Primary Plate Location", "The most common plate location for plates of this copy", TableColumn.UNGROUPED) { @Override public String getCellValue(Copy copy) { if (copy.getPrimaryPlateLocation() == null) { return null; } return copy.getPrimaryPlateLocation().toDisplayString(); } }); columns.add(new IntegerEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("plateLocationsCount"), "Plate Locations", "The number different plate locations found for plates of this copy", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getPlateLocationsCount(); } }); columns.add(new EnumEntityColumn<Copy, PlateStatus>( PropertyPath.from(Copy.class).toProperty("primaryPlateStatus"), "Primary Plate Status", "The most common plate status for plates of this copy", TableColumn.UNGROUPED, PlateStatus.values()) { @Override public PlateStatus getCellValue(Copy copy) { return copy.getPrimaryPlateStatus(); } }); buildConcentrationColumns(columns); columns.add(new IntegerEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("platesAvailable"), "Plates Available", "The number of plates with a status of \"Available\"", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getPlatesAvailable(); } }); columns.add(new FixedDecimalColumn<Copy>("Plate Screening Count Average", "The average number of times this copy's plates have been screened, ignoring replicates", TableColumn.UNGROUPED) { @Override public BigDecimal getCellValue(Copy copy) { if (copy.getScreeningStatistics().getPlateCount() == 0) return null; if (copy.getScreeningStatistics().getPlateScreeningCount() == 0) return BigDecimal.ZERO; BigDecimal val = new BigDecimal(copy.getScreeningStatistics().getPlateScreeningCount()).divide( new BigDecimal(copy.getScreeningStatistics().getPlateCount()), DECIMAL_SCALE, RoundingMode.CEILING); return val; } }); columns.add(new VolumeColumn<Copy>("Average Plate Remaining Volume", "The average well volume remaining across all library screening plates of this copy", TableColumn.UNGROUPED) { @Override public Volume getCellValue(Copy copy) { return getNullSafeVolumeStatistics(copy).getAverageRemaining(); } }); columns.add(new VolumeColumn<Copy>("Min Plate Remaining Volume", "The minimum well volume remaining across all library screening plates of this copy", TableColumn.UNGROUPED) { @Override public Volume getCellValue(Copy copy) { return getNullSafeVolumeStatistics(copy).getMinRemaining(); } }); columns.add(new VolumeColumn<Copy>("Max Plate Remaining Volume", "The maximum well volume remaining across all library screening plates of this copy", TableColumn.UNGROUPED) { @Override public Volume getCellValue(Copy copy) { return getNullSafeVolumeStatistics(copy).getMaxRemaining(); } }); columns.add(new DateColumn<Copy>("Last Date Screened", "The date the copy was last screened", TableColumn.UNGROUPED) { @Override public LocalDate getDate(Copy copy) { return copy.getScreeningStatistics().getLastDateScreened(); } }); columns.add(new DateColumn<Copy>("First Date Screened", "The date the copy was first screened", TableColumn.UNGROUPED) { @Override public LocalDate getDate(Copy copy) { return copy.getScreeningStatistics().getFirstDateScreened(); } }); columns.add( new DateEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("datePlated"), "Date Plated", "The earliest date on which a plate of this copy was created", TableColumn.UNGROUPED) { @Override public LocalDate getDate(Copy copy) { return copy.getDatePlated(); } }); columns.add(new IntegerEntityColumn<Copy>(Copy.library.toProperty("startPlate"), "Start Plate", "The first plate number of the library", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getLibrary().getStartPlate(); } }); Iterables.getLast(columns).setVisible(!isNested()); columns.add(new IntegerEntityColumn<Copy>(Copy.library.toProperty("startPlate"), "End Plate", "The last plate number of the library", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getLibrary().getEndPlate(); } }); Iterables.getLast(columns).setVisible(!isNested()); columns.add(new IntegerEntityColumn<Copy>(Copy.library, "Library Plate Count", "The number of plates in the library", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getLibrary().getEndPlate() - copy.getLibrary().getStartPlate() + 1; } }); Iterables.getLast(columns).setVisible(false); columns.add(new IntegerColumn<Copy>("Copy Plate Count", "The number of plates in this copy", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getScreeningStatistics().getPlateCount(); } @Override public boolean isCommandLink() { return true; } @Override public Object cellAction(Copy copy) { _libraryCopyPlateSearchResults.searchPlatesForCopy(copy); return BROWSE_LIBRARY_COPY_PLATES; } }); columns.add(new IntegerColumn<Copy>("Assay Plate Count", "The number of assay plates screened for this copy", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getScreeningStatistics().getAssayPlateCount(); } }); columns.add(new IntegerColumn<Copy>("Screening Count", "The total number of times this copy has been screened, ignoring replicates", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getScreeningStatistics().getScreeningCount(); } @Override public boolean isCommandLink() { return true; } @Override public Object cellAction(Copy copy) { _activitesBrowser.searchLibraryScreeningActivitiesForCopy(copy); return BROWSE_ACTIVITIES; } }); columns.add(new IntegerColumn<Copy>("Plate Screening Count", "The total number of times individual plates from this copy have been screened, ignoring replicates", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getScreeningStatistics().getPlateScreeningCount(); } }); Iterables.getLast(columns).setVisible(false); columns.add(new IntegerColumn<Copy>("Data Loading Count", "The number of screen results loaded for screens of this copy", TableColumn.UNGROUPED) { @Override public Integer getCellValue(Copy copy) { return copy.getScreeningStatistics().getDataLoadingCount(); } }); columns.add(new DateColumn<Copy>("First Date Data Loaded", "The date of the first screen result data loading activity", TableColumn.UNGROUPED) { @Override public LocalDate getDate(Copy copy) { return copy.getScreeningStatistics().getFirstDateDataLoaded(); } }); Iterables.getLast(columns).setVisible(false); columns.add(new DateColumn<Copy>("Last Date Data Loaded", "The date of the last screen result data loading activity", TableColumn.UNGROUPED) { @Override public LocalDate getDate(Copy copy) { return copy.getScreeningStatistics().getLastDateDataLoaded(); } }); Iterables.getLast(columns).setVisible(false); return columns; } private void buildConcentrationColumns(List<TableColumn<Copy, ?>> columns) { // Concentration Columns // molar values columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("minMolarConcentration"), "Minimum Well Molar Concentration", "The minimum molar concentration (diluted) of the wells of the copy's plates", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { MolarConcentration value = copy.getNullSafeConcentrationStatistics() .getDilutedMinMolarConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(true); columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("maxMolarConcentration"), "Maximum Well Molar Concentration", "The maximum molar concentration (diluted) of the wells of the copy's plates", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { MolarConcentration value = copy.getNullSafeConcentrationStatistics() .getDilutedMaxMolarConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(true); columns.add(new TextEntityColumn<Copy>( PropertyPath.from(Copy.class).toProperty("primaryWellMolarConcentration"), "Primary Well Molar Concentration", "The value of the most frequent plate well molar concentration (diluted)", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { MolarConcentration value = copy.getNullSafeConcentrationStatistics() .getDilutedPrimaryWellMolarConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(false); // mg/mL columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("minMgMlConcentration"), "Minimum Well Concentration (mg/mL)", "The minimum mg/mL concentration (diluted) of the wells of the copy's plates", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { BigDecimal value = copy.getNullSafeConcentrationStatistics() .getDilutedMinMgMlConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(true); columns.add(new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("maxMgMlConcentration"), "Maximum Well Concentration (mg/mL)", "The minimum mg/mL concentration (diluted) of the wells of the copy's plates", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { BigDecimal value = copy.getNullSafeConcentrationStatistics() .getDilutedMaxMgMlConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(true); columns.add( new TextEntityColumn<Copy>(PropertyPath.from(Copy.class).toProperty("primaryWellMgMlConcentration"), "Primary Well Concentration (mg/mL)", "The value of the most frequent plate well mg/mL concentration (diluted)", COLUMN_GROUP_CONCENTRATION) { @Override public String getCellValue(Copy copy) { BigDecimal value = copy.getNullSafeConcentrationStatistics() .getDilutedPrimaryWellMgMlConcentration(copy.getWellConcentrationDilutionFactor()); return value == null ? "n/a" : value.toString(); } }); Iterables.getLast(columns).setVisible(false); columns.add(new FixedDecimalEntityColumn<Copy>( PropertyPath.from(Copy.class).toProperty("wellConcentrationDilutionFactor"), "Primary Well Concentration Dilution Factor", "The most often ocurring factor by which the original library well concentration is diluted for this copy's plates", COLUMN_GROUP_CONCENTRATION) { @Override public BigDecimal getCellValue(Copy copy) { return copy.getWellConcentrationDilutionFactor(); } }); Iterables.getLast(columns).setVisible(true); } private static VolumeStatistics getNullSafeVolumeStatistics(Copy copy) { VolumeStatistics volumeStatistics = copy.getVolumeStatistics(); if (volumeStatistics == null) { return VolumeStatistics.Null; } return volumeStatistics; } @Override protected Copy rowToEntity(Copy row) { return row; } }