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.iccbl.screensaver.io.screens; import java.io.File; import java.io.FileNotFoundException; import java.util.Set; import java.util.SortedMap; import java.util.TreeMap; import org.apache.commons.cli.OptionBuilder; import org.apache.log4j.Logger; import edu.harvard.med.screensaver.db.DAOTransaction; import edu.harvard.med.screensaver.db.DAOTransactionRollbackException; import edu.harvard.med.screensaver.db.GenericEntityDAO; import edu.harvard.med.screensaver.db.LibrariesDAO; import edu.harvard.med.screensaver.db.ScreenDAO; import edu.harvard.med.screensaver.io.CommandLineApplication; import edu.harvard.med.screensaver.io.FatalParseException; import edu.harvard.med.screensaver.io.screens.StudyCreator; import edu.harvard.med.screensaver.io.workbook2.Cell; import edu.harvard.med.screensaver.io.workbook2.CellVocabularyParser; import edu.harvard.med.screensaver.io.workbook2.Workbook; import edu.harvard.med.screensaver.io.workbook2.WorkbookParseError; import edu.harvard.med.screensaver.io.workbook2.Worksheet; import edu.harvard.med.screensaver.model.libraries.Reagent; import edu.harvard.med.screensaver.model.libraries.ReagentVendorIdentifier; import edu.harvard.med.screensaver.model.libraries.Well; import edu.harvard.med.screensaver.model.libraries.WellKey; import edu.harvard.med.screensaver.model.screenresults.AnnotationType; import edu.harvard.med.screensaver.model.screens.ProjectPhase; import edu.harvard.med.screensaver.model.screens.Screen; import edu.harvard.med.screensaver.model.screens.ScreenType; import edu.harvard.med.screensaver.model.screens.StudyType; import edu.harvard.med.screensaver.model.users.LabAffiliation; import edu.harvard.med.screensaver.model.users.LabHead; import edu.harvard.med.screensaver.model.users.ScreeningRoomUser; public class MedicinalCompoundsStudyCreator extends CommandLineApplication { // static members private static Logger log = Logger.getLogger(MedicinalCompoundsStudyCreator.class); private static final String STUDY_NAME = "100002"; private static final String TITLE = "Annotations on Suitability of Compounds: G. Cuny & K. Lee"; private static final String SUMMARY = "Note for screeners regarding medchem annotation:\n" + "For historical reasons, the screening libraries contain many compounds that may be unsuitable for further study. These include compounds that are unstable and/or reactive, the very properties that may have contributed to apparent activity upon screening. Although experiments are needed to establish definitively whether compounds are false (or physiologically uninteresting) positives in a given screen, some compounds have obvious, chemically offensive functionalities from a structural point of view. Those compounds can be de-prioritized, so that attention can be directed to compounds that are more likely to be true positives. " + "The medicinal chemistry group evaluates the structures of library compounds on an ongoing basis, and the following annotations are applied:\n" + "'A': Compounds that have no obvious liabilities and that are deemed acceptable for initial follow-up work.\n" + "'B': Compounds that are deemed risky for follow-up and, if resources are limiting, should probably be given lower priority than Category A compounds.\n" + "'C': Compounds that are not recommended for follow-up, and, if resources are limiting, should be given lower priority than Category A and B compounds.\n" + "No flag: Compounds that have not yet been evaluated by the medicinal chemistry group."; private static final String A_NO_SPECIFIC_CONCERNS = "A: No specific concerns"; private static final String B_POTENTIAL_LIABILITY = "B: Potential liability"; private static final String C_SUBSTANTIAL_LIABILITY = "C: Substantial liability"; private static final SortedMap<String, String> VALID_MEDCHEM_COMMENT_VALUES = new TreeMap<String, String>(); static { VALID_MEDCHEM_COMMENT_VALUES.put("A", A_NO_SPECIFIC_CONCERNS); VALID_MEDCHEM_COMMENT_VALUES.put("a", A_NO_SPECIFIC_CONCERNS); VALID_MEDCHEM_COMMENT_VALUES.put("B", B_POTENTIAL_LIABILITY); VALID_MEDCHEM_COMMENT_VALUES.put("b", B_POTENTIAL_LIABILITY); VALID_MEDCHEM_COMMENT_VALUES.put("C", C_SUBSTANTIAL_LIABILITY); VALID_MEDCHEM_COMMENT_VALUES.put("c", C_SUBSTANTIAL_LIABILITY); VALID_MEDCHEM_COMMENT_VALUES.put("", null); } private static final String MECHEM_COMMENT_COLUMN_HEADER = "Medchem comment"; private static final String VENDOR_ID_COLUMN_HEADER = "Vendor_ID"; private static final String VENDOR_COLUMN_HEADER = "Vendor"; private static final String PLATE_COLUMN_HEADER = "Plate"; private static final String WELL_COLUMN_HEADER = "Well"; private static final String LAB_AFFILIATION_NAME = "Brigham and Women's Hospital"; private GenericEntityDAO _dao = null; private ScreenDAO _screenDao = null; private LibrariesDAO _librariesDao = null; public MedicinalCompoundsStudyCreator(String[] args) { super(args); _dao = (GenericEntityDAO) getSpringBean("genericEntityDao"); _screenDao = (ScreenDAO) getSpringBean("screenDao"); _librariesDao = (LibrariesDAO) getSpringBean("librariesDao"); } public static void main(String[] args) { final MedicinalCompoundsStudyCreator app = new MedicinalCompoundsStudyCreator(args); app.addCommandLineOption(OptionBuilder.isRequired().hasArg().withArgName("workbook file") .withLongOpt("input-file").create("f")); app.processOptions(true, true); app.run(); } public void run() { _dao.doInTransaction(new DAOTransaction() { public void runTransaction() { try { Screen study = _dao.findEntityByProperty(Screen.class, Screen.facilityId.getPath(), STUDY_NAME); if (study != null) { _screenDao.deleteStudy(study); } LabAffiliation labAffiliation = _dao.findEntityByProperty(LabAffiliation.class, "affiliationName", LAB_AFFILIATION_NAME); if (labAffiliation == null) { throw new RuntimeException( "expected lab affiliation " + LAB_AFFILIATION_NAME + " to exist"); } LabHead labHead = (LabHead) StudyCreator.findOrCreateScreeningRoomUser(_dao, "Gregory", "Cuny", "gcuny@rics.bwh.harvard.edu", true, labAffiliation); ScreeningRoomUser leadScreener = StudyCreator.findOrCreateScreeningRoomUser(_dao, "Kyungae", "Lee", "kyungae_lee@hms.harvard.edu", false, null); study = new Screen(findAdministratorUser(), STUDY_NAME, leadScreener, labHead, ScreenType.SMALL_MOLECULE, StudyType.IN_SILICO, ProjectPhase.ANNOTATION, TITLE); study.setSummary(SUMMARY); AnnotationType annotType = study.createAnnotationType("Notes on Suitability", A_NO_SPECIFIC_CONCERNS + ". " + B_POTENTIAL_LIABILITY + ". " + C_SUBSTANTIAL_LIABILITY + ". " + "No value indicates the compound has not yet been reviewed by this study.", false); int n = loadAndCreateReagents(getCommandLineOptionValue("f", File.class), annotType); _dao.saveOrUpdateEntity(study); log.info("created " + n + " annotations"); } catch (Exception e) { throw new DAOTransactionRollbackException(e); } } }); log.info("study successfully added to database"); } protected int loadAndCreateReagents(File workbookFile, AnnotationType annotType) throws FileNotFoundException { int n = 0; Workbook workbook = new Workbook(workbookFile); for (int iSheet = 0; iSheet < workbook.getWorkbook().getNumberOfSheets(); ++iSheet) { Worksheet sheet = workbook.getWorksheet(iSheet); n += loadAndCreateReagentsFromSheet(sheet, annotType); } if (workbook.getHasErrors()) { log.error("Encountered " + workbook.getErrors().size() + " error(s)."); for (WorkbookParseError error : workbook.getErrors()) { log.error(error.toString()); } } return n; } private int loadAndCreateReagentsFromSheet(Worksheet sheet, AnnotationType annotType) { int n = 0; try { short iVendorColumn = (short) findColumnForHeader(sheet, VENDOR_COLUMN_HEADER); short iVendorIdColumn = (short) findColumnForHeader(sheet, VENDOR_ID_COLUMN_HEADER); short iMedChemCommentColumn = (short) findColumnForHeader(sheet, MECHEM_COMMENT_COLUMN_HEADER); short iPlateColumn = (short) findColumnForHeader(sheet, PLATE_COLUMN_HEADER); short iWellColumn = (short) findColumnForHeader(sheet, WELL_COLUMN_HEADER); if (iVendorColumn >= 0 && iVendorIdColumn >= 0 && iMedChemCommentColumn >= 0) { for (int iRow = 1; iRow < sheet.getRows(); ++iRow) { // TODO: use iterator if (!sheet.getCell(iVendorColumn, iRow, true).isEmpty() && !sheet.getCell(iVendorIdColumn, iRow, true).isEmpty()) { Reagent reagent = findReagent(sheet.getCell(iPlateColumn, iRow, true).getInteger(), sheet.getCell(iWellColumn, iRow, true).getString(), sheet.getCell(iVendorIdColumn, iRow, true).getAsString(), sheet.getCell(iVendorIdColumn, iRow, true).getAsString()); if (reagent != null) { Cell medChemCommentCell = (Cell) sheet.getCell(iMedChemCommentColumn, iRow, false) .clone(); CellVocabularyParser<String> MEDCHEM_COMMENT_CELL_PARSER = new CellVocabularyParser<String>( VALID_MEDCHEM_COMMENT_VALUES, null, "bad annotation value"); String value = MEDCHEM_COMMENT_CELL_PARSER.parse(medChemCommentCell); if (annotType.createAnnotationValue(reagent, value) != null) { ++n; } } } } } return n; } catch (FatalParseException e) { sheet.addWorkbookError(e.getClass().getName() + ":" + e.getMessage()); return 0; } } private Reagent findReagent(Integer plateNumber, String wellName, String vendorName, String reagentIdentifier) { ReagentVendorIdentifier rvi = new ReagentVendorIdentifier(vendorName, reagentIdentifier); Set<Reagent> set = _librariesDao.findReagents(rvi, false); Reagent reagent = null; //Reagent reagent = _dao.findEntityById(Reagent.class, rvi); if (set.isEmpty()) { log.warn("no library contains reagent " + rvi); } else if (set.size() > 1) { throw new RuntimeException("more than one reagent found for RVI: " + rvi + ", reagents: " + set); } else { reagent = set.iterator().next(); } if (reagent == null) { WellKey wellKey = new WellKey(plateNumber, wellName); //log.warn("reagent does not exist with ID " + rvi); Well well = _dao.findEntityById(Well.class, wellKey.toString()); if (well == null) { log.error("unknown reagent " + rvi + "; looking for reagent in well, but no such well " + wellKey); } else { reagent = well.<Reagent>getLatestReleasedReagent(); if (reagent == null) { log.error("unknown reagent " + rvi + " and no reagent in well " + wellKey); } } } return reagent; } private static int findColumnForHeader(Worksheet sheet, String headerName) { for (Cell cell : sheet.getRow(0)) { if (cell.getAsString().equals(headerName)) return cell.getColumn(); } return -1; } }