Java tutorial
// $HeadURL: // http://seanderickson1@forge.abcd.harvard.edu/svn/screensaver/branches/iccbl/data-sharing-levels/src/edu/harvard/med/screensaver/io/screenresults/ScreenResultImporter.java // $ // $Id$ // // 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 javax.mail.MessagingException; import org.apache.commons.cli.OptionBuilder; import org.apache.log4j.Logger; import edu.harvard.med.iccbl.screensaver.io.AdminEmailApplication; import edu.harvard.med.screensaver.ScreensaverConstants; 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.ScreenDAO; import edu.harvard.med.screensaver.db.ScreenResultsDAO; import edu.harvard.med.screensaver.io.screenresults.ScreenResultReporter; import edu.harvard.med.screensaver.io.screens.StudyCreator; import edu.harvard.med.screensaver.model.screenresults.ScreenResult; import edu.harvard.med.screensaver.model.screens.Screen; import edu.harvard.med.screensaver.model.screens.ScreenType; import edu.harvard.med.screensaver.model.users.AdministratorUser; import edu.harvard.med.screensaver.model.users.LabHead; /** * TODO: Move the transactional code out of this class and into service methods * Create a studies to count overlapping positives and to count confirmed positive statistics.<br> * 1. Overlapping positives:<br> * see [#2268] new column to display # overlapping screens <br> * Details: <br> * <br> * 1. Overlapping positives:<br> * We want to provide a column in Well Search Results to display the number of screens that * have marked the well as a positive. I believe we can include even screens * w/DSL 3 (Private), but we should confirm this. It would be nice to be able to * calculate this number dynamically, but it almost certainly would not be * performant. Instead, we'll probably need to pre-compute this and store in the * database. To avoid creating new infrastructure for this, I propose that we * simply create a new study that provides a single data column ("annotation * type") for this pre-computed count. The study can be recreated via a batch * cron job that runs a command-line app for this purpose. If we come up with * new cross-screen comparison statistics, we can add them to this study, as * appropriate, as new data columns. <br> */ public class ScreenPositivesCountStudyCreator extends AdminEmailApplication { public static final String DEFAULT_SM_STUDY_TITLE = "Reagent Counts for Small Molecule Screens"; public static final String DEFAULT_SM_STUDY_SUMMARY = "Annotates each small molecule reagent with the number of times " + "it has been screened, and the count of positive hits per reagent (library well) " + "across all small molecule screens. This data is based on primary screening data " + "only and the \"positive\" designations were determined by the " + "investigator(s) responsible for each screen."; public static final String DEFAULT_RNAi_STUDY_TITLE = "Reagent Counts for RNAi Screens"; public static final String DEFAULT_RNAi_STUDY_SUMMARY = "Annotates each RNAi reagent with the number of times it has " + "been screened, and the count of positive hits per reagent (library well) across " + "all RNAi Screens. This data is based on primary screening data only and the " + "\"positive\" designations were determined by the investigator(s) " + "responsible for each screen."; public static final String DEFAULT_POSITIVES_ANNOTATION_NAME = "Screen Positives Count"; public static final String DEFAULT_SM_POSITIVES_ANNOTATION_DESC = "Number of times scored as positive across all Small Molecule Screens"; public static final String DEFAULT_RNAi_POSITIVES_ANNOTATION_DESC = "Number of times scored as positive across all RNAi Screens"; public static final String DEFAULT_OVERALL_ANNOTATION_NAME = "Screened Count"; public static final String DEFAULT_SM_OVERALL_ANNOTATION_DESC = "Number of times screened for all Small Molecule Screens"; public static final String DEFAULT_RNAi_OVERALL_ANNOTATION_DESC = "Number of times screened for all RNAi Screens"; public ScreenPositivesCountStudyCreator(String[] cmdLineArgs) { super(cmdLineArgs); } private static Logger log = Logger.getLogger(ScreenPositivesCountStudyCreator.class); public static final String[] OPTION_STUDY_TITLE = { "title", "title", "study-title", "Title for the study" }; public static final String[] OPTION_STUDY_SUMMARY = { "summary", "summary", "study-summary", "Summary for the study" }; // public static final String[] OPTION_ANNOTATION_NAME = { "annotation", "name", "annotation-name", "name for the annotation in the study" }; // public static final String[] OPTION_ANNOTATION_DESC = { "annotationdesc", "desc", "annotation-desc", "descriptive name of the annotation" }; public static final String[] OPTION_STUDY_NUMBER = { "number", "number", "study-number", "Study number (not required, recommended to use default values), (must be unique, unless specifying the \"replace\" option" }; public static final String[] OPTION_SCREEN_TYPE_SM = { "typesm", "", "screen-type-sm", "create the study for Small Molecule screens" }; public static final String[] OPTION_SCREEN_TYPE_RNAI = { "typernai", "", "screen-type-rnai", "create the study for RNAi screens" }; public static final String[] OPTION_REPLACE = { "replace", "", "replace-if-exists", "the default action is to replace the study if it is out of date; as determined by comparing the study date to the date of the latest screen result. If this option is specified, delete the existing study unconditionally." }; public static final String[] TEST_ONLY = { "testonly", "", "test-only", "run the entire operation specified, then roll-back." }; @SuppressWarnings("static-access") public static void main(String[] args) throws MessagingException { final ScreenPositivesCountStudyCreator app = new ScreenPositivesCountStudyCreator(args); String[] option = OPTION_STUDY_TITLE; app.addCommandLineOption( OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX]) .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX])); option = OPTION_STUDY_NUMBER; app.addCommandLineOption(OptionBuilder.hasArg().withType(Integer.class).withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); option = OPTION_STUDY_SUMMARY; app.addCommandLineOption( OptionBuilder.hasArg().withArgName(option[ARG_INDEX]).withDescription(option[DESCRIPTION_INDEX]) .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX])); option = OPTION_SCREEN_TYPE_SM; app.addCommandLineOption(OptionBuilder.withDescription(option[DESCRIPTION_INDEX]) .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX])); option = OPTION_SCREEN_TYPE_RNAI; app.addCommandLineOption(OptionBuilder.withDescription(option[DESCRIPTION_INDEX]) .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX])); option = OPTION_REPLACE; app.addCommandLineOption(OptionBuilder.withDescription(option[DESCRIPTION_INDEX]) .withLongOpt(option[LONG_OPTION_INDEX]).create(option[SHORT_OPTION_INDEX])); app.addCommandLineOption(OptionBuilder.withDescription(TEST_ONLY[DESCRIPTION_INDEX]) .withLongOpt(TEST_ONLY[LONG_OPTION_INDEX]).create(TEST_ONLY[SHORT_OPTION_INDEX])); app.processOptions(/* acceptDatabaseOptions= */true, /* acceptAdminUserOptions= */true); log.info("==== Running ScreenPositivesCountStudyCreator: " + app.toString() + "======"); try { app.execute(); } catch (Exception e) { String subject = "Execution failure for " + app.getClass().getName(); String msg = subject + "\n" + app.toString(); app.sendErrorMail(subject, msg, e); System.exit(1); } } private void execute() { final GenericEntityDAO dao = (GenericEntityDAO) getSpringBean("genericEntityDao"); final ScreenResultReporter report = (ScreenResultReporter) getSpringBean("screenResultReporter"); final ScreenResultsDAO screenResultsDao = (ScreenResultsDAO) getSpringBean("screenResultsDao"); final ScreenDAO screenDao = (ScreenDAO) getSpringBean("screenDao"); //TODO: Move the transactional code out of this class and into service methods dao.doInTransaction(new DAOTransaction() { public void runTransaction() { try { AdministratorUser admin = findAdministratorUser(); boolean replaceStudyIfExists = isCommandLineFlagSet(OPTION_REPLACE[SHORT_OPTION_INDEX]); String title = null; String summary = null; String annotationDesc = null; String overallAnnotationDesc = null; String studyFacilityId = null; ScreenType screenType = null; if (isCommandLineFlagSet(OPTION_SCREEN_TYPE_SM[SHORT_OPTION_INDEX])) { screenType = ScreenType.SMALL_MOLECULE; studyFacilityId = ScreensaverConstants.DEFAULT_BATCH_STUDY_ID_POSITIVE_COUNT_SM; if (isCommandLineFlagSet(OPTION_STUDY_NUMBER[SHORT_OPTION_INDEX])) { studyFacilityId = getCommandLineOptionValue(OPTION_STUDY_NUMBER[SHORT_OPTION_INDEX], String.class); } // todo: title = getMessages().getMessage("admin.studies.cross_screen_comparison_study.study_title"); title = DEFAULT_SM_STUDY_TITLE; summary = DEFAULT_SM_STUDY_SUMMARY; annotationDesc = DEFAULT_SM_POSITIVES_ANNOTATION_DESC; overallAnnotationDesc = DEFAULT_SM_OVERALL_ANNOTATION_DESC; } if (isCommandLineFlagSet(OPTION_SCREEN_TYPE_RNAI[SHORT_OPTION_INDEX])) { if (isCommandLineFlagSet(OPTION_SCREEN_TYPE_SM[SHORT_OPTION_INDEX])) { showHelpAndExit("Must specify either the \"" + OPTION_SCREEN_TYPE_SM[SHORT_OPTION_INDEX] + "\" or the \"" + OPTION_SCREEN_TYPE_RNAI[SHORT_OPTION_INDEX] + "\" Option"); } screenType = ScreenType.RNAI; studyFacilityId = ScreensaverConstants.DEFAULT_BATCH_STUDY_ID_POSITIVE_COUNT_RNAI; if (isCommandLineFlagSet(OPTION_STUDY_NUMBER[SHORT_OPTION_INDEX])) { studyFacilityId = getCommandLineOptionValue(OPTION_STUDY_NUMBER[SHORT_OPTION_INDEX], String.class); } title = DEFAULT_RNAi_STUDY_TITLE; summary = DEFAULT_RNAi_STUDY_SUMMARY; annotationDesc = DEFAULT_RNAi_POSITIVES_ANNOTATION_DESC; overallAnnotationDesc = DEFAULT_RNAi_OVERALL_ANNOTATION_DESC; } if (screenType == null) { showHelpAndExit("Must specify either the \"" + OPTION_SCREEN_TYPE_SM[SHORT_OPTION_INDEX] + "\" or the \"" + OPTION_SCREEN_TYPE_RNAI[SHORT_OPTION_INDEX] + "\" Option"); } if (isCommandLineFlagSet(OPTION_STUDY_TITLE[SHORT_OPTION_INDEX])) { title = getCommandLineOptionValue(OPTION_STUDY_TITLE[SHORT_OPTION_INDEX]); } if (isCommandLineFlagSet(OPTION_STUDY_SUMMARY[SHORT_OPTION_INDEX])) { summary = getCommandLineOptionValue(OPTION_STUDY_SUMMARY[SHORT_OPTION_INDEX]); } Screen study = dao.findEntityByProperty(Screen.class, Screen.facilityId.getPropertyName(), studyFacilityId); if (study != null) { // first check if the study is out of date ScreenResult latestScreenResult = screenResultsDao.getLatestScreenResult(); if (latestScreenResult == null) { log.info("No screen results found in the database"); System.exit(0); } else if (study.getDateCreated().compareTo(latestScreenResult.getDateCreated()) < 1) { screenDao.deleteStudy(study); } else if (replaceStudyIfExists) { screenDao.deleteStudy(study); } else { String msg = "study " + studyFacilityId + " already exists and is up-to-date (as determined by the date of the latest uploaded screen result). " + "Use the --" + OPTION_REPLACE[LONG_OPTION_INDEX] + " flag to delete the existing study first."; log.info(msg); System.exit(0); } } LabHead labHead = (LabHead) StudyCreator.findOrCreateScreeningRoomUser(dao, admin.getFirstName(), admin.getLastName(), admin.getEmail(), true, null); int count = report.createReagentCountStudy(admin, labHead, studyFacilityId, title, summary, DEFAULT_POSITIVES_ANNOTATION_NAME, annotationDesc, DEFAULT_OVERALL_ANNOTATION_NAME, overallAnnotationDesc, screenType); String subject = "Study created: " + study.getTitle(); //getMessages().getMessage("Study generated"); if (isCommandLineFlagSet(TEST_ONLY[SHORT_OPTION_INDEX])) { subject = "[TEST ONLY, no commits] " + subject; } String msg = "Study: " + study.getFacilityId() + ", " + study.getTitle() + ": " + study.getSummary() + "\nCross-screen Reagents found: " + count; sendAdminEmails(subject, msg); } catch (MessagingException e) { throw new DAOTransactionRollbackException(e); } if (isCommandLineFlagSet(TEST_ONLY[SHORT_OPTION_INDEX])) { throw new DAOTransactionRollbackException("Rollback, testing only"); } } }); log.info("==== finished ScreenPositivesCountStudyCreator ======"); } }