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.lincs.screensaver.io.libraries; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.util.Set; import com.google.common.collect.Sets; import org.apache.commons.cli.OptionBuilder; import org.apache.commons.cli.ParseException; 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.io.CommandLineApplication; import edu.harvard.med.screensaver.model.AttachedFile; import edu.harvard.med.screensaver.model.libraries.ReagentAttachedFileType; import edu.harvard.med.screensaver.model.libraries.SmallMoleculeReagent; /** * LINCS-only import attachments for reagents * * @author sde4 */ public class ReagentAttachmentImporter extends CommandLineApplication { private static Logger log = Logger.getLogger(ReagentAttachmentImporter.class); public static final int SHORT_OPTION_INDEX = 0; public static final int ARG_INDEX = 1; public static final int LONG_OPTION_INDEX = 2; public static final int DESCRIPTION_INDEX = 3; public static final String[] OPTION_INPUT_FILE = { "f", "file", "input-file", "Input file, to be converted to an sdf file (molfile not supported at this time)" }; public static final String[] OPTION_INPUT_FACILITY_ID = { "i", "facilityId", "facility-id", "facility id of the reagent to import the attachement for" }; public static final String[] OPTION_INPUT_SALT_ID = { "sid", "salt-id", "salt-id", "salt id the reagent to import the attachement for" }; public static final String[] OPTION_INPUT_BATCH_ID = { "bid", "batch-id", "batch-id", "batch id of the reagent to import the attachement for" }; public static final Set attachmentTypes = Sets .newHashSet(new String[] { "QC-NMR", "QC-LCMS", "QC-HPLC", "Data-File" }); public static final String[] OPTION_INPUT_QC_ATTACMENT_TYPE = { "type", "qc-type", "qc-type", "QC attachment type, one of: " + attachmentTypes }; @SuppressWarnings("static-access") public ReagentAttachmentImporter(String[] cmdLineArgs) { super(cmdLineArgs); String[] option = OPTION_INPUT_FILE; addCommandLineOption(OptionBuilder.hasArg().isRequired().withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); option = OPTION_INPUT_FACILITY_ID; addCommandLineOption(OptionBuilder.hasArg().isRequired().withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); option = OPTION_INPUT_SALT_ID; addCommandLineOption(OptionBuilder.hasArg().isRequired().withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); option = OPTION_INPUT_BATCH_ID; addCommandLineOption(OptionBuilder.hasArg().isRequired().withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); option = OPTION_INPUT_QC_ATTACMENT_TYPE; addCommandLineOption(OptionBuilder.hasArg().isRequired().withArgName(option[ARG_INDEX]) .withDescription(option[DESCRIPTION_INDEX]).withLongOpt(option[LONG_OPTION_INDEX]) .create(option[SHORT_OPTION_INDEX])); } @SuppressWarnings("static-access") public static void main(String[] args) { final ReagentAttachmentImporter app = new ReagentAttachmentImporter(args); app.processOptions(/* acceptDatabaseOptions= */false, /* acceptAdminUserOptions= */false); try { execute(app); } catch (Exception e) { log.error("application exception", e); System.exit(1); } } private static void execute(final ReagentAttachmentImporter app) { final GenericEntityDAO dao = (GenericEntityDAO) app.getSpringBean("genericEntityDao"); final LibrariesDAO librariesDao = (LibrariesDAO) app.getSpringBean("librariesDao"); dao.doInTransaction(new DAOTransaction() { @Override public void runTransaction() { String fileName = app.getCommandLineOptionValue(OPTION_INPUT_FILE[SHORT_OPTION_INDEX]); String facilityId = app.getCommandLineOptionValue(OPTION_INPUT_FACILITY_ID[SHORT_OPTION_INDEX]); Integer saltId = app.getCommandLineOptionValue(OPTION_INPUT_SALT_ID[SHORT_OPTION_INDEX], Integer.class); Integer batchId = app.getCommandLineOptionValue(OPTION_INPUT_BATCH_ID[SHORT_OPTION_INDEX], Integer.class); String attachmentType = app.getCommandLineOptionValue( OPTION_INPUT_QC_ATTACMENT_TYPE[SHORT_OPTION_INDEX], String.class); if (!attachmentTypes.contains(attachmentType)) { log.error( "unknown attachment type: " + attachmentType + ", must be one of: " + attachmentTypes); System.exit(1); } File file = new File(fileName); if (!file.exists()) { log.error("file does not exist: " + fileName); System.exit(1); } Set<SmallMoleculeReagent> reagents = librariesDao.findReagents(facilityId, saltId, batchId, true); if (reagents.isEmpty()) { log.error("no reagents found!"); System.exit(1); } ReagentAttachedFileType attachedFileType = dao.findEntityByProperty(ReagentAttachedFileType.class, "value", attachmentType); if (attachedFileType == null) { log.error("Could not find the attached file type: " + attachmentType + ", make sure that this value has been created in the database table."); System.exit(1); } for (SmallMoleculeReagent reagent : reagents) { try { AttachedFile attachedFile1 = reagent.createAttachedFile(file.getName(), attachedFileType, null, new FileInputStream(fileName)); dao.saveOrUpdateEntity(attachedFile1); dao.saveOrUpdateEntity(reagent); } catch (IOException e) { throw new DAOTransactionRollbackException("File not found: " + fileName, e); } } log.info("saved attachment for reagent(s): "); for (SmallMoleculeReagent reagent : reagents) { log.info("\tattached to:" + reagent.getWell().getWellKey() + ": " + reagent.getWell().getFacilityId() + "-" + reagent.getSaltFormId() + "-" + reagent.getFacilityBatchId()); } } }); } }