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.service.cherrypicks; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.io.Serializable; import java.math.RoundingMode; import java.util.Collections; import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.SortedSet; import java.util.TreeMap; import java.util.TreeSet; import java.util.zip.ZipEntry; import java.util.zip.ZipOutputStream; import org.apache.commons.collections.Factory; import org.apache.commons.collections.MultiMap; import org.apache.commons.collections.map.MultiValueMap; import org.apache.log4j.Logger; import com.google.common.collect.Lists; import com.google.common.collect.Sets; import edu.harvard.med.screensaver.db.GenericEntityDAO; import edu.harvard.med.screensaver.db.LibrariesDAO; import edu.harvard.med.screensaver.model.VolumeUnit; import edu.harvard.med.screensaver.model.cherrypicks.CherryPickAssayPlate; import edu.harvard.med.screensaver.model.cherrypicks.CherryPickRequest; import edu.harvard.med.screensaver.model.cherrypicks.LabCherryPick; import edu.harvard.med.screensaver.model.cherrypicks.LabCherryPick.LabCherryPickStatus; import edu.harvard.med.screensaver.model.libraries.Copy; import edu.harvard.med.screensaver.model.libraries.Plate; import edu.harvard.med.screensaver.model.libraries.PlateType; import edu.harvard.med.screensaver.util.CSVPrintWriter; import edu.harvard.med.screensaver.util.CustomNewlinePrintWriter; import edu.harvard.med.screensaver.util.Pair; /** * For a cherry pick request, builds the CSV files that define the assay plate * mapping. * * @author <a mailto="andrew_tolopko@hms.harvard.edu">Andrew Tolopko</a> * @author <a mailto="john_sullivan@hms.harvard.edu">John Sullivan</a> */ public class CherryPickRequestPlateMapFilesBuilder { /** * File extension for each plate map file in the zip file. * Stewart Rudnicki has indicated that this file extension should lower-case.. */ private static final String PLATE_MAP_FILE_EXTENSION = ".csv"; /** * Windows newline must be used! The consumer of the files we're generating is * a machine in the lab that has this requirement, so cross-platform concerns * are not a concern. */ private static final String NEWLINE = "\r\n"; private static final String[] CSV_FILE_HEADERS = { "Source Plate", "Source Copy", "Source Well", "Source Plate Type", "Destination Well", "Destination Plate Type", "Person Visiting", "Screen Number", "Volume" }; private static final String[] DISTINCT_PLATECOPYLIST_FILE_HEADERS = { "Source Plate", "Source Copy", "Location" }; private static final String README_FILE_NAME = "README.txt"; private static final String DISTINCT_PLATE_COPY_LIST_FILE_NAME = "plate-copy-location.csv"; // static members private static Logger log = Logger.getLogger(CherryPickRequestPlateMapFilesBuilder.class); // instance data members private GenericEntityDAO genericEntityDao; private CherryPickRequestPlateMapper cherryPickRequestPlateMapper; private LibrariesDAO librariesDao; // public constructors and methods public CherryPickRequestPlateMapFilesBuilder(GenericEntityDAO dao, LibrariesDAO librariesDao, CherryPickRequestPlateMapper cherryPickRequestPlateMapper) { this.genericEntityDao = dao; this.librariesDao = librariesDao; this.cherryPickRequestPlateMapper = cherryPickRequestPlateMapper; } // public constructors and methods public InputStream buildZip(final CherryPickRequest cherryPickRequestIn, final Set<CherryPickAssayPlate> plates) throws IOException { CherryPickRequest cherryPickRequest = (CherryPickRequest) genericEntityDao .reattachEntity(cherryPickRequestIn); return doBuildZip(cherryPickRequest, plates); } // private methods @SuppressWarnings("unchecked") private InputStream doBuildZip(CherryPickRequest cherryPickRequest, Set<CherryPickAssayPlate> forPlates) throws IOException { ByteArrayOutputStream zipOutRaw = new ByteArrayOutputStream(); ZipOutputStream zipOut = new ZipOutputStream(zipOutRaw); MultiMap/*<String,SortedSet<CherryPick>>*/ files2CherryPicks = buildCherryPickFiles(cherryPickRequest, forPlates); buildReadme(cherryPickRequest, zipOut); buildDistinctPlateCopyFile(cherryPickRequest, forPlates, zipOut); PrintWriter out = new CSVPrintWriter(new OutputStreamWriter(zipOut), NEWLINE); for (Iterator iter = files2CherryPicks.keySet().iterator(); iter.hasNext();) { String fileName = (String) iter.next(); ZipEntry zipEntry = new ZipEntry(fileName); zipOut.putNextEntry(zipEntry); writeHeadersRow(out); for (LabCherryPick cherryPick : (SortedSet<LabCherryPick>) files2CherryPicks.get(fileName)) { writeCherryPickRow(out, cherryPick); } out.flush(); } out.close(); return new ByteArrayInputStream(zipOutRaw.toByteArray()); } @SuppressWarnings("unchecked") private void buildReadme(CherryPickRequest cherryPickRequest, ZipOutputStream zipOut) throws IOException { ZipEntry zipEntry = new ZipEntry(README_FILE_NAME); zipOut.putNextEntry(zipEntry); PrintWriter writer = new CustomNewlinePrintWriter(zipOut, NEWLINE); writer.println("This zip file contains plate mappings for Cherry Pick Request " + cherryPickRequest.getCherryPickRequestNumber()); writer.println(); { StringBuilder buf = new StringBuilder(); for (CherryPickAssayPlate assayPlate : cherryPickRequest.getActiveCherryPickAssayPlates()) { buf.append(assayPlate.getName()).append("\t").append(assayPlate.getStatusLabel()); if (assayPlate.isPlatedAndScreened()) { buf.append("\t(").append(assayPlate.getCherryPickScreenings().last().getDateOfActivity()) .append(" by ").append(assayPlate.getCherryPickScreenings().last().getPerformedBy() .getFullNameFirstLast()) .append(')'); } else if (assayPlate.isPlated()) { buf.append("\t(").append(assayPlate.getCherryPickLiquidTransfer().getDateOfActivity()) .append(" by ").append(assayPlate.getCherryPickLiquidTransfer().getPerformedBy() .getFullNameFirstLast()) .append(')'); } buf.append(NEWLINE); } if (buf.length() > 0) { writer.println("Cherry pick plates:"); writer.print(buf.toString()); writer.println(); } } Map<CherryPickAssayPlate, Integer> platesRequiringReload = cherryPickRequestPlateMapper .getAssayPlatesRequiringSourcePlateReload(cherryPickRequest); if (platesRequiringReload.size() > 0) { writer.println("WARNING: Some cherry pick plates will be created from the same source plate!"); writer.println( "You will need to reload one or more source plates for each of the following cherry pick plates:"); for (CherryPickAssayPlate assayPlate : platesRequiringReload.keySet()) { writer.println("\tCherry pick plate '" + assayPlate.getName() + "' requires reload of source plate " + platesRequiringReload.get(assayPlate)); } writer.println(); } { StringBuilder buf = new StringBuilder(); MultiMap sourcePlateTypesForEachAssayPlate = getSourcePlateTypesForEachAssayPlate(cherryPickRequest); for (CherryPickAssayPlate assayPlate : cherryPickRequest.getActiveCherryPickAssayPlates()) { Set<PlateType> sourcePlateTypes = (Set<PlateType>) sourcePlateTypesForEachAssayPlate .get(assayPlate.getName()); if (sourcePlateTypes != null && sourcePlateTypes.size() > 1) { buf.append(assayPlate.getName()).append(NEWLINE); } } if (buf.length() > 0) { writer.println( "WARNING: Some cherry pick plates will be created from multiple source plates of non-uniform plate types!"); writer.println("The following cherry pick plates are specified across multiple files:"); writer.print(buf.toString()); writer.println(); } } writer.flush(); } /** * for [#3206] Generate a distinct plate/copy list for CPR download file */ private void buildDistinctPlateCopyFile(CherryPickRequest cherryPickRequest, Set<CherryPickAssayPlate> forPlates, ZipOutputStream zipOut) throws IOException { PrintWriter out = new CSVPrintWriter(new OutputStreamWriter(zipOut), NEWLINE); zipOut.putNextEntry(new ZipEntry(DISTINCT_PLATE_COPY_LIST_FILE_NAME)); for (String string : DISTINCT_PLATECOPYLIST_FILE_HEADERS) { out.print(string); } out.println(); // TODO: consider caching this while building the CPR Set<Plate> sourcePlates = Sets.newHashSet(); for (CherryPickAssayPlate plate : forPlates) { for (LabCherryPick lcp : plate.getLabCherryPicks()) { lcp = genericEntityDao.reloadEntity(lcp, true); sourcePlates.add(librariesDao.findPlate(lcp.getSourceWell().getPlateNumber(), lcp.getSourceCopy().getName())); } } // sort by plate/copy/location List<Plate> list = Lists.newArrayList(sourcePlates); Collections.sort(list, new Comparator<Plate>() { @Override public int compare(Plate o1, Plate o2) { if (o1.equals(o2)) { return o1.getLocation().compareTo(o2.getLocation()); } return o1.compareTo(o2); // note Plate.compare() does a plate/copy compare } }); for (Plate p : list) { out.print(p.getPlateNumber()); out.print(p.getCopy().getName()); out.print(p.getLocation() == null ? "" : p.getLocation().toDisplayString()); out.println(); } } @SuppressWarnings("unchecked") /** * Normally, we create 1 file per assay plate. However, in the case where an * assay plate is comprised of wells from library copy plates that have * different plate types, we need to generate a separate file for each source * plate type (i.e., the assay plate will be defined over multiple files). * @return a MultiMap that partitions the cherry picks by file, * ordering both the file names and cherry picks for each file. */ private MultiMap/*<String,SortedSet<CherryPick>>*/ buildCherryPickFiles(CherryPickRequest cherryPickRequest, Set<CherryPickAssayPlate> forPlates) { MultiMap assayPlate2SourcePlateTypes = getSourcePlateTypesForEachAssayPlate(cherryPickRequest); MultiMap result = MultiValueMap.decorate(new TreeMap<String, SortedSet<LabCherryPick>>(), new Factory() { public Object create() { return new TreeSet<LabCherryPick>(PlateMappingCherryPickComparator.getInstance()); } }); // HACK: transform set of CPAP into a set of IDs, for purpose of checking // set membership; we can't rely upon CPAP.equals(), since we're comparing // non-managed entities with managed entities, and therefore we do not have // the guarantee of instance equality for entities with the same ID Set<Serializable> forPlateIds = new HashSet<Serializable>(forPlates.size()); for (CherryPickAssayPlate cpap : forPlates) { if (cpap.getEntityId() == null) { throw new IllegalArgumentException( "all members of 'forPlates' must already be persisted and have a database identifier"); } forPlateIds.add(cpap.getEntityId()); } for (LabCherryPick cherryPick : cherryPickRequest.getLabCherryPicks()) { if (cherryPick.isAllocated()) { CherryPickAssayPlate assayPlate = cherryPick.getAssayPlate(); if (forPlates == null || (assayPlate != null && forPlateIds.contains(assayPlate.getEntityId()))) { Set<PlateType> sourcePlateTypes = (Set<PlateType>) assayPlate2SourcePlateTypes .get(assayPlate.getName()); String fileName = makeFilename(cherryPick, sourcePlateTypes.size()); result.put(fileName, cherryPick); } } } return result; } private String makeFilename(LabCherryPick cherryPick, int distinctSourcePlateTypes) { StringBuilder fileName = new StringBuilder(cherryPick.getAssayPlate().getName()); if (distinctSourcePlateTypes > 1) { fileName.append(' '); fileName.append(cherryPick.getSourceCopy().findPlate(cherryPick.getSourceWell().getPlateNumber()) .getPlateType().toString()); } int attempt = cherryPick.getAssayPlate().getAttemptOrdinal() + 1; if (attempt > 0) { fileName.append(" (Run").append(attempt).append(")"); } fileName.append(PLATE_MAP_FILE_EXTENSION); return fileName.toString(); } private MultiMap getSourcePlateTypesForEachAssayPlate(CherryPickRequest cherryPickRequest) { MultiMap assayPlateName2PlateTypes = MultiValueMap.decorate(new HashMap(), new Factory() { public Object create() { return new HashSet(); } }); for (LabCherryPick cherryPick : cherryPickRequest.getLabCherryPicks()) { if (cherryPick.isAllocated() && cherryPick.isMapped()) { assayPlateName2PlateTypes.put(cherryPick.getAssayPlate().getName(), cherryPick.getSourceCopy() .findPlate(cherryPick.getSourceWell().getPlateNumber()).getPlateType()); } } return assayPlateName2PlateTypes; } private void writeCherryPickRow(PrintWriter out, LabCherryPick cherryPick) { out.print(cherryPick.getSourceWell().getPlateNumber()); out.print(cherryPick.getSourceCopy().getName()); out.print(cherryPick.getSourceWell().getWellName()); out.print(cherryPick.getSourceCopy().findPlate(cherryPick.getSourceWell().getPlateNumber()).getPlateType()); out.print(cherryPick.getAssayPlateWellName()); out.print(cherryPick.getAssayPlate().getAssayPlateType()); out.print(cherryPick.getCherryPickRequest().getRequestedBy().getFullNameFirstLast()); out.print(cherryPick.getCherryPickRequest().getScreen().getFacilityId()); out.print(cherryPick.getCherryPickRequest().getTransferVolumePerWellApproved() .convert(VolumeUnit.MICROLITERS).getValue().setScale(2, RoundingMode.HALF_UP)); out.println(); } private void writeHeadersRow(PrintWriter out) { for (String string : CSV_FILE_HEADERS) { out.print(string); } out.println(); } }