cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/DerivationTreeSummaryDTO.java

   1 /**
   2 * Copyright (C) 2015 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.api.service.dto;
  10
  11 import java.io.Serializable;
  12 import java.net.URISyntaxException;
  13 import java.util.ArrayList;
  14 import java.util.Collection;
  15 import java.util.List;
  16 import java.util.UUID;
  17
  18 import org.apache.log4j.Logger;
  19
  20 import eu.etaxonomy.cdm.common.CdmUtils;
  21 import eu.etaxonomy.cdm.common.URI;
  22 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  23 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  24 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  25 import eu.etaxonomy.cdm.model.media.MediaUtils;
  26 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  27 import eu.etaxonomy.cdm.model.molecular.Sequence;
  28 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  29 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  30 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  31 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  32 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  33 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  34
  35 /**
  36  * Provides summary information on media, DNA, molecular data and scans
  37  * found in the derivation tree including the current {@link SpecimenOrObservationBase}
  38  * instance.
  39  *
  40  * @author pplitzner
  41  * @since Mar 26, 2015
  42  */
  43 public class DerivationTreeSummaryDTO implements Serializable {
  44
  45     private static final long serialVersionUID = 8329871164348514709L;
  46
  47     private static final Logger logger = Logger.getLogger(DerivationTreeSummaryDTO.class);
  48
  49     private List<Link> specimenScans = new ArrayList<>();
  50     private List<MolecularData> molecularDataList = new ArrayList<>();
  51     private List<Link> detailImages = new ArrayList<>();
  52     private List<UUID> specimenScanUuids = new ArrayList<>();
  53     private List<UUID> detailImageUuids = new ArrayList<>();
  54
  55     /**
  56      * Factory method to create the summary information on media, DNA, molecular data and scans
  57      * found in the derivation tree including the passed {@link SpecimenOrObservationBase specimenOrObservation}
  58      *
  59      * @param specimenOrObservation
  60      *      The {@link SpecimenOrObservationBase} to create the summary for.
  61      * @param specimenIdentifier
  62      *      In case of a {@link DerivedUnit} being passed to this factory method, the <code>specimenIdentifier</code> should
  63      *      be set to the result of {@link DerivedUnitDTO#composeSpecimenIdentifier(DerivedUnit)}
  64      * @return
  65      *      The new instance.
  66      */
  67     public static DerivationTreeSummaryDTO fromEntity(SpecimenOrObservationBase<?> specimenOrObservation, String specimenIdentifier) {
  68
  69         DerivationTreeSummaryDTO derivateDataDTO = new DerivationTreeSummaryDTO();
  70
  71         Collection<DerivedUnit> childDerivates = specimenOrObservation.collectDerivedUnits();
  72         for (DerivedUnit childDerivate : childDerivates) {
  73             // assemble molecular data
  74             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
  75             if (childDerivate.isInstanceOf(DnaSample.class)) {
  76                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
  77                     // TODO implement TissueSample assembly for web service
  78                 }
  79                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
  80                     DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
  81                     for (Sequence sequence : dna.getSequences()) {
  82                         URI boldUri = null;
  83                         try {
  84                             boldUri = sequence.getBoldUri();
  85                         } catch (URISyntaxException e1) {
  86                             // TODO consider better reporting of this incident
  87                             logger.error("Could not create BOLD URI", e1);
  88                         }
  89                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
  90                         Link providerLink = null;
  91                         if(boldUri!=null && dnaMarker!=null){
  92                             providerLink = new DerivationTreeSummaryDTO.Link(boldUri, dnaMarker.getLabel());
  93                         }
  94                         MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
  95
  96                         //contig file
  97                         ContigFile contigFile = null;
  98                         if (sequence.getContigFile() != null) {
  99                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 100                             if (contigMediaRepresentationPart != null) {
 101                                 contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
 102                             }
 103                         }
 104                         else{
 105                             contigFile = molecularData.addContigFile(null);
 106                         }
 107                         // primer files
 108                         if (sequence.getSingleReads() != null) {
 109                             int readCount = 1;
 110                             for (SingleRead singleRead : sequence.getSingleReads()) {
 111                                 MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 112                                 if (pherogramMediaRepresentationPart != null && contigFile != null) {
 113                                     contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
 114                                 }
 115                             }
 116                         }
 117                     }
 118                 }
 119             }
 120             // assemble media data
 121             else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
 122                 MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
 123
 124                 URI mediaUri = getMediaUri(media);
 125                 if (media.getKindOfUnit() != null) {
 126                     // specimen scan
 127                     if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
 128                         derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
 129                         String imageLinkText = "scan";
 130                         imageLinkText = specimenIdentifier;
 131                         derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
 132                     }
 133                     // detail image
 134                     else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
 135                         derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
 136                         String motif = "detail image";
 137                         if (media.getMediaSpecimen()!=null){
 138                             if(CdmUtils.isNotBlank(media.getMediaSpecimen().getTitleCache())) {
 139                                 motif = media.getMediaSpecimen().getTitleCache();
 140                             }
 141                         }
 142                         derivateDataDTO.addDetailImage(mediaUri, motif);
 143                     }
 144                 }
 145             }
 146         }
 147         return derivateDataDTO;
 148     }
 149
 150     @Deprecated
 151     private static URI getMediaUri(MediaSpecimen mediaSpecimen) {
 152         URI mediaUri = null;
 153         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 154         if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
 155             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 156             if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
 157                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 158                 if (part.getUri() != null) {
 159                     mediaUri = part.getUri();
 160                 }
 161             }
 162         }
 163         return mediaUri;
 164     }
 165
 166     /**
 167      * @return the molecularData
 168      */
 169     public List<MolecularData> getMolecularDataList() {
 170         return molecularDataList;
 171     }
 172
 173     public MolecularData addProviderLink(Link providerLink) {
 174         MolecularData molecularData = new MolecularData(providerLink);
 175         this.molecularDataList.add(molecularData);
 176         return molecularData;
 177     }
 178
 179     /**
 180      * @return the specimenScans
 181      */
 182     public List<Link> getSpecimenScans() {
 183         return specimenScans;
 184     }
 185
 186     public void addSpecimenScan(URI uri, String linkText){
 187         specimenScans.add(new Link(uri, linkText));
 188     }
 189
 190     /**
 191      * @return the detailImages
 192      */
 193     public List<Link> getDetailImages() {
 194         return detailImages;
 195     }
 196
 197     public void addDetailImage(URI uri, String motif){
 198         detailImages.add(new Link(uri, motif));
 199     }
 200
 201     /**
 202      * @return the specimenScanUuids
 203      */
 204     public List<UUID> getSpecimenScanUuids() {
 205         return specimenScanUuids;
 206     }
 207
 208     public void addSpecimenScanUuid(UUID uuid){
 209         specimenScanUuids.add(uuid);
 210     }
 211
 212     /**
 213      * @return the detailImageUuids
 214      */
 215     public List<UUID> getDetailImageUuids() {
 216         return detailImageUuids;
 217     }
 218
 219     public void addDetailImageUuid(UUID uuid){
 220         detailImageUuids.add(uuid);
 221     }
 222
 223     public class MolecularData implements Serializable{
 224
 225         private static final long serialVersionUID = -3509828381796659200L;
 226
 227         private final Link providerLink;
 228         private List<ContigFile> contigFiles;
 229
 230         public MolecularData(Link providerLink) {
 231             super();
 232             this.providerLink = providerLink;
 233         }
 234
 235         public ContigFile addContigFile(Link contigLink){
 236             if(contigFiles==null){
 237                 contigFiles = new ArrayList<ContigFile>();
 238             }
 239             ContigFile contigFile = new ContigFile(contigLink);
 240             contigFiles.add(contigFile);
 241             return contigFile;
 242         }
 243
 244         public synchronized Link getProviderLink() {
 245             return providerLink;
 246         }
 247
 248         public List<ContigFile> getContigFiles() {
 249             return contigFiles;
 250         }
 251
 252     }
 253
 254     public class ContigFile implements Serializable{
 255
 256         private final Link contigLink;
 257         private List<Link> primerLinks;
 258
 259         public ContigFile(Link contigLink) {
 260             this.contigLink = contigLink;
 261         }
 262
 263         public void addPrimerLink(URI uri, String linkText){
 264             if(primerLinks==null){
 265                 primerLinks = new ArrayList<Link>();
 266             }
 267             primerLinks.add(new Link(uri, linkText));
 268         }
 269
 270         public Link getContigLink() {
 271             return contigLink;
 272         }
 273
 274         public List<Link> getPrimerLinks() {
 275             return primerLinks;
 276         }
 277
 278     }
 279
 280     public static class Link implements Serializable{
 281
 282         private static final long serialVersionUID = 6635385359662624579L;
 283
 284         private String linkText;
 285         private URI uri;
 286
 287         public Link(URI uri, String linkText) {
 288             super();
 289             this.linkText = linkText;
 290             this.uri = uri;
 291         }
 292         /**
 293          * @return the linkText
 294          */
 295         public synchronized String getLinkText() {
 296             return linkText;
 297         }
 298         /**
 299          * @param linkText the linkText to set
 300          */
 301         public synchronized void setLinkText(String linkText) {
 302             this.linkText = linkText;
 303         }
 304         /**
 305          * @return the uri
 306          */
 307         public synchronized URI getUri() {
 308             return uri;
 309         }
 310         /**
 311          * @param uri the uri to set
 312          */
 313         public synchronized void setUri(URI uri) {
 314             this.uri = uri;
 315         }
 316
 317         @Override
 318         public int hashCode() {
 319             final int prime = 31;
 320             int result = 1;
 321             result = prime * result + ((linkText == null) ? 0 : linkText.hashCode());
 322             result = prime * result + ((uri == null) ? 0 : uri.hashCode());
 323             return result;
 324         }
 325
 326         @Override
 327         public boolean equals(Object obj) {
 328             if (this == obj) {
 329                 return true;
 330             }
 331             if (obj == null) {
 332                 return false;
 333             }
 334             if (getClass() != obj.getClass()) {
 335                 return false;
 336             }
 337             Link other = (Link) obj;
 338             if (linkText == null) {
 339                 if (other.linkText != null) {
 340                     return false;
 341                 }
 342             } else if (!linkText.equals(other.linkText)) {
 343                 return false;
 344             }
 345             if (uri == null) {
 346                 if (other.uri != null) {
 347                     return false;
 348                 }
 349             } else if (!uri.equals(other.uri)) {
 350                 return false;
 351             }
 352             return true;
 353         }
 354     }
 355
 356
 357 }