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.logging.log4j.LogManager;
  19 import org.apache.logging.log4j.Logger;
  20
  21 import eu.etaxonomy.cdm.common.CdmUtils;
  22 import eu.etaxonomy.cdm.common.URI;
  23 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  24 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  25 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  26 import eu.etaxonomy.cdm.model.media.MediaUtils;
  27 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  28 import eu.etaxonomy.cdm.model.molecular.Sequence;
  29 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  30 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  31 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  32 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  33 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  34 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  35
  36 /**
  37  * Provides summary information on media, DNA, molecular data and scans
  38  * found in the derivation tree including the current {@link SpecimenOrObservationBase}
  39  * instance.
  40  *
  41  * @author pplitzner
  42  * @since Mar 26, 2015
  43  */
  44 public class DerivationTreeSummaryDTO implements Serializable {
  45
  46     private static final long serialVersionUID = 8329871164348514709L;
  47
  48     private static final Logger logger = LogManager.getLogger();
  49
  50     private List<Link> specimenScans = new ArrayList<>();
  51     private List<MolecularData> molecularDataList = new ArrayList<>();
  52     private List<Link> detailImages = new ArrayList<>();
  53     private List<UUID> specimenScanUuids = new ArrayList<>();
  54     private List<UUID> detailImageUuids = new ArrayList<>();
  55
  56     /**
  57      * Factory method to create the summary information on media, DNA, molecular data and scans
  58      * found in the derivation tree including the passed {@link SpecimenOrObservationBase specimenOrObservation}
  59      *
  60      * @param specimenOrObservation
  61      *      The {@link SpecimenOrObservationBase} to create the summary for.
  62      * @param specimenIdentifier
  63      *      In case of a {@link DerivedUnit} being passed to this factory method, the <code>specimenIdentifier</code> should
  64      *      be set to the result of {@link DerivedUnitDTO#composeSpecimenShortTitle(DerivedUnit)}
  65      * @return
  66      *      The new instance.
  67      */
  68     public static DerivationTreeSummaryDTO fromEntity(SpecimenOrObservationBase<?> specimenOrObservation, String specimenIdentifier) {
  69
  70         DerivationTreeSummaryDTO derivateDataDTO = new DerivationTreeSummaryDTO();
  71
  72         Collection<DerivedUnit> childDerivates = specimenOrObservation.collectDerivedUnits(0);
  73         for (DerivedUnit childDerivate : childDerivates) {
  74             // assemble molecular data
  75             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
  76             if (childDerivate.isInstanceOf(DnaSample.class)) {
  77                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
  78                     // TODO implement TissueSample assembly for web service
  79                 }
  80                 if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
  81                     DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
  82                     for (Sequence sequence : dna.getSequences()) {
  83                         URI boldUri = null;
  84                         try {
  85                             boldUri = sequence.getBoldUri();
  86                         } catch (URISyntaxException e1) {
  87                             // TODO consider better reporting of this incident
  88                             logger.error("Could not create BOLD URI", e1);
  89                         }
  90                         final DefinedTerm dnaMarker = sequence.getDnaMarker();
  91                         Link providerLink = null;
  92                         if(boldUri!=null && dnaMarker!=null){
  93                             providerLink = new DerivationTreeSummaryDTO.Link(boldUri, dnaMarker.getLabel());
  94                         }
  95                         MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
  96
  97                         //contig file
  98                         ContigFile contigFile = null;
  99                         if (sequence.getContigFile() != null) {
 100                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 101                             if (contigMediaRepresentationPart != null) {
 102                                 contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
 103                             }
 104                         }
 105                         else{
 106                             contigFile = molecularData.addContigFile(null);
 107                         }
 108                         // primer files
 109                         if (sequence.getSingleReads() != null) {
 110                             int readCount = 1;
 111                             for (SingleRead singleRead : sequence.getSingleReads()) {
 112                                 MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
 113                                 if (pherogramMediaRepresentationPart != null && contigFile != null) {
 114                                     contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
 115                                 }
 116                             }
 117                         }
 118                     }
 119                 }
 120             }
 121             // assemble media data
 122             else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
 123                 MediaSpecimen mediaSpecimen = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
 124
 125                 URI mediaUri = getMediaUri(mediaSpecimen);
 126                 if (mediaSpecimen.getKindOfUnit() != null) {
 127                     // specimen scan
 128                     if (mediaSpecimen.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
 129                         derivateDataDTO.addSpecimenScanUuid(mediaSpecimen.getMediaSpecimen().getUuid());
 130                         String imageLinkText = "scan of " + specimenIdentifier;
 131                         if(CdmUtils.isNotBlank(mediaSpecimen.getMostSignificantIdentifier())) {
 132                             imageLinkText = mediaSpecimen.getMostSignificantIdentifier();
 133                         }
 134                         if(CdmUtils.isNotBlank(mediaSpecimen.getMediaSpecimen().getTitleCache())) {
 135                             imageLinkText += " (" + mediaSpecimen.getMediaSpecimen().getTitleCache() + ")";
 136                         }
 137                         derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText.trim());
 138                     }
 139                     // detail image
 140                     else if (mediaSpecimen.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
 141                         derivateDataDTO.addDetailImageUuid(mediaSpecimen.getMediaSpecimen().getUuid());
 142                         String motif = "detail image";
 143                         if (mediaSpecimen.getMediaSpecimen()!=null){
 144                             if(CdmUtils.isNotBlank(mediaSpecimen.getMediaSpecimen().getTitleCache())) {
 145                                 motif = mediaSpecimen.getMediaSpecimen().getTitleCache();
 146                             }
 147                         }
 148                         derivateDataDTO.addDetailImage(mediaUri, motif);
 149                     }
 150                 }
 151             }
 152         }
 153         return derivateDataDTO;
 154     }
 155
 156 //    private void updateDerivateTree(Set<DerivedUnitDTO> derivatives) {
 157 //       for (DerivedUnitDTO childDerivate : derivatives) {
 158 //               DerivationTreeSummaryDTO childTree = childDerivate.getDerivationTreeSummary();
 159 //               for (Link link:childTree.detailImages) {
 160 //                       this.addDetailImage(null, null);
 161 //               }
 162 //       }
 163 //
 164 //             // assemble molecular data
 165 //             //pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
 166 //             if (childDerivate instanceof DNASampleDTO) {
 167 //               DNASampleDTO dna = (DNASampleDTO)childDerivate;
 168 //                 if (childDerivate.getRecordBase() == SpecimenOrObservationType.TissueSample) {
 169 //                     // TODO implement TissueSample assembly for web service
 170 //                 }
 171 //                 if (childDerivate.getRecordBase() == SpecimenOrObservationType.DnaSample) {
 172 //
 173 //                     for (SequenceDTO sequence : dna.getSequences()) {
 174 //                         URI boldUri = null;
 175 //                         try {
 176 //                             boldUri = sequence.getBoldUri();
 177 //                         } catch (URISyntaxException e1) {
 178 //                             // TODO consider better reporting of this incident
 179 //                             logger.error("Could not create BOLD URI", e1);
 180 //                         }
 181 //                         final String dnaMarker = sequence.getDnaMarker();
 182 //                         Link providerLink = null;
 183 //                         if(boldUri!=null && dnaMarker!=null){
 184 //                             providerLink = new DerivationTreeSummaryDTO.Link(boldUri, dnaMarker);
 185 //                         }
 186 //                         MolecularData molecularData = this.addProviderLink(providerLink);
 187 //
 188 //                         //contig file
 189 //                         ContigFile contigFile = null;
 190 //                         if (sequence.getContigFile() != null) {
 191 //                             MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
 192 //                             if (contigMediaRepresentationPart != null) {
 193 //                                 contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
 194 //                             }
 195 //                         }
 196 //                         else{
 197 //                             contigFile = molecularData.addContigFile(null);
 198 //                         }
 199 //                         // primer files
 200 //                         if (sequence.getSingleReadAlignments() != null) {
 201 //                             int readCount = 1;
 202 //                             for (SingleReadAlignment singleRead : sequence.getSingleReadAlignments()) {
 203 //                                 MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getSingleRead().getPherogram());
 204 //                                 if (pherogramMediaRepresentationPart != null && contigFile != null) {
 205 //                                     contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
 206 //                                 }
 207 //                             }
 208 //                         }
 209 //                     }
 210 //                 }
 211 //             }
 212 //             // assemble media data
 213 //             else if (childDerivate.hasDetailImage) {
 214 //
 215 //
 216 //                     // specimen scan
 217 //                     if (childDerivate.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
 218 //                         this.addSpecimenScanUuid(childDerivate.get);
 219 //                         String imageLinkText = "scan of " + specimenIdentifier;
 220 //                         if(CdmUtils.isNotBlank(mediaSpecimen.getMostSignificantIdentifier())) {
 221 //                             imageLinkText = mediaSpecimen.getMostSignificantIdentifier();
 222 //                         }
 223 //                         if(CdmUtils.isNotBlank(mediaSpecimen.getMediaSpecimen().getTitleCache())) {
 224 //                             imageLinkText += " (" + mediaSpecimen.getMediaSpecimen().getTitleCache() + ")";
 225 //                         }
 226 //                         this.addSpecimenScan(mediaUri, imageLinkText.trim());
 227 //                     }
 228 //                     // detail image
 229 //                     else if (mediaSpecimen.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
 230 //                         derivateDataDTO.addDetailImageUuid(mediaSpecimen.getMediaSpecimen().getUuid());
 231 //                         String motif = "detail image";
 232 //                         if (mediaSpecimen.getMediaSpecimen()!=null){
 233 //                             if(CdmUtils.isNotBlank(mediaSpecimen.getMediaSpecimen().getTitleCache())) {
 234 //                                 motif = mediaSpecimen.getMediaSpecimen().getTitleCache();
 235 //                             }
 236 //                         }
 237 //                         derivateDataDTO.addDetailImage(mediaUri, motif);
 238 //                     }
 239 //                 }
 240 //             }
 241 //         }
 242 //    }
 243
 244     @Deprecated
 245     private static URI getMediaUri(MediaSpecimen mediaSpecimen) {
 246         URI mediaUri = null;
 247         Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
 248         if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
 249             Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
 250             if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
 251                 MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
 252                 if (part.getUri() != null) {
 253                     mediaUri = part.getUri();
 254                 }
 255             }
 256         }
 257         return mediaUri;
 258     }
 259
 260     /**
 261      * @return the molecularData
 262      */
 263     public List<MolecularData> getMolecularDataList() {
 264         return molecularDataList;
 265     }
 266
 267     public MolecularData addProviderLink(Link providerLink) {
 268         MolecularData molecularData = new MolecularData(providerLink);
 269         this.molecularDataList.add(molecularData);
 270         return molecularData;
 271     }
 272
 273     /**
 274      * @return the specimenScans
 275      */
 276     public List<Link> getSpecimenScans() {
 277         return specimenScans;
 278     }
 279
 280     public void addSpecimenScan(URI uri, String linkText){
 281         specimenScans.add(new Link(uri, linkText));
 282     }
 283
 284     /**
 285      * @return the detailImages
 286      */
 287     public List<Link> getDetailImages() {
 288         return detailImages;
 289     }
 290
 291     public void addDetailImage(URI uri, String motif){
 292         detailImages.add(new Link(uri, motif));
 293     }
 294
 295     /**
 296      * @return the specimenScanUuids
 297      */
 298     public List<UUID> getSpecimenScanUuids() {
 299         return specimenScanUuids;
 300     }
 301
 302     public void addSpecimenScanUuid(UUID uuid){
 303         specimenScanUuids.add(uuid);
 304     }
 305
 306     /**
 307      * @return the detailImageUuids
 308      */
 309     public List<UUID> getDetailImageUuids() {
 310         return detailImageUuids;
 311     }
 312
 313     public void addDetailImageUuid(UUID uuid){
 314         detailImageUuids.add(uuid);
 315     }
 316
 317     public class MolecularData implements Serializable{
 318
 319         private static final long serialVersionUID = -3509828381796659200L;
 320
 321         private final Link providerLink;
 322         private List<ContigFile> contigFiles;
 323
 324         public MolecularData(Link providerLink) {
 325             super();
 326             this.providerLink = providerLink;
 327         }
 328
 329         public ContigFile addContigFile(Link contigLink){
 330             if(contigFiles==null){
 331                 contigFiles = new ArrayList<ContigFile>();
 332             }
 333             ContigFile contigFile = new ContigFile(contigLink);
 334             contigFiles.add(contigFile);
 335             return contigFile;
 336         }
 337
 338         public synchronized Link getProviderLink() {
 339             return providerLink;
 340         }
 341
 342         public List<ContigFile> getContigFiles() {
 343             return contigFiles;
 344         }
 345
 346     }
 347
 348     public class ContigFile implements Serializable{
 349
 350         private final Link contigLink;
 351         private List<Link> primerLinks;
 352
 353         public ContigFile(Link contigLink) {
 354             this.contigLink = contigLink;
 355         }
 356
 357         public void addPrimerLink(URI uri, String linkText){
 358             if(primerLinks==null){
 359                 primerLinks = new ArrayList<Link>();
 360             }
 361             primerLinks.add(new Link(uri, linkText));
 362         }
 363
 364         public Link getContigLink() {
 365             return contigLink;
 366         }
 367
 368         public List<Link> getPrimerLinks() {
 369             return primerLinks;
 370         }
 371
 372     }
 373
 374     public static class Link implements Serializable{
 375
 376         private static final long serialVersionUID = 6635385359662624579L;
 377
 378         private String linkText;
 379         private URI uri;
 380
 381         public Link(URI uri, String linkText) {
 382             super();
 383             this.linkText = linkText;
 384             this.uri = uri;
 385         }
 386         /**
 387          * @return the linkText
 388          */
 389         public synchronized String getLinkText() {
 390             return linkText;
 391         }
 392         /**
 393          * @param linkText the linkText to set
 394          */
 395         public synchronized void setLinkText(String linkText) {
 396             this.linkText = linkText;
 397         }
 398         /**
 399          * @return the uri
 400          */
 401         public synchronized URI getUri() {
 402             return uri;
 403         }
 404         /**
 405          * @param uri the uri to set
 406          */
 407         public synchronized void setUri(URI uri) {
 408             this.uri = uri;
 409         }
 410
 411         @Override
 412         public int hashCode() {
 413             final int prime = 31;
 414             int result = 1;
 415             result = prime * result + ((linkText == null) ? 0 : linkText.hashCode());
 416             result = prime * result + ((uri == null) ? 0 : uri.hashCode());
 417             return result;
 418         }
 419
 420         @Override
 421         public boolean equals(Object obj) {
 422             if (this == obj) {
 423                 return true;
 424             }
 425             if (obj == null) {
 426                 return false;
 427             }
 428             if (getClass() != obj.getClass()) {
 429                 return false;
 430             }
 431             Link other = (Link) obj;
 432             if (linkText == null) {
 433                 if (other.linkText != null) {
 434                     return false;
 435                 }
 436             } else if (!linkText.equals(other.linkText)) {
 437                 return false;
 438             }
 439             if (uri == null) {
 440                 if (other.uri != null) {
 441                     return false;
 442                 }
 443             } else if (!uri.equals(other.uri)) {
 444                 return false;
 445             }
 446             return true;
 447         }
 448     }
 449
 450
 451 }