Workspace/Siman-Common/src/org/splat/service/StudyServiceImpl.java

   1 /*****************************************************************************
   2  * Company         OPEN CASCADE
   3  * Application     SIMAN
   4  * File            Id:
   5  * Creation date   02.10.2012
   6  * @author         Author: Maria KRUCHININA
   7  * @version        Revision:
   8  *****************************************************************************/
   9
  10 package org.splat.service;
  11
  12 import java.awt.Graphics2D;
  13 import java.io.File;
  14 import java.io.FileNotFoundException;
  15 import java.io.FileOutputStream;
  16 import java.io.IOException;
  17 import java.text.DecimalFormat;
  18 import java.text.SimpleDateFormat;
  19 import java.util.ArrayList;
  20 import java.util.Calendar;
  21 import java.util.Collections;
  22 import java.util.Date;
  23 import java.util.HashMap;
  24 import java.util.Iterator;
  25 import java.util.List;
  26 import java.util.Map;
  27 import java.util.Scanner;
  28 import java.util.Set;
  29
  30 import org.apache.lucene.index.IndexWriter;
  31 import org.apache.lucene.store.FSDirectory;
  32 import org.hibernate.Hibernate;
  33 import org.hibernate.criterion.Restrictions;
  34 import org.hibernate.proxy.HibernateProxy;
  35 import org.jfree.chart.ChartFactory;
  36 import org.jfree.chart.JFreeChart;
  37 import org.jfree.chart.plot.PlotOrientation;
  38 import org.jfree.data.xy.XYSeries;
  39 import org.jfree.data.xy.XYSeriesCollection;
  40 import org.splat.common.properties.MessageKeyEnum;
  41 import org.splat.dal.bo.kernel.Relation;
  42 import org.splat.dal.bo.kernel.User;
  43 import org.splat.dal.bo.som.ActorRelation;
  44 import org.splat.dal.bo.som.ContributorRelation;
  45 import org.splat.dal.bo.som.DescriptionAttribute;
  46 import org.splat.dal.bo.som.DocumentType;
  47 import org.splat.dal.bo.som.IDBuilder;
  48 import org.splat.dal.bo.som.ProgressState;
  49 import org.splat.dal.bo.som.ProjectElement;
  50 import org.splat.dal.bo.som.Publication;
  51 import org.splat.dal.bo.som.Scenario;
  52 import org.splat.dal.bo.som.SimulationContext;
  53 import org.splat.dal.bo.som.Study;
  54 import org.splat.dal.bo.som.Study.Properties;
  55 import org.splat.dal.bo.som.ValidationCycle;
  56 import org.splat.dal.bo.som.ValidationCycle.Actor;
  57 import org.splat.dal.bo.som.ValidationCycleRelation;
  58 import org.splat.dal.bo.som.ValidationStep;
  59 import org.splat.dal.bo.som.Visibility;
  60 import org.splat.dal.dao.som.DescriptionAttributeDAO;
  61 import org.splat.dal.dao.som.DocumentDAO;
  62 import org.splat.dal.dao.som.IDBuilderDAO;
  63 import org.splat.dal.dao.som.PublicationDAO;
  64 import org.splat.dal.dao.som.ScenarioDAO;
  65 import org.splat.dal.dao.som.StudyDAO;
  66 import org.splat.dal.dao.som.ValidationCycleDAO;
  67 import org.splat.exception.IncompatibleDataException;
  68 import org.splat.exception.InvalidParameterException;
  69 import org.splat.kernel.InvalidPropertyException;
  70 import org.splat.kernel.MismatchException;
  71 import org.splat.kernel.MissedPropertyException;
  72 import org.splat.kernel.MultiplyDefinedException;
  73 import org.splat.log.AppLogger;
  74 import org.splat.service.dto.DocToCompareDTO;
  75 import org.splat.service.dto.DocumentDTO;
  76 import org.splat.service.dto.StudyFacadeDTO;
  77 import org.splat.service.technical.IndexService;
  78 import org.splat.service.technical.ProjectSettingsService;
  79 import org.splat.service.technical.ProjectSettingsService.Step;
  80 import org.splat.service.technical.ProjectSettingsServiceImpl;
  81 import org.splat.service.technical.RepositoryService;
  82 import org.splat.som.Revision;
  83 import org.springframework.transaction.annotation.Transactional;
  84
  85 import com.lowagie.text.Document;
  86 import com.lowagie.text.DocumentException;
  87 import com.lowagie.text.Rectangle;
  88 import com.lowagie.text.pdf.DefaultFontMapper;
  89 import com.lowagie.text.pdf.PdfContentByte;
  90 import com.lowagie.text.pdf.PdfTemplate;
  91 import com.lowagie.text.pdf.PdfWriter;
  92
  93 /**
  94  * This class defines all methods for creation, modification the study.
  95  *
  96  * @author Maria KRUCHININA
  97  *
  98  */
  99 public class StudyServiceImpl implements StudyService {
 100
 101         /**
 102          * logger for the service.
 103          */
 104         public final static AppLogger LOG = AppLogger
 105                         .getLogger(StudyServiceImpl.class);
 106
 107         /**
 108          * Injected index service.
 109          */
 110         private IndexService _indexService;
 111
 112         /**
 113          * Injected step service.
 114          */
 115         private StepService _stepService;
 116
 117         /**
 118          * Injected project service.
 119          */
 120         private ProjectSettingsService _projectSettings;
 121
 122         /**
 123          * Injected project element service.
 124          */
 125         private ProjectElementService _projectElementService;
 126
 127         /**
 128          * Injected study DAO.
 129          */
 130         private StudyDAO _studyDAO;
 131
 132         /**
 133          * Injected scenario DAO.
 134          */
 135         private ScenarioDAO _scenarioDAO;
 136
 137         /**
 138          * Injected validation cycle DAO.
 139          */
 140         private ValidationCycleDAO _validationCycleDAO;
 141
 142         /**
 143          * Injected IDBuilder DAO.
 144          */
 145         private IDBuilderDAO _iDBuilderDAO;
 146
 147         /**
 148          * Injected document type service.
 149          */
 150         private DocumentTypeService _documentTypeService;
 151
 152         /**
 153          * Injected user service.
 154          */
 155         private UserService _userService;
 156
 157         /**
 158          * Injected publication DAO.
 159          */
 160         private PublicationDAO _publicationDAO;
 161
 162         /**
 163          * Injected repository service.
 164          */
 165         private RepositoryService _repositoryService;
 166
 167         /**
 168          * Injected document DAO.
 169          */
 170         private DocumentDAO _documentDAO;
 171
 172         /**
 173          * Injected description attribute DAO.
 174          */
 175         private DescriptionAttributeDAO _descriptionAttributeDAO;
 176
 177         /**
 178          * {@inheritDoc}
 179          *
 180          * @see org.splat.service.StudyService#selectStudy(long)
 181          */
 182         @Override
 183         @Transactional
 184         public Study selectStudy(final long index) {
 185                 Study result = getStudyDAO().get(index);
 186                 loadWorkflow(result);
 187                 return result;
 188         }
 189
 190         /**
 191          * {@inheritDoc}
 192          * @see org.splat.service.StudyService#removeStudy(long)
 193          */
 194         @Transactional
 195         public void removeStudy(final long index) {
 196                 Study study = getStudyDAO().get(index);
 197                 if (study != null) {
 198                         getStudyDAO().delete(study);
 199                 }
 200         }
 201
 202         /**
 203          * Get study by its reference.
 204          *
 205          * @param refid
 206          *            the study reference
 207          * @return found study or null
 208          */
 209         @Transactional(readOnly = true)
 210         public Study selectStudy(final String refid) {
 211                 Study result = getStudyDAO().findByCriteria(
 212                                 Restrictions.eq("sid", refid));
 213                 loadWorkflow(result);
 214                 return result;
 215         }
 216
 217         /**
 218          * {@inheritDoc}
 219          *
 220          * @see org.splat.service.StudyService#createStudy(org.splat.dal.bo.som.Study.Properties)
 221          */
 222         @Override
 223         @Transactional
 224         public Study createStudy(final Study.Properties sprop)
 225                         throws MissedPropertyException, InvalidPropertyException,
 226                         MultiplyDefinedException {
 227                 sprop.setReference(getProjectSettings().getReferencePattern());
 228                 Study study = new Study(sprop);
 229
 230                 buildReference(study);
 231                 getStudyDAO().create(study);
 232 //              try {
 233 //                      IndexService lucin = getIndex();
 234 //                      lucin.add(study);
 235 //              } catch (IOException error) {
 236 //                      LOG.error("Unable to index the study '" + study.getIndex()
 237 //                                      + "', reason:", error);
 238 //                      // Continue and try to index later
 239 //              }
 240                 return study;
 241         }
 242
 243         /**
 244          * {@inheritDoc}
 245          *
 246          * @see org.splat.service.StudyService#addProjectContext(org.splat.dal.bo.som.Study, org.splat.dal.bo.som.SimulationContext.Properties)
 247          */
 248         @Override
 249         @Transactional
 250         public SimulationContext addProjectContext(final Study aStudy,
 251                         final SimulationContext.Properties cprop)
 252                         throws MissedPropertyException, InvalidPropertyException,
 253                         MultiplyDefinedException {
 254                 SimulationContext added = getStepService().addSimulationContext(
 255                                 getProjectElementService().getFirstStep(aStudy), cprop);
 256                 update(aStudy);
 257                 return added;
 258         }
 259
 260         /**
 261          * {@inheritDoc}
 262          *
 263          * @see org.splat.service.StudyService#addProjectContext(org.splat.dal.bo.som.Study, org.splat.dal.bo.som.SimulationContext)
 264          */
 265         @Override
 266         @Transactional
 267         public SimulationContext addProjectContext(final Study aStudy,
 268                         final SimulationContext context) {
 269                 SimulationContext added = getStepService().addSimulationContext(
 270                                 getProjectElementService().getFirstStep(aStudy), context);
 271                 update(aStudy);
 272                 return added;
 273         }
 274
 275         /**
 276          * {@inheritDoc}
 277          *
 278          * @see org.splat.service.StudyService#addContributor(org.splat.dal.bo.som.Study, org.splat.dal.bo.kernel.User)
 279          */
 280         @Override
 281         public boolean addContributor(final Study aStudy, final User user) {
 282                 List<User> contributor = getModifiableContributors(aStudy); // Initializes contributor
 283                 for (Iterator<User> i = contributor.iterator(); i.hasNext();) {
 284                         User present = i.next();
 285                         if (present.equals(user)) {
 286                                 return false;
 287                         }
 288                 }
 289                 boolean absent = getModifiableActors(aStudy).add(user); // User may already be a reviewer or an approver
 290
 291                 aStudy.addRelation(new ContributorRelation(aStudy, user));
 292                 if (absent) {
 293                         update(aStudy); // Else, useless to re-index the study
 294                 }
 295                 contributor.add(user);
 296                 return true;
 297         }
 298
 299         /**
 300          * Moves this study from the Public to the Reference area of the repository. For being moved to the Reference area, the study must
 301          * previously be approved.
 302          *
 303          * @param aStudy
 304          *            the study to move
 305          * @return true if the move succeeded.
 306          * @see #moveToPublic()
 307          * @see #isPublic()
 308          * @see Publication#approve(Date)
 309          */
 310         @Override
 311         public boolean moveToReference(final Study aStudy) {
 312                 if (aStudy.getProgressState() != ProgressState.APPROVED) {
 313                         return false;
 314                 }
 315                 if (aStudy.getVisibility() != Visibility.PUBLIC) {
 316                         return false;
 317                 }
 318
 319                 aStudy.setVisibility(Visibility.REFERENCE);
 320                 if (update(aStudy)) {
 321                         return updateKnowledgeElementsIndex(aStudy); // If fails, the database roll-back is under responsibility of the caller
 322                 }
 323                 return false;
 324         }
 325
 326         /**
 327          * {@inheritDoc}
 328          *
 329          * @see org.splat.service.StudyService#update(org.splat.dal.bo.som.Study, org.splat.dal.bo.som.Study.Properties)
 330          */
 331         @Override
 332         public boolean update(final Study aStudy, final Properties sprop)
 333                         throws InvalidPropertyException {
 334                 if (sprop.getTitle() != null) {
 335                         aStudy.setTitle(sprop.getTitle());
 336                 }
 337                 if (sprop.getSummary() != null) {
 338                         aStudy.setAttribute(new DescriptionAttribute(aStudy, sprop
 339                                         .getSummary()));
 340                 }
 341                 // TODO: To be completed
 342                 return update(aStudy);
 343         }
 344
 345         /**
 346          * Check if the document is published in the study.
 347          *
 348          * @param aStudy
 349          *            the study
 350          * @param doc
 351          *            the document
 352          * @return true if the document is published in the study
 353          */
 354 /*      private boolean publishes(final Study aStudy, final Document doc) {
 355                 if (!aStudy.publishes(doc)) {
 356                         Scenario[] scene = aStudy.getScenarii();
 357                         for (int i = 0; i < scene.length; i++) {
 358                                 if (scene[i].publishes(doc)) {
 359                                         return true;
 360                                 }
 361                         }
 362                 }
 363                 return false;
 364         }
 365 */
 366         /**
 367          * {@inheritDoc}
 368          *
 369          * @see org.splat.service.StudyService#removeContributor(org.splat.dal.bo.som.Study, org.splat.dal.bo.kernel.User[])
 370          */
 371         @Override
 372         public boolean removeContributor(final Study aStudy, final User... users) {
 373                 List<User> contributor = getModifiableContributors(aStudy); // Initializes contributor
 374                 Boolean done = false;
 375                 for (int i = 0; i < users.length; i++) {
 376                         User user = users[i];
 377                         for (Iterator<User> j = contributor.iterator(); j.hasNext();) {
 378                                 User present = j.next();
 379                                 if (!present.equals(user)) {
 380                                         continue;
 381                                 }
 382
 383                                 aStudy.removeRelation(ContributorRelation.class, user);
 384                                 j.remove(); // Updates the contributor shortcut
 385                                 done = true;
 386                                 break;
 387                         }
 388                 }
 389                 if (done) {
 390                         update(aStudy);
 391                 }
 392                 return done;
 393         }
 394
 395         /**
 396          * {@inheritDoc}
 397          *
 398          * @see org.splat.service.StudyService#removeProjectContext(org.splat.dal.bo.som.Study, org.splat.dal.bo.som.SimulationContext)
 399          */
 400         @Override
 401         public boolean removeProjectContext(final Study aStudy,
 402                         final SimulationContext context) {
 403                 boolean done = getStepService().removeSimulationContext(
 404                                 getProjectElementService().getFirstStep(aStudy), context);
 405                 update(aStudy);
 406                 return done;
 407         }
 408
 409         /**
 410          * {@inheritDoc}
 411          *
 412          * @see org.splat.service.StudyService#setValidationCycle(org.splat.dal.bo.som.Study, org.splat.dal.bo.som.DocumentType,
 413          *      org.splat.dal.bo.som.ValidationCycle.Properties)
 414          */
 415         @Override
 416         @Transactional
 417         public void setValidationCycle(final Study aStudyDTO, final DocumentType type,
 418                         final ValidationCycle.Properties vprop) {
 419                 Map<String, ValidationCycle> validactor = aStudyDTO.getValidationCycles();
 420                 if (validactor == null) {
 421                         setShortCuts(aStudyDTO); // Initializes validactor and actor
 422                 }
 423
 424                 Study aStudy = selectStudy(aStudyDTO.getIndex());
 425
 426                 String cname = type.getName();
 427                 ValidationCycle cycle = validactor.get(cname);
 428
 429                 if (cycle != null && cycle.isAssigned()) {
 430                         resetActors(cycle, vprop);
 431                 } else {
 432                         try {
 433                                 cycle = new ValidationCycle(aStudy, vprop.setDocumentType(type));
 434
 435                                 getValidationCycleDAO().create(cycle); // RKV
 436
 437                                 ValidationCycleRelation link = cycle.getContext();
 438                                 aStudy.addRelation(link);
 439                                 aStudyDTO.getAllRelations().add(link); // RKV
 440
 441                                 validactor.put(cname, link.getTo()); // Replaces the cycle if exists as default,
 442                         } catch (Exception error) {
 443                                 LOG.error("Unable to re-index Knowledge Elements, reason:",
 444                                                 error);
 445                                 return;
 446                         }
 447                 }
 448                 resetActorsShortCut(aStudyDTO);
 449                 update(aStudy); // Re-index the study, just in case
 450         }
 451
 452         /**
 453          * Demotes this study from In-Check to In-Draft then In-Work states. This function is called internally when demoting the final result
 454          * document of the study.
 455          *
 456          * @param aStudy
 457          *            a study to demote
 458          * @return true if the demotion succeeded.
 459          */
 460         @Override
 461         public boolean demote(final Study aStudy) {
 462                 if (aStudy.getProgressState() == ProgressState.inCHECK) {
 463                         aStudy.setProgressState(ProgressState.inDRAFT);
 464                 } else if (aStudy.getProgressState() == ProgressState.inDRAFT) {
 465                         aStudy.setProgressState(ProgressState.inWORK);
 466                 } else {
 467                         return false;
 468                 }
 469                 return update(aStudy);
 470         }
 471
 472         /**
 473          * {@inheritDoc}
 474          *
 475          * @see org.splat.service.StudyService#generateLocalIndex(org.splat.dal.bo.som.Study)
 476          */
 477         @Override
 478         @Transactional
 479         public int generateLocalIndex(final Study aStudy) {
 480                 aStudy.setLastLocalIndex(aStudy.getLastLocalIndex() + 1);
 481                 return aStudy.getLastLocalIndex();
 482         }
 483
 484         /**
 485          * Promotes this study from In-Work to In-Draft then In-Check and APPROVED states. This function is called internally when promoting the
 486          * final result document of the study.
 487          *
 488          * @param aStudy
 489          *            a study to promote
 490          * @return true if the demotion succeeded.
 491          */
 492         @Override
 493         @Transactional
 494         public boolean promote(final Study aStudy) {
 495                 if (aStudy.getProgressState() == ProgressState.inWORK) {
 496                         aStudy.setProgressState(ProgressState.inDRAFT);
 497                 } else if (aStudy.getProgressState() == ProgressState.inDRAFT) {
 498                         aStudy.setProgressState(ProgressState.inCHECK);
 499                         Revision myvers = new Revision(aStudy.getVersion());
 500                         if (myvers.isMinor()) {
 501                                 aStudy.setVersion(myvers.incrementAs(aStudy.getProgressState())
 502                                                 .toString());
 503                         }
 504                 } else if (aStudy.getProgressState() == ProgressState.inCHECK) {
 505                         aStudy.setProgressState(ProgressState.APPROVED);
 506                 } else {
 507                         return false;
 508                 }
 509
 510                 return update(aStudy);
 511         }
 512
 513         /**
 514          * Moves this study from the Private to the Public area of the repository.
 515          *
 516          * @param aStudy
 517          *            a study to move
 518          * @return true if the move succeeded.
 519          * @see #isPublic()
 520          */
 521         @Override
 522         @Transactional
 523         public boolean moveToPublic(final Study aStudy) {
 524                 boolean isOk = false;
 525                 if (aStudy.getVisibility() == Visibility.PRIVATE) {
 526                         aStudy.setVisibility(Visibility.PUBLIC);
 527                         if (update(aStudy)) {
 528                                 isOk = updateKnowledgeElementsIndex(aStudy); // If fails, the database roll-back is under responsibility of the caller
 529                         }
 530                 }
 531                 return isOk;
 532         }
 533
 534         /**
 535          * Moves this study from the Public to the Private area of the repository.
 536          *
 537          * @param aStudy
 538          *            a study to move
 539          * @return true if the move succeeded.
 540          */
 541         @Override
 542         @Transactional
 543         public boolean moveToPrivate(final Study aStudy) {
 544                 boolean isOk = false;
 545                 if (aStudy.getVisibility() == Visibility.PUBLIC) {
 546                         aStudy.setVisibility(Visibility.PRIVATE);
 547                         if (update(aStudy)) {
 548                                 isOk = updateKnowledgeElementsIndex(aStudy); // If fails, the database roll-back is under responsibility of the caller
 549                         }
 550                 }
 551                 return isOk;
 552         }
 553
 554         /**
 555          * Update a study in the database.
 556          *
 557          * @param aStudy
 558          *            the study to update
 559          * @return true if the study is updated successfully
 560          */
 561         @Transactional
 562         private boolean update(final Study aStudy) {
 563                 boolean isOk = false;
 564                 try {
 565                         getStudyDAO().merge(aStudy); // Update of relational base
 566                         setShortCuts(aStudy); // RKV: initialize transient actors set
 567                         //RKV: getIndex().update(aStudy); // Update of Lucene index
 568                         isOk = true;
 569                 } catch (Exception e) {
 570                         LOG.error("STD-000001", e, aStudy.getIndex(), e.getMessage());
 571                 }
 572                 return isOk;
 573         }
 574
 575         /**
 576          * Build reference for the study. The reference of the study is stored as a new reference pattern (IDBuilder).
 577          *
 578          * @param aStudy
 579          *            the study
 580          * @return true if reference building is succeded
 581          */
 582         @Transactional
 583         private boolean buildReference(final Study aStudy) {
 584                 String pattern = aStudy.getReference(); // The study being supposed just created, its reference is the reference pattern
 585                 IDBuilder tool = selectIDBuilder(aStudy.getDate());
 586                 if (tool == null) {
 587                         tool = new IDBuilder(aStudy.getDate());
 588                         getIDBuilderDAO().create(tool);
 589                 }
 590                 aStudy.setReference(buildReference(tool, pattern, aStudy));
 591                 return true;
 592         }
 593
 594         /**
 595          * Build reference for the study. The reference of the study is stored as a new reference pattern (IDBuilder).
 596          *
 597          * @param aBuilder
 598          *            the id builder
 599          * @param study
 600          *            the study
 601          * @param pattern
 602          *            the reference pattern
 603          * @return true if reference building is succeded
 604          */
 605         @Transactional
 606         public String buildReference(final IDBuilder aBuilder,
 607                         final String pattern, final Study study) {
 608                 char[] format = pattern.toCharArray();
 609                 char[] ref = new char[80]; // Better evaluate the length of the generated string
 610                 int next = aBuilder.getBase() + 1;
 611
 612                 int count = 0;
 613                 for (int i = 0; i < format.length; i++) {
 614
 615                         // Insertion of attribute values
 616                         if (format[i] == '%') {
 617                                 i += 1;
 618
 619                                 if (format[i] == 'y') { // Insertion of year in format 2 (e.g. 09) or 4 (e.g. 2009) digits
 620                                         int n = i;
 621                                         while (format[i] == 'y') {
 622                                                 i += 1;
 623                                                 if (i == format.length) {
 624                                                         break;
 625                                                 }
 626                                         }
 627                                         SimpleDateFormat tostring = new SimpleDateFormat("yyyy"); //RKV: NOPMD: TODO: Use locale here?
 628                                         String year = tostring.format(study.getDate());
 629                                         year = year.substring(4 - (i - n), 4); // 4-(i-n) must be equal to either 0 or 2
 630                                         for (int j = 0; j < year.length(); j++) {
 631                                                 ref[count] = year.charAt(j);
 632                                                 count += 1;
 633                                         }
 634                                         i -= 1; // Back to the last 'y' character
 635                                 } else if (format[i] == '0') { // Insertion of the index
 636                                         int n = i;
 637                                         while (format[i] == '0') {
 638                                                 i += 1;
 639                                                 if (i == format.length) {
 640                                                         break;
 641                                                 }
 642                                         }
 643                                         DecimalFormat tostring = new DecimalFormat(pattern
 644                                                         .substring(n, i));
 645                                         String number = tostring.format(next);
 646                                         for (int j = 0; j < number.length(); j++) {
 647                                                 ref[count] = number.charAt(j);
 648                                                 count += 1;
 649                                         }
 650                                         i -= 1; // Back to the last '0' character
 651                                 }
 652                                 // Keep the character
 653                         } else {
 654                                 ref[count] = format[i];
 655                                 count += 1;
 656                         }
 657                 }
 658                 // Incrementation of the number of study
 659                 aBuilder.setBase(next);
 660                 getIDBuilderDAO().update(aBuilder);
 661                 return String.copyValueOf(ref, 0, count);
 662         }
 663
 664         /**
 665          * Find an id builder by date.
 666          *
 667          * @param date
 668          *            the date
 669          * @return found id builder
 670          */
 671         private IDBuilder selectIDBuilder(final Date date) {
 672                 Calendar aDate = Calendar.getInstance();
 673                 aDate.setTime(date);
 674                 return getIDBuilderDAO().findByCriteria(
 675                                 Restrictions.eq("cycle", aDate.get(Calendar.YEAR)));
 676         }
 677
 678         /**
 679          * Fill transient collection ModifiableActors of the study.
 680          *
 681          * @param aStudy
 682          *            the study
 683          */
 684         private void resetActorsShortCut(final Study aStudy) {
 685                 getModifiableActors(aStudy).clear();
 686                 // Get all actors involved in validation cycles
 687                 for (Iterator<ValidationCycle> i = aStudy.getValidationCycles()
 688                                 .values().iterator(); i.hasNext();) {
 689                         ValidationCycle cycle = i.next();
 690                         User[] user = cycle.getAllActors();
 691                         for (int j = 0; j < user.length; j++) {
 692                                 getModifiableActors(aStudy).add(user[j]);
 693                         }
 694                 }
 695                 // Get all other actors
 696                 for (Iterator<Relation> i = aStudy.getAllRelations().iterator(); i
 697                                 .hasNext();) {
 698                         Relation link = i.next();
 699                         Class<?> kindof = link.getClass().getSuperclass();
 700                         if (!kindof.equals(ActorRelation.class)) {
 701                                 continue;
 702                         }
 703                         getModifiableActors(aStudy).add(((ActorRelation) link).getTo());
 704                 }
 705         }
 706
 707         /**
 708          * Update lucene index for the study knowledge elements.
 709          *
 710          * @param aStudy
 711          *            the study
 712          * @return true if reindexing succeeded
 713          */
 714         private boolean updateKnowledgeElementsIndex(final Study aStudy) {
 715 //              boolean isOk = false;
 716 //              try {
 717 //                      IndexService lucin = getIndex();
 718 //
 719 //                      for (Iterator<Scenario> i = aStudy.getScenariiList().iterator(); i
 720 //                                      .hasNext();) {
 721 //                              Scenario scene = i.next();
 722 //                              for (Iterator<KnowledgeElement> j = scene
 723 //                                              .getAllKnowledgeElements().iterator(); j.hasNext();) {
 724 //                                      KnowledgeElement kelm = j.next();
 725 //                                      lucin.update(kelm);
 726 //                              }
 727 //                      }
 728 //                      isOk = true;
 729 //              } catch (Exception error) {
 730 //                      LOG.error("Unable to re-index Knowledge Elements, reason:",
 731 //                                      error);
 732 //              }
 733 //              return isOk;
 734                 return true;
 735         }
 736
 737         /**
 738          * Get lucene index service. Create a lucene index if it does not exist.
 739          *
 740          * @return index service
 741          * @throws IOException
 742          *             if error occurs during lucene index creation
 743          */
 744         private IndexService getIndex() throws IOException {
 745                 IndexService lucin = getIndexService();
 746                                 if (IndexWriter.isLocked(FSDirectory.open(getRepositoryService()
 747                                 .getRepositoryIndexDirectory()))) {
 748                         IndexWriter.unlock(FSDirectory.open(getRepositoryService()
 749                                         .getRepositoryIndexDirectory()));
 750                 }
 751                 if (!lucin.exists()) {
 752                         lucin.create(); // Happens when re-indexing all studies
 753                 }
 754                 return lucin;
 755         }
 756
 757         /**
 758          * Create a new validation cycle for documents of the given study.
 759          *
 760          * @param from
 761          *            the study
 762          * @param cycle
 763          *            the cycle description
 764          * @return the new validation cycle
 765          */
 766         protected ValidationCycle createValidationCycle(
 767                         final Study from,
 768                         final ProjectSettingsServiceImpl.ProjectSettingsValidationCycle cycle) {
 769                 Actor[] actype = cycle.getActorTypes();
 770                 User.Properties uprop = new User.Properties();
 771
 772                 ValidationCycle aValidationCycle = new ValidationCycle();
 773                 aValidationCycle.setDocumentType(getDocumentTypeService().selectType(
 774                                 cycle.getName())); // Null in case of default validation cycle
 775                 // context = new ValidationCycleRelation(from, vprop);
 776                 // RKV aValidationCycle.context = null; // Validation cycle defined in the workflow
 777                 for (int i = 0; i < actype.length; i++) {
 778                         User actor = null;
 779                         if (actype[i] != null) {
 780                                 try {
 781                                         if (actype[i] == Actor.manager) {
 782                                                 actor = from.getAuthor();
 783                                         } else if (actype[i] == Actor.Nx1) {
 784                                                 List<User> manager = getUserService().selectUsersWhere(
 785                                                                 uprop.setOrganizationName("Nx1"));
 786                                                 if (manager.size() == 1) {
 787                                                         actor = manager.get(0);
 788                                                 }
 789                                         } else if (actype[i] == Actor.Nx2) {
 790                                                 List<User> manager = getUserService().selectUsersWhere(
 791                                                                 uprop.setOrganizationName("Nx2"));
 792                                                 if (manager.size() == 1) {
 793                                                         actor = manager.get(0);
 794                                                 }
 795                                         } else { /* Actor.customer */
 796                                                 actor = from.getAuthor();
 797                                                 // TODO: Get the customer of the study, if exists
 798                                         }
 799                                 } catch (Exception e) { // Should not happen
 800                                         actor = null;
 801                                 }
 802                         }
 803                         if (i == 0) {
 804                                 aValidationCycle.setReviewer(actor);
 805                         } else if (i == 1) {
 806                                 aValidationCycle.setApprover(actor);
 807                         } else if (i == 2) {
 808                                 aValidationCycle.setSignatory(actor);
 809                         }
 810                 }
 811                 return aValidationCycle;
 812         }
 813
 814         /**
 815          * Remove a validation step from the validation cycle.
 816          *
 817          * @param aValidationCycle
 818          *            the validation cycle
 819          * @param step
 820          *            the validation step to remove
 821          */
 822         @Transactional
 823         protected void remove(final ValidationCycle aValidationCycle,
 824                         final ValidationStep step) {
 825                 if (step == ValidationStep.REVIEW) {
 826                         aValidationCycle.setReviewer(null);
 827                 } else if (step == ValidationStep.APPROVAL) {
 828                         aValidationCycle.setApprover(null);
 829                 } else if (step == ValidationStep.ACCEPTANCE
 830                                 || step == ValidationStep.REFUSAL) {
 831                         aValidationCycle.setSignatory(null);
 832                 }
 833                 if (aValidationCycle.isSaved()) {
 834                         getValidationCycleDAO().update(aValidationCycle);
 835                 }
 836         }
 837
 838         /**
 839          * Reset actors for the validation cycle.
 840          *
 841          * @param aValidationCycle
 842          *            the validation cycle to update
 843          * @param vprop
 844          *            new validation cycle properties containing new actors
 845          */
 846         @Transactional
 847         public void resetActors(final ValidationCycle aValidationCycle,
 848                         final ValidationCycle.Properties vprop) {
 849                 aValidationCycle.setPublisher(vprop.getPublisher()); // May be null
 850                 aValidationCycle.setReviewer(vprop.getReviewer()); // May be null
 851                 aValidationCycle.setApprover(vprop.getApprover()); // May be null
 852                 aValidationCycle.setSignatory(vprop.getSignatory()); // May be null
 853                 if (aValidationCycle.isSaved()) {
 854                         getValidationCycleDAO().merge(aValidationCycle);
 855                 }
 856         }
 857
 858         /**
 859          * Set actor for the given validation cycle and validation step.
 860          *
 861          * @param aValidationCycle
 862          *            the validation cycle
 863          * @param step
 864          *            the validation step
 865          * @param actor
 866          *            the actor to set
 867          */
 868         @Transactional
 869         protected void setActor(final ValidationCycle aValidationCycle,
 870                         final ValidationStep step, final User actor) {
 871                 if (step == ValidationStep.PROMOTION) {
 872                         aValidationCycle.setPublisher(actor);
 873                 } else if (step == ValidationStep.REVIEW) {
 874                         aValidationCycle.setReviewer(actor);
 875                 } else if (step == ValidationStep.APPROVAL) {
 876                         aValidationCycle.setApprover(actor);
 877                 } else if (step == ValidationStep.ACCEPTANCE
 878                                 || step == ValidationStep.REFUSAL) {
 879                         aValidationCycle.setSignatory(actor);
 880                 }
 881                 if (aValidationCycle.isSaved()) {
 882                         getValidationCycleDAO().update(aValidationCycle);
 883                 }
 884         }
 885
 886         /**
 887          * Returns all actors of this study other than the author, including contributors, reviewers and approvers.
 888          *
 889          * @param aStudy
 890          *            the study
 891          * @return the actors of this study
 892          * @see #hasActor(User)
 893          */
 894         public Set<User> getActors(final Study aStudy) {
 895                 if (aStudy.getActor() == null) {
 896                         setShortCuts(aStudy);
 897                 }
 898                 return Collections.unmodifiableSet(aStudy.getActor());
 899         }
 900
 901         /**
 902          * Returns all actors of this study other than the author, including contributors, reviewers and approvers.
 903          *
 904          * @param aStudy
 905          *            the study
 906          * @return the modifiable set of actors of this study
 907          * @see #hasActor(User)
 908          */
 909         public Set<User> getModifiableActors(final Study aStudy) {
 910                 if (aStudy.getActor() == null) {
 911                         setShortCuts(aStudy);
 912                 }
 913                 return aStudy.getActor();
 914         }
 915
 916         /**
 917          * Returns unmodifiable initialized transient list of contributors of this study.
 918          *
 919          * @param aStudy
 920          *            the study
 921          * @return the unmodifiable not null transient list of contributors of this study
 922          */
 923         @Override
 924         public List<User> getContributors(final Study aStudy) {
 925                 if (aStudy.getContributor() == null) {
 926                         setShortCuts(aStudy);
 927                 }
 928                 return Collections.unmodifiableList(aStudy.getContributor()); // May be empty
 929         }
 930
 931         /**
 932          * Returns modifiable initialized transient list of contributors of this study.
 933          *
 934          * @param aStudy
 935          *            the study
 936          * @return the modifiable not null transient list of contributors of this study
 937          */
 938         public List<User> getModifiableContributors(final Study aStudy) {
 939                 if (aStudy.getContributor() == null) {
 940                         setShortCuts(aStudy);
 941                 }
 942                 return aStudy.getContributor(); // May be empty
 943         }
 944
 945         /**
 946          * Returns the validation cycle of the given document type.
 947          *
 948          * @param aStudy
 949          *            the study
 950          * @param type
 951          *            the document type being subject of validation
 952          * @return the validation cycle of the document, or null if not defined.
 953          */
 954         @Override
 955         public ValidationCycle getValidationCycleOf(final Study aStudy,
 956                         final DocumentType type) {
 957                 if (aStudy.getValidationCycles() == null || aStudy.getValidationCycles().isEmpty()) {
 958                         setShortCuts(aStudy);
 959                 }
 960                 ValidationCycle result = aStudy.getValidationCycles().get(
 961                                 type.getName());
 962                 if (result == null) {
 963                         if (type.isStepResult()) {
 964                                 result = aStudy.getValidationCycles().get("default"); // "default" validation cycle defined in the configuration, if exist
 965                         }
 966                         if (result == null) {
 967                                 result = aStudy.getValidationCycles().get("built-in");
 968                         }
 969                 }
 970                 return result;
 971         }
 972
 973         /**
 974          * Checks if the given user is actor of this study. Actors include contributors, reviewers and approvers.
 975          *
 976          * @param aStudy
 977          *            the study
 978          * @param user
 979          *            the user to look for
 980          * @return true if the given user is actor of this study.
 981          * @see #getActors()
 982          */
 983         @Override
 984         public boolean hasActor(final Study aStudy, final User user) {
 985                 if (user == null) {
 986                         return false;
 987                 }
 988                 for (Iterator<User> i = getActors(aStudy).iterator(); i.hasNext();) {
 989                         User involved = i.next();
 990                         if (involved.equals(user)) {
 991                                 return true;
 992                         }
 993                 }
 994                 return false;
 995         }
 996
 997         /**
 998          * Checks if the given user participates to this study. The Study staff includes the author and contributors.
 999          *
1000          * @param aStudy
1001          *            the study
1002          * @param user
1003          *            the user to look for
1004          * @return true if the given user is actor of this study.
1005          * @see #getContributors()
1006          */
1007         @Override
1008         public boolean isStaffedBy(final Study aStudy, final User user) {
1009                 if (user == null) {
1010                         return false;
1011                 }
1012                 if (aStudy == null) {
1013                         return false;
1014                 }
1015                 if (aStudy.getAuthor() == null) {
1016                         return false;
1017                 }
1018                 if (aStudy.getAuthor().equals(user)) {
1019                         return true;
1020                 }
1021                 for (Iterator<User> i = getContributors(aStudy).iterator(); i.hasNext();) {
1022                         if (i.next().equals(user)) {
1023                                 return true;
1024                         }
1025                 }
1026                 return false;
1027         }
1028
1029         /**
1030          * Initialize shortcuts of the study as its transient collections.
1031          *
1032          * @param aStudy
1033          *            the study
1034          */
1035         @Override
1036         public void loadWorkflow(final Study aStudy) {
1037                 setShortCuts(aStudy);
1038         }
1039
1040         /**
1041          * Initialize shortcuts of the study as its transient collections.
1042          *
1043          * @param aStudy
1044          *            the study
1045          */
1046         public void setShortCuts(final Study aStudy) {
1047                 aStudy.getContributor().clear();
1048                 aStudy.getValidationCycles().clear();
1049                 aStudy.getActor().clear();
1050
1051                 // Get the contributors
1052                 for (Iterator<Relation> i = aStudy.getRelations(
1053                                 ContributorRelation.class).iterator(); i.hasNext();) {
1054                         ContributorRelation link = (ContributorRelation) i.next();
1055                         aStudy.getContributor().add(link.getTo());
1056                 }
1057                 // Get the validation cycles specific to this study
1058                 for (Iterator<Relation> i = aStudy.getRelations(
1059                                 ValidationCycleRelation.class).iterator(); i.hasNext();) {
1060                         ValidationCycleRelation link = (ValidationCycleRelation) i.next();
1061                         aStudy.getValidationCycles().put(link.getDocumentType().getName(),
1062                                         link.getTo()); // The associated document type is necessarily not null in this
1063                         // context
1064                 }
1065                 // Get the validation cycles coming from the configured workflow and not overridden in this study
1066                 for (Iterator<ProjectSettingsServiceImpl.ProjectSettingsValidationCycle> i = getProjectSettings()
1067                                 .getAllValidationCycles().iterator(); i.hasNext();) {
1068                         ProjectSettingsServiceImpl.ProjectSettingsValidationCycle cycle = i
1069                                         .next();
1070                         String type = cycle.getName();
1071                         if (!aStudy.getValidationCycles().containsKey(type)) {
1072                                 aStudy.getValidationCycles().put(type,
1073                                                 createValidationCycle(aStudy, cycle));
1074                         }
1075                 }
1076                 // Get all corresponding actors
1077                 for (Iterator<ValidationCycle> i = aStudy.getValidationCycles()
1078                                 .values().iterator(); i.hasNext();) {
1079                         ValidationCycle cycle = i.next();
1080                         User[] user = cycle.getAllActors();
1081                         for (int j = 0; j < user.length; j++) {
1082                                 aStudy.getActor().add(user[j]);
1083                         }
1084                 }
1085                 // Get all other actors
1086                 for (Iterator<Relation> i = aStudy.getAllRelations().iterator(); i
1087                                 .hasNext();) {
1088                         Relation link = i.next();
1089                         Class<?> kindof = link.getClass().getSuperclass();
1090                         if (!kindof.equals(ActorRelation.class)) {
1091                                 continue;
1092                         }
1093                         aStudy.getActor().add(((ActorRelation) link).getTo());
1094                 }
1095         }
1096
1097         /**
1098          *
1099          * {@inheritDoc}
1100          * @see org.splat.service.StudyService#markStudyAsReference(org.splat.dal.bo.som.Study)
1101          */
1102         @Override
1103         @Transactional
1104         public void markStudyAsReference (final Study aStudy) {
1105
1106                 aStudy.setMarkreference(1);
1107                 aStudy.setProgressState(ProgressState.TEMPLATE);
1108                 getStudyDAO().merge(aStudy);
1109         }
1110
1111         /**
1112          *
1113          * {@inheritDoc}
1114          * @see org.splat.service.StudyService#removeStudyAsReference(org.splat.dal.bo.som.Study)
1115          */
1116         @Override
1117         @Transactional
1118         public void removeStudyAsReference(final Study aStudy) {
1119
1120                 aStudy.setMarkreference(0);
1121                 aStudy.setProgressState(ProgressState.APPROVED);
1122                 getStudyDAO().merge(aStudy);
1123         }
1124
1125
1126         /**
1127          * {@inheritDoc}
1128          * @see org.splat.service.StudyService#getDescription(java.lang.Long)
1129          */
1130         @Override
1131         @Transactional(readOnly = true)
1132         public String getDescription(final Long studyId) throws InvalidParameterException {
1133                 if(studyId == null) {
1134                         throw new InvalidParameterException("studyId", "null");
1135                 }
1136                 Study study = _studyDAO.get(studyId);
1137                 if(study == null) {
1138                         throw new InvalidParameterException("studyId", studyId.toString());
1139                 }
1140                 return study.getDescription();
1141         }
1142
1143
1144         /**
1145          * {@inheritDoc}
1146          * @see org.splat.service.StudyService#setDescription(java.lang.Long, java.lang.String)
1147          */
1148         @Override
1149         @Transactional
1150         public void setDescription(final Long studyId, final String descriptionText)
1151                         throws InvalidParameterException {
1152                 if(studyId == null) {
1153                         throw new InvalidParameterException("studyId", "null");
1154                 }
1155                 Study study = _studyDAO.get(studyId);
1156                 if(study == null) {
1157                         throw new InvalidParameterException("studyId", studyId.toString());
1158                 }
1159                 study.setAttribute(new DescriptionAttribute(study, descriptionText));
1160         }
1161
1162         /**
1163          * {@inheritDoc}
1164          * @see org.splat.service.StudyService#removeStudyDescription(java.lang.Long)
1165          */
1166         @Override
1167         @Transactional
1168         public boolean removeDescription(final Long studyId) throws InvalidParameterException {
1169                 if(studyId == null) {
1170                         throw new InvalidParameterException("studyId", String.valueOf(studyId));
1171                 }
1172                 Study study = _studyDAO.get(studyId);
1173                 if(study == null) {
1174                         throw new InvalidParameterException("studyId", String.valueOf(studyId));
1175                 }
1176                 return study.removeAttribute(study.getAttribute(DescriptionAttribute.class));
1177         }
1178
1179
1180         /**
1181          *
1182          * {@inheritDoc}
1183          * @see org.splat.service.StudyService#compare(java.util.List)
1184          */
1185         @Override
1186         public String compare (final List<DocToCompareDTO> docsList, final String userName) throws IncompatibleDataException{
1187
1188                 String axis1Name = "";
1189                 String axis2Name = "";
1190                 String resultPath = "";
1191
1192                 XYSeriesCollection dataset = new XYSeriesCollection();
1193
1194                 Iterator<DocToCompareDTO> docListIter = docsList.iterator();
1195
1196                 for (; docListIter.hasNext();) {
1197
1198                         DocToCompareDTO docDTO = docListIter.next();
1199                         String pathToFile = docDTO.getPathToFile();
1200                         File compDocFile = new File(pathToFile);
1201
1202                         resultPath = pathToFile.substring(0, pathToFile.indexOf("vault")) + "downloads" + File.separator + userName + File.separator + "ComparisonResult.pdf";
1203
1204                         XYSeries series = new XYSeries("Study: " + docDTO.getStudyTitle() + " Scenario: " + docDTO.getScenarioTitle() + "Document: " + docDTO.getDocumentTitle());
1205
1206                         //read the file and get points information.
1207                         try {
1208                                 Scanner input = new Scanner(compDocFile);
1209
1210                                 //get the name of the axis.
1211                                 if (input.hasNext()) {
1212                                         String[] tokens = input.nextLine().split(",");
1213
1214                                         if (tokens.length < 2)
1215                                                 throw new IncompatibleDataException(MessageKeyEnum.IDT_000001.toString());
1216
1217                                         if ("".equals(axis1Name)) {
1218                                                 axis1Name = tokens[0];
1219                                         } else if (!axis1Name.equals(tokens[0])) {
1220                                                 LOG.debug("Axis must be the same for all documents");
1221                                                 throw new IncompatibleDataException(MessageKeyEnum.IDT_000001.toString());
1222                                         }
1223
1224                                         if ("".equals(axis2Name)) {
1225                                                 axis2Name = tokens[1];
1226                                         } else if (!axis2Name.equals(tokens[1])) {
1227                                                 LOG.debug("Axis must be the same for all documents");
1228                                                 throw new IncompatibleDataException(MessageKeyEnum.IDT_000001.toString());
1229                                         }
1230                                 }
1231
1232                                 //Get the XY points series.
1233                                 while(input.hasNext()) {
1234
1235                                         String currentString = input.nextLine();
1236
1237                                         if ("".equals(currentString)) {
1238                                                 continue;
1239                                         }
1240                                         else {
1241                                                 String[] tokens = currentString.split(" ");
1242                                                 series.add(Double.valueOf(tokens[0]), Double.valueOf(tokens[1]));
1243                                         }
1244
1245                                 } //while
1246
1247                                 dataset.addSeries(series);
1248
1249                         } catch (FileNotFoundException e) {
1250                                 // TODO Auto-generated catch block
1251                                 e.printStackTrace();
1252                                 return "ERROR";
1253                         }
1254                 } //for
1255
1256                 JFreeChart chart = ChartFactory.createXYLineChart(
1257                                 "Comparision of Studies Results", // Title
1258                                 axis1Name, // x-axis Label
1259                                 axis2Name, // y-axis Label
1260                                 dataset, // Dataset
1261                                 PlotOrientation.VERTICAL, // Plot Orientation
1262                                 true, // Show Legend
1263                                 true, // Use tooltips
1264                                 false // Configure chart to generate URLs?
1265                                 );
1266
1267                 //export to PDF - file.
1268                 int x = 500;
1269                 int y = 300;
1270                 Rectangle pagesize = new Rectangle(x, y);
1271                 Document document = new Document(pagesize, 50, 50, 50, 50);
1272         PdfWriter writer;
1273                 try {
1274                         File resFile = new File(resultPath);
1275                         File resFolder = new File(resultPath.substring(0, resultPath.lastIndexOf(File.separator)));
1276                         resFolder.mkdirs();
1277                         writer = PdfWriter.getInstance(document, new FileOutputStream(resFile));
1278
1279                 document.open();
1280                 PdfContentByte cb = writer.getDirectContent();
1281                 PdfTemplate tp = cb.createTemplate(x, y);
1282                 Graphics2D g2 = tp.createGraphics(x, y, new DefaultFontMapper());
1283                 chart.draw(g2, new java.awt.Rectangle(x,y));
1284                 g2.dispose();
1285                 cb.addTemplate(tp, 0, 0);
1286                 document.close();
1287
1288                 } catch (FileNotFoundException e) {
1289                         // TODO Auto-generated catch block
1290                         e.printStackTrace();
1291                 } catch (DocumentException e) {
1292                         // TODO Auto-generated catch block
1293                         e.printStackTrace();
1294                 }
1295
1296                 return resultPath;
1297         }
1298
1299         /**
1300          * Get project settings.
1301          *
1302          * @return Project settings service
1303          */
1304         private ProjectSettingsService getProjectSettings() {
1305                 return _projectSettings;
1306         }
1307
1308         /**
1309          * Set project settings service.
1310          *
1311          * @param projectSettingsService
1312          *            project settings service
1313          */
1314         public void setProjectSettings(
1315                         final ProjectSettingsService projectSettingsService) {
1316                 _projectSettings = projectSettingsService;
1317         }
1318
1319         /**
1320          * Get the projectElementService.
1321          *
1322          * @return the projectElementService
1323          */
1324         public ProjectElementService getProjectElementService() {
1325                 return _projectElementService;
1326         }
1327
1328         /**
1329          * Set the projectElementService.
1330          *
1331          * @param projectElementService
1332          *            the projectElementService to set
1333          */
1334         public void setProjectElementService(
1335                         final ProjectElementService projectElementService) {
1336                 _projectElementService = projectElementService;
1337         }
1338
1339         /**
1340          * Get the stepService.
1341          *
1342          * @return the stepService
1343          */
1344         public StepService getStepService() {
1345                 return _stepService;
1346         }
1347
1348         /**
1349          * Set the stepService.
1350          *
1351          * @param stepService
1352          *            the stepService to set
1353          */
1354         public void setStepService(final StepService stepService) {
1355                 _stepService = stepService;
1356         }
1357
1358         /**
1359          * Get the indexService.
1360          *
1361          * @return the indexService
1362          */
1363         public IndexService getIndexService() {
1364                 return _indexService;
1365         }
1366
1367         /**
1368          * Set the indexService.
1369          *
1370          * @param indexService
1371          *            the indexService to set
1372          */
1373         public void setIndexService(final IndexService indexService) {
1374                 _indexService = indexService;
1375         }
1376
1377         /**
1378          * Get the studyDAO.
1379          *
1380          * @return the studyDAO
1381          */
1382         public StudyDAO getStudyDAO() {
1383                 return _studyDAO;
1384         }
1385
1386         /**
1387          * Set the studyDAO.
1388          *
1389          * @param studyDAO
1390          *            the studyDAO to set
1391          */
1392         public void setStudyDAO(final StudyDAO studyDAO) {
1393                 _studyDAO = studyDAO;
1394         }
1395
1396         /**
1397          * Get the iDBuilderDAO.
1398          *
1399          * @return the iDBuilderDAO
1400          */
1401         public IDBuilderDAO getIDBuilderDAO() {
1402                 return _iDBuilderDAO;
1403         }
1404
1405         /**
1406          * Set the iDBuilderDAO.
1407          *
1408          * @param builderDAO
1409          *            the iDBuilderDAO to set
1410          */
1411         public void setIDBuilderDAO(final IDBuilderDAO builderDAO) {
1412                 _iDBuilderDAO = builderDAO;
1413         }
1414
1415         /**
1416          * Get the scenarioDAO.
1417          *
1418          * @return the scenarioDAO
1419          */
1420         public ScenarioDAO getScenarioDAO() {
1421                 return _scenarioDAO;
1422         }
1423
1424         /**
1425          * Set the scenarioDAO.
1426          *
1427          * @param scenarioDAO
1428          *            the scenarioDAO to set
1429          */
1430         public void setScenarioDAO(final ScenarioDAO scenarioDAO) {
1431                 _scenarioDAO = scenarioDAO;
1432         }
1433
1434         /**
1435          * Get the validationCycleDAO.
1436          *
1437          * @return the validationCycleDAO
1438          */
1439         public ValidationCycleDAO getValidationCycleDAO() {
1440                 return _validationCycleDAO;
1441         }
1442
1443         /**
1444          * Set the validationCycleDAO.
1445          *
1446          * @param validationCycleDAO
1447          *            the validationCycleDAO to set
1448          */
1449         public void setValidationCycleDAO(
1450                         final ValidationCycleDAO validationCycleDAO) {
1451                 _validationCycleDAO = validationCycleDAO;
1452         }
1453
1454         /**
1455          * Get the documentTypeService.
1456          *
1457          * @return the documentTypeService
1458          */
1459         public DocumentTypeService getDocumentTypeService() {
1460                 return _documentTypeService;
1461         }
1462
1463         /**
1464          * Set the documentTypeService.
1465          *
1466          * @param documentTypeService
1467          *            the documentTypeService to set
1468          */
1469         public void setDocumentTypeService(
1470                         final DocumentTypeService documentTypeService) {
1471                 _documentTypeService = documentTypeService;
1472         }
1473
1474         /**
1475          * Get the userService.
1476          *
1477          * @return the userService
1478          */
1479         public UserService getUserService() {
1480                 return _userService;
1481         }
1482
1483         /**
1484          * Set the userService.
1485          *
1486          * @param userService
1487          *            the userService to set
1488          */
1489         public void setUserService(final UserService userService) {
1490                 _userService = userService;
1491         }
1492
1493         /**
1494          * {@inheritDoc}
1495          *
1496          * @see org.splat.service.StudyService#getComparableStudies()
1497          */
1498         @Transactional(readOnly = true)
1499         public List<StudyFacadeDTO> getComparableStudies(final long userId) throws MismatchException {
1500                 //retrieve the number of the "Analyze the results" step
1501                 List<Step> allSteps = _projectSettings.getAllSteps();
1502                 Step theAnalyzeStep = null;
1503                 for(Step step : allSteps) {
1504                         if(step.getKey().equals("postprocessing")) {
1505                                 theAnalyzeStep = step;
1506                         }
1507                 }
1508                 if(theAnalyzeStep == null) {    //TODO: throw some other exception
1509                         throw new MismatchException("no step with key 'postprocessing' found." +
1510                                         "Probably, customization settings have been changed.");
1511                 }
1512
1513                 List<Publication> publications = _publicationDAO.getFilteredList("mydoc",
1514                                 Restrictions.eq("step", Integer.valueOf(theAnalyzeStep.getNumber())));
1515
1516                 //split retrieved publications into groups by studies and scenarios
1517                 Map<Study, List<ProjectElement>> studyMap = new HashMap<Study, List<ProjectElement>>();
1518                 Map<ProjectElement, List<Publication>> scenarioMap =
1519                                 new HashMap<ProjectElement, List<Publication>>();
1520
1521                 for(Publication publication : publications) {
1522                         //filter out publications corresponding to a document of given step which is not a _result_ document
1523                         if(!publication.value().getType().isResultOf(theAnalyzeStep)
1524                                         || !"srd".equals(publication.getSourceFile().getFormat())) {
1525                                 continue;
1526                         }
1527
1528                         //check the study visibility to the user
1529                         if(!isStaffedBy(publication.getOwnerStudy(), _userService.selectUser(userId))
1530                                         && Visibility.PUBLIC.equals(publication.getOwnerStudy().getVisibility())) {
1531                                 continue;
1532                         }
1533
1534                         Study study = publication.getOwnerStudy();
1535                         ProjectElement scenario = publication.getOwner();
1536
1537                         Hibernate.initialize(scenario);
1538                     if (scenario instanceof HibernateProxy) {
1539                         scenario = (ProjectElement) ((HibernateProxy) scenario).getHibernateLazyInitializer()
1540                                 .getImplementation();
1541                     }
1542
1543                         if(!(scenario instanceof Scenario)) {
1544                                 throw new MismatchException(
1545                                                 "publications from postprocessing step are supposed to have owner scenario");
1546                         }
1547
1548                         if(!studyMap.containsKey(study)) {
1549                                 studyMap.put(study, new ArrayList<ProjectElement>());
1550                         }
1551
1552                         if(!studyMap.get(study).contains(scenario)) {
1553                                 studyMap.get(study).add(scenario);
1554                         }
1555
1556                         if(!scenarioMap.containsKey(scenario)) {
1557                                 scenarioMap.put(scenario, new ArrayList<Publication>());
1558                         }
1559                         scenarioMap.get(scenario).add(publication);
1560                 }
1561
1562                 //Create the result DTOs
1563                 List<StudyFacadeDTO> result = new ArrayList<StudyFacadeDTO>();
1564                 for(Study study : studyMap.keySet()) {
1565
1566                         StudyFacadeDTO studyDTO = new StudyFacadeDTO();
1567                         studyDTO.setName(study.getTitle());
1568                         studyDTO.setScenarios(new ArrayList<StudyFacadeDTO.ScenarioDTO>());
1569                         result.add(studyDTO);
1570
1571                         for(ProjectElement scenario : studyMap.get(study)) {
1572
1573                                 StudyFacadeDTO.ScenarioDTO scenarioDTO = new StudyFacadeDTO.ScenarioDTO();
1574                                 scenarioDTO.setName(scenario.getTitle());
1575                                 scenarioDTO.setDocs(new ArrayList<DocumentDTO>());
1576                                 studyDTO.getScenarios().add(scenarioDTO);
1577
1578                                 for(Publication publication : scenarioMap.get(scenario)) {
1579
1580                                         DocumentDTO documentDTO = new DocumentDTO();
1581                                         documentDTO.setId(publication.getIndex());
1582                                         documentDTO.setTitle(publication.value().getTitle());
1583
1584                                         scenarioDTO.getDocs().add(documentDTO);
1585                                 }
1586                         }
1587                 }
1588                 return result;
1589         }
1590
1591         /**
1592          * Get the publicationDAO.
1593          * @return the publicationDAO
1594          */
1595         public PublicationDAO getPublicationDAO() {
1596                 return _publicationDAO;
1597         }
1598
1599         /**
1600          * Set the publicationDAO.
1601          * @param publicationDAO the publicationDAO to set
1602          */
1603         public void setPublicationDAO(final PublicationDAO publicationDAO) {
1604                 _publicationDAO = publicationDAO;
1605         }
1606
1607         /**
1608          * Get the repositoryService.
1609          * @return the repositoryService
1610          */
1611         public RepositoryService getRepositoryService() {
1612                 return _repositoryService;
1613         }
1614
1615         /**
1616          * Set the repositoryService.
1617          * @param repositoryService the repositoryService to set
1618          */
1619         public void setRepositoryService(final RepositoryService repositoryService) {
1620                 _repositoryService = repositoryService;
1621         }
1622
1623         /**
1624          * Get the documentDAO.
1625          * @return the documentDAO
1626          */
1627         public DocumentDAO getDocumentDAO() {
1628                 return _documentDAO;
1629         }
1630
1631         /**
1632          * Set the documentDAO.
1633          * @param documentDAO the documentDAO to set
1634          */
1635         public void setDocumentDAO(final DocumentDAO documentDAO) {
1636                 _documentDAO = documentDAO;
1637         }
1638
1639         /**
1640          * Get the descriptionAttributeDAO.
1641          * @return the descriptionAttributeDAO
1642          */
1643         public DescriptionAttributeDAO getDescriptionAttributeDAO() {
1644                 return _descriptionAttributeDAO;
1645         }
1646
1647         /**
1648          * Set the descriptionAttributeDAO.
1649          * @param descriptionAttributeDAO the descriptionAttributeDAO to set
1650          */
1651         public void setDescriptionAttributeDAO(
1652                         final DescriptionAttributeDAO descriptionAttributeDAO) {
1653                 _descriptionAttributeDAO = descriptionAttributeDAO;
1654         }
1655 }