cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiNoteExport.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2009 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.io.pesi.out;
  11
  12 import java.sql.Connection;
  13 import java.sql.PreparedStatement;
  14 import java.sql.SQLException;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.joda.time.DateTime;
  21 import org.springframework.stereotype.Component;
  22 import org.springframework.transaction.TransactionStatus;
  23
  24 import eu.etaxonomy.cdm.io.common.DbExportStateBase;
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper;
  27 import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.common.Extension;
  30 import eu.etaxonomy.cdm.model.common.ExtensionType;
  31 import eu.etaxonomy.cdm.model.common.Language;
  32 import eu.etaxonomy.cdm.model.common.LanguageString;
  33 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  34 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  35 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  36 import eu.etaxonomy.cdm.model.description.Distribution;
  37 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  38 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  39 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  40 import eu.etaxonomy.cdm.model.description.TextData;
  41 import eu.etaxonomy.cdm.model.location.NamedArea;
  42 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  43 import eu.etaxonomy.cdm.model.taxon.Taxon;
  44
  45 /**
  46  * The export class for {@link eu.etaxonomy.cdm.model.description.DescriptionElementBase DescriptionElements}.<p>
  47  * Inserts into DataWarehouse database table <code>Note</code>.<p>
  48  * It is divided into two phases:<ul>
  49  * <li>Phase 1: Export of DescriptionElements as Notes.
  50  * <li>Phase 2: Export of TaxonName extensions <code>taxComment</code>, <code>fauComment</code> and <code>fauExtraCodes</code> as Notes.</ul>
  51  * @author e.-m.lee
  52  * @date 23.02.2010
  53  *
  54  */
  55 @Component
  56 public class PesiNoteExport extends PesiExportBase {
  57         private static final Logger logger = Logger.getLogger(PesiNoteExport.class);
  58         private static final Class<? extends CdmBase> standardMethodParameter = DescriptionElementBase.class;
  59
  60         private static int modCount = 1000;
  61         private static final String dbTableName = "Note";
  62         private static final String pluralString = "Notes";
  63         private static final String parentPluralString = "Taxa";
  64
  65         public PesiNoteExport() {
  66                 super();
  67         }
  68
  69         /* (non-Javadoc)
  70          * @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter()
  71          */
  72         @Override
  73         public Class<? extends CdmBase> getStandardMethodParameter() {
  74                 return standardMethodParameter;
  75         }
  76
  77         /* (non-Javadoc)
  78          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
  79          */
  80         @Override
  81         protected boolean doCheck(PesiExportState state) {
  82                 boolean result = true;
  83                 return result;
  84         }
  85
  86         /* (non-Javadoc)
  87          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
  88          */
  89         @Override
  90         protected void doInvoke(PesiExportState state) {
  91                 try {
  92                         logger.error("*** Started Making " + pluralString + " ...");
  93
  94                         // Get the limit for objects to save within a single transaction.
  95                         int limit = state.getConfig().getLimitSave();
  96                         int pageSize = 1000;
  97
  98                         // Calculate the pageNumber
  99                         int pageNumber = 1;
 100
 101                         // Stores whether this invoke was successful or not.
 102                         boolean success = true;
 103
 104                         // PESI: Clear the database table Note.
 105                         doDelete(state);
 106
 107                         // Get specific mappings: (CDM) DescriptionElement -> (PESI) Note
 108                         PesiExportMapping mapping = getMapping();
 109
 110                         // Initialize the db mapper
 111                         mapping.initialize(state);
 112
 113                         // PESI: Create the Notes
 114                         int count = 0;
 115                         int pastCount = 0;
 116                         TransactionStatus txStatus = null;
 117                         List<DescriptionElementBase> list = null;
 118
 119                         // Start transaction
 120                         logger.error("PHASE 1...");
 121                         txStatus = startTransaction(true);
 122                         logger.error("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ...");
 123                         while ((list = getDescriptionService().listDescriptionElements(null, null, null, pageSize, pageNumber, null)).size() > 0) {
 124
 125                                 logger.error("Fetched " + list.size() + " " + pluralString + ". Exporting...");
 126                                 for (DescriptionElementBase description : list) {
 127
 128                                         if (getNoteCategoryFk(description) != null) {
 129                                                 doCount(count++, modCount, pluralString);
 130                                                 success &= mapping.invoke(description);
 131                                         }
 132                                 }
 133
 134                                 // Commit transaction
 135                                 commitTransaction(txStatus);
 136                                 logger.error("Committed transaction.");
 137                                 logger.error("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
 138                                 pastCount = count;
 139
 140                                 // Start transaction
 141                                 txStatus = startTransaction(true);
 142                                 logger.error("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ...");
 143
 144                                 // Increment pageNumber
 145                                 pageNumber++;
 146                         }
 147                         if (list.size() == 0) {
 148                                 logger.error("No " + pluralString + " left to fetch.");
 149                         }
 150                         // Commit transaction
 151                         commitTransaction(txStatus);
 152                         logger.error("Committed transaction.");
 153
 154
 155                         logger.error("PHASE 2...");
 156                         txStatus = startTransaction(true);
 157                         List<TaxonNameBase> taxonNameList = null;
 158                         ExtensionType taxCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.taxCommentUuid);
 159                         ExtensionType fauCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.fauCommentUuid);
 160                         ExtensionType fauExtraCodesExtensionType = (ExtensionType)getTermService().find(PesiTransformer.fauExtraCodesUuid);
 161                         String taxComment = null;
 162                         String fauComment = null;
 163                         String fauExtraCodes = null;
 164
 165                         Connection connection = state.getConfig().getDestination().getConnection();
 166                         logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
 167                         while ((taxonNameList = getNameService().list(null, limit, count, null, null)).size() > 0) {
 168
 169                                 logger.error("Fetched " + list.size() + " " + parentPluralString + ". Exporting...");
 170                                 for (TaxonNameBase<?,?> taxonName : taxonNameList) {
 171                                         Set<Extension> extensions = taxonName.getExtensions();
 172                                         for (Extension extension : extensions) {
 173                                                 if (extension.getType().equals(taxCommentExtensionType)) {
 174                                                         taxComment = extension.getValue();
 175                                                         invokeNotes(taxComment,
 176                                                                         PesiTransformer.getNoteCategoryFk(PesiTransformer.taxCommentUuid),
 177                                                                         PesiTransformer.getNoteCategoryCache(PesiTransformer.taxCommentUuid),
 178                                                                         null, null, getTaxonFk(taxonName, state),connection);
 179                                                 } else if (extension.getType().equals(fauCommentExtensionType)) {
 180                                                         fauComment = extension.getValue();
 181                                                         invokeNotes(fauComment,
 182                                                                         PesiTransformer.getNoteCategoryFk(PesiTransformer.fauCommentUuid),
 183                                                                         PesiTransformer.getNoteCategoryCache(PesiTransformer.fauCommentUuid),
 184                                                                         null, null, getTaxonFk(taxonName, state),connection);
 185                                                 } else if (extension.getType().equals(fauExtraCodesExtensionType)) {
 186                                                         fauExtraCodes = extension.getValue();
 187                                                         invokeNotes(fauExtraCodes,
 188                                                                         PesiTransformer.getNoteCategoryFk(PesiTransformer.fauExtraCodesUuid),
 189                                                                         PesiTransformer.getNoteCategoryCache(PesiTransformer.fauExtraCodesUuid),
 190                                                                         null, null, getTaxonFk(taxonName, state),connection);
 191                                                 }
 192                                         }
 193
 194                                         doCount(count++, modCount, pluralString);
 195                                 }
 196
 197                                 // Commit transaction
 198                                 commitTransaction(txStatus);
 199                                 logger.error("Committed transaction.");
 200                                 logger.error("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
 201                                 pastCount = count;
 202
 203                                 // Start transaction
 204                                 txStatus = startTransaction(true);
 205                                 logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
 206                         }
 207                         if (list.size() == 0) {
 208                                 logger.error("No " + parentPluralString + " left to fetch.");
 209                         }
 210                         // Commit transaction
 211                         commitTransaction(txStatus);
 212                         logger.error("Committed transaction.");
 213
 214
 215                         logger.error("*** Finished Making " + pluralString + " ..." + getSuccessString(success));
 216
 217                         if (!success){
 218                                 state.setUnsuccessfull();
 219                         }
 220                         return;
 221                 } catch (SQLException e) {
 222                         e.printStackTrace();
 223                         logger.error(e.getMessage());
 224                         state.setUnsuccessfull();
 225                 }
 226         }
 227
 228         /**
 229          * @param taxComment
 230          * @param noteCategoryFk
 231          * @param noteCategoryCache
 232          * @param object
 233          * @param object2
 234          */
 235         private void invokeNotes(String note, Integer noteCategoryFk,
 236                         String noteCategoryCache, Integer languageFk, String languageCache,
 237                         Integer taxonFk, Connection connection) {
 238                 String notesSql = "UPDATE Note SET Note_1 = ?, NoteCategoryFk = ?, NoteCategoryCache = ?, LanguageFk = ?, LanguageCache = ? WHERE TaxonFk = ?";
 239                 try {
 240                         PreparedStatement notesStmt = connection.prepareStatement(notesSql);
 241
 242                         if (note != null) {
 243                                 notesStmt.setString(1, note);
 244                         } else {
 245                                 notesStmt.setObject(1, null);
 246                         }
 247
 248                         if (noteCategoryFk != null) {
 249                                 notesStmt.setInt(2, noteCategoryFk);
 250                         } else {
 251                                 notesStmt.setObject(2, null);
 252                         }
 253
 254                         if (noteCategoryCache != null) {
 255                                 notesStmt.setString(3, noteCategoryCache);
 256                         } else {
 257                                 notesStmt.setObject(3, null);
 258                         }
 259
 260                         if (languageFk != null) {
 261                                 notesStmt.setInt(4, languageFk);
 262                         } else {
 263                                 notesStmt.setObject(4, null);
 264                         }
 265
 266                         if (languageCache != null) {
 267                                 notesStmt.setString(5, languageCache);
 268                         } else {
 269                                 notesStmt.setObject(5, null);
 270                         }
 271
 272                         if (taxonFk != null) {
 273                                 notesStmt.setInt(6, taxonFk);
 274                         } else {
 275                                 notesStmt.setObject(6, null);
 276                         }
 277
 278                         notesStmt.executeUpdate();
 279                 } catch (SQLException e) {
 280                         logger.error("Note could not be created: " + note);
 281                         e.printStackTrace();
 282                 }
 283
 284
 285         }
 286
 287         /**
 288          * Deletes all entries of database tables related to <code>Note</code>.
 289          * @param state The PesiExportState
 290          * @return Whether the delete operation was successful or not.
 291          */
 292         protected boolean doDelete(PesiExportState state) {
 293                 PesiExportConfigurator pesiConfig = (PesiExportConfigurator) state.getConfig();
 294
 295                 String sql;
 296                 Source destination =  pesiConfig.getDestination();
 297
 298                 // Clear NoteSource
 299                 sql = "DELETE FROM NoteSource";
 300                 destination.setQuery(sql);
 301                 destination.update(sql);
 302
 303                 // Clear Note
 304                 sql = "DELETE FROM " + dbTableName;
 305                 destination.setQuery(sql);
 306                 destination.update(sql);
 307                 return true;
 308         }
 309
 310         /* (non-Javadoc)
 311          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
 312          */
 313         @Override
 314         protected boolean isIgnore(PesiExportState state) {
 315                 // TODO Auto-generated method stub
 316                 return false;
 317         }
 318
 319         /**
 320          * Returns the <code>Note_1</code> attribute.
 321          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 322          * @return The <code>Note_1</code> attribute.
 323          * @see MethodMapper
 324          */
 325         @SuppressWarnings("unused")
 326         private static String getNote_1(DescriptionElementBase descriptionElement) {
 327                 String result = null;
 328
 329                 if (descriptionElement.isInstanceOf(TextData.class)) {
 330                         TextData textData = CdmBase.deproxy(descriptionElement, TextData.class);
 331                         result = textData.getText(Language.DEFAULT());
 332                 }
 333
 334                 return result;
 335         }
 336
 337         /**
 338          * Returns the <code>Note_2</code> attribute.
 339          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 340          * @return The <code>Note_2</code> attribute.
 341          * @see MethodMapper
 342          */
 343         @SuppressWarnings("unused")
 344         private static String getNote_2(DescriptionElementBase descriptionElement) {
 345                 logger.warn("Not yet implemented");
 346                 return null;
 347         }
 348
 349         /**
 350          * Returns the <code>NoteCategoryFk</code> attribute.
 351          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 352          * @return The <code>NoteCategoryFk</code> attribute.
 353          * @see MethodMapper
 354          */
 355         private static Integer getNoteCategoryFk(DescriptionElementBase descriptionElement) {
 356                 Integer result = null;
 357
 358                 result = PesiTransformer.textData2NodeCategoryFk(descriptionElement.getFeature());
 359
 360                 return result;
 361         }
 362
 363         /**
 364          * Returns the <code>NoteCategoryCache</code> attribute.
 365          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 366          * @return The <code>NoteCategoryCache</code> attribute.
 367          * @see MethodMapper
 368          */
 369         @SuppressWarnings("unused")
 370         private static String getNoteCategoryCache(DescriptionElementBase descriptionElement) {
 371                 String result = null;
 372
 373                 if (descriptionElement.isInstanceOf(TextData.class)) {
 374                         result = PesiTransformer.textData2NodeCategoryCache(descriptionElement.getFeature());
 375                 }
 376
 377                 return result;
 378         }
 379
 380         /**
 381          * Returns the <code>LanguageFk</code> attribute.
 382          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 383          * @return The <code>LanguageFk</code> attribute.
 384          * @see MethodMapper
 385          */
 386         @SuppressWarnings("unused")
 387         private static Integer getLanguageFk(DescriptionElementBase descriptionElement) {
 388                 Language language = getLanguage(descriptionElement);
 389
 390                 return PesiTransformer.language2LanguageId(language);
 391         }
 392
 393         /**
 394          * Returns the <code>LanguageCache</code> attribute.
 395          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 396          * @return The <code>LanguageCache</code> attribute.
 397          * @see MethodMapper
 398          */
 399         @SuppressWarnings("unused")
 400         private static String getLanguageCache(DescriptionElementBase descriptionElement) {
 401                 Language language = getLanguage(descriptionElement);
 402
 403                 return PesiTransformer.language2LanguageCache(language);
 404         }
 405
 406         private static Language getLanguage(DescriptionElementBase descriptionElement) {
 407                 Language language = null;
 408
 409                 Map<Language, LanguageString> multilanguageText = null;
 410                 if (descriptionElement.isInstanceOf(CommonTaxonName.class)) {
 411                         CommonTaxonName commonTaxonName = CdmBase.deproxy(descriptionElement, CommonTaxonName.class);
 412                         language = commonTaxonName.getLanguage();
 413                 } else if (descriptionElement.isInstanceOf(TextData.class)) {
 414                         TextData textData = CdmBase.deproxy(descriptionElement, TextData.class);
 415                         multilanguageText = textData.getMultilanguageText();
 416                 } else if (descriptionElement.isInstanceOf(IndividualsAssociation.class)) {
 417                         IndividualsAssociation individualsAssociation = CdmBase.deproxy(descriptionElement, IndividualsAssociation.class);
 418                         multilanguageText = individualsAssociation.getDescription();
 419                 } else if (descriptionElement.isInstanceOf(TaxonInteraction.class)) {
 420                         TaxonInteraction taxonInteraction = CdmBase.deproxy(descriptionElement, TaxonInteraction.class);
 421                         multilanguageText = taxonInteraction.getDescriptions();
 422                 } else {
 423                         logger.debug("Given descriptionElement does not support languages. Hence LanguageCache could not be determined: " + descriptionElement.getUuid());
 424                 }
 425
 426                 if (multilanguageText != null) {
 427                         Set<Language> languages = multilanguageText.keySet();
 428
 429                         // TODO: Think of something more sophisticated than this
 430                         if (languages.size() > 0) {
 431                                 language = languages.iterator().next();
 432                         }
 433                         if (languages.size() > 1){
 434                                 logger.warn("There is more than 1 language for a given description (" + descriptionElement.getClass().getSimpleName() + "):" + descriptionElement.getUuid());
 435                         }
 436                 }
 437                 return language;
 438         }
 439
 440         /**
 441          * Returns the <code>Region</code> attribute.
 442          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 443          * @return The <code>Region</code> attribute.
 444          * @see MethodMapper
 445          */
 446         @SuppressWarnings("unused")
 447         private static String getRegion(DescriptionElementBase descriptionElement) {
 448                 String result = null;
 449                 DescriptionBase<?> inDescription = descriptionElement.getInDescription();
 450
 451                 // Area information are associated to TaxonDescriptions and Distributions.
 452                 if (descriptionElement.isInstanceOf(Distribution.class)) {
 453                         Distribution distribution = CdmBase.deproxy(descriptionElement, Distribution.class);
 454                         result = PesiTransformer.area2AreaCache(distribution.getArea());
 455                 } else if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) {
 456                         TaxonDescription taxonDescription = CdmBase.deproxy(inDescription, TaxonDescription.class);
 457                         Set<NamedArea> namedAreas = taxonDescription.getGeoScopes();
 458                         if (namedAreas.size() == 1) {
 459                                 result = PesiTransformer.area2AreaCache(namedAreas.iterator().next());
 460                         } else if (namedAreas.size() > 1) {
 461                                 logger.warn("This TaxonDescription contains more than one NamedArea: " + taxonDescription.getTitleCache());
 462                         }
 463                 }
 464                 return result;
 465         }
 466
 467         /**
 468          * Returns the <code>TaxonFk</code> attribute.
 469          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 470          * @param state The {@link PesiExportState PesiExportState}.
 471          * @return The <code>TaxonFk</code> attribute.
 472          * @see MethodMapper
 473          */
 474         @SuppressWarnings("unused")
 475         private static Integer getTaxonFk(DescriptionElementBase descriptionElement, DbExportStateBase<?> state) {
 476                 Integer result = null;
 477                 DescriptionBase<?> inDescription = descriptionElement.getInDescription();
 478                 if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) {
 479                         TaxonDescription taxonDescription = CdmBase.deproxy(inDescription, TaxonDescription.class);
 480                         Taxon taxon = taxonDescription.getTaxon();
 481                         result = state.getDbId(taxon.getName());
 482                 }
 483                 return result;
 484         }
 485
 486         /**
 487          * Returns the TaxonFk for a given TaxonName.
 488          * @param taxonName The {@link TaxonNameBase TaxonName}.
 489          * @param state The {@link DbExportStateBase DbExportState}.
 490          * @return
 491          */
 492         private static Integer getTaxonFk(TaxonNameBase<?,?> taxonName, DbExportStateBase<?> state) {
 493                 return state.getDbId(taxonName);
 494         }
 495
 496         /**
 497          * Returns the <code>LastAction</code> attribute.
 498          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 499          * @return The <code>LastAction</code> attribute.
 500          * @see MethodMapper
 501          */
 502         @SuppressWarnings("unused")
 503         private static String getLastAction(DescriptionElementBase descriptionElement) {
 504                 // TODO
 505                 return null;
 506         }
 507
 508         /**
 509          * Returns the <code>LastActionDate</code> attribute.
 510          * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.
 511          * @return The <code>LastActionDate</code> attribute.
 512          * @see MethodMapper
 513          */
 514         @SuppressWarnings("unused")
 515         private static DateTime getLastActionDate(DescriptionElementBase descriptionElement) {
 516                 DateTime result = null;
 517                 return result;
 518         }
 519
 520         /**
 521          * Returns the CDM to PESI specific export mappings.
 522          * @return The {@link PesiExportMapping PesiExportMapping}.
 523          */
 524         private PesiExportMapping getMapping() {
 525                 PesiExportMapping mapping = new PesiExportMapping(dbTableName);
 526
 527                 mapping.addMapper(IdMapper.NewInstance("NoteId"));
 528                 mapping.addMapper(MethodMapper.NewInstance("Note_1", this));
 529                 mapping.addMapper(MethodMapper.NewInstance("Note_2", this));
 530                 mapping.addMapper(MethodMapper.NewInstance("NoteCategoryFk", this));
 531                 mapping.addMapper(MethodMapper.NewInstance("NoteCategoryCache", this));
 532                 mapping.addMapper(MethodMapper.NewInstance("LanguageFk", this));
 533                 mapping.addMapper(MethodMapper.NewInstance("LanguageCache", this));
 534                 mapping.addMapper(MethodMapper.NewInstance("Region", this));
 535                 mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this.getClass(), "getTaxonFk", standardMethodParameter, DbExportStateBase.class));
 536                 mapping.addMapper(MethodMapper.NewInstance("LastAction", this));
 537                 mapping.addMapper(MethodMapper.NewInstance("LastActionDate", this));
 538
 539                 return mapping;
 540         }
 541
 542 }