cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestDatabase.java

   1 /* just for testing */
   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
  11 package eu.etaxonomy.cdm.test.function;
  12
  13 import static org.junit.Assert.assertNotNull;
  14
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import junit.framework.Assert;
  21
  22 import org.apache.log4j.Logger;
  23 import org.hibernate.mapping.Column;
  24 import org.junit.Test;
  25 import org.springframework.core.io.ClassPathResource;
  26 import org.springframework.core.io.Resource;
  27
  28 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  29 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  30 import eu.etaxonomy.cdm.common.AccountStore;
  31 import eu.etaxonomy.cdm.common.CdmUtils;
  32 import eu.etaxonomy.cdm.database.CdmDataSource;
  33 import eu.etaxonomy.cdm.database.CdmPersistentDataSource;
  34 import eu.etaxonomy.cdm.database.DataSourceNotFoundException;
  35 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
  36 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  37 import eu.etaxonomy.cdm.database.ICdmDataSource;
  38 import eu.etaxonomy.cdm.model.agent.AgentBase;
  39 import eu.etaxonomy.cdm.model.agent.Contact;
  40 import eu.etaxonomy.cdm.model.agent.Person;
  41 import eu.etaxonomy.cdm.model.common.Annotation;
  42 import eu.etaxonomy.cdm.model.common.AnnotationType;
  43 import eu.etaxonomy.cdm.model.common.Language;
  44 import eu.etaxonomy.cdm.model.common.init.TermNotFoundException;
  45 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  46 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  47 import eu.etaxonomy.cdm.model.description.Feature;
  48 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  49 import eu.etaxonomy.cdm.model.description.TextData;
  50 import eu.etaxonomy.cdm.model.name.BotanicalName;
  51 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  52 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  53 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  54 import eu.etaxonomy.cdm.model.name.Rank;
  55 import eu.etaxonomy.cdm.model.reference.Journal;
  56 import eu.etaxonomy.cdm.model.taxon.Taxon;
  57 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  58
  59
  60 public class TestDatabase {
  61         private static final Logger logger = Logger.getLogger(TestDatabase.class);
  62
  63         private void test(){
  64                 System.out.println("Start TestDatabase");
  65                 //testNewDatabaseConnection();
  66                 //testFacts();
  67 //              testNewDatasourceClass();
  68                 testHybridRelationships();
  69         //      testPaddie();
  70                 System.out.println("\nEnd TestDatabase");
  71         }
  72
  73         public void testNewDatabaseConnection(){
  74                 try {
  75
  76                         Column coL;
  77                         boolean omitTermLoading = false;
  78                         Resource applicationContextResource = new ClassPathResource(CdmApplicationController.DEFAULT_APPLICATION_CONTEXT_RESOURCE);
  79                         CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance();
  80                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(applicationContextResource, dataSource, DbSchemaValidation.CREATE, omitTermLoading);
  81                         appCtr.NewConversation();
  82                         appCtr.NewConversation();
  83
  84                         //CdmApplicationController appCtr = CdmApplicationController.NewInstance(DbSchemaValidation.CREATE);
  85                         appCtr.close();
  86                 } catch (DataSourceNotFoundException e) {
  87                         logger.error("datasource error");
  88                 } catch (TermNotFoundException e) {
  89                         logger.error("defined terms not found");
  90                 }
  91         }
  92
  93         public void testNewDatasourceClass(){
  94                 try {
  95 //                      String server = "192.168.2.10";
  96 //                      String database = "cdm_test_andreasM";
  97 //                      String username = "edit";
  98 //                      String password = CdmUtils.readInputLine("Password: ");
  99                         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
 100
 101 //                      ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password);
 102                         ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
 103                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 104
 105                         Rank genus = Rank.GENUS();
 106                         BotanicalName botanicalName = BotanicalName.NewInstance(genus);
 107                         botanicalName.setGenusOrUninomial("GenusName");
 108
 109                         Journal journal = Journal.NewInstance();
 110                         journal.setTitleCache("Afro+Doc");
 111
 112                         //                      Taxon taxon = Taxon.NewInstance(botanicalName, journal);
 113 //                      Taxon taxon2 = Taxon.NewInstance(botanicalName2, null);
 114         //              botanicalName.getTitleCache();
 115
 116                         Taxon taxon1 = Taxon.NewInstance(botanicalName,journal);
 117                         appCtr.getTaxonService().save(taxon1);
 118                         BotanicalName homotypName = BotanicalName.NewInstance(Rank.SUBGENUS(), botanicalName.getHomotypicalGroup());
 119                         homotypName.setGenusOrUninomial("Subgenus");
 120                         homotypName.setInfraGenericEpithet("homotyp");
 121
 122                         //Synonym synonym = Synonym.NewInstance(homotypName, journal);
 123
 124                         System.out.println("Taxa of " + botanicalName + ": " + botanicalName.getTaxonBases());
 125                         System.out.println("Synonyms of " + homotypName + ": " + homotypName.getSynonyms());
 126
 127                         HomotypicalGroup homotypicalGroup = taxon1.getHomotypicGroup();
 128                         System.out.println("HomotypicNames of " + botanicalName + ":" + homotypicalGroup.getTypifiedNames());
 129                         System.out.println("HomotypicSynonymsByGroup of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicGroup());
 130                         System.out.println("HomotypicSynonymsBySynonymy of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicRelationship());
 131
 132 //                      appCtr.getTaxonService().saveTaxon(taxon2);
 133 //                      appCtr.getTaxonService().saveTaxon(taxon);
 134
 135                         appCtr.close();
 136
 137                 } catch (DataSourceNotFoundException e) {
 138                         logger.error("datasource error");
 139                 } catch (TermNotFoundException e) {
 140                         logger.error("defined terms not found");
 141                 }
 142         }
 143
 144
 145         public void testFacts(){
 146                 try {
 147                         String server = "192.168.2.10";
 148                         String database = "cdm_test_andreasM";
 149                         String username = "edit";
 150                         String password = CdmUtils.readInputLine("Password: ");
 151                         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;
 152                         ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password);
 153                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 154
 155                         Rank genus = Rank.GENUS();
 156                         BotanicalName botanicalName = BotanicalName.NewInstance(genus);
 157                         botanicalName.setGenusOrUninomial("GenusName");
 158
 159                         Journal journal = Journal.NewInstance();
 160                         journal.setTitleCache("Afro+Doc");
 161
 162                         Taxon taxon = Taxon.NewInstance(botanicalName,journal);
 163                         appCtr.getTaxonService().save(taxon);
 164
 165                         TaxonDescription taxonDescription = TaxonDescription.NewInstance();
 166                         taxon.addDescription(taxonDescription);
 167
 168                         //textData
 169                         TextData textData = TextData.NewInstance();
 170                         textData.putText("XXX", Language.DEFAULT());
 171                         taxonDescription.addElement(textData);
 172
 173                         //commonNames
 174                         String commonNameString;
 175                         if (taxon.getName() != null){
 176                                 commonNameString = "Common " + taxon.getName().getTitleCache();
 177                         }else{
 178                                 commonNameString = "Common (null)";
 179                         }
 180                         CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, Language.DEFAULT());
 181                         taxonDescription.addElement(commonName);
 182
 183                         //save
 184                         appCtr.getTaxonService().save(taxon);
 185
 186
 187                         appCtr.close();
 188
 189                 } catch (DataSourceNotFoundException e) {
 190                         logger.error("datasource error");
 191                 } catch (TermNotFoundException e) {
 192                         logger.error("defined terms not found");
 193                 }
 194         }
 195
 196
 197         public void testHybridRelationships(){
 198                 try {
 199 //                      String database = "cdm";
 200 //                      String username = "sa";
 201
 202                         String server = "192.168.2.10";
 203                         String database = "cdm_test_andreasM";
 204                         String username = "edit";
 205                         String password = CdmUtils.readInputLine("Password: ");
 206                         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
 207                         ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password);
 208                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 209
 210                         Rank genus = Rank.GENUS();
 211                         BotanicalName parentName = BotanicalName.NewInstance(genus);
 212                         parentName.setGenusOrUninomial("parent");
 213
 214                         BotanicalName childName = BotanicalName.NewInstance(genus);
 215                         childName.setGenusOrUninomial("child");
 216                         parentName.addHybridChild(childName, HybridRelationshipType.FIRST_PARENT(), null);
 217
 218                         //save
 219                         appCtr.getNameService().save(parentName);
 220
 221
 222                         appCtr.close();
 223
 224                 } catch (DataSourceNotFoundException e) {
 225                         logger.error("datasource error");
 226                 } catch (TermNotFoundException e) {
 227                         logger.error("defined terms not found");
 228                 }
 229         }
 230
 231         public void testPaddie(){
 232
 233
 234                 try {
 235                         String server = "PADDIE";
 236                         String database = "edit_test";
 237                         String username = "andreas";
 238                         String password = CdmUtils.readInputLine("Password: ");
 239                         DbSchemaValidation validation = DbSchemaValidation.VALIDATE;
 240                         ICdmDataSource datasource = CdmDataSource.NewSqlServer2005Instance(server, database, -1, username, password, null);
 241                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, validation);
 242
 243                         Rank genus = Rank.GENUS();
 244                         BotanicalName botanicalName = BotanicalName.NewInstance(genus);
 245                         botanicalName.setGenusOrUninomial("GenusName");
 246
 247                         Journal journal = Journal.NewInstance();
 248                         journal.setTitle("JournalTitel");
 249
 250                         //                      Taxon taxon = Taxon.NewInstance(botanicalName, journal);
 251 //                      Taxon taxon2 = Taxon.NewInstance(botanicalName2, null);
 252         //              botanicalName.getTitleCache();
 253                         Rank.SPECIES();
 254                         appCtr.getNameService().save(botanicalName);
 255
 256 //                      appCtr.getTaxonService().saveTaxon(taxon2);
 257 //                      appCtr.getTaxonService().saveTaxon(taxon);
 258
 259                         appCtr.close();
 260                 } catch (DataSourceNotFoundException e) {
 261                         logger.error("datasource error");
 262                 } catch (TermNotFoundException e) {
 263                         logger.error("defined terms not found");
 264                 }
 265         }
 266
 267
 268         public void testContact(){
 269                 try {
 270 //                      String server = "192.168.2.10";
 271 //                      String database = "cdm_test_andreasM";
 272 //                      String username = "edit";
 273 //                      String password = CdmUtils.readInputLine("Password: ");
 274                         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
 275
 276 //                      ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password);
 277                         //ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "");
 278                         ICdmDataSource datasource = cdm_test_anahit2();
 279                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 280                         AgentBase person = Person.NewTitledInstance("TestPerson");
 281                         Contact contact1 = new Contact();
 282                         Set<String> set = new HashSet<String>();
 283                         set.add("email1");
 284                         set.add("c@d.org");
 285 //                      contact1.setEmail(set);
 286 //                      person.setContact(contact1);
 287                         appCtr.getAgentService().save(person);
 288                         appCtr.close();
 289                         System.out.println("End");
 290                 } catch (DataSourceNotFoundException e) {
 291                         logger.error("datasource error");
 292                 } catch (TermNotFoundException e) {
 293                         logger.error("defined terms not found");
 294                 }
 295         }
 296
 297
 298         public void testNewVersion(){
 299                 try {
 300                         System.out.println("Start");
 301                         DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
 302
 303 //                      ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password);
 304                         ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
 305                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
 306                         BotanicalName botName = BotanicalName.NewInstance(Rank.SPECIES());
 307                         botName.setGenusOrUninomial("Genus");
 308                         botName.setSpecificEpithet("species");
 309                         appCtr.getNameService().save(botName);
 310                         List<?> names = appCtr.getNameService().findNamesByTitle("Genus species");
 311
 312                         names.size();
 313 //                      AgentBase person = Person.NewTitledInstance("TestPerson");
 314 //                      Contact contact1 = new Contact();
 315 //                      Set<String> set = new HashSet<String>();
 316 //                      set.add("email1");
 317 //                      set.add("c@d.org");
 318 ////                    contact1.setEmail(set);
 319 //                      person.setContact(contact1);
 320 //                      appCtr.getAgentService().save(person);
 321                         appCtr.close();
 322                         System.out.println("End");
 323                 } catch (DataSourceNotFoundException e) {
 324                         logger.error("datasource error");
 325                 } catch (TermNotFoundException e) {
 326                         logger.error("defined terms not found");
 327                 }
 328         }
 329
 330         public void testDataSourceWithNomenclaturalCode(){
 331                 String dataSourceName = "test";
 332                 NomenclaturalCode code = NomenclaturalCode.ICZN;
 333 //              ICdmDataSource dataSource = CdmDataSource.NewH2EmbeddedInstance("test", "sa", "", code);
 334                 String password = CdmUtils.readInputLine("Password: ");
 335                 ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, code);
 336                 CdmPersistentDataSource.save(dataSourceName, dataSource);
 337
 338                 try {
 339                         CdmPersistentDataSource loadedDataSource = CdmPersistentDataSource.NewInstance(dataSourceName);
 340 //                      CdmApplicationController.NewInstance(loadedDataSource, DbSchemaValidation.CREATE);
 341
 342                         NomenclaturalCode loadedCode = loadedDataSource.getNomenclaturalCode();
 343                         Assert.assertEquals(code, loadedCode);
 344
 345                         CdmPersistentDataSource.delete(loadedDataSource);
 346
 347                 } catch (DataSourceNotFoundException e) {
 348                         // TODO Auto-generated catch block
 349                         e.printStackTrace();
 350                 }
 351
 352
 353         }
 354
 355         public void testLoadedAnnotationGetAnnotatedObjectCall(){
 356                 String password = CdmUtils.readInputLine("Password: ");
 357                 ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, NomenclaturalCode.ICBN);
 358                 try {
 359                         CdmApplicationController appCtr = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.UPDATE);
 360
 361                         ConversationHolder conversation = appCtr.NewConversation();
 362
 363                         // make the taxon and description elements
 364                         Taxon taxon = Taxon.NewInstance(null, null);
 365
 366                         TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
 367
 368                         UUID taxonDescriptionUuid = taxonDescription.getUuid();
 369
 370                         Feature featureAnatomy = Feature.ANATOMY();
 371
 372                         TextData textData = TextData.NewInstance();
 373                         textData.addAnnotation(Annotation.NewInstance(null, null));
 374
 375                         assertNotNull(textData.getAnnotations().iterator().next().getAnnotatedObj());
 376
 377                         textData.setFeature(featureAnatomy);
 378
 379                         taxonDescription.addElement(textData);
 380
 381                         appCtr.getTaxonService().save(taxon);
 382
 383                         conversation.commit(false);
 384                         // end of creation phase
 385
 386
 387                         // load the new taxon in a new conversation to assure that it was loaded into a new session
 388                         // if you are willing to blame it on conversations, please rewrite into two methods
 389                         // the result will be the same
 390                         ConversationHolder newConversation = appCtr.NewConversation();
 391                         DescriptionBase loadedDescription = appCtr.getDescriptionService().load(taxonDescriptionUuid);
 392
 393                         TextData descriptionElement = (TextData) loadedDescription.getElements().iterator().next();
 394
 395                         Annotation annotation = descriptionElement.getAnnotations().iterator().next();
 396
 397                         // this should not be null
 398                         assertNotNull(annotation.getAnnotatedObj());
 399
 400
 401                 } catch (DataSourceNotFoundException e) {
 402                         // TODO Auto-generated catch block
 403                         e.printStackTrace();
 404                 } catch (TermNotFoundException e) {
 405                         // TODO Auto-generated catch block
 406                         e.printStackTrace();
 407                 }
 408
 409         }
 410
 411
 412         public static ICdmDataSource cdm_test_anahit2(){
 413                 DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
 414                 String cdmServer = "192.168.2.10";
 415                 String cdmDB = "cdm_test_anahit2";
 416                 String cdmUserName = "edit";
 417                 return makeDestination(cdmServer, cdmDB, -1, cdmUserName, null);
 418         }
 419
 420         /**
 421          * initializes source
 422          * @return true, if connection establisehd
 423          */
 424         private static ICdmDataSource makeDestination(String cdmServer, String cdmDB, int port, String cdmUserName, String pwd ){
 425                 //establish connection
 426                 pwd = AccountStore.readOrStorePassword(cdmServer, cdmDB, cdmUserName, pwd);
 427                 //TODO not MySQL
 428                 ICdmDataSource destination = CdmDataSource.NewMySqlInstance(cdmServer, cdmDB, port, cdmUserName, pwd, null);
 429                 return destination;
 430
 431         }
 432
 433         /**
 434          * @param args
 435          */
 436         public static void  main(String[] args) {
 437                 TestDatabase sc = new TestDatabase();
 438 //      sc.testNewDatabaseConnection();
 439 //              sc.testDataSourceWithNomenclaturalCode();
 440                 sc.testLoadedAnnotationGetAnnotatedObjectCall();
 441         }
 442
 443 }