app-import/src/main/java/eu/etaxonomy/cdm/app/util/TestDatabase.java

   1 /**
   2 * Copyright (C) 2008 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 */
   6
   7 package eu.etaxonomy.cdm.app.util;
   8
   9 import java.util.ArrayList;
  10 import java.util.GregorianCalendar;
  11 import java.util.List;
  12
  13 import org.apache.log4j.Logger;
  14 import org.springframework.transaction.TransactionStatus;
  15
  16 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  17 import eu.etaxonomy.cdm.common.AccountStore;
  18 import eu.etaxonomy.cdm.database.CdmDataSource;
  19 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  20 import eu.etaxonomy.cdm.database.ICdmDataSource;
  21 import eu.etaxonomy.cdm.io.jaxb.DataSet;
  22 import eu.etaxonomy.cdm.model.agent.AgentBase;
  23 import eu.etaxonomy.cdm.model.agent.Institution;
  24 import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
  25 import eu.etaxonomy.cdm.model.agent.Person;
  26 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  27 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  28 import eu.etaxonomy.cdm.model.common.TimePeriod;
  29 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  30 import eu.etaxonomy.cdm.model.description.Feature;
  31 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  32 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  33 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  34 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  35 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  36 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  37 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  38 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  39 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  40 import eu.etaxonomy.cdm.model.name.BotanicalName;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  42 import eu.etaxonomy.cdm.model.name.Rank;
  43 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  44 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  48 import eu.etaxonomy.cdm.model.taxon.Synonym;
  49 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  50 import eu.etaxonomy.cdm.model.taxon.Taxon;
  51 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  53 import eu.etaxonomy.cdm.model.taxon.Classification;
  54
  55 /**
  56  * @author a.babadshanjan
  57  * @created 28.10.2008
  58  */
  59 public class TestDatabase {
  60
  61         private static final String server = "192.168.2.10";
  62         private static final String username = "edit";
  63
  64         private static final Logger logger = Logger.getLogger(TestDatabase.class);
  65
  66         public static ICdmDataSource CDM_DB(String dbname) {
  67
  68                 logger.info("Setting DB " + dbname);
  69                 String password = AccountStore.readOrStorePassword(dbname, server, username, null);
  70                 ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, dbname, username, password, NomenclaturalCode.ICBN);
  71                 return datasource;
  72         }
  73
  74     public static CdmApplicationController
  75     initDb(ICdmDataSource db, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {
  76
  77                 logger.info("Initializing database '" + db.getName() + "'");
  78
  79                 CdmApplicationController appCtrInit = null;
  80                 appCtrInit = CdmApplicationController.NewInstance(db, dbSchemaValidation, omitTermLoading);
  81
  82                 return appCtrInit;
  83     }
  84
  85         public static void loadTestData(String dbname, CdmApplicationController appCtr) {
  86
  87                 logger.info("Loading test data into " + dbname);
  88
  89                 TransactionStatus txStatus = appCtr.startTransaction();
  90                 DataSet dataSet = buildDataSet();
  91
  92                 appCtr.getTermService().save(dataSet.getTerms());
  93                 appCtr.getTaxonService().save(dataSet.getTaxonBases());
  94
  95                 appCtr.commitTransaction(txStatus);
  96                 appCtr.close();
  97     }
  98
  99         /**
 100          * This method constructs a small sample classification to test JAXB marshaling.
 101          * The sample tree contains four taxa. The root taxon has two children taxa, and
 102          * there is one "free" taxon without a parent and children.
 103          */
 104         private static DataSet buildDataSet() {
 105
 106                 List<AgentBase> agents = new ArrayList<AgentBase>();
 107             List<VersionableEntity> agentData = new ArrayList<VersionableEntity>();
 108             //List<Agent> agentData = new ArrayList<Agent>();
 109
 110             //List<TermBase> terms = new ArrayList<TermBase>();
 111             List<DefinedTermBase> terms = new ArrayList<DefinedTermBase>();
 112             List<Reference> references = new ArrayList<Reference>();
 113             List<TaxonNameBase> taxonomicNames = new ArrayList<TaxonNameBase>();
 114             List<TaxonBase> taxonBases = new ArrayList<TaxonBase>();
 115
 116             List<Feature> features = new ArrayList<Feature>();
 117
 118             Feature feature1 = Feature.BIOLOGY_ECOLOGY();
 119
 120             TaxonNameDescription taxNameDescription = TaxonNameDescription.NewInstance();
 121             taxNameDescription.addFeature(feature1);
 122             QuantitativeData element = QuantitativeData.NewInstance();
 123             StatisticalMeasurementValue statisticalValue = StatisticalMeasurementValue.NewInstance();
 124             statisticalValue.setType(StatisticalMeasure.MAX());
 125             statisticalValue.setValue((float) 2.1);
 126             element.addStatisticalValue(statisticalValue);
 127             taxNameDescription.addElement(element);
 128
 129             SpecimenOrObservationBase<?> specimen = Specimen.NewInstance();
 130
 131             specimen.setIndividualCount(12);
 132
 133
 134             Feature featureIndAss = Feature.INDIVIDUALS_ASSOCIATION();
 135             TaxonNameDescription newTaxNameDesc = TaxonNameDescription.NewInstance();
 136             newTaxNameDesc.addFeature(featureIndAss);
 137             IndividualsAssociation indAss = IndividualsAssociation.NewInstance();
 138             indAss.setAssociatedSpecimenOrObservation(specimen);
 139
 140             newTaxNameDesc.addElement(indAss);
 141
 142
 143
 144
 145 //          List<Synonym> synonyms = new ArrayList<Synonym>();
 146             List<AnnotatableEntity> homotypicalGroups;
 147
 148                 Reference<?> citRef, sec;
 149                 BotanicalName name1, name2, name21, nameRoot1, nameFree, synName11, synName12, synName2, synNameFree;
 150                 BotanicalName nameRoot2, nameR2_1, nameR2_2;
 151                 Taxon child1, child2, child21, root1T, root2T, freeT;
 152                 Taxon childR2_1, childR2_2;
 153                 TaxonNode child1Node, child2Node, child21Node, root1TNode, root2TNode, freeTNode;
 154                 TaxonNode childR2_1Node, childR2_2Node;
 155                 Classification taxTree, taxTree2;
 156                 Synonym syn11, syn12, syn2, synFree;
 157                 Rank rankSpecies, rankSubspecies, rankGenus;
 158
 159                 // agents
 160                 // - persons, institutions
 161
 162                 Person linne = new Person("Carl", "Linne", "L.");
 163                 linne.setTitleCache("Linne & Karl", true);
 164                 GregorianCalendar birth = new GregorianCalendar(1707, 4, 23);
 165                 GregorianCalendar death = new GregorianCalendar(1778, 0, 10);
 166                 TimePeriod period = TimePeriod.NewInstance(birth, death);
 167                 linne.setLifespan(period);
 168
 169 //              Keyword keyword = Keyword.NewInstance("plantarum", "lat", "");
 170 //              linne.addKeyword(keyword);
 171
 172                 Institution institute = Institution.NewInstance();
 173
 174                 agents.add(linne);
 175                 agents.add(institute);
 176
 177                 // agent data
 178                 // - contacts, addresses, memberships
 179
 180                 //Contact contact1 = new Contact();
 181                 //contact1.setEmail("someone@somewhere.org");
 182                 InstitutionalMembership membership
 183                 = new InstitutionalMembership(institute, linne, period, "Biodiversity", "Head");
 184                 //agentData.add(contact1);
 185
 186                 agentData.add(membership);
 187
 188                 // terms
 189                 // - ranks, keywords
 190
 191                 rankSpecies = Rank.SPECIES();
 192                 rankSubspecies = Rank.SUBSPECIES();
 193                 rankGenus = Rank.GENUS();
 194
 195 //              terms.add(keyword);
 196
 197         // taxonomic names
 198
 199                 nameRoot1 = BotanicalName.NewInstance(rankGenus,"Calendula",null,null,null,linne,null,"p.100", null);
 200                 nameRoot1.addDescription(taxNameDescription);
 201                 nameRoot1.addDescription(newTaxNameDesc);
 202                 name1 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"arvensis",null,linne,null,"p.1", null);
 203                 synName11 = BotanicalName.NewInstance(rankSpecies,"Caltha",null,"arvensis",null,linne,null,"p.11", null);
 204                 synName12 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"sancta",null,linne,null,"p.12", null);
 205
 206                 name2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzae",null,linne,null,"p.2", null);
 207                 synName2 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"echinata",null,linne,null,"p.2", null);
 208
 209                 name21 = BotanicalName.NewInstance(rankSubspecies,"Calendula",null,"lanzea","something",linne,null,"p.1", null);
 210                 //name211 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
 211                 //name212 = BotanicalName.NewInstance(rankSpecies,"Calendula",null,"lanzea",null,linne,null,"p.1", null);
 212
 213                 nameRoot2 =
 214                         BotanicalName.NewInstance(rankGenus,"Sonchus",null,null,null,linne,null,"p.200", null);
 215                 nameR2_1 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child1",null,linne,null,"p.1", null);
 216                 nameR2_2 = BotanicalName.NewInstance(rankSpecies,"Sonchus",null,"child2",null,linne,null,"p.2", null);
 217
 218                 nameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"intybus",null,linne,null,"p.200", null);
 219                 synNameFree = BotanicalName.NewInstance(rankSpecies,"Cichorium",null,"balearicum",null,linne,null,"p.2", null);
 220
 221                 taxonomicNames.add(nameRoot1);
 222                 taxonomicNames.add(name1);
 223                 taxonomicNames.add(synName11);
 224                 taxonomicNames.add(synName12);
 225                 taxonomicNames.add(name2);
 226                 taxonomicNames.add(name21);
 227                 taxonomicNames.add(synName2);
 228                 taxonomicNames.add(nameFree);
 229                 taxonomicNames.add(synNameFree);
 230                 taxonomicNames.add(nameRoot2);
 231
 232         // references
 233                 sec = ReferenceFactory.newBook();
 234                 sec.setAuthorTeam(linne);
 235                 sec.setTitleCache("Plant Specification & Taxonomy", true);
 236                 references.add(sec);
 237
 238                 citRef = ReferenceFactory.newDatabase();
 239                 citRef.setAuthorTeam(linne);
 240                 citRef.setTitleCache("BioCASE", true);
 241                 references.add(citRef);
 242
 243                 // taxa
 244
 245                 root1T = Taxon.NewInstance(nameRoot1, sec);
 246                 root2T = Taxon.NewInstance(nameRoot2, sec);
 247                 freeT = Taxon.NewInstance(nameFree, sec);
 248                 child1 = Taxon.NewInstance(name1, sec);
 249                 child2 = Taxon.NewInstance(name2, sec);
 250                 child21 = Taxon.NewInstance(name21, sec);
 251                 childR2_1 = Taxon.NewInstance(nameR2_1, sec);
 252                 childR2_2 = Taxon.NewInstance(nameR2_2, sec);
 253
 254                 //TaxonInteractions
 255
 256                 TaxonInteraction descBase = TaxonInteraction.NewInstance();
 257                 descBase.setTaxon2(root1T);
 258                 Feature hostplant = Feature.HOSTPLANT();
 259
 260                 descBase.setFeature(hostplant);
 261                 TaxonDescription taxDesc = TaxonDescription.NewInstance();
 262                 taxDesc.addElement(descBase);
 263                 root2T.addDescription(taxDesc);
 264
 265                 //locations
 266
 267                 taxDesc = TaxonDescription.NewInstance();
 268                 Feature locationFeature = Feature.DISTRIBUTION();
 269
 270
 271                 //locationFeature.
 272                 WaterbodyOrCountry area = WaterbodyOrCountry.NewInstance("", "locationTest", null);
 273                 area.setType(NamedAreaType.NATURAL_AREA());
 274
 275                 //WaterbodyOrCountry woC= WaterbodyOrCountry.NewInstance();
 276                 area.addWaterbodyOrCountry(WaterbodyOrCountry.AFGHANISTAN());
 277                 taxDesc.addGeoScope(area);
 278                 taxDesc.addFeature(locationFeature);
 279                 root1T.addDescription(taxDesc);
 280
 281
 282                 // synonyms
 283
 284                 synFree = Synonym.NewInstance(synNameFree, sec);
 285                 syn11 = Synonym.NewInstance(synName11, sec);
 286                 syn12 = Synonym.NewInstance(synName12, sec);
 287                 syn2 = Synonym.NewInstance(synName2, sec);
 288
 289                 child1.addSynonym(syn11, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
 290                 child1.addSynonym(syn12, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
 291                 child2.addSynonym(syn2, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
 292                 freeT.addSynonym(synFree, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
 293
 294                 taxonBases.add(synFree);
 295                 taxonBases.add(syn11);
 296                 taxonBases.add(syn12);
 297                 taxonBases.add(syn2);
 298
 299                 // taxonomic children
 300
 301                 //TODO: Adapt to classification
 302                 taxTree = Classification.NewInstance("TestTree");
 303
 304                 root1TNode = taxTree.addChildTaxon(root1T, sec, null, null);
 305                 child1Node = root1TNode.addChildTaxon(child1, null, null, null);
 306                 child2Node = root1TNode.addChildTaxon(child2, null, null, null);
 307                 child21Node = child2Node.addChildTaxon(child21, null, null, null);
 308
 309                 taxTree2 = Classification.NewInstance("TestTree2");
 310
 311                 root2TNode = taxTree2.addChildTaxon(root2T, sec, null, null);
 312                 root2TNode.addChildTaxon(child1, sec, "p.1010", syn11);
 313                 root2TNode.addChildTaxon(child2, null, null, null);
 314
 315                 /*
 316                 root1T.addTaxonomicChild(child1, sec, "p.1010");
 317                 root1T.addTaxonomicChild(child2, sec, "p.1020");
 318                 child2.addTaxonomicChild(child21, sec, "p.2000");
 319
 320                 root2T.addTaxonomicChild(child1, sec, "p.1010");
 321                 root2T.addTaxonomicChild(child2, sec, "p.1020");
 322                 */
 323                 //
 324
 325
 326                 taxonBases.add(root1T);
 327                 taxonBases.add(root2T);
 328                 taxonBases.add(freeT);
 329                 taxonBases.add(child1);
 330                 taxonBases.add(child2);
 331                 taxonBases.add(child21);
 332                 taxonBases.add(childR2_1);
 333                 taxonBases.add(childR2_2);
 334
 335                 DataSet dataSet = new DataSet();
 336
 337                 logger.warn("WARNING: TestDatabase has been commented in parts. Mainly, must be adapted to classification.");
 338
 339                 dataSet.setTerms(terms);
 340                 dataSet.setAgents(agents);
 341 //              dataSet.setAgentData(agentData); //TODO
 342                 dataSet.setReferences(references);
 343                 dataSet.setTaxonomicNames(taxonomicNames);
 344                 dataSet.setTaxonBases(taxonBases);
 345
 346
 347                 return dataSet;
 348
 349         }
 350 }