cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/package-info.java

   1 /* Package Annotations*/
   2
   3 @javax.xml.bind.annotation.XmlSchema(namespace = "http://etaxonomy.eu/cdm/model/common/1.0", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
   4 @com.sun.xml.bind.XmlAccessorFactory(eu.etaxonomy.cdm.jaxb.CdmAccessorFactoryImpl.class)
   5 @org.hibernate.annotations.GenericGenerators(
   6         {
   7                 /* @see {@link eu.etaxonomy.cdm.persistence.hibernate.TableGenerator} */
   8                 @GenericGenerator(
   9                                 name="custom-enhanced-table",
  10                                 strategy = "eu.etaxonomy.cdm.persistence.hibernate.TableGenerator",
  11                                 parameters = {
  12                                     @Parameter(name="table_name", value = "hibernate_sequences"),
  13                                     @Parameter(name="optimizer", value = "pooled"),
  14                                     /* initial_value = increment_size as proposed to fix an issue with pooled optimizer
  15                                      * http://opensource.atlassian.com/projects/hibernate/browse/HHH-3608?focusedCommentId=37112&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_37112
  16                                      */
  17                                     @Parameter(name="initial_value", value= "10"),
  18                                     @Parameter(name="increment_size", value = "10"),
  19                                     /* we want to have a sequence per table */
  20                                     @Parameter(name="prefer_entity_table_as_segment_value", value="true")
  21                                 }
  22                 ),
  23                 /* Steve Ebersole of Hibernate highly recommends the use of the two new generators
  24                  * http://relation.to/2082.lace
  25                  * Also see: http://docs.jboss.org/hibernate/core/3.3/reference/en/html/mapping.html#mapping-declaration-id-enhanced
  26                  */
  27                 /* new table generator
  28                  * always stores sequences in a table. May be configured to return a sequence on a per table basis
  29                  * RECOMMENDED WHEN RUNNING A CDM DATASOURCE IN A MULTI CLIENT ENVIRONMENT
  30                  */
  31                 @GenericGenerator(
  32                                 name="enhanced-table",
  33                                 strategy = "org.hibernate.id.enhanced.TableGenerator",
  34                                 parameters = {
  35                                     @Parameter(name="table_name", value = "hibernate_sequences"),
  36                         @Parameter(name="optimizer", value = "pooled"),
  37                                     /* initial_value = increment_size as proposed to fix an issue with pooled optimizer
  38                                      * http://opensource.atlassian.com/projects/hibernate/browse/HHH-3608?focusedCommentId=37112&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_37112
  39                                      */
  40                                     @Parameter(name="initial_value", value= "10"),
  41                                     @Parameter(name="increment_size", value = "10"),
  42                                     /* we want to have a sequence per table */
  43                                     @Parameter(name="prefer_entity_table_as_segment_value", value="true")
  44                                 }
  45                 ),
  46                 /* new sequence generator
  47                  * Using sequence when the dialect supports it, otherwise it will emulate a sequence using a table in the db
  48                  * This method will result in database wide unique id's */
  49                 @GenericGenerator(
  50                                 name="enhanced-sequence",
  51                                 strategy = "org.hibernate.id.enhanced.SequenceStyleGenerator",
  52                                 parameters = {
  53                                 @Parameter(name="optimizer", value = "pooled"),
  54                                 /* initial_value = increment_size as proposed to fix an issue with pooled optimizer
  55                                      * http://opensource.atlassian.com/projects/hibernate/browse/HHH-3608?focusedCommentId=37112&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#action_37112
  56                                      */
  57                                     @Parameter(name="initial_value", value= "10"),
  58                                     @Parameter(name="increment_size", value = "10")
  59                             }
  60                 ),
  61                 /* A couple of old style generators */
  62                 /* generates identifiers of type long, short or int that are unique only when no other process
  63                  * is inserting data into the same table.
  64                  * DO NOT USE IN A CLUSTER OR MULTIPLE CLIENT ENVIRONMENT */
  65                 @GenericGenerator(
  66                                 name="system-increment",
  67                                 strategy = "increment"
  68                 ),
  69                 /* supports identity columns in DB2, MySQL, MS SQL Server, Sybase and HypersonicSQL.
  70                  * The returned identifier is of type long, short or int. */
  71                 @GenericGenerator(
  72                                 name="system-identity",
  73                                 strategy = "identity"
  74
  75                 ),
  76                 /* uses a hi/lo algorithm to efficiently generate identifiers of type long, short or int,
  77                  * given a table and column (by default hibernate_unique_key and next_hi respectively) as
  78                  * a source of hi values. The hi/lo algorithm generates identifiers that are unique only
  79                  * for a particular database. */
  80                 @GenericGenerator(
  81                                 name="system-hilo",
  82                                 strategy = "hilo"
  83                 ),
  84                 /* uses a sequence in DB2, PostgreSQL, Oracle, SAP DB, McKoi or a generator in Interbase.
  85                  * The returned identifier is of type long, short or int */
  86                 @GenericGenerator(
  87                                 name="system-sequence",
  88                                 strategy = "sequence"
  89                 ),
  90                 /* selects identity, sequence or hilo depending upon the capabilities of the underlying database. */
  91                 @GenericGenerator(
  92                                 name="system-native",
  93                                 strategy = "native"
  94                 )
  95         }
  96 )
  97
  98 @org.hibernate.annotations.TypeDefs( {
  99         //TODO needed ??
 100         @org.hibernate.annotations.TypeDef(name="persistentDuration", typeClass=org.jadira.usertype.dateandtime.joda.PersistentDurationAsString.class),
 101         @org.hibernate.annotations.TypeDef(name="dateTimeUserType", typeClass=org.jadira.usertype.dateandtime.joda.PersistentDateTime.class),
 102         @org.hibernate.annotations.TypeDef(name="partialUserType", typeClass=eu.etaxonomy.cdm.hibernate.PartialUserType.class),
 103         @org.hibernate.annotations.TypeDef(name="uuidUserType", typeClass=eu.etaxonomy.cdm.hibernate.UUIDUserType.class),
 104         @org.hibernate.annotations.TypeDef(name="uriUserType", typeClass=eu.etaxonomy.cdm.hibernate.URIUserType.class),
 105         @org.hibernate.annotations.TypeDef(name="enumUserType", typeClass=eu.etaxonomy.cdm.hibernate.EnumUserType.class),
 106         @org.hibernate.annotations.TypeDef(name="doiUserType", typeClass=eu.etaxonomy.cdm.hibernate.DOIUserType.class),
 107         @org.hibernate.annotations.TypeDef(name="orcidUserType", typeClass=eu.etaxonomy.cdm.hibernate.OrcidUserType.class),
 108     @org.hibernate.annotations.TypeDef(name="shiftUserType", typeClass=eu.etaxonomy.cdm.hibernate.ShiftUserType.class),
 109     @org.hibernate.annotations.TypeDef(name="bigDecimalUserType", typeClass=eu.etaxonomy.cdm.hibernate.BigDecimalUserType.class),
 110 })
 111 @org.hibernate.annotations.AnyMetaDef(name = "CdmBase" ,
 112                                               metaType="string",
 113                                               idType="integer",
 114                                               metaValues={
 115                 //Identifiable Entities
 116                 @MetaValue(value = "Institution", targetEntity = Institution.class),
 117                 @MetaValue(value = "Person", targetEntity = Person.class),
 118                 @MetaValue(value = "Team", targetEntity = Team.class),
 119         @MetaValue(value = "MediaKey", targetEntity = MediaKey.class),
 120         @MetaValue(value = "SpecimenDescription", targetEntity = SpecimenDescription.class),
 121         @MetaValue(value = "TaxonDescription", targetEntity = TaxonDescription.class),
 122         @MetaValue(value = "TaxonNameDescription", targetEntity = TaxonNameDescription.class),
 123         @MetaValue(value = "PolytomousKey", targetEntity = PolytomousKey.class),
 124         @MetaValue(value = "Media", targetEntity = Media.class),
 125         @MetaValue(value = "DnaSample", targetEntity = DnaSample.class),
 126         @MetaValue(value = "TaxonName", targetEntity = TaxonName.class),
 127         @MetaValue(value = "Collection", targetEntity = Collection.class),
 128         @MetaValue(value = "FieldUnit", targetEntity = FieldUnit.class),
 129         @MetaValue(value = "DerivedUnit", targetEntity = DerivedUnit.class),
 130         @MetaValue(value = "Reference", targetEntity = Reference.class),
 131         @MetaValue(value = "Classification", targetEntity = Classification.class),
 132         @MetaValue(value = "Synonym", targetEntity = Synonym.class),
 133         @MetaValue(value = "Taxon", targetEntity = Taxon.class),
 134
 135         @MetaValue(value = "TermTree", targetEntity = TermTree.class),
 136         @MetaValue(value = "PhylogeneticTree", targetEntity = PhylogeneticTree.class),
 137         @MetaValue(value = "MediaSpecimen", targetEntity = MediaSpecimen.class),
 138         @MetaValue(value = "TermVocabulary", targetEntity = TermVocabulary.class),
 139         @MetaValue(value = "OrderedTermVocabulary", targetEntity = OrderedTermVocabulary.class),
 140
 141         @MetaValue(value = "AnnotationType", targetEntity = AnnotationType.class),
 142         @MetaValue(value = "DefinedTerm", targetEntity = DefinedTerm.class),
 143         @MetaValue(value = "DerivationEventType", targetEntity = DerivationEventType.class),
 144         @MetaValue(value = "ExtensionType", targetEntity = ExtensionType.class),
 145         @MetaValue(value = "Feature", targetEntity = Feature.class),
 146         @MetaValue(value = "Language", targetEntity = Language.class),
 147         @MetaValue(value = "MarkerType", targetEntity = MarkerType.class),
 148         @MetaValue(value = "MeasurementUnit", targetEntity = MeasurementUnit.class),
 149         @MetaValue(value = "NamedAreaType", targetEntity = NamedAreaType.class),
 150         @MetaValue(value = "NaturalLanguageTerm", targetEntity = NaturalLanguageTerm.class),
 151         @MetaValue(value = "ReferenceSystem", targetEntity = ReferenceSystem.class),
 152         @MetaValue(value = "RightsType", targetEntity = RightsType.class),
 153         @MetaValue(value = "StatisticalMeasure", targetEntity = StatisticalMeasure.class),
 154         @MetaValue(value = "TextFormat", targetEntity = TextFormat.class),
 155
 156         @MetaValue(value = "NamedArea", targetEntity = NamedArea.class),
 157         @MetaValue(value = "Country", targetEntity = Country.class),
 158         @MetaValue(value = "NamedAreaLevel", targetEntity = NamedAreaLevel.class),
 159         @MetaValue(value = "NomenclaturalStatusType", targetEntity = NomenclaturalStatusType.class),
 160         @MetaValue(value = "OrderedTerm", targetEntity = OrderedTerm.class),
 161         @MetaValue(value = "PresenceAbsenceTerm", targetEntity = PresenceAbsenceTerm.class),
 162         @MetaValue(value = "Rank", targetEntity = Rank.class),
 163         @MetaValue(value = "HybridRelationshipType", targetEntity = HybridRelationshipType.class),
 164         @MetaValue(value = "NameRelationshipType", targetEntity = NameRelationshipType.class),
 165         @MetaValue(value = "SynonymType", targetEntity = SynonymType.class),
 166         @MetaValue(value = "TaxonRelationshipType", targetEntity = TaxonRelationshipType.class),
 167         @MetaValue(value = "State", targetEntity = State.class),
 168         @MetaValue(value = "NameTypeDesignationStatus", targetEntity = NameTypeDesignationStatus.class),
 169         @MetaValue(value = "SpecimenTypeDesignationStatus", targetEntity = SpecimenTypeDesignationStatus.class),
 170
 171
 172         //Annotatable Entities
 173         @MetaValue(value = "TextData", targetEntity = TextData.class),
 174                 @MetaValue(value = "CategoricalData", targetEntity = CategoricalData.class),
 175                 @MetaValue(value = "CommonTaxonName", targetEntity = CommonTaxonName.class),
 176                 @MetaValue(value = "Distribution", targetEntity = Distribution.class),
 177                 @MetaValue(value = "IndividualsAssociation", targetEntity = IndividualsAssociation.class),
 178                 @MetaValue(value = "QuantitativeData", targetEntity = QuantitativeData.class),
 179                 @MetaValue(value = "TaxonInteraction", targetEntity = TaxonInteraction.class),
 180
 181
 182                 @MetaValue(value = "Sequence", targetEntity = Sequence.class),
 183                 @MetaValue(value = "NomenclaturalStatus", targetEntity = NomenclaturalStatus.class),
 184
 185                 @MetaValue(value = "Annotation", targetEntity = Annotation.class),
 186
 187                 @MetaValue(value = "User", targetEntity = User.class),  //required?
 188
 189
 190                 @MetaValue(value = "AmplificationResult", targetEntity = AmplificationResult.class),
 191                 @MetaValue(value = "Amplification", targetEntity = Amplification.class),
 192         @MetaValue(value = "DerivationEvent", targetEntity = DerivationEvent.class),
 193         @MetaValue(value = "DeterminationEvent", targetEntity = DeterminationEvent.class),
 194         @MetaValue(value = "GatheringEvent", targetEntity = GatheringEvent.class),
 195         @MetaValue(value = "MaterialOrMethodEvent", targetEntity = MaterialOrMethodEvent.class),
 196         @MetaValue(value = "Cloning", targetEntity = Cloning.class),
 197         @MetaValue(value = "PreservationMethod", targetEntity = PreservationMethod.class),
 198         @MetaValue(value = "SingleRead", targetEntity = SingleRead.class),
 199         @MetaValue(value = "HomotypicalGroup", targetEntity = HomotypicalGroup.class),
 200         @MetaValue(value = "Identifier", targetEntity = Identifier.class),
 201         @MetaValue(value = "Credit", targetEntity = Credit.class),
 202         @MetaValue(value = "LanguageString", targetEntity = LanguageString.class),
 203         @MetaValue(value = "Representation", targetEntity = Representation.class),
 204         @MetaValue(value = "Rights", targetEntity = Rights.class),
 205         @MetaValue(value = "Primer", targetEntity = Primer.class),
 206         @MetaValue(value = "TaxonNode", targetEntity = TaxonNode.class),
 207         @MetaValue(value = "TaxonNodeAgentRelation", targetEntity = TaxonNodeAgentRelation.class),
 208         @MetaValue(value = "DescriptiveDataSet", targetEntity = DescriptiveDataSet.class),
 209         @MetaValue(value = "MultiAccessKey", targetEntity = MultiAccessKey.class),
 210
 211         @MetaValue(value = "DescriptionElementSource", targetEntity = DescriptionElementSource.class),
 212         @MetaValue(value = "IdentifiableSource", targetEntity = IdentifiableSource.class),
 213         @MetaValue(value = "HybridRelationship", targetEntity = HybridRelationship.class),
 214         @MetaValue(value = "NameRelationship", targetEntity = NameRelationship.class),
 215         @MetaValue(value = "TaxonRelationship", targetEntity = TaxonRelationship.class),
 216         @MetaValue(value = "NameTypeDesignation", targetEntity = NameTypeDesignation.class),
 217         @MetaValue(value = "SpecimenTypeDesignation", targetEntity = SpecimenTypeDesignation.class),
 218 })
 219 package eu.etaxonomy.cdm.model.common;
 220
 221 import org.hibernate.annotations.GenericGenerator;
 222 import org.hibernate.annotations.MetaValue;
 223 import org.hibernate.annotations.Parameter;
 224
 225 import eu.etaxonomy.cdm.model.agent.Institution;
 226 import eu.etaxonomy.cdm.model.agent.Person;
 227 import eu.etaxonomy.cdm.model.agent.Team;
 228 import eu.etaxonomy.cdm.model.description.CategoricalData;
 229 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
 230 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
 231 import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
 232 import eu.etaxonomy.cdm.model.description.Distribution;
 233 import eu.etaxonomy.cdm.model.description.Feature;
 234 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 235 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
 236 import eu.etaxonomy.cdm.model.description.MediaKey;
 237 import eu.etaxonomy.cdm.model.description.MultiAccessKey;
 238 import eu.etaxonomy.cdm.model.description.NaturalLanguageTerm;
 239 import eu.etaxonomy.cdm.model.description.PolytomousKey;
 240 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
 241 import eu.etaxonomy.cdm.model.description.QuantitativeData;
 242 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
 243 import eu.etaxonomy.cdm.model.description.State;
 244 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
 245 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 246 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
 247 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
 248 import eu.etaxonomy.cdm.model.description.TextData;
 249 import eu.etaxonomy.cdm.model.description.TextFormat;
 250 import eu.etaxonomy.cdm.model.location.Country;
 251 import eu.etaxonomy.cdm.model.location.NamedArea;
 252 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
 253 import eu.etaxonomy.cdm.model.location.NamedAreaType;
 254 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
 255 import eu.etaxonomy.cdm.model.media.Media;
 256 import eu.etaxonomy.cdm.model.media.Rights;
 257 import eu.etaxonomy.cdm.model.media.RightsType;
 258 import eu.etaxonomy.cdm.model.molecular.Amplification;
 259 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
 260 import eu.etaxonomy.cdm.model.molecular.Cloning;
 261 import eu.etaxonomy.cdm.model.molecular.DnaSample;
 262 import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;
 263 import eu.etaxonomy.cdm.model.molecular.Primer;
 264 import eu.etaxonomy.cdm.model.molecular.Sequence;
 265 import eu.etaxonomy.cdm.model.molecular.SingleRead;
 266 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
 267 import eu.etaxonomy.cdm.model.name.HybridRelationship;
 268 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
 269 import eu.etaxonomy.cdm.model.name.NameRelationship;
 270 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
 271 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
 272 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
 273 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 274 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 275 import eu.etaxonomy.cdm.model.name.Rank;
 276 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 277 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
 278 import eu.etaxonomy.cdm.model.name.TaxonName;
 279 import eu.etaxonomy.cdm.model.occurrence.Collection;
 280 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
 281 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
 282 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 283 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 284 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 285 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 286 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
 287 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 288 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
 289 import eu.etaxonomy.cdm.model.permission.User;
 290 import eu.etaxonomy.cdm.model.reference.Reference;
 291 import eu.etaxonomy.cdm.model.taxon.Classification;
 292 import eu.etaxonomy.cdm.model.taxon.Synonym;
 293 import eu.etaxonomy.cdm.model.taxon.SynonymType;
 294 import eu.etaxonomy.cdm.model.taxon.Taxon;
 295 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
 296 import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
 297 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 298 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 299 import eu.etaxonomy.cdm.model.term.DefinedTerm;
 300 import eu.etaxonomy.cdm.model.term.OrderedTerm;
 301 import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
 302 import eu.etaxonomy.cdm.model.term.Representation;
 303 import eu.etaxonomy.cdm.model.term.TermTree;
 304 import eu.etaxonomy.cdm.model.term.TermVocabulary;
 305