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Revision 4208745a

Added by Ben Clark over 15 years ago

Lots of changes, but primarily:
Enabled the marshalling / unmarshalling of LSIDAuthority
Renamed the User table to UserAccount to avoid problems on SQLServer
Major refactoring of CacheStrategyGenerators so that the generic framework extends across all IIdentifiableEntities, allowing (but not requiring) the use of @Configurable and aop to inject custom cache strategy generators at runtime

View differences:

.gitattributes
829 829 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/datagenerator/TaxonGenerator.java -text
830 830 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/hibernate/HibernateProxyHelper.java -text
831 831 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/CdmNamespacePrefixMapper.java -text
832 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/ClassAdapter.java -text
832 833 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/DateTimeAdapter.java -text
833 834 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/FormattedText.java -text
834 835 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/FormattedTextAdapter.java -text
835 836 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/LSIDAdapter.java -text
836 837 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/MultilanguageTextAdapter.java -text
837 838 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/MultilanguageTextElement.java -text
839 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/Namespace.java -text
840 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/NamespacesAdapter.java -text
841 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/NamespacesElement.java -text
838 842 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/PartialAdapter.java -text
839 843 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/TDWGNamespacePrefixMapper.java -text
840 844 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/UUIDAdapter.java -text
......
1029 1033 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/InProceedings.java -text
1030 1034 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Journal.java -text
1031 1035 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Map.java -text
1032 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/NomenclaturalReferenceHelper.java -text
1033 1036 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/Patent.java -text
1034 1037 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/PersonalCommunication.java -text
1035 1038 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/reference/PrintSeries.java -text
......
1074 1077 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/agent/PersonDefaultCacheStrategy.java -text
1075 1078 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/agent/TeamDefaultCacheStrategy.java -text
1076 1079 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/common/IIdentifiableEntityCacheStrategy.java -text
1080 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/common/IdentifiableEntityDefaultCacheStrategy.java -text
1077 1081 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/BotanicNameDefaultCacheStrategy.java -text
1078 1082 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/INameCacheStrategy.java -text
1079 1083 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/cache/name/INonViralNameCacheStrategy.java -text
......
1095 1099 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/exceptions/UnknownCdmTypeException.java -text
1096 1100 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/INonViralNameParser.java -text
1097 1101 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImpl.java -text
1102 
cdmlib-model/src/main/java/eu/etaxonomy/cdm/strategy/taxon/TaxonBaseDefaultCacheStrategy.java -text
1098 1103 
cdmlib-model/src/main/resources/log4j.properties -text
1099 1104 
cdmlib-model/src/main/resources/terms/AbsenceTerm.csv -text
1100 1105 
cdmlib-model/src/main/resources/terms/AnnotationType.csv -text
......
1177 1182 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonTest.java -text
1178 1183 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonomicViewTest.java -text
1179 1184 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/name/BotanicNameCacheStrategyTest.java -text
1180 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/name/CdDvdDefaultCacheStrategyTest.java -text
1181 1185 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/name/NonViralNameDefaultCacheStrategyTest.java -text
1182 1186 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/name/ZoologicalNameCacheStrategyTest.java -text
1187 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/cache/reference/CdDvdDefaultCacheStrategyTest.java -text
1183 1188 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/strategy/parser/NonViralNameParserImplTest.java -text
1184 1189 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/TestFullReferenceParser.java -text
1185 1190 
cdmlib-model/src/test/java/eu/etaxonomy/cdm/test/function/TestModel.java -text
cdmlib-model/pom.xml
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    <plugins>
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      <plugin>
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        <artifactId>maven-antrun-plugin</artifactId>
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<!--        <executions>-->
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<!--          <execution>-->
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<!--            <id>aspectj-main</id>-->
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<!--            <phase>process-sources</phase>-->
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<!--            <goals>-->
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<!--              <goal>run</goal>-->
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<!--            <configuration>-->
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<!--              <tasks>-->
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<!--                <taskdef classname="org.aspectj.tools.ant.taskdefs.AjcTask" name="iajc">-->
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<!--                  <classpath refid="maven.plugin.classpath" />-->
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<!--                </taskdef>-->
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<!--                <iajc verbose="false" source="1.5" destDir="target/classes">-->
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<!--                  <classpath refid="maven.plugin.classpath" />-->
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<!--                  <classpath refid="maven.compile.classpath" />-->
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<!--                  <sourceroots>-->
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<!--                    <pathelement location="src/main/java" />-->
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<!--                  </sourceroots>-->
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<!--            </configuration>-->
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<!--          </execution>-->
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<!--          <execution>-->
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<!--            <id>aspectj-test</id>-->
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<!--            <phase>process-test-sources</phase>-->
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<!--            <goals>-->
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<!--              <goal>run</goal>-->
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<!--            <configuration>-->
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<!--              <tasks>-->
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<!--                <taskdef classname="org.aspectj.tools.ant.taskdefs.AjcTask" name="iajc">-->
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<!--                  <classpath refid="maven.plugin.classpath" />-->
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<!--                </taskdef>-->
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<!--                <iajc verbose="false" source="1.5" destDir="target/test-classes">-->
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<!--                  <classpath refid="maven.plugin.classpath" />-->
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<!--                  <classpath refid="maven.compile.classpath" />-->
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<!--                  <classpath refid="maven.test.classpath" />-->
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<!--                  <sourceroots>-->
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<!--                    <pathelement location="src/test/java" />-->
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<!--                  </sourceroots>-->
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<!--                </iajc>-->
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<!--              </tasks>-->
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<!--            </configuration>-->
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<!--          </execution>-->
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<!--        </executions>-->
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        <executions>
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          <execution>
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            <id>aspectj-main</id>
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            <phase>process-sources</phase>
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            <goals>
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              <goal>run</goal>
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            </goals>
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            <configuration>
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              <tasks>
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                <property name="spring.aspects.jar" value="${settings.localRepository}/org/springframework/spring-aspects/2.5.6/spring-aspects-2.5.6.jar"/>
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                <path id="aspectPath">
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                  <pathelement location="${spring.aspects.jar}"/>
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                </path>
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                <taskdef classname="org.aspectj.tools.ant.taskdefs.AjcTask" name="iajc">
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                  <classpath refid="maven.plugin.classpath" />
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                </taskdef>
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                <iajc verbose="false" source="1.5" destDir="target/classes"
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                  aspectPathRef="aspectPath">
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                  <classpath refid="maven.plugin.classpath" />
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                  <classpath refid="maven.compile.classpath" />
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                  <sourceroots>
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                    <pathelement location="src/main/java" />
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                  </sourceroots>
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                </iajc>
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              </tasks>
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            </configuration>
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          </execution>
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          <execution>
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            <id>aspectj-test</id>
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            <phase>process-test-sources</phase>
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            <goals>
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              <goal>run</goal>
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            </goals>
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            <configuration>
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              <tasks>
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                <taskdef classname="org.aspectj.tools.ant.taskdefs.AjcTask" name="iajc">
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                  <classpath refid="maven.plugin.classpath" />
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                </taskdef>
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                <iajc verbose="false" source="1.5" destDir="target/test-classes">
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                  <classpath refid="maven.plugin.classpath" />
60 
                  <classpath refid="maven.compile.classpath" />
61 
                  <classpath refid="maven.test.classpath" />
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                  <sourceroots>
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                    <pathelement location="src/test/java" />
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                  </sourceroots>
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                </iajc>
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              </tasks>
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            </configuration>
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          </execution>
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        </executions>
65 70 
        <dependencies>
66 71 
          <dependency>
67 72 
            <groupId>org.aspectj</groupId>
68 73 
            <artifactId>aspectjtools</artifactId>
69 
            <version>1.5.4</version>
74 
            <version>1.6.3</version>
70 75 
          </dependency>
71 76 
          <dependency>
72 77 
            <groupId>org.aspectj</groupId>
73 78 
            <artifactId>aspectjrt</artifactId>
74 
            <version>1.5.4</version>
79 
            <version>1.6.3</version>
75 80 
          </dependency>
76 81 
        </dependencies>
77 82 
      </plugin>
......
138 143 
      <groupId>org.springframework</groupId>
139 144 
      <artifactId>spring-test</artifactId>
140 145 
    </dependency>
146 
    <dependency>
147 
      <groupId>org.springframework</groupId>
148 
      <artifactId>spring-aspects</artifactId>
149 
    </dependency>
141 150 
    <dependency>
142 151 
      <groupId>net.sf.opencsv</groupId>
143 152 
      <artifactId>opencsv</artifactId>
cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/ClassAdapter.java
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package eu.etaxonomy.cdm.jaxb;
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import javax.xml.bind.annotation.adapters.XmlAdapter;


  		




  
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public class ClassAdapter extends XmlAdapter<String, Class> {


  		




  
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	@Override


  		




  
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	public String marshal(Class clazz) throws Exception {


  		




  
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		return clazz.getCanonicalName();


  		




  
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	}


  		




  
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	@Override


  		




  
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	public Class unmarshal(String string) throws Exception {


  		




  
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		return Class.forName(string);


  		




  
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	}


  		




  
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}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/Namespace.java
    
  





  
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package eu.etaxonomy.cdm.jaxb;


  		




  
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import javax.xml.bind.annotation.XmlAccessType;


  		




  
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import javax.xml.bind.annotation.XmlAccessorType;


  		




  
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import javax.xml.bind.annotation.XmlElement;


  		




  
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import javax.xml.bind.annotation.XmlType;


  		




  
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import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;


  		




  
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import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;


  		




  
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@XmlAccessorType(XmlAccessType.FIELD)


  		




  
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@XmlType(name = "Namespace", namespace="http://etaxonomy.eu/cdm/model/common/1.0", propOrder = {


  		




  
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    "nspace",


  		




  
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	"clazz"


  		




  
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})


  		




  
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public class Namespace {


  		




  
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	@XmlElement(name = "NSpace", namespace="http://etaxonomy.eu/cdm/model/common/1.0", required = true)


  		




  
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	private String nspace;


  		




  
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	@XmlElement(name = "Class", namespace="http://etaxonomy.eu/cdm/model/common/1.0", required = true)


  		




  
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	@XmlJavaTypeAdapter(ClassAdapter.class)


  		




  
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	private Class<? extends IIdentifiableEntity> clazz;


  		




  
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	public String getNSpace() {


  		




  
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		return nspace;


  		




  
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	}


  		




  
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	public void setNSpace(String nspace) {


  		




  
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		this.nspace = nspace;


  		




  
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	}


  		




  
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	public Class<? extends IIdentifiableEntity> getClazz() {


  		




  
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		return clazz;


  		




  
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	}


  		




  
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	public void setClazz(Class<? extends IIdentifiableEntity> clazz) {


  		




  
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		this.clazz = clazz;


  		




  
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	}


  		




  
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}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/NamespacesAdapter.java
    
  





  
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/**


  		




  
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* Copyright (C) 2009 EDIT


  		




  
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* European Distributed Institute of Taxonomy 


  		




  
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* http://www.e-taxonomy.eu


  		




  
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* 


  		




  
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* The contents of this file are subject to the Mozilla Public License Version 1.1


  		




  
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* See LICENSE.TXT at the top of this package for the full license terms.


  		




  
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*/


  		




  
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package eu.etaxonomy.cdm.jaxb;


  		




  
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import java.util.Map;


  		




  
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import java.util.concurrent.ConcurrentHashMap;


  		




  
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import javax.xml.bind.annotation.adapters.XmlAdapter;


  		




  
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import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;


  		




  
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/**


  		




  
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 * @author a.babadshanjan


  		




  
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 * @version 1.0


  		




  
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 */


  		




  
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public class NamespacesAdapter extends XmlAdapter<NamespacesElement, Map<String,Class<? extends IIdentifiableEntity>>> {


  		




  
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	@Override


  		




  
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	public NamespacesElement marshal(Map<String,Class<? extends IIdentifiableEntity>> value)


  		




  
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			throws Exception {


  		




  
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		NamespacesElement namespacesElement = new NamespacesElement();


  		




  
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		for(String s : value.keySet()) {


  		




  
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			Namespace namespace = new Namespace();


  		




  
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			namespace.setNSpace(s);


  		




  
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			namespace.setClazz(value.get(s));


  		




  
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			namespacesElement.getNamespace().add(namespace);


  		




  
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		}


  		




  
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		return namespacesElement;


  		




  
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	}


  		




  
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    @Override


  		




  
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	public Map<String,Class<? extends IIdentifiableEntity>> unmarshal(NamespacesElement value)


  		




  
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			throws Exception {


  		




  
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        Map<String, Class<? extends IIdentifiableEntity>> map = new ConcurrentHashMap<String, Class<? extends IIdentifiableEntity>>();


  		




  
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		for(Namespace n : value.getNamespace()) {


  		




  
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			map.put(n.getNSpace(),n.getClazz());


  		




  
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		}


  		




  
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		return map;


  		




  
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	}


  		




  
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}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/NamespacesElement.java
    
  





  
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//


  		




  
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// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.1-b02-fcs 


  		




  
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// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 


  		




  
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// Any modifications to this file will be lost upon recompilation of the source schema. 


  		




  
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// Generated on: 2007.12.21 at 08:13:35 PM GMT 


  		




  
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//


  		




  
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package eu.etaxonomy.cdm.jaxb;


  		




  
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import java.util.ArrayList;


  		




  
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import java.util.List;


  		




  
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import javax.xml.bind.annotation.XmlAccessType;


  		




  
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import javax.xml.bind.annotation.XmlAccessorType;


  		




  
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import javax.xml.bind.annotation.XmlElement;


  		




  
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import javax.xml.bind.annotation.XmlType;


  		




  
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/**


  		




  
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 * <p>Java class for Namespaces complex type.


  		




  
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 */


  		




  
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@XmlAccessorType(XmlAccessType.FIELD)


  		




  
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@XmlType(name = "Namespaces", namespace="http://etaxonomy.eu/cdm/model/common/1.0", propOrder = {


  		




  
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    "namespace"


  		




  
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})


  		




  
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public class NamespacesElement {


  		




  
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    @XmlElement(name = "Namespace", namespace="http://etaxonomy.eu/cdm/model/common/1.0", required = true)


  		




  
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    protected List<Namespace> namespace = new ArrayList<Namespace>();


  		




  
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    /**


  		




  
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     * Gets the value of the languageString property.


  		




  
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     * 


  		




  
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     * <p>


  		




  
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     * This accessor method returns a reference to the live list,


  		




  
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     * not a snapshot. Therefore any modification you make to the


  		




  
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     * returned list will be present inside the JAXB object.


  		




  
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     * This is why there is not a <CODE>set</CODE> method for the languageString property.


  		




  
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     * 


  		




  
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     * <p>


  		




  
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     * For example, to add a new item, do as follows:


  		




  
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     * <pre>


  		




  
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     *    getLanguageString().add(newItem);


  		




  
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     * </pre>


  		




  
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     * 


  		




  
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     * 


  		




  
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     * <p>


  		




  
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     * Objects of the following type(s) are allowed in the list


  		




  
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     * {@link Namespace }


  		




  
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     * 


  		




  
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     * 


  		




  
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     */


  		




  
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    public List<Namespace> getNamespace() {


  		




  
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        return this.namespace;


  		




  
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    }


  		




  
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}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/jaxb/PartialAdapter.java
    
  





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				dateTimeFieldTypes[1] = DateTimeFieldType.monthOfYear();


  		




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				values[1] = Integer.parseInt(matcher.group(2));


  		




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			case 1:


  		




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				dateTimeFieldTypes[0] = DateTimeFieldType.yearOfEra();


  		




  
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				dateTimeFieldTypes[0] = DateTimeFieldType.year();


  		




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				values[0] = Integer.parseInt(matcher.group(1));


  		




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			}


  		




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			return new Partial(dateTimeFieldTypes, values);


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/AgentBase.java
    
  





  11
  11
  
    

  		




  12
  12
  
    
import javax.persistence.Embedded;


  		




  13
  13
  
    
import javax.persistence.Entity;


  		




  
  14
  
    
import javax.persistence.Transient;


  		




  14
  15
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  15
  16
  
    
import javax.xml.bind.annotation.XmlAccessorType;


  		




  16
  17
  
    
import javax.xml.bind.annotation.XmlElement;


  		




  
  18
  
    
import javax.xml.bind.annotation.XmlTransient;


  		




  17
  19
  
    
import javax.xml.bind.annotation.XmlType;


  		




  18
  20
  
    

  		




  19
  21
  
    
import org.hibernate.annotations.Index;


  		




  ......




  21
  23
  
    
import org.hibernate.envers.Audited;


  		




  22
  24
  
    

  		




  23
  25
  
    
import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;


  		




  
  26
  
    
import eu.etaxonomy.cdm.strategy.cache.agent.INomenclaturalAuthorCacheStrategy;


  		




  
  27
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  24
  28
  
    

  		




  25
  29
  
    
/**


  		




  26
  30
  
    
 * The upmost (abstract) class for agents such as persons, teams or institutions.


  		




  ......




  40
  44
  
    
@Entity


  		




  41
  45
  
    
@Audited


  		




  42
  46
  
    
@Table(appliesTo="AgentBase", indexes = { @Index(name = "agentTitleCacheIndex", columnNames = { "titleCache" }) })


  		




  43
  
  
    
public abstract class AgentBase extends IdentifiableMediaEntity{


  		




  
  47
  
    
public abstract class AgentBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S>{


  		




  44
  48
  
    

  		




  45
  49
  
    
	/**


  		




  46
  50
  
    
	 * 


  		




  ......




  66
  70
  
    
	public void setContact(Contact contact){


  		




  67
  71
  
    
		this.contact = contact;


  		




  68
  72
  
    
	}


  		




  69
  
  
    

  		




  70
  73
  
    
}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/Contact.java
    
  





  9
  9
  
    

  		




  10
  10
  
    
package eu.etaxonomy.cdm.model.agent;


  		




  11
  11
  
    

  		




  
  12
  
    
import java.io.Serializable;


  		




  12
  13
  
    
import java.util.ArrayList;


  		




  13
  14
  
    
import java.util.HashSet;


  		




  14
  15
  
    
import java.util.List;


  		




  ......




  56
  57
  
    
@XmlRootElement(name = "Contact")


  		




  57
  58
  
    
@Embeddable


  		




  58
  59
  
    
@Audited


  		




  59
  
  
    
public class Contact {


  		




  
  60
  
    
public class Contact implements Serializable {


  		




  60
  61
  
    
	private static final long serialVersionUID = -1851305307069277625L;


  		




  61
  62
  
    
	private static final Logger logger = Logger.getLogger(Contact.class);


  		




  62
  63
  
    
	


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/Institution.java
    
  





  17
  17
  
    
import javax.persistence.FetchType;


  		




  18
  18
  
    
import javax.persistence.ManyToMany;


  		




  19
  19
  
    
import javax.persistence.ManyToOne;


  		




  
  20
  
    
import javax.persistence.Transient;


  		




  20
  21
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  21
  22
  
    
import javax.xml.bind.annotation.XmlAccessorType;


  		




  22
  23
  
    
import javax.xml.bind.annotation.XmlElement;


  		




  ......




  24
  25
  
    
import javax.xml.bind.annotation.XmlIDREF;


  		




  25
  26
  
    
import javax.xml.bind.annotation.XmlRootElement;


  		




  26
  27
  
    
import javax.xml.bind.annotation.XmlSchemaType;


  		




  
  28
  
    
import javax.xml.bind.annotation.XmlTransient;


  		




  27
  29
  
    
import javax.xml.bind.annotation.XmlType;


  		




  28
  30
  
    

  		




  29
  31
  
    
import org.apache.log4j.Logger;


  		




  30
  32
  
    
import org.hibernate.annotations.Cascade;


  		




  31
  33
  
    
import org.hibernate.annotations.CascadeType;


  		




  32
  34
  
    
import org.hibernate.envers.Audited;


  		




  
  35
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  
  36
  
    

  		




  
  37
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  
  38
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;


  		




  33
  39
  
    

  		




  34
  40
  
    
/**


  		




  35
  41
  
    
 * This class represents public or private institutions.


  		




  ......




  55
  61
  
    
@XmlRootElement(name = "Institution")


  		




  56
  62
  
    
@Entity


  		




  57
  63
  
    
@Audited


  		




  58
  
  
    
public class Institution extends AgentBase {


  		




  
  64
  
    
@Configurable


  		




  
  65
  
    
public class Institution extends AgentBase<IIdentifiableEntityCacheStrategy<Institution>> {


  		




  59
  66
  
    
	private static final long serialVersionUID = -951321271656955808L;


  		




  60
  67
  
    
	public static final Logger logger = Logger.getLogger(Institution.class);


  		




  61
  68
  
    
	


  		




  ......




  92
  99
  
    
	 */


  		




  93
  100
  
    
	public Institution() {


  		




  94
  101
  
    
		super();


  		




  
  102
  
    
		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Institution>();


  		




  95
  103
  
    
	}


  		




  96
  104
  
    

  		




  97
  105
  
    
	/** 


  		




  ......




  175
  183
  
    
	public void setName(String name){


  		




  176
  184
  
    
		this.name = name;


  		




  177
  185
  
    
	}


  		




  178
  
  
    

  		




  179
  
  
    
	/**


  		




  180
  
  
    
	 * Generates the identification string for this institution.


  		




  181
  
  
    
	 * The string is based on its name and code as well as on the name and code of


  		




  182
  
  
    
	 * its parent institution, if existing.


  		




  183
  
  
    
	 * This method overrides {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() generateTitle}.


  		




  184
  
  
    
	 * The result might be kept as {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#setTitleCache(String) titleCache} if the


  		




  185
  
  
    
	 * flag {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#protectedTitleCache protectedTitleCache} is not set.


  		




  186
  
  
    
	 * 


  		




  187
  
  
    
	 * @return  the identification string


  		




  188
  
  
    
	 */


  		




  189
  
  
    
	@Override


  		




  190
  
  
    
	public String generateTitle(){


  		




  191
  
  
    
		return "";


  		




  192
  
  
    
	}


  		




  193
  
  
    

  		




  194
  186
  
    
}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/Person.java
    
  





  17
  17
  
    
import org.hibernate.annotations.Cascade;


  		




  18
  18
  
    
import org.hibernate.annotations.CascadeType;


  		




  19
  19
  
    
import org.hibernate.envers.Audited;


  		




  
  20
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  20
  21
  
    

  		




  21
  22
  
    
import java.util.*;


  		




  22
  23
  
    
import javax.persistence.*;


  		




  ......




  62
  63
  
    
@XmlRootElement(name = "Person")


  		




  63
  64
  
    
@Entity


  		




  64
  65
  
    
@Audited


  		




  
  66
  
    
@Configurable


  		




  65
  67
  
    
public class Person extends TeamOrPersonBase<Person> {


  		




  66
  68
  
    
	private static final long serialVersionUID = 4153566493065539763L;


  		




  67
  69
  
    
	public static final Logger logger = Logger.getLogger(Person.class);


  		




  ......




  318
  320
  
    
		this.lifespan = lifespan;


  		




  319
  321
  
    
	}


  		




  320
  322
  
    

  		




  321
  
  
    
	/**


  		




  322
  
  
    
	 * Generates the "full" name string of <i>this</i> person according to the strategy


  		




  323
  
  
    
	 * defined in {@link eu.etaxonomy.cdm.strategy.cache.agent.PersonDefaultCacheStrategy PersonDefaultCacheStrategy}.


  		




  324
  
  
    
	 * The used attributes are:


  		




  325
  
  
    
	 * {@link #getPrefix() prefix}, {@link #getFirstname() firstname}, {@link #getLastname() lastname} and {@link #getSuffix() suffix}.


  		




  326
  
  
    
	 * This method overrides {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() generateTitle}.


  		




  327
  
  
    
	 * The result might be kept as {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#setTitleCache(String) titleCache} if the


  		




  328
  
  
    
	 * flag {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#protectedTitleCache protectedTitleCache} is not set.


  		




  329
  
  
    
	 * 


  		




  330
  
  
    
	 * @return  the string with the full name of <i>this</i> person


  		




  331
  
  
    
	 */


  		




  332
  
  
    
	@Override


  		




  333
  
  
    
	public String generateTitle() {


  		




  334
  
  
    
		String title = null;


  		




  335
  
  
    
		if (cacheStrategy != null) {


  		




  336
  
  
    
		title = cacheStrategy.getTitleCache(this);


  		




  337
  
  
    
		} 


  		




  338
  
  
    
        return title;


  		




  339
  
  
    
	}


  		




  
  323
  
    
//	/**


  		




  
  324
  
    
//	 * Generates the "full" name string of <i>this</i> person according to the strategy


  		




  
  325
  
    
//	 * defined in {@link eu.etaxonomy.cdm.strategy.cache.agent.PersonDefaultCacheStrategy PersonDefaultCacheStrategy}.


  		




  
  326
  
    
//	 * The used attributes are:


  		




  
  327
  
    
//	 * {@link #getPrefix() prefix}, {@link #getFirstname() firstname}, {@link #getLastname() lastname} and {@link #getSuffix() suffix}.


  		




  
  328
  
    
//	 * This method overrides {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() generateTitle}.


  		




  
  329
  
    
//	 * The result might be kept as {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#setTitleCache(String) titleCache} if the


  		




  
  330
  
    
//	 * flag {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#protectedTitleCache protectedTitleCache} is not set.


  		




  
  331
  
    
//	 * 


  		




  
  332
  
    
//	 * @return  the string with the full name of <i>this</i> person


  		




  
  333
  
    
//	 */


  		




  
  334
  
    
//	@Override


  		




  
  335
  
    
//	public String generateTitle() {


  		




  
  336
  
    
//		String title = null;


  		




  
  337
  
    
//		if (cacheStrategy != null) {


  		




  
  338
  
    
//		title = cacheStrategy.getTitleCache(this);


  		




  
  339
  
    
//		} 


  		




  
  340
  
    
//        return title;


  		




  
  341
  
    
//	}


  		




  340
  342
  
    

  		




  341
  343
  
    
}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/Team.java
    
  





  30
  30
  
    
import org.hibernate.annotations.CascadeType;


  		




  31
  31
  
    
import org.hibernate.annotations.IndexColumn;


  		




  32
  32
  
    
import org.hibernate.envers.Audited;


  		




  
  33
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  33
  34
  
    

  		




  34
  35
  
    
import eu.etaxonomy.cdm.strategy.cache.agent.TeamDefaultCacheStrategy;


  		




  35
  36
  
    

  		




  ......




  60
  61
  
    
@XmlRootElement


  		




  61
  62
  
    
@Entity


  		




  62
  63
  
    
@Audited


  		




  
  64
  
    
@Configurable


  		




  63
  65
  
    
public class Team extends TeamOrPersonBase<Team> {


  		




  64
  66
  
    
	private static final long serialVersionUID = 97640416905934622L;


  		




  65
  67
  
    
	public static final Logger logger = Logger.getLogger(Team.class);


  		




  ......




  156
  158
  
    
	 * 


  		




  157
  159
  
    
	 * @return  a string which identifies <i>this</i> team


  		




  158
  160
  
    
	 */


  		




  159
  
  
    
	@Override


  		




  160
  
  
    
	public String generateTitle() {


  		




  161
  
  
    
		return cacheStrategy.getTitleCache(this);


  		




  162
  
  
    
	}


  		




  
  161
  
    
//	@Override


  		




  
  162
  
    
//	public String generateTitle() {


  		




  
  163
  
    
//		return cacheStrategy.getTitleCache(this);


  		




  
  164
  
    
//	}


  		




  163
  165
  
    
	


  		




  164
  166
  
    
	


  		




  165
  167
  
    
	/**


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/agent/TeamOrPersonBase.java
    
  





  36
  36
  
    
})


  		




  37
  37
  
    
@Entity


  		




  38
  38
  
    
@Audited


  		




  39
  
  
    
public abstract class TeamOrPersonBase<T extends TeamOrPersonBase<?>> extends AgentBase implements INomenclaturalAuthor {


  		




  
  39
  
    
public abstract class TeamOrPersonBase<T extends TeamOrPersonBase<?>> extends AgentBase<INomenclaturalAuthorCacheStrategy<T>> implements INomenclaturalAuthor {


  		




  40
  40
  
    
	private static final long serialVersionUID = 5216821307314001961L;


  		




  41
  41
  
    
	public static final Logger logger = Logger.getLogger(TeamOrPersonBase.class);


  		




  42
  42
  
    

  		




  43
  43
  
    
	@XmlElement(name="NomenclaturalTitle")


  		




  44
  44
  
    
	protected String nomenclaturalTitle;


  		




  45
  
  
    
	


  		




  46
  
  
    
	@XmlTransient


  		




  47
  
  
    
	@Transient


  		




  48
  
  
    
	protected INomenclaturalAuthorCacheStrategy<T> cacheStrategy;


  		




  49
  45
  
    

  		




  50
  46
  
    
	/**


  		




  51
  47
  
    
	 * Returns the identification string (nomenclatural abbreviation) used in


  		




  ......




  63
  59
  
    
	public void setNomenclaturalTitle(String nomenclaturalTitle) {


  		




  64
  60
  
    
		this.nomenclaturalTitle = nomenclaturalTitle;


  		




  65
  61
  
    
	}


  		




  66
  
  
    

  		




  67
  62
  
    
}


  		












  

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





  71
  71
  
    
		}


  		




  72
  72
  
    
	}


  		




  73
  73
  
    
	public void removeMarker(Marker marker){


  		




  74
  
  
    
		marker.setMarkedObj(null);


  		




  
  74
  
    
		if(this.markers.contains(marker)) {


  		




  
  75
  
    
		    this.markers.remove(marker);


  		




  
  76
  
    
		    marker.setMarkedObj(null);


  		




  
  77
  
    
		}


  		




  75
  78
  
    
	}


  		




  76
  79
  
    

  		




  77
  80
  
    
//*************** ANNOTATIONS **********************************************


  		




  ......




  87
  90
  
    
	}


  		




  88
  91
  
    
	


  		




  89
  92
  
    
	public void removeAnnotation(Annotation annotation){


  		




  90
  
  
    
		this.annotations.remove(annotation);


  		




  91
  
  
    
		annotation.setAnnotatedObj(null);


  		




  
  93
  
    
		if(this.annotations.contains(annotation)) {


  		




  
  94
  
    
		    this.annotations.remove(annotation);


  		




  
  95
  
    
		    annotation.setAnnotatedObj(null);


  		




  
  96
  
    
		}


  		




  92
  97
  
    
	}


  		




  93
  98
  
    
	


  		




  94
  99
  
    
//********************** CLONE *****************************************/


  		












  

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





  20
  20
  
    
import javax.persistence.FetchType;


  		




  21
  21
  
    
import javax.persistence.MappedSuperclass;


  		




  22
  22
  
    
import javax.persistence.OneToMany;


  		




  
  23
  
    
import javax.persistence.Transient;


  		




  23
  24
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  24
  25
  
    
import javax.xml.bind.annotation.XmlAccessorType;


  		




  25
  26
  
    
import javax.xml.bind.annotation.XmlElement;


  		




  ......




  43
  44
  
    
import eu.etaxonomy.cdm.model.name.NonViralName;


  		




  44
  45
  
    
import eu.etaxonomy.cdm.model.name.TaxonNameBase;


  		




  45
  46
  
    
import eu.etaxonomy.cdm.model.taxon.TaxonBase;


  		




  
  47
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  46
  48
  
    

  		




  47
  49
  
    
/**


  		




  48
  50
  
    
 * Superclass for the primary CDM classes that can be referenced from outside via LSIDs and contain a simple generated title string as a label for human reading.


  		




  ......




  67
  69
  
    
    "sources"


  		




  68
  70
  
    
})


  		




  69
  71
  
    
@MappedSuperclass


  		




  70
  
  
    
public abstract class IdentifiableEntity extends AnnotatableEntity 


  		




  
  72
  
    
public abstract class IdentifiableEntity<S extends IIdentifiableEntityCacheStrategy> extends AnnotatableEntity 


  		




  71
  73
  
    
implements ISourceable, IIdentifiableEntity, Comparable<IdentifiableEntity> {


  		




  72
  74
  
    
	private static final long serialVersionUID = -5610995424730659058L;


  		




  73
  75
  
    
	private static final Logger logger = Logger.getLogger(IdentifiableEntity.class);


  		




  ......




  119
  121
  
    
    @OneToMany(fetch = FetchType.LAZY)		


  		




  120
  122
  
    
	@Cascade({CascadeType.SAVE_UPDATE})


  		




  121
  123
  
    
	private Set<OriginalSource> sources = new HashSet<OriginalSource>();


  		




  122
  
  
    

  		




  
  124
  
    
    


  		




  
  125
  
    
    @XmlTransient


  		




  
  126
  
    
	@Transient


  		




  
  127
  
    
	protected S cacheStrategy;


  		




  123
  128
  
    
	


  		




  124
  129
  
    
	/* (non-Javadoc)


  		




  125
  130
  
    
	 * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getLsid()


  		




  ......




  144
  149
  
    
		return null;


  		




  145
  150
  
    
	}


  		




  146
  151
  
    

  		




  147
  
  
    
	/* (non-Javadoc)


  		




  148
  
  
    
	 * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#generateTitle()


  		




  149
  
  
    
	 */


  		




  150
  
  
    
	public abstract String generateTitle();


  		




  151
  
  
    

  		




  152
  152
  
    
	/* (non-Javadoc)


  		




  153
  153
  
    
	 * @see eu.etaxonomy.cdm.model.common.IIdentifiableEntity#getTitleCache()


  		




  154
  154
  
    
	 */


  		




  ......




  426
  426
  
    
		}


  		




  427
  427
  
    
		return result;


  		




  428
  428
  
    
	}


  		




  
  429
  
    
	


  		




  
  430
  
    
	/**


  		




  
  431
  
    
	 * Returns the {@link eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy cache strategy} used to generate


  		




  
  432
  
    
	 * several strings corresponding to <i>this</i> identifiable entity


  		




  
  433
  
    
	 * (in particular taxon name caches and author strings).


  		




  
  434
  
    
	 * 


  		




  
  435
  
    
	 * @return  the cache strategy used for <i>this</i> identifiable entity


  		




  
  436
  
    
	 * @see     eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy


  		




  
  437
  
    
	 */


  		




  
  438
  
    
	public S getCacheStrategy() {


  		




  
  439
  
    
		return this.cacheStrategy;


  		




  
  440
  
    
	}


  		




  
  441
  
    
	/** 


  		




  
  442
  
    
	 * @see 	#getCacheStrategy()


  		




  
  443
  
    
	 */


  		




  
  444
  
    
	


  		




  
  445
  
    
	public void setCacheStrategy(S cacheStrategy) {


  		




  
  446
  
    
		this.cacheStrategy = cacheStrategy;


  		




  
  447
  
    
	}


  		




  
  448
  
    
	


  		




  
  449
  
    
	public String generateTitle() {


  		




  
  450
  
    
		if (cacheStrategy == null){


  		




  
  451
  
    
			logger.warn("No CacheStrategy defined for "+ this.getClass() + ": " + this.getUuid());


  		




  
  452
  
    
			return null;


  		




  
  453
  
    
		}else{


  		




  
  454
  
    
			return cacheStrategy.getTitleCache(this);


  		




  
  455
  
    
		}


  		




  
  456
  
    
	}


  		




  429
  457
  
    
}


  		












  

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





  1
  1
  
    
package eu.etaxonomy.cdm.model.common;


  		




  2
  2
  
    

  		




  
  3
  
    
import java.io.Serializable;


  		




  3
  4
  
    
import java.util.NoSuchElementException;


  		




  4
  5
  
    
import java.util.StringTokenizer;


  		




  5
  6
  
    

  		




  6
  7
  
    
import javax.persistence.Embeddable;


  		




  7
  
  
    
import javax.persistence.FetchType;


  		




  8
  
  
    
import javax.persistence.ManyToOne;


  		




  9
  8
  
    

  		




  10
  9
  
    
import com.ibm.lsid.MalformedLSIDException;


  		




  11
  10
  
    

  		




  ......




  19
  18
  
    
 * @see com.ibm.lsid.client.LSID


  		




  20
  19
  
    
 */


  		




  21
  20
  
    
@Embeddable


  		




  22
  
  
    
public class LSID {


  		




  
  21
  
    
public class LSID implements Serializable {


  		




  23
  22
  
    

  		




  24
  23
  
    
	private String lsid;


  		




  25
  24
  
    
	


  		












  

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





  7
  7
  
    
import javax.persistence.FetchType;


  		




  8
  8
  
    
import javax.persistence.Transient;


  		




  9
  9
  
    
import javax.wsdl.Definition;


  		




  
  10
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  
  11
  
    
import javax.xml.bind.annotation.XmlAccessorType;


  		




  
  12
  
    
import javax.xml.bind.annotation.XmlElement;


  		




  
  13
  
    
import javax.xml.bind.annotation.XmlRootElement;


  		




  
  14
  
    
import javax.xml.bind.annotation.XmlTransient;


  		




  
  15
  
    
import javax.xml.bind.annotation.XmlType;


  		




  
  16
  
    
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;


  		




  10
  17
  
    

  		




  11
  18
  
    
import org.hibernate.annotations.CollectionOfElements;


  		




  12
  19
  
    
import org.hibernate.annotations.NaturalId;


  		




  13
  20
  
    
import org.hibernate.annotations.Type;


  		




  14
  21
  
    
import org.hibernate.annotations.TypeDef;


  		




  15
  22
  
    
import org.hibernate.annotations.TypeDefs;


  		




  
  23
  
    
import org.hibernate.envers.Audited;


  		




  16
  24
  
    

  		




  17
  25
  
    
import com.ibm.lsid.MalformedLSIDException;


  		




  18
  26
  
    

  		




  
  27
  
    
import eu.etaxonomy.cdm.jaxb.NamespacesAdapter;


  		




  
  28
  
    

  		




  
  29
  
    
@XmlAccessorType(XmlAccessType.FIELD)


  		




  
  30
  
    
@XmlType(name = "LSIDAuthority", propOrder = {


  		




  
  31
  
    
		"authority",


  		




  
  32
  
    
		"server",


  		




  
  33
  
    
		"port",


  		




  
  34
  
    
		"url",


  		




  
  35
  
    
		"namespaces"


  		




  
  36
  
    
})


  		




  
  37
  
    
@XmlRootElement(name = "LSIDAuthority")


  		




  19
  38
  
    
@Entity


  		




  20
  39
  
    
@TypeDefs(@TypeDef(name="wsdlDefinitionUserType", typeClass=WSDLDefinitionUserType.class))


  		




  21
  40
  
    
public class LSIDAuthority extends CdmBase {


  		




  ......




  30
  49
  
    
	private static final String AUTHORITY_PROTOCOL="http";


  		




  31
  50
  
    
    private static final String AUTHORITY_PATH="/authority/";


  		




  32
  51
  
    

  		




  
  52
  
    
    @XmlElement(name = "Authority")


  		




  33
  53
  
    
    @NaturalId


  		




  34
  54
  
    
	private String authority;


  		




  35
  55
  
    
	


  		




  36
  56
  
    
	// the resolved components of the lsid


  		




  
  57
  
    
    @XmlElement(name = "Server")


  		




  37
  58
  
    
	private String server;


  		




  
  59
  
    
    @XmlElement(name = "Port")


  		




  38
  60
  
    
	private int port = -1;


  		




  
  61
  
    
    @XmlElement(name = "Url")


  		




  39
  62
  
    
	private String url;


  		




  40
  63
  
    
	


  		




  41
  64
  
    
	// the wsdl describing how to invoke operations on the authority


  		




  
  65
  
    
    @XmlTransient


  		




  42
  66
  
    
	@Type(type = "wsdlDefinitionUserType")


  		




  43
  67
  
    
	private Definition authorityWSDL;


  		




  44
  68
  
    
	


  		




  
  69
  
    
    @XmlElement(name = "Namespaces")


  		




  
  70
  
    
    @XmlJavaTypeAdapter(NamespacesAdapter.class)


  		




  45
  71
  
    
	@CollectionOfElements(fetch = FetchType.LAZY)


  		




  46
  72
  
    
	private Map<String,Class<? extends IIdentifiableEntity>> namespaces = new HashMap<String,Class<? extends IIdentifiableEntity>>();


  		




  47
  73
  
    
	


  		












  

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





  45
  45
  
    
	


  		




  46
  46
  
    
	@XmlElementWrapper(name = "Representations")


  		




  47
  47
  
    
	@XmlElement(name = "Representation")


  		




  48
  
  
    
    @OneToMany(fetch=FetchType.LAZY)


  		




  
  48
  
    
    @OneToMany(fetch=FetchType.EAGER)


  		




  49
  49
  
    
	@Cascade( { CascadeType.SAVE_UPDATE, CascadeType.DELETE })


  		




  50
  50
  
    
	private Set<Representation> representations = new HashSet<Representation>();


  		




  51
  51
  
    
	


  		












  

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





  9
  9
  
    

  		




  10
  10
  
    
package eu.etaxonomy.cdm.model.common;


  		




  11
  11
  
    

  		




  
  12
  
    
import java.io.Serializable;


  		




  12
  13
  
    
import java.util.Calendar;


  		




  13
  14
  
    

  		




  14
  15
  
    
import javax.persistence.Embeddable;


  		




  ......




  43
  44
  
    
})


  		




  44
  45
  
    
@XmlRootElement(name = "TimePeriod")


  		




  45
  46
  
    
@Embeddable


  		




  46
  
  
    
public class TimePeriod implements Cloneable {


  		




  
  47
  
    
public class TimePeriod implements Cloneable, Serializable {


  		




  47
  48
  
    
	private static final Logger logger = Logger.getLogger(TimePeriod.class);


  		




  48
  49
  
    
	private static final DateTimeFieldType monthType = DateTimeFieldType.monthOfYear();


  		




  49
  50
  
    
	private static final DateTimeFieldType yearType = DateTimeFieldType.year();


  		












  

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





  17
  17
  
    
import javax.persistence.FetchType;


  		




  18
  18
  
    
import javax.persistence.ManyToMany;


  		




  19
  19
  
    
import javax.persistence.OneToOne;


  		




  
  20
  
    
import javax.persistence.Table;


  		




  20
  21
  
    
import javax.persistence.Transient;


  		




  21
  22
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  22
  23
  
    
import javax.xml.bind.annotation.XmlAccessorType;


  		




  ......




  28
  29
  
    
import javax.xml.bind.annotation.XmlTransient;


  		




  29
  30
  
    
import javax.xml.bind.annotation.XmlType;


  		




  30
  31
  
    

  		




  
  32
  
    
import org.hibernate.annotations.Cascade;


  		




  
  33
  
    
import org.hibernate.annotations.CascadeType;


  		




  31
  34
  
    
import org.hibernate.annotations.NaturalId;


  		




  32
  35
  
    
import org.hibernate.envers.Audited;


  		




  33
  36
  
    
import org.hibernate.envers.NotAudited;


  		




  ......




  52
  55
  
    
@XmlRootElement(name = "User")


  		




  53
  56
  
    
@Entity


  		




  54
  57
  
    
@Audited


  		




  
  58
  
    
@Table(name = "UserAccount")


  		




  55
  59
  
    
public class User extends CdmBase implements UserDetails {


  		




  56
  60
  
    

  		




  57
  61
  
    
	/**


  		




  ......




  105
  109
  
    
	@XmlIDREF


  		




  106
  110
  
    
	@XmlSchemaType(name = "IDREF")


  		




  107
  111
  
    
	@OneToOne(fetch = FetchType.LAZY)


  		




  
  112
  
    
	@Cascade({CascadeType.SAVE_UPDATE})


  		




  108
  113
  
    
	protected Person person;


  		




  109
  114
  
    
	


  		




  110
  115
  
    
	@XmlTransient


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/DescriptionBase.java
    
  





  44
  44
  
    
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;


  		




  45
  45
  
    
import eu.etaxonomy.cdm.model.reference.ReferenceBase;


  		




  46
  46
  
    
import eu.etaxonomy.cdm.model.taxon.Taxon;


  		




  
  47
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  47
  48
  
    

  		




  48
  49
  
    
/**


  		




  49
  50
  
    
 * The upmost (abstract) class for a description as a whole (with possibly


  		




  ......




  72
  73
  
    
@Entity


  		




  73
  74
  
    
@Audited


  		




  74
  75
  
    
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)


  		




  75
  
  
    
public abstract class DescriptionBase extends IdentifiableEntity {


  		




  
  76
  
    
public abstract class DescriptionBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> {


  		




  76
  77
  
    
	private static final long serialVersionUID = 5504218413819040193L;


  		




  77
  78
  
    
	private static final Logger logger = Logger.getLogger(DescriptionBase.class);


  		




  78
  79
  
    
	


  		




  ......




  303
  304
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()


  		




  304
  305
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()


  		




  305
  306
  
    
	 */


  		




  306
  
  
    
	@Override


  		




  307
  
  
    
	public String generateTitle() {


  		




  308
  
  
    
		//TODO generate title "generate Title not yet implemented"


  		




  309
  
  
    
		return this.toString();


  		




  310
  
  
    
	}


  		




  
  307
  
    
//	@Override


  		




  
  308
  
    
//	public String generateTitle() {


  		




  
  309
  
    
//		//TODO generate title "generate Title not yet implemented"


  		




  
  310
  
    
//		return this.toString();


  		




  
  311
  
    
//	}


  		




  311
  312
  
    

  		




  312
  
  
    
	/**


  		




  
  313
  
    
    /**


  		




  313
  314
  
    
	 * @return the imageGallery


  		




  314
  315
  
    
	 */


  		




  315
  316
  
    
	public boolean isImageGallery() {


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/IdentificationKey.java
    
  





  55
  55
  
    
	@SuppressWarnings("unused")


  		




  56
  56
  
    
	private static final Logger logger = Logger.getLogger(IdentificationKey.class);


  		




  57
  57
  
    
	


  		




  58
  
  
    
	/*


  		




  59
  
  
    
     * FIXME - shouldn't this be @ManyToMany - i.e. many keys can refer to the


  		




  60
  
  
    
	 * same taxon and some taxa will be covered by multiple keys?


  		




  61
  
  
    
	 */


  		




  62
  58
  
    
	@XmlElementWrapper(name = "CoveredTaxa")


  		




  63
  59
  
    
	@XmlElement(name = "CoveredTaxon")


  		




  64
  60
  
    
	@XmlIDREF


  		




  65
  61
  
    
	@XmlSchemaType(name = "IDREF")


  		




  66
  
  
    
	@OneToMany(fetch = FetchType.LAZY)


  		




  
  62
  
    
	@ManyToMany(fetch = FetchType.LAZY)


  		




  67
  63
  
    
	private Set<Taxon> coveredTaxa = new HashSet<Taxon>();


  		




  68
  64
  
    
	


  		




  69
  65
  
    
	@XmlElementWrapper( name = "GeoScopes")


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/SpecimenDescription.java
    
  





  18
  18
  
    
import org.apache.log4j.Logger;


  		




  19
  19
  
    
import org.hibernate.envers.Audited;


  		




  20
  20
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  21
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  21
  22
  
    

  		




  22
  23
  
    
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;


  		




  
  24
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  
  25
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;


  		




  23
  26
  
    

  		




  24
  27
  
    
/**


  		




  25
  28
  
    
 * This class represents descriptions for {@link SpecimenOrObservationBase specimens or observations}.


  		




  ......




  37
  40
  
    
@Entity


  		




  38
  41
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionBase")


  		




  39
  42
  
    
@Audited


  		




  40
  
  
    
public class SpecimenDescription extends DescriptionBase {


  		




  
  43
  
    
@Configurable


  		




  
  44
  
    
public class SpecimenDescription extends DescriptionBase<IIdentifiableEntityCacheStrategy<SpecimenDescription>> {


  		




  41
  45
  
    
	private static final long serialVersionUID = -8506790426682192703L;


  		




  42
  46
  
    
	@SuppressWarnings("unused")


  		




  43
  47
  
    
	private static final Logger logger = Logger.getLogger(SpecimenDescription.class);


  		




  ......




  48
  52
  
    
	 */


  		




  49
  53
  
    
	public SpecimenDescription() {


  		




  50
  54
  
    
		super();


  		




  
  55
  
    
		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<SpecimenDescription>();


  		




  51
  56
  
    
	}


  		




  52
  57
  
    
	


  		




  53
  58
  
    

  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TaxonDescription.java
    
  





  35
  35
  
    
import org.hibernate.annotations.CascadeType;


  		




  36
  36
  
    
import org.hibernate.envers.Audited;


  		




  37
  37
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  38
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  38
  39
  
    

  		




  39
  40
  
    
import eu.etaxonomy.cdm.model.location.NamedArea;


  		




  40
  41
  
    
import eu.etaxonomy.cdm.model.taxon.Taxon;


  		




  
  42
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  
  43
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;


  		




  41
  44
  
    

  		




  42
  45
  
    
/**


  		




  43
  46
  
    
 * This class represents descriptions that delimit or circumscribe a real taxon.


  		




  ......




  62
  65
  
    
@Entity


  		




  63
  66
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionBase")


  		




  64
  67
  
    
@Audited


  		




  65
  
  
    
public class TaxonDescription extends DescriptionBase {


  		




  
  68
  
    
@Configurable


  		




  
  69
  
    
public class TaxonDescription extends DescriptionBase<IIdentifiableEntityCacheStrategy<TaxonDescription>> {


  		




  66
  70
  
    
	private static final long serialVersionUID = 8065879180505546803L;


  		




  67
  71
  
    
	@SuppressWarnings("unused")


  		




  68
  72
  
    
	private static final Logger logger = Logger.getLogger(TaxonDescription.class);


  		




  ......




  101
  105
  
    
	 */


  		




  102
  106
  
    
	public TaxonDescription(){


  		




  103
  107
  
    
		super();


  		




  
  108
  
    
		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<TaxonDescription>();


  		




  104
  109
  
    
	}


  		




  105
  110
  
    
	


  		




  106
  111
  
    
	/**


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TaxonNameDescription.java
    
  





  26
  26
  
    
import org.hibernate.annotations.CascadeType;


  		




  27
  27
  
    
import org.hibernate.envers.Audited;


  		




  28
  28
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  29
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  29
  30
  
    

  		




  30
  31
  
    
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;


  		




  31
  32
  
    
import eu.etaxonomy.cdm.model.name.TaxonNameBase;


  		




  
  33
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  
  34
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;


  		




  32
  35
  
    

  		




  33
  36
  
    
/**


  		




  34
  37
  
    
 * This class represents all piece of information (not ruled by a {@link NomenclaturalCode nomenclatural code})


  		




  ......




  47
  50
  
    
@Entity


  		




  48
  51
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionBase")


  		




  49
  52
  
    
@Audited


  		




  50
  
  
    
public class TaxonNameDescription extends DescriptionBase {


  		




  
  53
  
    
@Configurable


  		




  
  54
  
    
public class TaxonNameDescription extends DescriptionBase<IIdentifiableEntityCacheStrategy<TaxonNameDescription>> {


  		




  51
  55
  
    
	private static final long serialVersionUID = -7349160369642038687L;


  		




  52
  56
  
    
	@SuppressWarnings("unused")


  		




  53
  57
  
    
	private static final Logger logger = Logger.getLogger(TaxonNameDescription.class);


  		




  ......




  65
  69
  
    
	 */


  		




  66
  70
  
    
	public TaxonNameDescription() {


  		




  67
  71
  
    
		super();


  		




  
  72
  
    
		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy();


  		




  68
  73
  
    
	}


  		




  69
  74
  
    
	


  		




  70
  75
  
    
	/**


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/description/TextData.java
    
  





  71
  71
  
    
	@XmlElement(name = "MultiLanguageText")


  		




  72
  72
  
    
    @XmlJavaTypeAdapter(MultilanguageTextAdapter.class)


  		




  73
  73
  
    
    @OneToMany (fetch= FetchType.LAZY)


  		




  74
  
  
    
	@MapKey(name="language")


  		




  75
  74
  
    
    @Cascade({CascadeType.SAVE_UPDATE})


  		




  76
  75
  
    
    @IndexedEmbedded


  		




  77
  76
  
    
	private Map<Language, LanguageString> multilanguageText = new HashMap<Language,LanguageString>();


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/location/Point.java
    
  





  8
  8
  
    
*/


  		




  9
  9
  
    

  		




  10
  10
  
    
package eu.etaxonomy.cdm.model.location;


  		




  
  11
  
    
import java.io.Serializable;


  		




  
  12
  
    

  		




  11
  13
  
    
import javax.persistence.Embeddable;


  		




  12
  14
  
    
import javax.persistence.FetchType;


  		




  13
  15
  
    
import javax.persistence.ManyToOne;


  		




  ......




  38
  40
  
    
})


  		




  39
  41
  
    
@XmlRootElement(name = "Point")


  		




  40
  42
  
    
@Embeddable


  		




  41
  
  
    
public class Point implements Cloneable {


  		




  
  43
  
    
public class Point implements Cloneable, Serializable {


  		




  42
  44
  
    
	private static final Logger logger = Logger.getLogger(Point.class);


  		




  43
  45
  
    
	


  		




  44
  46
  
    
	//TODO was Float but H2 threw errors


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/media/IdentifiableMediaEntity.java
    
  





  19
  19
  
    
import org.hibernate.annotations.CascadeType;


  		




  20
  20
  
    

  		




  21
  21
  
    
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;


  		




  
  22
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  22
  23
  
    

  		




  23
  24
  
    
@XmlAccessorType(XmlAccessType.FIELD)


  		




  24
  25
  
    
@XmlType(name = "IdentifiableMediaEntity", propOrder = {


  		




  25
  26
  
    
    "media"


  		




  26
  27
  
    
})


  		




  27
  28
  
    
@MappedSuperclass


  		




  28
  
  
    
public abstract class IdentifiableMediaEntity extends IdentifiableEntity implements IMediaDocumented, IMediaEntity{


  		




  
  29
  
    
public abstract class IdentifiableMediaEntity<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableEntity<S> implements IMediaDocumented, IMediaEntity{


  		




  29
  30
  
    

  		




  30
  31
  
    
	private static final long serialVersionUID = 4038647011021908313L;


  		




  31
  32
  
    

  		




  32
  
  
    
	static Logger logger = Logger.getLogger(IdentifiableMediaEntity.class);


  		




  
  33
  
    
	protected static Logger logger = Logger.getLogger(IdentifiableMediaEntity.class);


  		




  33
  34
  
    

  		




  34
  35
  
    
    @XmlElementWrapper(name = "Media")


  		




  35
  36
  
    
    @XmlElement(name = "Medium")


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.java
    
  





  15
  15
  
    
import eu.etaxonomy.cdm.model.reference.ReferenceBase;


  		




  16
  16
  
    
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;


  		




  17
  17
  
    
import eu.etaxonomy.cdm.model.common.IReferencedEntity;


  		




  
  18
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;


  		




  
  19
  
    
import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;


  		




  
  20
  
    

  		




  18
  21
  
    
import org.apache.log4j.Logger;


  		




  19
  22
  
    
import org.hibernate.annotations.Cascade;


  		




  20
  23
  
    
import org.hibernate.annotations.CascadeType;


  		




  21
  24
  
    
import org.hibernate.annotations.Index;


  		




  22
  25
  
    
import org.hibernate.annotations.Table;


  		




  23
  26
  
    
import org.hibernate.envers.Audited;


  		




  
  27
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  24
  28
  
    

  		




  25
  29
  
    
import java.util.*;


  		




  26
  30
  
    

  		




  ......




  56
  60
  
    
@XmlRootElement(name = "Sequence")


  		




  57
  61
  
    
@Entity


  		




  58
  62
  
    
@Audited


  		




  
  63
  
    
@Configurable


  		




  59
  64
  
    
@Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })


  		




  60
  
  
    
public class Sequence extends IdentifiableEntity implements IReferencedEntity, IMediaDocumented{


  		




  
  65
  
    
public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{


  		




  61
  66
  
    
	private static final long serialVersionUID = 8298983152731241775L;


  		




  62
  67
  
    
	private static final Logger logger = Logger.getLogger(Sequence.class);


  		




  63
  68
  
    
	


  		




  ......




  115
  120
  
    
    @OneToMany(fetch = FetchType.LAZY)


  		




  116
  121
  
    
	private Set<Media> chromatograms = new HashSet<Media>();


  		




  117
  122
  
    
	


  		




  
  123
  
    
	protected Sequence() {


  		




  
  124
  
    
		super(); // FIXME I think this is explicit - do we really need to call this?


  		




  
  125
  
    
		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();


  		




  
  126
  
    
	}


  		




  
  127
  
    
	


  		




  118
  128
  
    
	public Locus getLocus(){


  		




  119
  129
  
    
		logger.debug("getLocus");


  		




  120
  130
  
    
		return this.locus;


  		




  ......




  234
  244
  
    
		this.citationMicroReference = citationMicroReference;


  		




  235
  245
  
    
	}


  		




  236
  246
  
    

  		




  237
  
  
    
	@Override


  		




  238
  
  
    
	public String generateTitle(){


  		




  239
  
  
    
		return "";


  		




  240
  
  
    
	}


  		




  241
  
  
    

  		




  242
  247
  
    
	public ReferenceBase getCitation(){


  		




  243
  248
  
    
		return publishedIn;


  		




  244
  249
  
    
	}


  		




  245
  
  
    

  		




  246
  250
  
    
}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/BacterialName.java
    
  





  21
  21
  
    
import org.apache.log4j.Logger;


  		




  22
  22
  
    
import org.hibernate.envers.Audited;


  		




  23
  23
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  24
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  24
  25
  
    

  		




  25
  26
  
    
/**


  		




  26
  27
  
    
 * The taxon name class for bacteria.


  		




  ......




  40
  41
  
    
@Entity


  		




  41
  42
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")


  		




  42
  43
  
    
@Audited


  		




  
  44
  
    
@Configurable


  		




  43
  45
  
    
public class BacterialName extends NonViralName<BacterialName> {


  		




  44
  46
  
    
	


  		




  45
  47
  
    
	/**


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/BotanicalName.java
    
  





  29
  29
  
    
import org.hibernate.annotations.CascadeType;


  		




  30
  30
  
    
import org.hibernate.envers.Audited;


  		




  31
  31
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  32
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  32
  33
  
    

  		




  33
  34
  
    
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;


  		




  34
  35
  
    
import eu.etaxonomy.cdm.model.common.RelationshipBase;


  		




  ......




  59
  60
  
    
@Entity


  		




  60
  61
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")


  		




  61
  62
  
    
@Audited


  		




  
  63
  
    
@Configurable


  		




  62
  64
  
    
public class BotanicalName extends NonViralName<BotanicalName> {


  		




  63
  65
  
    
	


  		




  64
  66
  
    
	/**


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/CultivarPlantName.java
    
  





  12
  12
  
    
import org.apache.log4j.Logger;


  		




  13
  13
  
    
import org.hibernate.envers.Audited;


  		




  14
  14
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  15
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  15
  16
  
    

  		




  16
  17
  
    
import javax.persistence.*;


  		




  17
  18
  
    
import javax.xml.bind.annotation.XmlAccessType;


  		




  ......




  40
  41
  
    
@Entity


  		




  41
  42
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")


  		




  42
  43
  
    
@Audited


  		




  
  44
  
    
@Configurable


  		




  43
  45
  
    
public class CultivarPlantName extends BotanicalName {


  		




  44
  46
  
    
	static Logger logger = Logger.getLogger(CultivarPlantName.class);


  		




  45
  47
  
    
	


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/NonViralName.java
    
  





  32
  32
  
    
import org.hibernate.search.annotations.Fields;


  		




  33
  33
  
    
import org.hibernate.search.annotations.Index;


  		




  34
  34
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  35
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  35
  36
  
    

  		




  36
  37
  
    
import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;


  		




  37
  38
  
    
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;


  		




  ......




  76
  77
  
    
@Entity


  		




  77
  78
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")


  		




  78
  79
  
    
@Audited


  		




  
  80
  
    
@Configurable


  		




  79
  81
  
    
public class NonViralName<T extends NonViralName> extends TaxonNameBase<T, INonViralNameCacheStrategy> {


  		




  80
  82
  
    
	


  		




  81
  83
  
    
	private static final Logger logger = Logger.getLogger(NonViralName.class);


  		




  ......




  144
  146
  
    
	@XmlElement(name = "ProtectedNameCache")


  		




  145
  147
  
    
	protected boolean protectedNameCache;


  		




  146
  148
  
    

  		




  147
  
  
    
    @XmlTransient


  		




  148
  
  
    
    @Transient


  		




  149
  
  
    
	protected INonViralNameCacheStrategy cacheStrategy;


  		




  
  149
  
    
//    @XmlTransient


  		




  
  150
  
    
//    @Transient


  		




  
  151
  
    
//	protected INonViralNameCacheStrategy cacheStrategy;


  		




  150
  152
  
    
	


  		




  151
  153
  
    
	// ************* CONSTRUCTORS *************/	


  		




  152
  154
  
    
	


  		




  ......




  290
  292
  
    
	 * @see 	eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy


  		




  291
  293
  
    
	 * @see     eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy


  		




  292
  294
  
    
	 */


  		




  293
  
  
    
	@Override


  		




  294
  
  
    
	@Transient


  		




  295
  
  
    
	public INonViralNameCacheStrategy getCacheStrategy() {


  		




  296
  
  
    
		return cacheStrategy;


  		




  297
  
  
    
	}


  		




  
  295
  
    
//	@Override


  		




  
  296
  
    
//	@Transient


  		




  
  297
  
    
//	public INonViralNameCacheStrategy getCacheStrategy() {


  		




  
  298
  
    
//		return cacheStrategy;


  		




  
  299
  
    
//	}


  		




  298
  300
  
    
	


  		




  299
  301
  
    
	/**


  		




  300
  302
  
    
	 * @see  #getCacheStrategy()


  		




  301
  303
  
    
	 */


  		




  302
  
  
    
	@Override


  		




  303
  
  
    
	public void setCacheStrategy(INonViralNameCacheStrategy cacheStrategy) {


  		




  304
  
  
    
		this.cacheStrategy = cacheStrategy;


  		




  305
  
  
    
	}


  		




  
  304
  
    
//	@Override


  		




  
  305
  
    
//	public void setCacheStrategy(INonViralNameCacheStrategy cacheStrategy) {


  		




  
  306
  
    
//		this.cacheStrategy = cacheStrategy;


  		




  
  307
  
    
//	}


  		




  306
  308
  
    

  		




  307
  309
  
    
	/**


  		




  308
  310
  
    
	 * Returns the {@link eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor author (team)} that published <i>this</i> non viral


  		




  ......




  499
  501
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()


  		




  500
  502
  
    
	 * @see  	TaxonNameBase#generateTitle()


  		




  501
  503
  
    
	 */


  		




  502
  
  
    
	@Override


  		




  503
  
  
    
	public String generateTitle(){


  		




  504
  
  
    
		if (cacheStrategy == null){


  		




  505
  
  
    
			logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());


  		




  506
  
  
    
			return null;


  		




  507
  
  
    
		}else{


  		




  508
  
  
    
			return cacheStrategy.getTitleCache(this);


  		




  509
  
  
    
		}


  		




  510
  
  
    
	}


  		




  
  504
  
    
//	@Override


  		




  
  505
  
    
//	public String generateTitle(){


  		




  
  506
  
    
//		if (cacheStrategy == null){


  		




  
  507
  
    
//			logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());


  		




  
  508
  
    
//			return null;


  		




  
  509
  
    
//		}else{


  		




  
  510
  
    
//			return cacheStrategy.getTitleCache(this);


  		




  
  511
  
    
//		}


  		




  
  512
  
    
//	}


  		




  511
  513
  
    
	


  		




  512
  514
  
    
	@Override


  		




  513
  515
  
    
	public String generateFullTitle(){


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonNameBase.java
    
  





  96
  96
  
    
@Audited


  		




  97
  97
  
    
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)


  		




  98
  98
  
    
@Table(appliesTo="TaxonNameBase", indexes = { @Index(name = "taxonNameBaseTitleCacheIndex", columnNames = { "titleCache" }) })


  		




  99
  
  
    
public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INameCacheStrategy> extends IdentifiableEntity implements IReferencedEntity, IParsable, IRelated {


  		




  
  99
  
    
public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INameCacheStrategy> extends IdentifiableEntity<S> implements IReferencedEntity, IParsable, IRelated {


  		




  100
  100
  
    

  		




  101
  101
  
    
	private static final long serialVersionUID = -4530368639601532116L;


  		




  102
  102
  
    
	private static final Logger logger = Logger.getLogger(TaxonNameBase.class);


  		




  ......




  180
  180
  
    
    @XmlElement(name = "Rank")


  		




  181
  181
  
    
	@XmlIDREF


  		




  182
  182
  
    
	@XmlSchemaType(name = "IDREF")


  		




  183
  
  
    
	@ManyToOne(fetch = FetchType.LAZY)


  		




  
  183
  
    
	@ManyToOne(fetch = FetchType.EAGER)


  		




  184
  184
  
    
	private Rank rank;


  		




  185
  185
  
    

  		




  186
  
  
    

  		




  187
  186
  
    
	@XmlElement(name = "NomenclaturalReference")


  		




  188
  187
  
    
    @XmlIDREF


  		




  189
  188
  
    
    @XmlSchemaType(name = "IDREF")


  		




  ......




  606
  605
  
    
		//TODO implement


  		




  607
  606
  
    
		logger.warn("not yet implemented");


  		




  608
  607
  
    
	}


  		




  609
  
  
    

  		




  610
  
  
    
	/**


  		




  611
  
  
    
	 * Returns the {@link eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy cache strategy} used to generate


  		




  612
  
  
    
	 * several strings corresponding to <i>this</i> taxon name


  		




  613
  
  
    
	 * (in particular taxon name caches and author strings).


  		




  614
  
  
    
	 * 


  		




  615
  
  
    
	 * @return  the cache strategy used for <i>this</i> taxon name


  		




  616
  
  
    
	 * @see 	eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy


  		




  617
  
  
    
	 * @see     eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy


  		




  618
  
  
    
	 */


  		




  619
  
  
    
	@Transient


  		




  620
  
  
    
	public abstract S getCacheStrategy();


  		




  621
  
  
    
	/** 


  		




  622
  
  
    
	 * @see 	#getCacheStrategy()


  		




  623
  
  
    
	 */


  		




  624
  
  
    
	


  		




  625
  
  
    
	public abstract void setCacheStrategy(S cacheStrategy);


  		




  626
  608
  
    
	


  		




  627
  609
  
    
	/** 


  		




  628
  610
  
    
	 * Returns the taxonomic {@link Rank rank} of <i>this</i> taxon name.


  		




  ......




  1277
  1259
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()


  		




  1278
  1260
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()


  		




  1279
  1261
  
    
	 */


  		




  1280
  
  
    
	@Override


  		




  1281
  
  
    
	public String generateTitle() {


  		




  1282
  
  
    
		// TODO Auto-generated method stub


  		




  1283
  
  
    
		logger.warn("not yet implemented");


  		




  1284
  
  
    
		return null;


  		




  1285
  
  
    
	}	


  		




  
  1262
  
    
//	@Override


  		




  
  1263
  
    
//	public abstract String generateTitle();


  		




  1286
  1264
  
    
}


  		












  

    
      cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ViralName.java
    
  





  24
  24
  
    
import org.hibernate.search.annotations.Field;


  		




  25
  25
  
    
import org.hibernate.search.annotations.Index;


  		




  26
  26
  
    
import org.hibernate.search.annotations.Indexed;


  		




  
  27
  
    
import org.springframework.beans.factory.annotation.Configurable;


  		




  27
  28
  
    

  		




  28
  29
  
    
import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;


  		




  29
  30
  
    

  		




  ......




  50
  51
  
    
@Entity


  		




  51
  52
  
    
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")


  		




  52
  53
  
    
@Audited


  		




  
  54
  
    
@Configurable


  		




  53
  55
  
    
public class ViralName extends TaxonNameBase<ViralName, INameCacheStrategy<ViralName>>  {


  		




  54
  56
  
    
	


  		




  55
  57
  
    
	private static final Logger logger = Logger.getLogger(ViralName.class);


  		




  56
  58
  
    

  		




  57
  
  
    
    @XmlTransient


  		




  58
  
  
    
    @Transient


  		




  59
  
  
    
	protected INameCacheStrategy<ViralName> cacheStrategy;


  		




  
  59
  
    
//    @XmlTransient


  		




  
  60
  
    
//    @Transient


  		




  
  61
  
    
//	protected INameCacheStrategy<ViralName> cacheStrategy;


  		




  60
  62
  
    
	


  		




  61
  63
  
    
	@XmlElement(name = "Acronym")


  		




  62
  64
  
    
	@Field(index=Index.TOKENIZED)


  		




  ......




  120
  122
  
    
	 * @see  	eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()


  		




  121
  123
  
    
	 * @see  	TaxonNameBase#generateTitle()


  		




  122
  124
  
    
	 */


  		




  123
  
  
    
	@Override


  		




  124
  
  
    
	public String generateTitle(){


  		




  125
  
  
    
		logger.warn("not yet implemented");


  		




  126
  
  
    
		return this.toString();


  		




  127
  
  
    
	}


  		




  
  125
  
    
//	@Override


  		




  
  126
  
    
//	public String generateTitle(){


  		




  
  127
  
    
//		logger.warn("not yet implemented");


  		




  
  128
  
    
//		return this.toString();


  		




  
  129
  
    
//	}


  		




  128
  130
  
    

  		




  129
  131
  
    
	@Override


  		




  130
  132
  
    
	public String generateFullTitle(){


  		




  ......




  176
  178
  
    
	 * @see 	eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy


  		




  177
  179
  
    
	 * @see     eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy


  		




  178
  180
  
    
	 */


  		




  179
  
  
    
	@Override


  		




  180
  
  
    
	@Transient


  		




  181
  
  
    
	public INameCacheStrategy getCacheStrategy() {


  		




  182
  
  
    
		return cacheStrategy;


  		




  183
  
  
    
	}


  		




  
  181
  
    
//	@Override


  		




  
  182
  
    
//	@Transient


  		




  
  183
  
    
//	public INameCacheStrategy getCacheStrategy() {


  		




  
  184
  
    
//		return cacheStrategy;


  		




  
  185
  
    
//	}


  		




  184
  186
  
    

  		




  185
  187
  
    

  		




  186
  188
  
    
	/**


  		




  187
  189
  
    
	 * @see  #getCacheStrategy()


  		




  188
  190
  
    
	 */


  		




  189
  
  
    
	@Override


  		




  190
  
  
    
	public void setCacheStrategy(INameCacheStrategy cacheStrategy) {


  		




  191
  
  
    
		this.cacheStrategy = cacheStrategy;


  		




  192
  
  
    
	}


  		




  
  191
  
    
//	@Override


  		




  
  192
  
    
//	public void setCacheStrategy(INameCacheStrategy cacheStrategy) {


  		




  
  193
  
    
//		this.cacheStrategy = cacheStrategy;


  		




  
  194
  
    
//	}


  		








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