Revision 94d72025
Added by Andreas Müller almost 6 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/OriginalSourceType.java | ||
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import org.apache.log4j.Logger; |
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import eu.etaxonomy.cdm.model.name.TaxonName; |
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/** |
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* The original source type is used to define the type of an {@link OriginalSourceBase original source}.<BR>
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* It is used to distinguish e.g. data lineage when importing data from one database to another from e.g. content oriented |
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* sources such as the citation in a book. |
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* In future they may come further source types.
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* In future they may come further source types. |
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* @author a.mueller |
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* @since 15.05.2013 |
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*/ |
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@XmlEnum |
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public enum OriginalSourceType implements IEnumTerm<OriginalSourceType>, Serializable{
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//0 |
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/** |
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* Unknown provenance is the type to be used if no information is available about the type |
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* of activity that happened. |
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*
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* |
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*/ |
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@XmlEnumValue("Unknown")
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Unknown(UUID.fromString("b48a443c-05f2-47ff-b885-1d3bd31118e1"), "Unknown Provenance", "UNK", null),
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//1 |
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/** |
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* Primary Taxonomic Source describes the sources a taxonomist uses to gather certain information.
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* Primary Taxonomic Source describes the sources a taxonomist uses to gather certain information. |
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* E.g. a taxonomist may have used three books/articles/other references to gather information |
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* about the distribution status of a taxon. |
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* He/she will store these references as original source of type Primary Taxonomic Source. |
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* This is a specialization of PROV-O Primary Source
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* This is a specialization of PROV-O Primary Source |
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* ({@link http://www.w3.org/TR/2013/REC-prov-o-20130430/#PrimarySource})
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*
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* |
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*/ |
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@XmlEnumValue("Primary Taxonomic Source")
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PrimaryTaxonomicSource(UUID.fromString("c990beb3-3bc9-4dad-bbdf-9c11683493da"), "Primary Taxonomic Source", "PTS", null),
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//2 |
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/** |
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* Data Lineage describes the data life cycle of electronically available data. A typical |
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* use-case for data lineage is a data import from one database to another. Sources of
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* type data lineage will store information about the original database and the identifier
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* use-case for data lineage is a data import from one database to another. Sources of |
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* type data lineage will store information about the original database and the identifier |
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* and table (->namespace) used in the original database. |
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* There are multiple types of data lineage: Blackbox, Dispatcher, Aggregator
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* ({@link http://de.wikipedia.org/wiki/Data-Lineage})
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* There are multiple types of data lineage: Blackbox, Dispatcher, Aggregator |
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* ({@link http://de.wikipedia.org/wiki/Data-Lineage})
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*/ |
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@XmlEnumValue("Data Lineage")
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Lineage(UUID.fromString("4f9fdf9a-f3b5-490c-96f0-90e050599b0e"), "Data Lineage", "DLI", null),
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//4 |
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/** |
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* Data Transformation is a specialization of {@value #Lineage} and describes a data
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* transformation process that happens primarily on the given dataset but may also
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* Data Transformation is a specialization of {@value #Lineage} and describes a data
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* transformation process that happens primarily on the given dataset but may also |
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* include external data. |
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*/ |
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@XmlEnumValue("Data Transformation")
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//5 |
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/** |
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* Data aggregation is a specification of {@value #Lineage} and describes the
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* data transformation process that primarily includes data aggregation processes
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* Data aggregation is a specification of {@value #Lineage} and describes the
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* data transformation process that primarily includes data aggregation processes |
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* but may also include data imports and transformations. |
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*/ |
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@XmlEnumValue("Data Aggregation")
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//6 |
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/** |
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* Primary Media Source describes the original source for any media file.
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* E.g. a media may be copy of figure in book. The book itself will then be the primary media source.
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* Primary Media Source describes the original source for any media file. |
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* E.g. a media may be copy of figure in book. The book itself will then be the primary media source. |
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* |
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* This is a specialization of PROV-O Primary Source
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* This is a specialization of PROV-O Primary Source |
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* ({@link http://www.w3.org/TR/2013/REC-prov-o-20130430/#PrimarySource})
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*
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* |
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*/ |
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@XmlEnumValue("Primary Media Source")
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PrimaryMediaSource(UUID.fromString("72be3615-a6da-4728-948a-b3c5797fa4bc"), "Primary Media Source", "PMS", null),
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//6 |
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/** |
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* Nomenclatural reference as used for {@link TaxonName taxon names} and
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* type designations. |
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* E.g. a media may be copy of figure in book. The book itself will then be the primary media source. |
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* |
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*/ |
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@XmlEnumValue("Nomenclatural Reference")
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NomenclaturalReference(UUID.fromString(""), "Nomenclatural Reference", "NOR", null),
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//7 |
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/** |
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Other(UUID.fromString("b7c4b7fe-0aef-428a-bb7b-9153a11bf845"), "Other", "OTH", null),
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; |
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(OriginalSourceType.class); |
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// *************************** DELEGATE **************************************/
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// *************************** DELEGATE **************************************/ |
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private static EnumeratedTermVoc<OriginalSourceType> delegateVoc; |
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private IEnumTerm<OriginalSourceType> delegateVocTerm; |
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static {
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delegateVoc = EnumeratedTermVoc.getVoc(OriginalSourceType.class); |
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} |
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@Override |
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public String getKey(){return delegateVocTerm.getKey();}
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@Override |
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public String getMessage(){return delegateVocTerm.getMessage();}
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@Override |
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public String getMessage(Language language){return delegateVocTerm.getMessage(language);}
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@Override |
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public UUID getUuid() {return delegateVocTerm.getUuid();}
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@Override |
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public OriginalSourceType getKindOf() {return delegateVocTerm.getKindOf();}
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@Override |
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public Set<OriginalSourceType> getGeneralizationOf() {return delegateVocTerm.getGeneralizationOf();}
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@Override |
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public boolean isKindOf(OriginalSourceType ancestor) {return delegateVocTerm.isKindOf(ancestor); }
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@Override |
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public Set<OriginalSourceType> getGeneralizationOf(boolean recursive) {return delegateVocTerm.getGeneralizationOf(recursive);}
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public static OriginalSourceType getByKey(String key){return delegateVoc.getByKey(key);}
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public static OriginalSourceType getByUuid(UUID uuid) {return delegateVoc.getByUuid(uuid);}
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|
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ITaxonNameBase.java | ||
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import eu.etaxonomy.cdm.model.common.IParsable; |
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import eu.etaxonomy.cdm.model.common.IRelated; |
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
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public void setRank(Rank rank); |
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/** |
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* Returns the {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
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* Returns the {@link eu.etaxonomy.cdm.model.reference.Reference nomenclatural reference} of <i>this</i> taxon name.
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* The nomenclatural reference is here meant to be the one publication |
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* <i>this</i> taxon name was originally published in while fulfilling the formal |
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* requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural code}.
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* |
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* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference |
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* @see eu.etaxonomy.cdm.model.reference.Reference |
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* @see #getNomenclaturalSource() |
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*/ |
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public INomenclaturalReference getNomenclaturalReference();
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public Reference getNomenclaturalReference(); |
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/** |
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* Assigns a {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
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* The corresponding {@link eu.etaxonomy.cdm.model.reference.Reference.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
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* as it is obviously used for nomenclatural purposes. |
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* |
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* @throws IllegalArgumentException if parameter <code>nomenclaturalReference</code> is not assignable from {@link INomenclaturalReference}
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* @see #getNomenclaturalReference() |
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*/ |
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public void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference); |
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/** |
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* Returns the appended phrase string assigned to <i>this</i> taxon name. |
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* The appended phrase is a non-atomised addition to a name. It is |
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* not ruled by a nomenclatural code. |
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*/ |
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public String getAppendedPhrase(); |
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/** |
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* @see #getAppendedPhrase() |
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*/ |
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public void setAppendedPhrase(String appendedPhrase); |
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public void setNomenclaturalReference(Reference nomenclaturalReference); |
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/** |
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* Returns the details string of the {@link #getNomenclaturalReference() nomenclatural reference} assigned
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* (implicitly) pages but can also be figures or tables or any other |
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* element of a publication. A nomenclatural micro reference (details) |
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* requires the existence of a nomenclatural reference. |
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* |
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* @see #getNomenclaturalReference() |
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* @see #getNomenclaturalSource() |
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*/ |
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//Details of the nomenclatural reference (protologue). |
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public String getNomenclaturalMicroReference(); |
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/** |
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*/ |
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public void setNomenclaturalMicroReference(String nomenclaturalMicroReference); |
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/** |
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* Sets the nomenclatural source which is a combination of the nomenclatural reference |
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* and the detail information (exact page, table, figure, ...) where to find this name |
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* for the first time. |
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* |
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* @see #getNomenclaturalReference() |
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* @see #getNomenclaturalMicroReference() |
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*/ |
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public DescriptionElementSource getNomenclaturalSource(); |
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/** |
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* Sets the nomenclatural source |
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* @param nomenclaturalSource |
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*/ |
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public void setNomenclaturalSource(DescriptionElementSource nomenclaturalSource); |
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/** |
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* Returns the appended phrase string assigned to <i>this</i> taxon name. |
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* The appended phrase is a non-atomised addition to a name. It is |
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* not ruled by a nomenclatural code. |
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*/ |
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public String getAppendedPhrase(); |
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/** |
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* @see #getAppendedPhrase() |
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*/ |
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public void setAppendedPhrase(String appendedPhrase); |
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/** |
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* @param warnings |
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*/ |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TaxonName.java | ||
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import eu.etaxonomy.cdm.model.common.IParsable; |
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import eu.etaxonomy.cdm.model.common.IRelated; |
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
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import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
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import eu.etaxonomy.cdm.model.common.TermType; |
| ... | ... | |
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"appendedPhrase", |
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"nomenclaturalMicroReference", |
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"nomenclaturalReference", |
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"nomenclaturalSource", |
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"rank", |
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"fullTitleCache", |
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"protectedFullTitleCache", |
| ... | ... | |
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// @NullOrNotEmpty |
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@Column(length=255) |
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private String appendedPhrase; |
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@XmlElement(name = "NomenclaturalMicroReference") |
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@Field |
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@CacheUpdate(noUpdate ="titleCache") |
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//TODO Val #3379 |
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// @NullOrNotEmpty |
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@Column(length=255) |
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private String nomenclaturalMicroReference; |
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// |
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// @XmlElement(name = "NomenclaturalMicroReference")
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// @Field
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// @CacheUpdate(noUpdate ="titleCache")
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// //TODO Val #3379
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//// @NullOrNotEmpty
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// @Column(length=255)
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// private String nomenclaturalMicroReference;
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@XmlAttribute |
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@CacheUpdate(noUpdate ={"titleCache","fullTitleCache"})
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// @NotNull |
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@IndexedEmbedded(depth=1) |
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private Rank rank; |
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@XmlElement(name = "NomenclaturalReference") |
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// |
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// @XmlElement(name = "NomenclaturalReference") |
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// @XmlIDREF |
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// @XmlSchemaType(name = "IDREF") |
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// @ManyToOne(fetch = FetchType.LAZY) |
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// @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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// @CacheUpdate(noUpdate ="titleCache") |
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// @IndexedEmbedded |
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// private Reference nomenclaturalReference; |
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@XmlElement(name = "NomenclaturalSource") |
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@XmlIDREF |
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@XmlSchemaType(name = "IDREF") |
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@ManyToOne(fetch = FetchType.LAZY) |
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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@CacheUpdate(noUpdate ="titleCache") |
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@IndexedEmbedded |
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private Reference nomenclaturalReference; |
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private DescriptionElementSource nomenclaturalSource; |
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@XmlElementWrapper(name = "Registrations") |
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@XmlElement(name = "Registration") |
| ... | ... | |
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* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy |
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* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy |
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*/ |
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protected TaxonName(NomenclaturalCode type, Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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protected TaxonName(NomenclaturalCode type, Rank rank, String genusOrUninomial, |
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String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, |
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TeamOrPersonBase combinationAuthorship, Reference nomenclaturalReference, |
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String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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this(type, rank, homotypicalGroup); |
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setGenusOrUninomial(genusOrUninomial); |
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setInfraGenericEpithet (infraGenericEpithet); |
| ... | ... | |
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this.rank = rank; |
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} |
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/** |
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* Returns the {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
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* The nomenclatural reference is here meant to be the one publication |
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* <i>this</i> taxon name was originally published in while fulfilling the formal |
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* requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural code}.
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* |
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* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference |
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* @see eu.etaxonomy.cdm.model.reference.Reference |
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*/ |
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@Override |
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public INomenclaturalReference getNomenclaturalReference(){
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return this.nomenclaturalReference; |
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public Reference getNomenclaturalReference(){
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if (this.nomenclaturalSource == null){
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return null; |
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} |
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return this.nomenclaturalSource.getCitation(); |
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} |
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@Override |
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public DescriptionElementSource getNomenclaturalSource(){
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return this.nomenclaturalSource; |
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} |
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protected DescriptionElementSource getNomenclaturalSource(boolean createIfNotExist){
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if (this.nomenclaturalSource == null){
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if (!createIfNotExist){
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return null; |
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} |
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this.nomenclaturalSource = DescriptionElementSource.NewInstance(OriginalSourceType.NomenclaturalReference); |
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} |
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return this.nomenclaturalSource; |
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} |
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|
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/** |
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* Assigns a {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
|
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* The corresponding {@link eu.etaxonomy.cdm.model.reference.Reference.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
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* as it is obviously used for nomenclatural purposes. |
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* |
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* Shortcut to set the nomenclatural reference. |
|
| 2272 |
* |
|
| 2244 | 2273 |
* @throws IllegalArgumentException if parameter <code>nomenclaturalReference</code> is not assignable from {@link INomenclaturalReference}
|
| 2245 | 2274 |
* @see #getNomenclaturalReference() |
| 2246 | 2275 |
*/ |
| 2276 |
|
|
| 2247 | 2277 |
@Override |
| 2248 |
public void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference){
|
|
| 2249 |
if(nomenclaturalReference != null){
|
|
| 2250 |
if(!INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
|
|
| 2251 |
throw new IllegalArgumentException("Parameter nomenclaturalReference is not assignable from INomenclaturalReference");
|
|
| 2252 |
} |
|
| 2253 |
this.nomenclaturalReference = (Reference)nomenclaturalReference; |
|
| 2254 |
} else {
|
|
| 2255 |
this.nomenclaturalReference = null; |
|
| 2278 |
public void setNomenclaturalReference(Reference nomenclaturalReference){
|
|
| 2279 |
getNomenclaturalSource(true).setCitation(nomenclaturalReference); |
|
| 2280 |
checkNullSource(); |
|
| 2281 |
} |
|
| 2282 |
|
|
| 2283 |
|
|
| 2284 |
/** |
|
| 2285 |
* |
|
| 2286 |
*/ |
|
| 2287 |
private void checkNullSource() {
|
|
| 2288 |
if (this.nomenclaturalSource == null){
|
|
| 2289 |
return; |
|
| 2290 |
}else if (this.nomenclaturalSource.getCitation() != null |
|
| 2291 |
|| this.nomenclaturalSource.getCitationMicroReference() != null |
|
| 2292 |
|| this.nomenclaturalSource.getNameUsedInSource() != null |
|
| 2293 |
|| isBlank(this.nomenclaturalSource.getOriginalNameString())){
|
|
| 2294 |
//TODO what about supplemental data? |
|
| 2295 |
return; |
|
| 2296 |
}else{
|
|
| 2297 |
this.nomenclaturalSource = null; |
|
| 2256 | 2298 |
} |
| 2257 | 2299 |
} |
| 2258 | 2300 |
|
| 2301 |
|
|
| 2302 |
@Override |
|
| 2303 |
public void setNomenclaturalSource(DescriptionElementSource nomenclaturalSource) throws IllegalArgumentException {
|
|
| 2304 |
if (!OriginalSourceType.NomenclaturalReference.equals(nomenclaturalSource.getType()) ){
|
|
| 2305 |
throw new IllegalArgumentException("Nomenclatural source must be of type " + OriginalSourceType.NomenclaturalReference.getMessage());
|
|
| 2306 |
} |
|
| 2307 |
this.nomenclaturalSource = nomenclaturalSource; |
|
| 2308 |
} |
|
| 2309 |
|
|
| 2259 | 2310 |
/** |
| 2260 | 2311 |
* Returns the appended phrase string assigned to <i>this</i> taxon name. |
| 2261 | 2312 |
* The appended phrase is a non-atomised addition to a name. It is |
| ... | ... | |
| 2285 | 2336 |
//Details of the nomenclatural reference (protologue). |
| 2286 | 2337 |
@Override |
| 2287 | 2338 |
public String getNomenclaturalMicroReference(){
|
| 2288 |
return this.nomenclaturalMicroReference; |
|
| 2339 |
if (this.nomenclaturalSource == null){
|
|
| 2340 |
return null; |
|
| 2341 |
} |
|
| 2342 |
return this.nomenclaturalSource.getCitationMicroReference(); |
|
| 2289 | 2343 |
} |
| 2290 | 2344 |
/** |
| 2291 | 2345 |
* @see #getNomenclaturalMicroReference() |
| 2292 | 2346 |
*/ |
| 2293 | 2347 |
@Override |
| 2294 | 2348 |
public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
|
| 2295 |
this.nomenclaturalMicroReference = StringUtils.isBlank(nomenclaturalMicroReference)? null : nomenclaturalMicroReference; |
|
| 2349 |
this.getNomenclaturalSource(true).setCitationMicroReference(StringUtils.isBlank(nomenclaturalMicroReference)? null : nomenclaturalMicroReference); |
|
| 2350 |
checkNullSource(); |
|
| 2296 | 2351 |
} |
| 2297 | 2352 |
|
| 2298 | 2353 |
@Override |
Also available in: Unified diff
ref #6581 first incomplete version for making nomenclatural reference an orginal source