* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
-
package eu.etaxonomy.cdm.model.taxon;
import java.util.ArrayList;
import javax.persistence.JoinTable;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
import javax.persistence.OrderColumn;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-import org.apache.log4j.Logger;
-import org.hibernate.LazyInitializationException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.Parameter;
import org.hibernate.search.annotations.Store;
import eu.etaxonomy.cdm.common.CdmUtils;
-import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
"taxon",
"parent",
"treeIndex",
- "sortIndex",
"childNodes",
+ "sortIndex",
"countChildren",
"agentRelations",
"synonymToBeUsed",
})
@XmlRootElement(name = "TaxonNode")
@Entity
-//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
-//@Indexed(index = "eu.etaxonomy.cdm.model.taxon.TaxonNode")
@Audited
@Table(name="TaxonNode", indexes = { @javax.persistence.Index(name = "taxonNodeTreeIndex", columnList = "treeIndex") })
@ChildTaxaMustBeLowerRankThanParent(groups = Level3.class)
implements ITaxonTreeNode, ITreeNode<TaxonNode>{
private static final long serialVersionUID = -4743289894926587693L;
- private static final Logger logger = Logger.getLogger(TaxonNode.class);
+ private static final Logger logger = LogManager.getLogger(TaxonNode.class);
@XmlElement(name = "taxon")
@XmlIDREF
// @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
private TaxonNode parent;
+ @XmlElementWrapper(name = "childNodes")
+ @XmlElement(name = "childNode")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ //see https://dev.e-taxonomy.eu/redmine/issues/3722
+ //see https://dev.e-taxonomy.eu/redmine/issues/4200
+ //see https://dev.e-taxonomy.eu/redmine/issues/8127
+ //see https://dev.e-taxonomy.eu/redmine/issues/10067
+ @OrderColumn(name="sortIndex", nullable=true)
+ @OneToMany(mappedBy="parent", fetch=FetchType.LAZY)
+ //do not cascade
+ private List<TaxonNode> childNodes = new ArrayList<>();
+
+ @XmlElement(name = "countChildren")
+ private int countChildren;
+
@XmlElement(name = "treeIndex")
@Column(length=255)
@Field(store = Store.YES, index = Index.YES, analyze = Analyze.NO)
@IndexedEmbedded(includeEmbeddedObjectId=true)
private Classification classification;
- @XmlElementWrapper(name = "childNodes")
- @XmlElement(name = "childNode")
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- //see https://dev.e-taxonomy.eu/redmine/issues/3722
- @OrderColumn(name="sortIndex")
- @OrderBy("sortIndex")
- @OneToMany(mappedBy="parent", fetch=FetchType.LAZY)
- //@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
- private List<TaxonNode> childNodes = new ArrayList<>();
-
- //see https://dev.e-taxonomy.eu/redmine/issues/3722
- //see https://dev.e-taxonomy.eu/redmine/issues/4200
- private Integer sortIndex = -1;
-
-// //the source for this placement
-// @XmlElement(name = "source")
-// @XmlIDREF
-// @XmlSchemaType(name = "IDREF")
-// @OneToOne(fetch = FetchType.LAZY, orphanRemoval=true)
-// @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE, CascadeType.DELETE, CascadeType.PERSIST})
-// private DescriptionElementSource source;
-
- @XmlElement(name = "countChildren")
- private int countChildren;
-
@XmlElementWrapper(name = "agentRelations")
@XmlElement(name = "agentRelation")
@XmlIDREF
// ******************** CONSTRUCTOR **********************************************/
- protected TaxonNode(){super();}
+ //for hibernate use only, *packet* private required by bytebuddy
+ @Deprecated
+ TaxonNode(){}
/**
* to create nodes either use {@link Classification#addChildTaxon(Taxon, Reference, String, Synonym)}
// ************************* GETTER / SETTER *******************************/
- @Transient
- public Integer getSortIndex() {
- return sortIndex;
- }
- /**
- * SortIndex shall be handled only internally, therefore not public.
- * However, as javaassist only supports protected methods it needs to be protected, not private.
- * Alternatively we could use deproxy on every call of this method (see commented code)
- * @param i
- * @return
- * @deprecated for internal use only
- */
- @Deprecated
- protected void setSortIndex(Integer i) {
-// CdmBase.deproxy(this, TaxonNode.class).sortIndex = i; //alternative solution for private, DON'T remove
- sortIndex = i;
- }
-
public Taxon getTaxon() {
return taxon;
}
//#8281 indicates a preliminary placement
public boolean isDoubtful() {return hasStatus(TaxonNodeStatus.DOUBTFUL);}
- public boolean isExcluded() {return hasStatus(TaxonNodeStatus.EXCLUDED);}
-
-//************************* SOURCE *********************/
-
-// @Override
-// @Transient
-// public String getMicroReference() {
-// return source == null ? null : this.source.getCitationMicroReference();
-// }
-// public void setMicroReference(String microReference) {
-// this.getSource(true).setCitationMicroReference(StringUtils.isBlank(microReference)? null : microReference);
-// checkNullSource();
-// }
-//
-// @Override
-// @Transient
-// public Reference getReference() {
-// return (this.source == null) ? null : source.getCitation();
-// }
-// public void setReference(Reference reference) {
-// getSource(true).setCitation(reference);
-// checkNullSource();
-// }
-
-// @Override
-// public DescriptionElementSource getSource() {
-// return source;
-// }
-// @Override
-// public void setSource(DescriptionElementSource source) {
-// this.source = source;
-// }
+ /**
+ * <code>true</code> if status is {@link TaxonNodeStatus#EXCLUDED} or any
+ * of its child status
+ */
+ public boolean isExcluded() {return isOrIsKindOf(TaxonNodeStatus.EXCLUDED);}
+ /**
+ * <code>true</code> if status is {@link TaxonNodeStatus#EXCLUDED} but not
+ * a sub-status (more specific excluded status)
+ */
+ public boolean isExcludedExact() {return hasStatus(TaxonNodeStatus.EXCLUDED);}
+ public boolean isGeographicallyExcluded() {return hasStatus(TaxonNodeStatus.EXCLUDED_GEO);}
+
+ public boolean isTaxonomicallyExcluded() {return hasStatus(TaxonNodeStatus.EXCLUDED_TAX);}
+
+ public boolean isNomenclaturallyExcluded() {return hasStatus(TaxonNodeStatus.EXCLUDED_NOM);}
+
+ public boolean isUncertainApplication() {return hasStatus(TaxonNodeStatus.UNCERTAIN_APPLICATION);}
+
+ public boolean isUnresolved() {return hasStatus(TaxonNodeStatus.UNRESOLVED);}
//************************************************************/
+ /**
+ * The computed order index of this node being a child in the parents
+ * childnode list.
+ */
+ @Transient
+ public Integer getSortIndex() {
+ return getParent() == null ? null : getParent().getChildNodes().indexOf(CdmBase.deproxy(this));
+ }
+
//countChildren
public int getCountChildren() {
return countChildren;
}
// check if this node is a descendant of the childNode
if(child.getParent() != this && child.isAncestor(this)){
- throw new IllegalAncestryException("New parent node is a descendant of the node to be moved.");
+ throw new IllegalStateException("New parent node is a descendant of the node to be moved.");
}
child.setParentTreeNode(this, index);
child.setSource(source);
-
return child;
}
childNodes.remove(index);
child.setClassification(null);
- //update sortindex
- //TODO workaround (see sortIndex doc)
this.countChildren = childNodes.size();
child.setParent(null);
child.setTreeIndex(null);
- updateSortIndex(index);
- child.setSortIndex(null);
}
}
-
/**
* Remove this taxonNode From its taxonomic parent
*
/**
* Sets the parent of this taxon node to the given parent. Cleans up references to
* old parents and sets the classification to the new parents classification
- *
- * @param parent
*/
@Transient
protected void setParentTreeNode(TaxonNode parent, int index){
// add this node to the parent's child nodes
parent = CdmBase.deproxy(parent);
List<TaxonNode> parentChildren = parent.getChildNodes();
- //TODO: Only as a workaround. We have to find out why merge creates null entries.
-// HHH_9751_Util.removeAllNull(parentChildren);
-// parent.updateSortIndex(0);
if (index > parent.getChildNodes().size()){
index = parent.getChildNodes().size();
}
parentChildren.add(index, this);
}
-
- //sortIndex
- //TODO workaround (see sortIndex doc)
- // this.getParent().removeNullValueFromChildren();
- this.getParent().updateSortIndex(index);
- //only for debugging
- if (this.getSortIndex() == null){
- logger.warn("sortindex is null. This should not happen.");
- }else if (! this.getSortIndex().equals(index)){
- logger.warn("index and sortindex are not equal: " + this.getSortIndex() + ";" + index);
- }
+// //only for debugging
+// if (this.getSortIndex() == null){
+// logger.warn("sortindex is null. This should not happen.");
+// }else if (! this.getSortIndex().equals(index)){
+// logger.warn("index and sortindex are not equal: " + this.getSortIndex() + ";" + index);
+// }
// update the children count
parent.setCountChildren(parent.getChildNodes().size());
}
- /**
- * As long as the sort index is not correctly handled through hibernate this is a workaround method
- * to update the sort index manually
- * @param parentChildren
- * @param index
- */
- private void updateSortIndex(int index) {
- if (this.hasChildNodes()){
- List<TaxonNode> children = this.getChildNodes();
- HHH_9751_Util.removeAllNull(children);
- for(int i = index; i < children.size(); i++){
- TaxonNode child = children.get(i);
- if (child != null){
- // child = CdmBase.deproxy(child, TaxonNode.class); //deproxy not needed as long as setSortIndex is protected or public #4200
- child.setSortIndex(i);
- }else{
- String message = "A node in a taxon tree must never be null but is (ParentId: %d; sort index: %d; index: %d; i: %d)";
- throw new IllegalStateException(String.format(message, getId(), sortIndex, index, i));
- }
- }
- }
- }
-
/**
* Returns a set containing this node and all nodes that are descendants of this node.
*/
return getTaxon() == null? null: getTaxon().getName();
}
- public void removeNullValueFromChildren(){
- try {
- //HHH_9751_Util.removeAllNull(childNodes);
- this.updateSortIndex(0);
- } catch (LazyInitializationException e) {
- logger.info("Cannot clean up uninitialized children without a session, skipping.");
- }
- }
-
private boolean hasStatus(TaxonNodeStatus status) {
return CdmUtils.nullSafeEqual(this.status, status);
}
+ private boolean isOrIsKindOf(TaxonNodeStatus status) {
+ if (this.status == null) {
+ return status == null;
+ }else {
+ return hasStatus(status) || this.status.isKindOf(status);
+ }
+ }
+
//*********************** CLONE ********************************************************/
/**
* Clones <i>this</i> taxon node. This is a shortcut that enables to create
BGBM BDI Projects / cdmlib.git / blobdiff