Revision 22abd4ac
Added by Andreas Müller over 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/taxonx/TaxonXNomenclatureImport.java | ||
|---|---|---|
| 50 | 50 |
*/ |
| 51 | 51 |
@Component |
| 52 | 52 |
public class TaxonXNomenclatureImport extends CdmIoBase<TaxonXImportState> implements ICdmIO<TaxonXImportState> {
|
| 53 |
private static final Logger logger = Logger.getLogger(TaxonXNomenclatureImport.class); |
|
| 53 |
private static final long serialVersionUID = 796115831082828758L; |
|
| 54 |
|
|
| 55 |
private static final Logger logger = Logger.getLogger(TaxonXNomenclatureImport.class); |
|
| 54 | 56 |
|
| 55 | 57 |
@SuppressWarnings("unused")
|
| 56 | 58 |
private static int modCount = 10000; |
| ... | ... | |
| 320 | 322 |
} |
| 321 | 323 |
|
| 322 | 324 |
|
| 323 |
private TaxonNameBase getChildrenNameType(TaxonNameBase name, String typeStr, String authorStr){
|
|
| 324 |
TaxonNameBase result = null; |
|
| 325 |
Set<TaxonBase> list = name.getTaxonBases(); |
|
| 326 |
for (TaxonBase taxonBase : list){
|
|
| 327 |
Taxon taxon; |
|
| 328 |
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
| 329 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
| 330 |
}else{
|
|
| 331 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 332 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
|
| 333 |
} |
|
| 334 |
Set<Taxon> children = taxon.getTaxonomicChildren(); |
|
| 335 |
for (Taxon child: children){
|
|
| 336 |
NonViralName childName = (CdmBase.deproxy(child.getName(), NonViralName.class)); |
|
| 337 |
if (childName.getNameCache().equals(typeStr)){
|
|
| 338 |
if (compareAuthorship(childName, authorStr)){
|
|
| 339 |
return childName; |
|
| 340 |
} |
|
| 341 |
} |
|
| 342 |
} |
|
| 343 |
} |
|
| 344 |
return result; |
|
| 345 |
} |
|
| 325 |
// private TaxonNameBase getChildrenNameType(TaxonNameBase name, String typeStr, String authorStr){
|
|
| 326 |
// TaxonNameBase result = null;
|
|
| 327 |
// Set<TaxonBase> list = name.getTaxonBases();
|
|
| 328 |
// for (TaxonBase taxonBase : list){
|
|
| 329 |
// Taxon taxon;
|
|
| 330 |
// if (taxonBase.isInstanceOf(Taxon.class)){
|
|
| 331 |
// taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
| 332 |
// }else{
|
|
| 333 |
// Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
| 334 |
// taxon = syn.getAcceptedTaxa().iterator().next();
|
|
| 335 |
// }
|
|
| 336 |
// Set<Taxon> children = taxon.getTaxonomicChildren();
|
|
| 337 |
// for (Taxon child: children){
|
|
| 338 |
// NonViralName childName = (CdmBase.deproxy(child.getName(), NonViralName.class));
|
|
| 339 |
// if (childName.getNameCache().equals(typeStr)){
|
|
| 340 |
// if (compareAuthorship(childName, authorStr)){
|
|
| 341 |
// return childName;
|
|
| 342 |
// }
|
|
| 343 |
// }
|
|
| 344 |
// }
|
|
| 345 |
// }
|
|
| 346 |
// return result;
|
|
| 347 |
// }
|
|
| 346 | 348 |
|
| 347 | 349 |
private boolean compareAuthorship(NonViralName typeName, String authorStr){
|
| 348 | 350 |
boolean result = false; |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/Taxon.java | ||
|---|---|---|
| 615 | 615 |
this.relationsFromThisTaxon.remove(rel); |
| 616 | 616 |
Taxon fromTaxon = rel.getFromTaxon(); |
| 617 | 617 |
Taxon toTaxon = rel.getToTaxon(); |
| 618 |
// check if this removes the taxonomical parent. If so, also remove shortcut to the higher taxon |
|
| 619 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) ){
|
|
| 620 |
if (fromTaxon != null && fromTaxon.equals(this)){
|
|
| 621 |
this.taxonomicParentCache = null; |
|
| 622 |
}else if (toTaxon != null && toTaxon.equals(this)){
|
|
| 623 |
this.setTaxonomicChildrenCount(computeTaxonomicChildrenCount()); |
|
| 624 |
} |
|
| 625 |
} |
|
| 618 |
|
|
| 626 | 619 |
//delete Relationship from other related Taxon |
| 627 | 620 |
if (fromTaxon != this){
|
| 628 | 621 |
rel.setToTaxon(null); //remove this Taxon from relationship |
| ... | ... | |
| 672 | 665 |
if (toTaxon!=null){
|
| 673 | 666 |
toTaxon.addTaxonRelation(rel); |
| 674 | 667 |
} |
| 675 |
// check if this sets the taxonomical parent. If so, remember a shortcut to this taxon |
|
| 676 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && toTaxon!=null ){
|
|
| 677 |
this.taxonomicParentCache = toTaxon; |
|
| 678 |
} |
|
| 679 | 668 |
}else if (this.equals(toTaxon)){
|
| 680 | 669 |
relationsToThisTaxon.add(rel); |
| 681 | 670 |
// also add relation to other taxon object |
| 682 | 671 |
if (fromTaxon!=null){
|
| 683 | 672 |
fromTaxon.addTaxonRelation(rel); |
| 684 | 673 |
} |
| 685 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && fromTaxon!=null ){
|
|
| 686 |
this.taxonomicChildrenCount++; |
|
| 687 |
} |
|
| 688 |
|
|
| 689 | 674 |
} |
| 690 | 675 |
}else if (toTaxon == null || fromTaxon == null){
|
| 691 | 676 |
if (toTaxon == null){
|
| ... | ... | |
| 694 | 679 |
if (fromTaxon!= null){
|
| 695 | 680 |
fromTaxon.addTaxonRelation(rel); |
| 696 | 681 |
} |
| 697 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && fromTaxon!=null ){
|
|
| 698 |
this.taxonomicChildrenCount++; |
|
| 699 |
} |
|
| 700 | 682 |
}else if (fromTaxon == null && toTaxon != null){
|
| 701 | 683 |
fromTaxon = this; |
| 702 | 684 |
relationsFromThisTaxon.add(rel); |
| 703 |
if (toTaxon!=null){
|
|
| 704 |
toTaxon.addTaxonRelation(rel); |
|
| 705 |
} |
|
| 706 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && toTaxon!=null ){
|
|
| 707 |
this.taxonomicParentCache = toTaxon; |
|
| 708 |
} |
|
| 685 |
toTaxon.addTaxonRelation(rel); |
|
| 709 | 686 |
} |
| 710 | 687 |
} |
| 711 | 688 |
} |
| 712 | 689 |
} |
| 713 | 690 |
|
| 714 |
/* (non-Javadoc) |
|
| 715 |
* @see eu.etaxonomy.cdm.model.common.IRelated#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase) |
|
| 716 |
*/ |
|
| 691 |
|
|
| 717 | 692 |
@Override |
| 718 | 693 |
@Deprecated //for inner use by RelationshipBase only |
| 719 | 694 |
public void addRelationship(RelationshipBase rel){
|
| ... | ... | |
| 806 | 781 |
} |
| 807 | 782 |
} |
| 808 | 783 |
|
| 809 |
/** |
|
| 810 |
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
|
| 811 |
* "taxonomically included in") instance where <i>this</i> taxon plays the target |
|
| 812 |
* role (parent) and adds it to the set of |
|
| 813 |
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to <i>this</i> taxon.
|
|
| 814 |
* The taxon relationship will also be added to the set of |
|
| 815 |
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the second taxon
|
|
| 816 |
* (child) involved in the created relationship.<P> |
|
| 817 |
* Since the taxon relationship concerns the modifications |
|
| 818 |
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
| 819 |
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
| 820 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 821 |
* than the rank of the taxon name used as a child taxon. |
|
| 822 |
* |
|
| 823 |
* @param child the taxon which plays the source role (child) in the new taxon relationship |
|
| 824 |
* @param citation the reference source for the new taxon relationship |
|
| 825 |
* @param microcitation the string with the details describing the exact localisation within the reference |
|
| 826 |
* @see #setTaxonomicParent(Taxon, Reference, String) |
|
| 827 |
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String) |
|
| 828 |
* @see #addTaxonRelation(TaxonRelationship) |
|
| 829 |
* @see #getTaxonRelations() |
|
| 830 |
* @see #getRelationsFromThisTaxon() |
|
| 831 |
* @see #getRelationsToThisTaxon() |
|
| 832 |
* @see #getTaxonomicParent() |
|
| 833 |
* @see #getTaxonomicChildrenCount() |
|
| 834 |
*/ |
|
| 835 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 836 |
public void addTaxonomicChild(Taxon child, Reference citation, String microcitation){
|
|
| 837 |
if (child == null){
|
|
| 838 |
throw new NullPointerException("Child Taxon is 'null'");
|
|
| 839 |
}else{
|
|
| 840 |
child.setTaxonomicParent(this, citation, microcitation); |
|
| 841 |
} |
|
| 842 |
} |
|
| 843 |
|
|
| 844 |
/** |
|
| 845 |
* Removes one {@link TaxonRelationship taxon relationship} with {@link TaxonRelationshipType taxon relationship type}
|
|
| 846 |
* "taxonomically included in" and with the given child taxon playing the |
|
| 847 |
* source role from the set of {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging
|
|
| 848 |
* to <i>this</i> taxon. The taxon relationship will also be removed from the set |
|
| 849 |
* of {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the child taxon.
|
|
| 850 |
* Furthermore the inherited RelatedFrom and RelatedTo attributes of the |
|
| 851 |
* taxon relationship will be nullified.<P> |
|
| 852 |
* Since the taxon relationship concerns the classification modifications |
|
| 853 |
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
| 854 |
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
| 855 |
* |
|
| 856 |
* @param child the taxon playing the source role in the relationship to be removed |
|
| 857 |
* @see #removeTaxonRelation(TaxonRelationship) |
|
| 858 |
* @see #getRelationsToThisTaxon() |
|
| 859 |
* @see #getRelationsFromThisTaxon() |
|
| 860 |
* @see #getTaxonomicParent() |
|
| 861 |
* @see #getTaxonomicChildrenCount() |
|
| 862 |
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom() |
|
| 863 |
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedTo() |
|
| 864 |
* |
|
| 865 |
*/ |
|
| 866 |
@Deprecated //will be removed in future versions. Use classification/TaxonNode instead |
|
| 867 |
public void removeTaxonomicChild(Taxon child){
|
|
| 868 |
Set<TaxonRelationship> taxRels = this.getTaxonRelations(); |
|
| 869 |
for (TaxonRelationship taxRel : taxRels ){
|
|
| 870 |
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) |
|
| 871 |
&& taxRel.getFromTaxon().equals(child)){
|
|
| 872 |
this.removeTaxonRelation(taxRel); |
|
| 873 |
} |
|
| 874 |
} |
|
| 875 |
} |
|
| 876 |
|
|
| 877 |
/** |
|
| 878 |
* Returns the taxon which is the next higher taxon (parent) of <i>this</i> taxon |
|
| 879 |
* within the classification and which is stored in the |
|
| 880 |
* TaxonomicParentCache attribute. Each taxon can have only one parent taxon. |
|
| 881 |
* The child taxon and the parent taxon play the source respectively the |
|
| 882 |
* target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 883 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 884 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 885 |
* than the rank of the taxon name used as a child taxon. |
|
| 886 |
* |
|
| 887 |
* @see #setTaxonomicParent(Taxon, Reference, String) |
|
| 888 |
* @see #getTaxonomicChildren() |
|
| 889 |
* @see #getTaxonomicChildrenCount() |
|
| 890 |
* @see #getRelationsFromThisTaxon() |
|
| 891 |
*/ |
|
| 892 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 893 |
public Taxon getTaxonomicParent() {
|
|
| 894 |
return this.taxonomicParentCache; |
|
| 895 |
} |
|
| 896 |
|
|
| 897 |
/** |
|
| 898 |
* Sets the taxononomic parent of <i>this</i> taxon to null. |
|
| 899 |
* Note that this method does not handle taxonomic relationships. |
|
| 900 |
*/ |
|
| 901 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 902 |
public void nullifyTaxonomicParent() {
|
|
| 903 |
this.taxonomicParentCache = null; |
|
| 904 |
} |
|
| 905 |
|
|
| 906 |
/** |
|
| 907 |
* Replaces both the taxonomic parent cache with the given new parent taxon |
|
| 908 |
* and the corresponding taxon relationship with a new {@link TaxonRelationship taxon relationship}
|
|
| 909 |
* (with {@link TaxonRelationshipType taxon relationship type} "taxonomically included in") instance.
|
|
| 910 |
* In the new taxon relationship <i>this</i> taxon plays the source role (child). |
|
| 911 |
* This method creates and adds the new taxon relationship to the set of |
|
| 912 |
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to <i>this</i> taxon.
|
|
| 913 |
* The taxon relationship will also be added to the set of |
|
| 914 |
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to the second taxon
|
|
| 915 |
* (parent) involved in the new relationship.<P> |
|
| 916 |
* Since the taxon relationship concerns the classification modifications |
|
| 917 |
* of the {@link #getTaxonomicParent() parent taxon} for <i>this</i> taxon and of the number of
|
|
| 918 |
* {@link #getTaxonomicChildrenCount() childrens} for the child taxon will be stored.
|
|
| 919 |
* |
|
| 920 |
* @param newParent the taxon which plays the target role (parent) in the new taxon relationship |
|
| 921 |
* @param citation the reference source for the new taxon relationship |
|
| 922 |
* @param microcitation the string with the details describing the exact localisation within the reference |
|
| 923 |
* @see #removeTaxonRelation(TaxonRelationship) |
|
| 924 |
* @see #getTaxonomicParent() |
|
| 925 |
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String) |
|
| 926 |
* @see #addTaxonRelation(TaxonRelationship) |
|
| 927 |
* @see #getTaxonRelations() |
|
| 928 |
* @see #getRelationsFromThisTaxon() |
|
| 929 |
* @see #getRelationsToThisTaxon() |
|
| 930 |
* @see #getTaxonomicChildrenCount() |
|
| 931 |
*/ |
|
| 932 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 933 |
public void setTaxonomicParent(Taxon newParent, Reference citation, String microcitation){
|
|
| 934 |
//remove previously existing parent relationship!!! |
|
| 935 |
Taxon oldParent = this.getTaxonomicParent(); |
|
| 936 |
Set<TaxonRelationship> taxRels = this.getTaxonRelations(); |
|
| 937 |
for (TaxonRelationship taxRel : taxRels ){
|
|
| 938 |
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && taxRel.getToTaxon().equals(oldParent)){
|
|
| 939 |
this.removeTaxonRelation(taxRel); |
|
| 940 |
} |
|
| 941 |
} |
|
| 942 |
//add new parent |
|
| 943 |
if (newParent != null){
|
|
| 944 |
addTaxonRelation(newParent, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),citation,microcitation); |
|
| 945 |
} |
|
| 946 |
} |
|
| 947 |
|
|
| 948 |
/** |
|
| 949 |
* Returns the set of taxa which have <i>this</i> taxon as next higher taxon |
|
| 950 |
* (parent) within the classification. Each taxon can have several child |
|
| 951 |
* taxa. The child taxon and the parent taxon play the source respectively |
|
| 952 |
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 953 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 954 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 955 |
* than the rank of the taxon name used as a child taxon. |
|
| 956 |
* |
|
| 957 |
* @see #getTaxonomicParent() |
|
| 958 |
* @see #addTaxonomicChild(Taxon, Reference, String) |
|
| 959 |
* @see #getTaxonomicChildrenCount() |
|
| 960 |
* @see #getRelationsToThisTaxon() |
|
| 961 |
*/ |
|
| 962 |
@Transient |
|
| 963 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 964 |
public Set<Taxon> getTaxonomicChildren() {
|
|
| 965 |
Set<Taxon> taxa = new HashSet<Taxon>(); |
|
| 966 |
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon(); |
|
| 967 |
for (TaxonRelationship rel: rels){
|
|
| 968 |
TaxonRelationshipType tt = rel.getType(); |
|
| 969 |
TaxonRelationshipType incl = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); |
|
| 970 |
if (tt.equals(incl)){
|
|
| 971 |
taxa.add(rel.getFromTaxon()); |
|
| 972 |
} |
|
| 973 |
} |
|
| 974 |
return taxa; |
|
| 975 |
} |
|
| 976 |
|
|
| 977 |
/** |
|
| 978 |
* Returns the number of taxa which have <i>this</i> taxon as next higher taxon |
|
| 979 |
* (parent) within the classification and the number of which is stored in |
|
| 980 |
* the TaxonomicChildrenCount attribute. Each taxon can have several child |
|
| 981 |
* taxa. The child taxon and the parent taxon play the source respectively |
|
| 982 |
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
| 983 |
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
| 984 |
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
| 985 |
* than the rank of the taxon name used as a child taxon. |
|
| 986 |
* |
|
| 987 |
* @see #getTaxonomicChildren() |
|
| 988 |
* @see #getRelationsToThisTaxon() |
|
| 989 |
*/ |
|
| 990 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 991 |
public int getTaxonomicChildrenCount(){
|
|
| 992 |
return taxonomicChildrenCount; |
|
| 993 |
} |
|
| 994 |
|
|
| 995 |
/** |
|
| 996 |
* @see #getTaxonomicChildrenCount() |
|
| 997 |
*/ |
|
| 998 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 999 |
public void setTaxonomicChildrenCount(int taxonomicChildrenCount) {
|
|
| 1000 |
this.taxonomicChildrenCount = taxonomicChildrenCount; |
|
| 1001 |
} |
|
| 1002 |
|
|
| 1003 |
/** |
|
| 1004 |
* Returns the boolean value indicating whether <i>this</i> taxon has at least one |
|
| 1005 |
* taxonomic child taxon within the classification (true) or not (false). |
|
| 1006 |
* |
|
| 1007 |
* @see #getTaxonomicChildrenCount() |
|
| 1008 |
* @see #getTaxonomicChildren() |
|
| 1009 |
*/ |
|
| 1010 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 1011 |
@Transient |
|
| 1012 |
public boolean hasTaxonomicChildren(){
|
|
| 1013 |
return this.taxonomicChildrenCount > 0; |
|
| 1014 |
} |
|
| 1015 |
|
|
| 1016 |
@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead |
|
| 1017 |
private int computeTaxonomicChildrenCount(){
|
|
| 1018 |
int count = 0; |
|
| 1019 |
for (TaxonRelationship rel: this.getRelationsToThisTaxon()){
|
|
| 1020 |
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
|
|
| 1021 |
count++; |
|
| 1022 |
} |
|
| 1023 |
} |
|
| 1024 |
return count; |
|
| 1025 |
} |
|
| 1026 |
|
|
| 1027 |
|
|
| 1028 | 784 |
/** |
| 1029 | 785 |
* Returns the boolean value indicating whether <i>this</i> taxon is a misaplication |
| 1030 | 786 |
* (misapplied name) for at least one other taxon. |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/datagenerator/TaxonGenerator.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.datagenerator; |
| 11 | 11 |
|
| 12 |
import java.util.Random; |
|
| 13 |
|
|
| 14 | 12 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 15 | 13 |
import eu.etaxonomy.cdm.model.common.Language; |
| 16 | 14 |
import eu.etaxonomy.cdm.model.common.LanguageString; |
| ... | ... | |
| 19 | 17 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 20 | 18 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 21 | 19 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 22 |
//import eu.etaxonomy.cdm.model.reference.Book; |
|
| 23 |
//import eu.etaxonomy.cdm.model.reference.Database; |
|
| 24 | 20 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 25 | 21 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 26 | 22 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 38 | 34 |
private static String[] epitheta = {"vulgaris", "magdalena", "officinalis", "alba", "negra", "communa", "alpina", "rotundifolia", "greutheriana", "helventica", "allemania", "franca"};
|
| 39 | 35 |
private static String[] ranks = {"subsp", "var", "f"};
|
| 40 | 36 |
|
| 41 |
private Random rnd = new Random(); |
|
| 42 |
|
|
| 43 | 37 |
public static Taxon getTestTaxon(){
|
| 44 | 38 |
Person deCandolle = Person.NewInstance(); |
| 45 | 39 |
deCandolle.setTitleCache("DC.", true);
|
| ... | ... | |
| 71 | 65 |
botSpecies.setCombinationAuthorship(Person.NewInstance()); |
| 72 | 66 |
botSpecies.getCombinationAuthorship().setNomenclaturalTitle("Pau");
|
| 73 | 67 |
Taxon childTaxon = Taxon.NewInstance(botSpecies, sec); |
| 74 |
childTaxon.setTaxonomicParent(genusTaxon, citationRef, "456"); |
|
| 68 |
// childTaxon.setTaxonomicParent(genusTaxon, citationRef, "456");
|
|
| 75 | 69 |
|
| 76 | 70 |
//homotypic synonym of childTaxon1 |
| 77 | 71 |
BotanicalName botSpecies4= BotanicalName.NewInstance(Rank.SPECIES()); |
| ... | ... | |
| 91 | 85 |
botSpecies2.setCombinationAuthorship(Person.NewInstance()); |
| 92 | 86 |
botSpecies2.getCombinationAuthorship().setNomenclaturalTitle("Zahn");
|
| 93 | 87 |
Taxon childTaxon2 = Taxon.NewInstance(botSpecies2, sec); |
| 94 |
childTaxon2.setTaxonomicParent(genusTaxon, citationRef, "499"); |
|
| 88 |
// childTaxon2.setTaxonomicParent(genusTaxon, citationRef, "499");
|
|
| 95 | 89 |
|
| 96 | 90 |
//heterotypic synonym of childTaxon2 |
| 97 | 91 |
BotanicalName botSpecies3= BotanicalName.NewInstance(Rank.SPECIES()); |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/TaxonTest.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.test.unit.EntityTestBase; |
| 39 | 39 |
|
| 40 | 40 |
public class TaxonTest extends EntityTestBase {
|
| 41 |
private static final Logger logger = Logger.getLogger(TaxonTest.class);
|
|
| 42 |
|
|
| 41 |
@SuppressWarnings("unused")
|
|
| 42 |
private static final Logger logger = Logger.getLogger(TaxonTest.class); |
|
| 43 | 43 |
|
| 44 | 44 |
private Reference sec; |
| 45 | 45 |
private Reference misSec; |
| ... | ... | |
| 85 | 85 |
// newTree.addParentChild(rootT, child1, sec, "p.998"); |
| 86 | 86 |
// newTree.addParentChild(rootT, child2, sec, "p.987"); |
| 87 | 87 |
|
| 88 |
rootT.addTaxonomicChild(child1, sec, "p.998"); |
|
| 89 |
rootT.addTaxonomicChild(child2, sec, "p.987"); |
|
| 90 | 88 |
// synonymy |
| 91 | 89 |
syn1=Synonym.NewInstance(name1,sec); |
| 92 | 90 |
syn2=Synonym.NewInstance(name2,sec); |
| ... | ... | |
| 104 | 102 |
assertTrue(rootT.generateTitle().startsWith(rootT.getName().getTitleCache())); |
| 105 | 103 |
} |
| 106 | 104 |
|
| 107 |
@Test |
|
| 108 |
public void testAddTaxonomicChild() {
|
|
| 109 |
|
|
| 110 |
rootT.addTaxonomicChild(freeT, null, null); |
|
| 111 |
Assert.assertEquals(Integer.valueOf(3), Integer.valueOf(rootT.getTaxonomicChildren().size())); |
|
| 112 |
} |
|
| 113 |
|
|
| 114 |
@Test |
|
| 115 |
public void testGetTaxonomicParent() {
|
|
| 116 |
assertEquals(rootT, child2.getTaxonomicParent()); |
|
| 117 |
} |
|
| 118 |
|
|
| 119 |
@Test |
|
| 120 |
public void testSetTaxonomicParent() {
|
|
| 121 |
child2.setTaxonomicParent(child1, null, null); |
|
| 122 |
assertEquals(child1, child2.getTaxonomicParent()); |
|
| 123 |
} |
|
| 124 |
|
|
| 125 |
@Test |
|
| 126 |
public void testGetTaxonomicChildren() {
|
|
| 127 |
Set<Taxon> kids=rootT.getTaxonomicChildren(); |
|
| 128 |
assertTrue(kids.size()==2 && kids.contains(child1) && kids.contains(child2)); |
|
| 129 |
} |
|
| 130 |
|
|
| 131 |
@Test |
|
| 132 |
public void testHasTaxonomicChildren() {
|
|
| 133 |
assertFalse(child2.hasTaxonomicChildren()); |
|
| 134 |
assertTrue(rootT.hasTaxonomicChildren()); |
|
| 135 |
rootT.removeTaxonomicChild(child1); |
|
| 136 |
assertTrue(rootT.hasTaxonomicChildren()); |
|
| 137 |
rootT.removeTaxonomicChild(child2); |
|
| 138 |
assertFalse(rootT.hasTaxonomicChildren()); |
|
| 139 |
} |
|
| 140 |
|
|
| 141 |
@Test |
|
| 142 |
public void testGetTaxonomicChildrenCount() {
|
|
| 143 |
assertEquals(0, child2.getTaxonomicChildrenCount()); |
|
| 144 |
assertEquals(2, rootT.getTaxonomicChildrenCount()); |
|
| 145 |
rootT.removeTaxonomicChild(child1); |
|
| 146 |
assertEquals(1, rootT.getTaxonomicChildrenCount()); |
|
| 147 |
rootT.removeTaxonomicChild(child2); |
|
| 148 |
assertEquals(0, rootT.getTaxonomicChildrenCount()); |
|
| 149 |
} |
|
| 150 |
|
|
| 151 | 105 |
@Test |
| 152 | 106 |
public void testIsMisappliedName() {
|
| 153 | 107 |
assertFalse(child2.isMisapplication()); |
| ... | ... | |
| 189 | 143 |
assertEquals("The taxon has not properly been removed from the description", null, desc.getTaxon());
|
| 190 | 144 |
} |
| 191 | 145 |
|
| 192 |
/** |
|
| 193 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getDescriptions()}.
|
|
| 194 |
*/ |
|
| 195 |
@Test |
|
| 196 |
public void testGetDescriptions() {
|
|
| 197 |
logger.warn("Not yet implemented");
|
|
| 198 |
} |
|
| 199 |
|
|
| 200 |
/** |
|
| 201 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#setDescriptions(java.util.Set)}.
|
|
| 202 |
*/ |
|
| 203 |
@Test |
|
| 204 |
public void testSetDescriptions() {
|
|
| 205 |
logger.warn("Not yet implemented");
|
|
| 206 |
} |
|
| 207 |
|
|
| 208 |
/** |
|
| 209 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addDescription(eu.etaxonomy.cdm.model.description.TaxonDescription)}.
|
|
| 210 |
*/ |
|
| 211 |
@Test |
|
| 212 |
public void testAddDescription() {
|
|
| 213 |
logger.warn("Not yet implemented");
|
|
| 214 |
} |
|
| 215 |
|
|
| 216 |
/** |
|
| 217 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeDescription(eu.etaxonomy.cdm.model.description.TaxonDescription)}.
|
|
| 218 |
*/ |
|
| 219 |
@Test |
|
| 220 |
public void testRemoveDescription() {
|
|
| 221 |
logger.warn("Not yet implemented");
|
|
| 222 |
} |
|
| 223 |
|
|
| 224 |
/** |
|
| 225 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getSynonymRelations()}.
|
|
| 226 |
*/ |
|
| 227 |
@Test |
|
| 228 |
public void testGetSynonymRelations() {
|
|
| 229 |
logger.warn("Not yet implemented");
|
|
| 230 |
} |
|
| 231 |
|
|
| 232 |
/** |
|
| 233 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#setSynonymRelations(java.util.Set)}.
|
|
| 234 |
*/ |
|
| 235 |
@Test |
|
| 236 |
public void testSetSynonymRelations() {
|
|
| 237 |
logger.warn("Not yet implemented");
|
|
| 238 |
} |
|
| 239 |
|
|
| 240 |
/** |
|
| 241 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonymRelation(eu.etaxonomy.cdm.model.taxon.SynonymRelationship)}.
|
|
| 242 |
*/ |
|
| 243 |
@Test |
|
| 244 |
public void testAddSynonymRelation() {
|
|
| 245 |
logger.warn("Not yet implemented");
|
|
| 246 |
} |
|
| 247 |
|
|
| 248 |
/** |
|
| 249 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeSynonymRelation(eu.etaxonomy.cdm.model.taxon.SynonymRelationship)}.
|
|
| 250 |
*/ |
|
| 251 |
@Test |
|
| 252 |
public void testRemoveSynonymRelation() {
|
|
| 253 |
logger.warn("Not yet implemented");
|
|
| 254 |
} |
|
| 255 |
|
|
| 256 |
/** |
|
| 257 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getRelationsFromThisTaxon()}.
|
|
| 258 |
*/ |
|
| 259 |
@Test |
|
| 260 |
public void testGetRelationsFromThisTaxon() {
|
|
| 261 |
logger.warn("Not yet implemented");
|
|
| 262 |
} |
|
| 263 |
|
|
| 264 |
/** |
|
| 265 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#setRelationsFromThisTaxon(java.util.Set)}.
|
|
| 266 |
*/ |
|
| 267 |
@Test |
|
| 268 |
public void testSetRelationsFromThisTaxon() {
|
|
| 269 |
logger.warn("Not yet implemented");
|
|
| 270 |
} |
|
| 271 |
|
|
| 272 |
/** |
|
| 273 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getRelationsToThisTaxon()}.
|
|
| 274 |
*/ |
|
| 275 |
@Test |
|
| 276 |
public void testGetRelationsToThisTaxon() {
|
|
| 277 |
logger.warn("Not yet implemented");
|
|
| 278 |
} |
|
| 279 |
|
|
| 280 |
/** |
|
| 281 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#setRelationsToThisTaxon(java.util.Set)}.
|
|
| 282 |
*/ |
|
| 283 |
@Test |
|
| 284 |
public void testSetRelationsToThisTaxon() {
|
|
| 285 |
logger.warn("Not yet implemented");
|
|
| 286 |
} |
|
| 287 |
|
|
| 288 | 146 |
/** |
| 289 | 147 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getTaxonRelations()}.
|
| 290 | 148 |
*/ |
| ... | ... | |
| 326 | 184 |
assertEquals("There should be exactly one taxon relationships", 1, taxon.getTaxonRelations().size());
|
| 327 | 185 |
} |
| 328 | 186 |
|
| 329 |
/** |
|
| 330 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase)}.
|
|
| 331 |
*/ |
|
| 332 |
@Test |
|
| 333 |
public void testAddRelationship() {
|
|
| 334 |
logger.warn("Not yet implemented");
|
|
| 335 |
} |
|
| 336 |
|
|
| 337 |
/** |
|
| 338 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addTaxonRelation(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 339 |
*/ |
|
| 340 |
@Test |
|
| 341 |
public void testAddTaxonRelationTaxonTaxonRelationshipTypeReferenceBaseString() {
|
|
| 342 |
logger.warn("Not yet implemented");
|
|
| 343 |
} |
|
| 344 |
|
|
| 345 |
/** |
|
| 346 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addMisappliedName(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 347 |
*/ |
|
| 348 |
@Test |
|
| 349 |
public void testAddMisappliedName() {
|
|
| 350 |
logger.warn("Not yet implemented");
|
|
| 351 |
} |
|
| 352 |
|
|
| 353 |
|
|
| 354 |
/** |
|
| 355 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#hasSynonyms()}.
|
|
| 356 |
*/ |
|
| 357 |
@Test |
|
| 358 |
public void testHasSynonyms() {
|
|
| 359 |
logger.warn("Not yet implemented");
|
|
| 360 |
} |
|
| 361 |
|
|
| 362 |
/** |
|
| 363 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getMisappliedNames()}.
|
|
| 364 |
*/ |
|
| 365 |
@Test |
|
| 366 |
public void testGetMisappliedNames() {
|
|
| 367 |
logger.warn("Not yet implemented");
|
|
| 368 |
} |
|
| 369 |
|
|
| 370 |
|
|
| 371 |
/** |
|
| 372 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getSynonymsSortedByType()}.
|
|
| 373 |
*/ |
|
| 374 |
@Test |
|
| 375 |
public void testGetSynonymsSortedByType() {
|
|
| 376 |
logger.warn("Not yet implemented");
|
|
| 377 |
} |
|
| 378 |
|
|
| 379 |
/** |
|
| 380 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)}.
|
|
| 381 |
*/ |
|
| 382 |
@Test |
|
| 383 |
public void testAddSynonymSynonymSynonymRelationshipType() {
|
|
| 384 |
logger.warn("Not yet implemented");
|
|
| 385 |
} |
|
| 386 |
|
|
| 387 |
/** |
|
| 388 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 389 |
*/ |
|
| 390 |
@Test |
|
| 391 |
public void testAddSynonymSynonymSynonymRelationshipTypeReferenceBaseString() {
|
|
| 392 |
logger.warn("Not yet implemented");
|
|
| 393 |
} |
|
| 394 |
|
|
| 395 |
/** |
|
| 396 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)}.
|
|
| 397 |
*/ |
|
| 398 |
@Test |
|
| 399 |
public void testAddSynonymNameTaxonNameBaseSynonymRelationshipType() {
|
|
| 400 |
logger.warn("Not yet implemented");
|
|
| 401 |
} |
|
| 402 |
|
|
| 403 |
/** |
|
| 404 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 405 |
*/ |
|
| 406 |
@Test |
|
| 407 |
public void testAddSynonymNameTaxonNameBaseSynonymRelationshipTypeReferenceBaseString() {
|
|
| 408 |
logger.warn("Not yet implemented");
|
|
| 409 |
} |
|
| 410 |
|
|
| 411 |
/** |
|
| 412 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHeterotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase)}.
|
|
| 413 |
*/ |
|
| 414 |
@Test |
|
| 415 |
public void testAddHeterotypicSynonymNameTaxonNameBase() {
|
|
| 416 |
logger.warn("Not yet implemented");
|
|
| 417 |
} |
|
| 418 |
|
|
| 419 |
/** |
|
| 420 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHeterotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 421 |
*/ |
|
| 422 |
@Test |
|
| 423 |
public void testAddHeterotypicSynonymNameTaxonNameBaseHomotypicalGroupReferenceBaseString() {
|
|
| 424 |
logger.warn("Not yet implemented");
|
|
| 425 |
} |
|
| 426 |
|
|
| 427 |
/** |
|
| 428 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHomotypicSynonymName(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 429 |
*/ |
|
| 430 |
@Test |
|
| 431 |
public void testAddHomotypicSynonymName() {
|
|
| 432 |
logger.warn("Not yet implemented");
|
|
| 433 |
} |
|
| 434 |
|
|
| 435 |
/** |
|
| 436 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#addHomotypicSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)}.
|
|
| 437 |
*/ |
|
| 438 |
@Test |
|
| 439 |
public void testAddHomotypicSynonym() {
|
|
| 440 |
logger.warn("Not yet implemented");
|
|
| 441 |
} |
|
| 442 |
|
|
| 443 |
/** |
|
| 444 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#removeSynonym(eu.etaxonomy.cdm.model.taxon.Synonym)}.
|
|
| 445 |
*/ |
|
| 446 |
@Test |
|
| 447 |
public void testRemoveSynonym() {
|
|
| 448 |
logger.warn("Not yet implemented");
|
|
| 449 |
} |
|
| 450 |
|
|
| 451 |
/** |
|
| 452 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#iterator()}.
|
|
| 453 |
*/ |
|
| 454 |
@Test |
|
| 455 |
public void testIterator() {
|
|
| 456 |
logger.warn("Not yet implemented");
|
|
| 457 |
} |
|
| 458 |
|
|
| 459 |
/** |
|
| 460 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymsByHomotypicGroup()}.
|
|
| 461 |
*/ |
|
| 462 |
@Test |
|
| 463 |
public void testGetHomotypicSynonymsByHomotypicGroup() {
|
|
| 464 |
logger.warn("Not yet implemented");
|
|
| 465 |
} |
|
| 466 |
|
|
| 467 |
/** |
|
| 468 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymsByHomotypicRelationship()}.
|
|
| 469 |
*/ |
|
| 470 |
@Test |
|
| 471 |
public void testGetHomotypicSynonymsByHomotypicRelationship() {
|
|
| 472 |
logger.warn("Not yet implemented");
|
|
| 473 |
} |
|
| 474 |
|
|
| 475 |
/** |
|
| 476 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHomotypicSynonymyGroups()}.
|
|
| 477 |
*/ |
|
| 478 |
@Test |
|
| 479 |
public void testGetHomotypicSynonymyGroups() {
|
|
| 480 |
logger.warn("Not yet implemented");
|
|
| 481 |
} |
|
| 482 |
|
|
| 483 |
/** |
|
| 484 |
* Test method for {@link eu.etaxonomy.cdm.model.taxon.Taxon#getHeterotypicSynonymyGroups()}.
|
|
| 485 |
*/ |
|
| 486 |
@Test |
|
| 487 |
public void testGetHeterotypicSynonymyGroups() {
|
|
| 488 |
logger.warn("Not yet implemented");
|
|
| 489 |
} |
|
| 490 |
|
|
| 491 | 187 |
|
| 492 | 188 |
@Test |
| 493 | 189 |
public void testAddRemoveSynonymInSameGroup(){
|
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java | ||
|---|---|---|
| 66 | 66 |
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao; |
| 67 | 67 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao; |
| 68 | 68 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 69 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 70 | 69 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
| 71 | 70 |
import eu.etaxonomy.cdm.persistence.query.OrderHint; |
| 72 | 71 |
|
| ... | ... | |
| 98 | 97 |
// this.alternativeSpellingSuggestionParser = alternativeSpellingSuggestionParser; |
| 99 | 98 |
// } |
| 100 | 99 |
|
| 101 |
@Override |
|
| 102 |
public List<Taxon> getRootTaxa(Reference sec) {
|
|
| 103 |
return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true, false); |
|
| 104 |
} |
|
| 105 |
|
|
| 106 |
@Override |
|
| 107 |
public List<Taxon> getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {
|
|
| 108 |
checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");
|
|
| 109 |
if (onlyWithChildren == null){
|
|
| 110 |
onlyWithChildren = true; |
|
| 111 |
} |
|
| 112 |
if (withMisapplications == null){
|
|
| 113 |
withMisapplications = true; |
|
| 114 |
} |
|
| 115 |
if (cdmFetch == null){
|
|
| 116 |
cdmFetch = CdmFetch.NO_FETCH(); |
|
| 117 |
} |
|
| 118 |
|
|
| 119 |
Criteria crit = getSession().createCriteria(Taxon.class); |
|
| 120 |
|
|
| 121 |
crit.setFetchMode("name", FetchMode.JOIN);
|
|
| 122 |
crit.createAlias("name", "name");
|
|
| 123 |
|
|
| 124 |
if (rank != null) {
|
|
| 125 |
crit.add(Restrictions.eq("name.rank", rank));
|
|
| 126 |
}else{
|
|
| 127 |
crit.add(Restrictions.isNull("taxonomicParentCache"));
|
|
| 128 |
} |
|
| 129 |
|
|
| 130 |
if (sec != null){
|
|
| 131 |
crit.add(Restrictions.eq("sec", sec) );
|
|
| 132 |
} |
|
| 133 |
|
|
| 134 |
if (! cdmFetch.includes(CdmFetch.FETCH_CHILDTAXA())){
|
|
| 135 |
logger.info("Not fetching child taxa");
|
|
| 136 |
//TODO overwrite LAZY (SELECT) does not work (bug in hibernate?) |
|
| 137 |
crit.setFetchMode("relationsToThisTaxon.fromTaxon", FetchMode.LAZY);
|
|
| 138 |
} |
|
| 139 |
|
|
| 140 |
List<Taxon> results = new ArrayList<Taxon>(); |
|
| 141 |
@SuppressWarnings("unchecked")
|
|
| 142 |
List<Taxon> taxa = crit.list(); |
|
| 143 |
for(Taxon taxon : taxa){
|
|
| 144 |
|
|
| 145 |
|
|
| 146 |
//childTaxa |
|
| 147 |
//TODO create restriction instead |
|
| 148 |
// (a) not using cache fields |
|
| 149 |
/*Hibernate.initialize(taxon.getRelationsFromThisTaxon()); |
|
| 150 |
if (onlyWithChildren == false || taxon.getRelationsFromThisTaxon().size() > 0){
|
|
| 151 |
if (withMisapplications == true || ! taxon.isMisappliedName()){
|
|
| 152 |
defaultBeanInitializer.initialize(taxon, propertyPaths); |
|
| 153 |
results.add(taxon); |
|
| 154 |
} |
|
| 155 |
}*/ |
|
| 156 |
// (b) using cache fields |
|
| 157 |
if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){
|
|
| 158 |
if (withMisapplications == true || ! taxon.isMisapplication()){
|
|
| 159 |
defaultBeanInitializer.initialize(taxon, propertyPaths); |
|
| 160 |
results.add(taxon); |
|
| 161 |
} |
|
| 162 |
} |
|
| 163 |
} |
|
| 164 |
return results; |
|
| 165 |
} |
|
| 166 |
|
|
| 167 |
@Override |
|
| 168 |
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {
|
|
| 169 |
return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null); |
|
| 170 |
} |
|
| 171 | 100 |
|
| 172 | 101 |
@Override |
| 173 | 102 |
public List<TaxonBase> getTaxaByName(String queryString, Reference sec) {
|
| ... | ... | |
| 979 | 908 |
for (Iterator<TaxonRelationship> iterator = ((Taxon)taxonBase).getRelationsFromThisTaxon().iterator(); iterator.hasNext();){
|
| 980 | 909 |
TaxonRelationship relationFromThisTaxon = iterator.next(); |
| 981 | 910 |
|
| 982 |
// decrease children count of taxonomic parent by one |
|
| 983 |
if (relationFromThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {
|
|
| 984 |
Taxon toTaxon = relationFromThisTaxon.getToTaxon(); // parent |
|
| 985 |
if (toTaxon != null) {
|
|
| 986 |
toTaxon.setTaxonomicChildrenCount(toTaxon.getTaxonomicChildrenCount() - 1); |
|
| 987 |
} |
|
| 988 |
} |
|
| 989 | 911 |
} |
| 990 | 912 |
} |
| 991 | 913 |
|
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java | ||
|---|---|---|
| 36 | 36 |
import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao; |
| 37 | 37 |
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer; |
| 38 | 38 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 39 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 40 | 39 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
| 41 | 40 |
import eu.etaxonomy.cdm.persistence.query.OrderHint; |
| 42 | 41 |
|
| ... | ... | |
| 225 | 224 |
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, |
| 226 | 225 |
Integer pageNumber, List<String> propertyPaths); |
| 227 | 226 |
|
| 228 |
|
|
| 229 |
/** |
|
| 230 |
* Computes all Taxon instances that do not have a taxonomic parent and has at least one child. |
|
| 231 |
* @return The List<Taxon> of root taxa. |
|
| 232 |
* @deprecated obsolete when using classification |
|
| 233 |
*/ |
|
| 234 |
@Deprecated |
|
| 235 |
public List<Taxon> getRootTaxa(Reference sec); |
|
| 236 |
|
|
| 237 |
|
|
| 238 |
/** |
|
| 239 |
* Computes all Taxon instances that do not have a taxonomic parent. |
|
| 240 |
* @param sec The concept reference that the taxon belongs to |
|
| 241 |
* @param cdmFetch not used yet !! TODO |
|
| 242 |
* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true. |
|
| 243 |
* @param withMisaplications if false only taxa are returned that have no isMisappliedNameFor relationship. |
|
| 244 |
* <Br>Default: true. |
|
| 245 |
* @return The List<Taxon> of root taxa. |
|
| 246 |
* @deprecated obsolete when using classification |
|
| 247 |
*/ |
|
| 248 |
@Deprecated |
|
| 249 |
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications); |
|
| 250 |
|
|
| 251 |
|
|
| 252 | 227 |
/** |
| 253 |
* Computes all Taxon instances which name is of a certain Rank. |
|
| 254 |
* |
|
| 255 |
* @param rank |
|
| 256 |
* The rank of the taxon name |
|
| 257 |
* @param sec |
|
| 258 |
* The concept reference that the taxon belongs to |
|
| 259 |
* @param cdmFetch |
|
| 260 |
* not used yet !! TODO |
|
| 261 |
* @param onlyWithChildren |
|
| 262 |
* if true only taxa are returned that have taxonomic children. <Br> |
|
| 263 |
* Default: true. |
|
| 264 |
* @param withMisaplications |
|
| 265 |
* if false only taxa are returned that have no |
|
| 266 |
* isMisappliedNameFor relationship. |
|
| 267 |
* @param propertyPaths |
|
| 268 |
* properties to be initialized, For detailed description and |
|
| 269 |
* examples <b>please refer to:</b> |
|
| 270 |
* {@link IBeanInitializer#initialize(Object, List)}. <Br>
|
|
| 271 |
* Default: true. |
|
| 272 |
* @return The List<Taxon> of root taxa. |
|
| 273 |
* @deprecated obsolete when using classification |
|
| 274 |
*/ |
|
| 275 |
@Deprecated |
|
| 276 |
public List<Taxon> |
|
| 277 |
getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths); |
|
| 278 |
|
|
| 279 |
/** |
|
| 280 | 228 |
* TODO necessary? |
| 281 | 229 |
* @param pagesize max maximum number of returned taxa |
| 282 | 230 |
* @param page page to start, with 0 being first page |
| cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImplTest.java | ||
|---|---|---|
| 13 | 13 |
import static org.junit.Assert.assertFalse; |
| 14 | 14 |
import static org.junit.Assert.assertNotNull; |
| 15 | 15 |
import static org.junit.Assert.assertNull; |
| 16 |
import static org.junit.Assert.assertSame; |
|
| 17 | 16 |
import static org.junit.Assert.assertTrue; |
| 18 | 17 |
import static org.junit.Assert.fail; |
| 19 | 18 |
|
| ... | ... | |
| 43 | 42 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 44 | 43 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 45 | 44 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 46 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 47 | 45 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 48 | 46 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 49 | 47 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 64 | 62 |
import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao; |
| 65 | 63 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao; |
| 66 | 64 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 67 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 68 | 65 |
import eu.etaxonomy.cdm.persistence.query.GroupByCount; |
| 69 | 66 |
import eu.etaxonomy.cdm.persistence.query.GroupByDate; |
| 70 | 67 |
import eu.etaxonomy.cdm.persistence.query.Grouping; |
| ... | ... | |
| 162 | 159 |
assertNotNull("Instance of IReferenceDao expected",referenceDao);
|
| 163 | 160 |
} |
| 164 | 161 |
|
| 165 |
/** |
|
| 166 |
* Test method for |
|
| 167 |
* {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference)}
|
|
| 168 |
* . |
|
| 169 |
*/ |
|
| 170 |
@Test |
|
| 171 |
@DataSet |
|
| 172 |
public void testGetRootTaxa() {
|
|
| 173 |
Reference sec1 = referenceDao.findById(1); |
|
| 174 |
assert sec1 != null : "sec1 must exist"; |
|
| 175 |
Reference sec2 = referenceDao.findById(2); |
|
| 176 |
assert sec2 != null : "sec2 must exist"; |
|
| 177 |
|
|
| 178 |
List<Taxon> rootTaxa = taxonDao.getRootTaxa(sec1); |
|
| 179 |
assertNotNull("getRootTaxa should return a List", rootTaxa);
|
|
| 180 |
assertFalse("The list should not be empty", rootTaxa.isEmpty());
|
|
| 181 |
assertEquals("There should be one root taxon", 1, rootTaxa.size());
|
|
| 182 |
|
|
| 183 |
rootTaxa = taxonDao.getRootTaxa(sec1, CdmFetch.FETCH_CHILDTAXA(), true, false); |
|
| 184 |
assertNotNull("getRootTaxa should return a List", rootTaxa);
|
|
| 185 |
assertFalse("The list should not be empty", rootTaxa.isEmpty());
|
|
| 186 |
assertEquals("There should be one root taxon", 1, rootTaxa.size());
|
|
| 187 |
|
|
| 188 |
rootTaxa = taxonDao.getRootTaxa(Rank.GENUS(), sec1, CdmFetch.FETCH_CHILDTAXA(), true, false, null); |
|
| 189 |
assertNotNull("getRootTaxa should return a List", rootTaxa);
|
|
| 190 |
assertFalse("The list should not be empty", rootTaxa.isEmpty());
|
|
| 191 |
assertEquals("There should be one root taxon", 1, rootTaxa.size());
|
|
| 192 |
|
|
| 193 |
rootTaxa = taxonDao.getRootTaxa(Rank.FAMILY(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null); |
|
| 194 |
if (logger.isDebugEnabled()) {
|
|
| 195 |
logger.debug("Root taxa rank Family (" + rootTaxa.size() + "):");
|
|
| 196 |
for (Taxon taxon : rootTaxa) {
|
|
| 197 |
logger.debug(taxon.getTitleCache()); |
|
| 198 |
} |
|
| 199 |
} |
|
| 200 |
assertEquals("There should be one root taxon rank Family", 1, rootTaxa.size());
|
|
| 201 |
rootTaxa = taxonDao.getRootTaxa(Rank.GENUS(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null); |
|
| 202 |
assertNotNull("getRootTaxa should return a List", rootTaxa);
|
|
| 203 |
assertFalse("The list should not be empty", rootTaxa.isEmpty());
|
|
| 204 |
if (logger.isDebugEnabled()) {
|
|
| 205 |
logger.debug("Root taxa rank Genus (" + rootTaxa.size() + "):");
|
|
| 206 |
for (Taxon taxon : rootTaxa) {
|
|
| 207 |
logger.debug(taxon.getTitleCache()); |
|
| 208 |
} |
|
| 209 |
} |
|
| 210 |
assertEquals("There should be 22 root taxa rank Genus", 22, rootTaxa.size());
|
|
| 211 |
|
|
| 212 |
rootTaxa = taxonDao.getRootTaxa(Rank.SPECIES(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null); |
|
| 213 |
if (logger.isDebugEnabled()) {
|
|
| 214 |
logger.debug("Root taxa rank Species (" + rootTaxa.size() + "):");
|
|
| 215 |
for (Taxon taxon : rootTaxa) {
|
|
| 216 |
logger.debug(taxon.getTitleCache()); |
|
| 217 |
} |
|
| 218 |
} |
|
| 219 |
assertEquals("There should be 4 root taxa rank Species", 3, rootTaxa.size());
|
|
| 220 |
} |
|
| 221 |
|
|
| 222 | 162 |
/** |
| 223 | 163 |
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
|
| 224 | 164 |
*/ |
| ... | ... | |
| 790 | 730 |
// } |
| 791 | 731 |
} |
| 792 | 732 |
|
| 793 |
@Test |
|
| 794 |
@DataSet |
|
| 795 |
public void testDeleteWithChildren() {
|
|
| 796 |
Taxon taxonWithChildren = (Taxon)taxonDao.findByUuid(mimas); |
|
| 797 |
assert taxonWithChildren != null : "taxon must exist"; |
|
| 798 |
assertEquals(taxonWithChildren.getTaxonomicChildrenCount(), 2); |
|
| 799 |
Taxon parent = (Taxon)taxonDao.findByUuid(sphingidae); |
|
| 800 |
assertSame(taxonWithChildren.getTaxonomicParent(), parent); |
|
| 801 |
assertEquals(parent.getTaxonomicChildrenCount(), 204); |
|
| 802 |
taxonDao.delete(taxonWithChildren); |
|
| 803 |
assertEquals(parent.getTaxonomicChildrenCount(), 203); |
|
| 804 |
} |
|
| 805 |
|
|
| 806 | 733 |
@Test |
| 807 | 734 |
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
| 808 | 735 |
public void testFindDeleted() {
|
| ... | ... | |
| 929 | 856 |
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis); |
| 930 | 857 |
assert taxon != null : "taxon cannot be null"; |
| 931 | 858 |
|
| 932 |
assertEquals("getTaxonomicChildrenCount should return 1 in this view",1,taxon.getTaxonomicChildrenCount());
|
|
| 933 |
assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
|
|
| 859 |
assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
|
|
| 934 | 860 |
} |
| 935 | 861 |
|
| 936 | 862 |
@Test |
| ... | ... | |
| 940 | 866 |
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis); |
| 941 | 867 |
assert taxon != null : "taxon cannot be null"; |
| 942 | 868 |
|
| 943 |
assertEquals("getTaxonomicChildrenCount should return 0 in this view",0,taxon.getTaxonomicChildrenCount());
|
|
| 944 | 869 |
assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon.getRelationsToThisTaxon().isEmpty());
|
| 945 | 870 |
} |
| 946 | 871 |
|
| cdmlib-remote/src/test/java/eu/etaxonomy/cdm/remote/dto/assembler/lsid/AssemblerTest.java | ||
|---|---|---|
| 126 | 126 |
for(int i = 0; i < 10; i++) {
|
| 127 | 127 |
Taxon child = Taxon.NewInstance(name, (Reference)sec); |
| 128 | 128 |
child.setLsid(new LSID("urn:lsid:example.org:taxonconcepts:" + (2 + i )));
|
| 129 |
taxon.addTaxonomicChild(child, null,null); |
|
| 129 |
// taxon.addTaxonomicChild(child, null,null);
|
|
| 130 | 130 |
} |
| 131 | 131 |
|
| 132 | 132 |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonService.java | ||
|---|---|---|
| 35 | 35 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.common.Language; |
| 38 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
|
| 39 | 38 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
| 40 | 39 |
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
| 41 | 40 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| ... | ... | |
| 59 | 58 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
| 60 | 59 |
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer; |
| 61 | 60 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 62 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 63 | 61 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
| 64 | 62 |
import eu.etaxonomy.cdm.persistence.query.OrderHint; |
| 65 | 63 |
|
| 66 | 64 |
|
| 67 | 65 |
public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
|
| 68 | 66 |
|
| 69 |
/** |
|
| 70 |
* Computes all Taxon instances that do not have a taxonomic parent. |
|
| 71 |
* @param sec The concept reference that the taxon belongs to |
|
| 72 |
* |
|
| 73 |
* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true. |
|
| 74 |
* @return The List<Taxon> of root taxa. |
|
| 75 |
* @deprecated obsolete when using classification |
|
| 76 |
*/ |
|
| 77 |
@Deprecated |
|
| 78 |
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren); |
|
| 79 |
|
|
| 80 |
/** |
|
| 81 |
* Computes all Taxon instances which name is of a certain Rank. |
|
| 82 |
* @param rank The rank of the taxon name |
|
| 83 |
* @param sec The concept reference that the taxon belongs to |
|
| 84 |
* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true. |
|
| 85 |
* @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are |
|
| 86 |
* the misapplied name are not returned.<Br>Default: true. |
|
| 87 |
* @param propertyPaths |
|
| 88 |
* properties to be initialized, For detailed description and |
|
| 89 |
* examples <b>please refer to:</b> |
|
| 90 |
* {@link IBeanInitializer#initialize(Object, List)}. <Br>
|
|
| 91 |
* Default: true. |
|
| 92 |
* @return The List<Taxon> of root taxa. |
|
| 93 |
* @deprecated obsolete when using classification |
|
| 94 |
*/ |
|
| 95 |
@Deprecated |
|
| 96 |
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths); |
|
| 97 |
|
|
| 98 | 67 |
/** |
| 99 | 68 |
* Computes all relationships. |
| 100 | 69 |
* @param limit |
| ... | ... | |
| 104 | 73 |
*/ |
| 105 | 74 |
public List<RelationshipBase> getAllRelationships(int limit, int start); |
| 106 | 75 |
|
| 107 |
/** |
|
| 108 |
* Returns TaxonRelationshipType vocabulary |
|
| 109 |
* @return |
|
| 110 |
* @deprecated use TermService#getVocabulary(VocabularyType) instead |
|
| 111 |
*/ |
|
| 112 |
@Deprecated |
|
| 113 |
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary(); |
|
| 114 |
|
|
| 115 | 76 |
/** |
| 116 | 77 |
* Returns a list of taxa that matches the name string and the sec reference |
| 117 | 78 |
* @param name the name string to search for |
| ... | ... | |
| 215 | 176 |
public Synonym changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon, |
| 216 | 177 |
TaxonRelationshipType oldRelationshipType, |
| 217 | 178 |
SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException; |
| 218 |
/** |
|
| 219 |
* Deletes all synonym relationships of a given synonym. If taxon is given |
|
| 220 |
* only those relationships to the taxon are deleted. |
|
| 221 |
* |
|
| 222 |
* @param syn |
|
| 223 |
* the synonym |
|
| 224 |
* @param taxon |
|
| 225 |
* @return |
|
| 226 |
* @deprecated This method must no longer being used since the |
|
| 227 |
* SynonymRelationship is annotated at the {@link Taxon} and at
|
|
| 228 |
* the {@link Synonym} with <code>orphanDelete=true</code>. Just
|
|
| 229 |
* remove the from and to entities from the relationship and |
|
| 230 |
* hibernate will care for the deletion. Using this method can cause |
|
| 231 |
* <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797) |
|
| 232 |
* |
|
| 233 |
*/ |
|
| 234 |
@Deprecated |
|
| 235 |
public long deleteSynonymRelationships(Synonym syn, Taxon taxon); |
|
| 236 |
|
|
| 237 | 179 |
|
| 238 | 180 |
/** |
| 239 | 181 |
* Changes the homotypic group of a synonym into the new homotypic group. |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java | ||
|---|---|---|
| 75 | 75 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 76 | 76 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 77 | 77 |
import eu.etaxonomy.cdm.model.common.Language; |
| 78 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
|
| 79 | 78 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
| 80 | 79 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
| 81 | 80 |
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
| ... | ... | |
| 123 | 122 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao; |
| 124 | 123 |
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao; |
| 125 | 124 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
| 126 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 127 | 125 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
| 128 | 126 |
import eu.etaxonomy.cdm.persistence.query.OrderHint; |
| 129 | 127 |
import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder; |
| ... | ... | |
| 198 | 196 |
return dao.getTaxaByName(name, sec); |
| 199 | 197 |
} |
| 200 | 198 |
|
| 201 |
/** |
|
| 202 |
* FIXME Candidate for harmonization |
|
| 203 |
* merge with getRootTaxa(Reference sec, ..., ...) |
|
| 204 |
* (non-Javadoc) |
|
| 205 |
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean) |
|
| 206 |
*/ |
|
| 207 |
@Override |
|
| 208 |
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
|
|
| 209 |
if (cdmFetch == null){
|
|
| 210 |
cdmFetch = CdmFetch.NO_FETCH(); |
|
| 211 |
} |
|
| 212 |
return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false); |
|
| 213 |
} |
|
| 214 |
|
|
| 215 |
@Override |
|
| 216 |
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {
|
|
| 217 |
return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths); |
|
| 218 |
} |
|
| 219 |
|
|
| 220 | 199 |
@Override |
| 221 | 200 |
public List<RelationshipBase> getAllRelationships(int limit, int start){
|
| 222 | 201 |
return dao.getAllRelationships(limit, start); |
| 223 | 202 |
} |
| 224 | 203 |
|
| 225 |
/** |
|
| 226 |
* FIXME Candidate for harmonization |
|
| 227 |
* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ? |
|
| 228 |
*/ |
|
| 229 |
@Override |
|
| 230 |
@Deprecated |
|
| 231 |
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
|
|
| 232 |
|
|
| 233 |
String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac"; |
|
| 234 |
UUID uuid = UUID.fromString(taxonRelTypeVocabularyId); |
|
| 235 |
OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary = |
|
| 236 |
(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid); |
|
| 237 |
return taxonRelTypeVocabulary; |
|
| 238 |
} |
|
| 239 |
|
|
| 240 | 204 |
@Override |
| 241 | 205 |
@Transactional(readOnly = false) |
| 242 | 206 |
public UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
|
| ... | ... | |
| 1351 | 1315 |
return this.dao.getPhylumName(name); |
| 1352 | 1316 |
} |
| 1353 | 1317 |
|
| 1354 |
@Override |
|
| 1355 |
public long deleteSynonymRelationships(Synonym syn, Taxon taxon) {
|
|
| 1356 |
return dao.deleteSynonymRelationships(syn, taxon); |
|
| 1357 |
} |
|
| 1358 |
|
|
| 1359 | 1318 |
@Override |
| 1360 | 1319 |
public long deleteSynonymRelationships(Synonym syn) {
|
| 1361 | 1320 |
return dao.deleteSynonymRelationships(syn, null); |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestService.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.api.service.DeleteResult; |
| 24 | 24 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
| 25 | 25 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
| 26 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 27 | 26 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 28 | 27 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 29 | 28 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| ... | ... | |
| 40 | 39 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 41 | 40 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| 42 | 41 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 43 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
| 44 | 42 |
|
| 45 | 43 |
|
| 46 | 44 |
|
| ... | ... | |
| 82 | 80 |
|
| 83 | 81 |
Taxon parentTaxon = Taxon.NewInstance(zn, sec); |
| 84 | 82 |
parentTaxon.setUuid(TEST_TAXON_UUID); |
| 85 |
parentTaxon.addTaxonomicChild(childTaxon, sec, null); |
|
| 83 |
// parentTaxon.addTaxonomicChild(childTaxon, sec, null);
|
|
| 86 | 84 |
|
| 87 | 85 |
|
| 88 | 86 |
// test |
| ... | ... | |
| 105 | 103 |
} |
| 106 | 104 |
} |
| 107 | 105 |
|
| 108 |
public void testRootTaxa(){
|
|
| 109 |
// load Name list |
|
| 110 |
logger.info("Load existing names from db...");
|
|
| 111 |
List<TaxonNameBase> tnList = appCtr.getNameService().list(null,1000, 0,null,null); |
|
| 112 |
for (TaxonNameBase tn2: tnList){
|
|
| 113 |
logger.info("Title: "+ tn2.getTitleCache() + " UUID: " + tn2.getUuid()+";");
|
|
| 114 |
} |
|
| 115 |
|
|
| 116 |
// load Root taxa |
|
| 117 |
logger.info("Load taxon from db...");
|
|
| 118 |
List<Taxon> taxa = appCtr.getTaxonService().getRootTaxa(null, CdmFetch.NO_FETCH(), false); |
|
| 119 |
for (Taxon rt: taxa){
|
|
| 120 |
logger.info("Root taxon: "+ rt.toString());
|
|
| 121 |
for (Taxon child: rt.getTaxonomicChildren()){
|
|
| 122 |
logger.info("Child: "+ child.toString());
|
|
| 123 |
logger.info(" Child.higherTaxon: "+ child.getTaxonomicParent().toString());
|
|
| 124 |
for (Synonym synonym: child.getSynonyms()){
|
|
| 125 |
logger.info(" Child synonyms: "+ synonym.toString());
|
|
| 126 |
} |
|
| 127 |
} |
|
| 128 |
} |
|
| 129 |
} |
|
| 130 |
|
|
| 131 |
public void testTermApi(){
|
|
| 132 |
ITermService ts = appCtr.getTermService(); |
|
| 133 |
//DefinedTermBase dt = ts.getTermByUri("e9f8cdb7-6819-44e8-95d3-e2d0690c3523");
|
|
| 134 |
//logger.warn(dt.toString()); |
|
| 135 |
//TODO: fix ts.listTerms(0,100) |
|
| 136 |
// List<DefinedTermBase> dts = ts.listTerms(0,100); |
|
| 137 |
// int i = 0; |
|
| 138 |
// for (DefinedTermBase d: dts){
|
|
| 139 |
// i++; |
|
| 140 |
// if (i > 10) break; |
|
| 141 |
// logger.info(d.toString()); |
|
| 142 |
// } |
|
| 143 |
} |
|
| 144 |
|
|
| 145 | 106 |
public void testDeleteTaxa(){
|
| 146 | 107 |
ITaxonService taxonService = appCtr.getTaxonService(); |
| 147 | 108 |
TaxonNameBase<?,?> taxonName = BotanicalName.NewInstance(Rank.SPECIES()); |
| ... | ... | |
| 192 | 153 |
Reference ref = ReferenceFactory.newJournal(); |
| 193 | 154 |
Taxon parent = Taxon.NewInstance(taxonName, ref); |
| 194 | 155 |
Taxon child = Taxon.NewInstance(taxonName, null); |
| 195 |
parent.addTaxonomicChild(child, null, null); |
|
| 156 |
// parent.addTaxonomicChild(child, null, null);
|
|
| 196 | 157 |
|
| 197 | 158 |
logger.info("Save taxon ...");
|
| 198 | 159 |
UUID uuidTaxon1 = taxonService.save(parent).getUuid(); |
Also available in: Unified diff
ref #6089 Remove all calls and methods for taxonomicChildrenCount and taxonomicParentCache