Revision 165e1209
Added by Andreas Müller over 4 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java | ||
|---|---|---|
| 43 | 43 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR; |
| 44 | 44 |
import eu.etaxonomy.cdm.io.common.Source; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 46 |
import eu.etaxonomy.cdm.model.common.GrantedAuthorityImpl; |
|
| 47 |
import eu.etaxonomy.cdm.model.common.Group; |
|
| 48 | 46 |
import eu.etaxonomy.cdm.model.common.Language; |
| 49 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 50 | 47 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 51 | 48 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 52 | 49 |
import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
| ... | ... | |
| 55 | 52 |
import eu.etaxonomy.cdm.model.metadata.PreferencePredicate; |
| 56 | 53 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 57 | 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 55 |
import eu.etaxonomy.cdm.model.permission.GrantedAuthorityImpl; |
|
| 56 |
import eu.etaxonomy.cdm.model.permission.Group; |
|
| 57 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 58 | 58 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 59 | 59 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 60 | 60 |
import eu.etaxonomy.cdm.model.term.DefinedTermBase; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.java | ||
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| 130 | 130 |
|
| 131 | 131 |
//user defined features |
| 132 | 132 |
String [] featureList = new String[]{"Red Book", "Endemism"};
|
| 133 |
addFeataureNodesByStringList(featureList, root, transformer, service);
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|
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addFeatureNodesByStringList(featureList, root, transformer, service); |
|
| 134 | 134 |
|
| 135 | 135 |
return result; |
| 136 | 136 |
} |
| ... | ... | |
| 159 | 159 |
} |
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} |
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|
| 162 |
public void addFeataureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
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|
| 162 |
public void addFeatureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
|
| 163 | 163 |
try {
|
| 164 | 164 |
for (String featureString : featureStringList){
|
| 165 | 165 |
UUID featureUuid; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java | ||
|---|---|---|
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR; |
| 26 | 26 |
import eu.etaxonomy.cdm.io.common.Source; |
| 27 | 27 |
import eu.etaxonomy.cdm.io.globis.GlobisImportConfigurator; |
| 28 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 29 | 28 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 30 | 29 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| 30 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 31 | 31 |
import eu.etaxonomy.cdm.model.reference.ISourceable; |
| 32 | 32 |
|
| 33 | 33 |
/** |
| app-import/src/main/java/eu/etaxonomy/cdm/app/salvador/SalvadorActivator.java | ||
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| 28 | 28 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
| 29 | 29 |
import eu.etaxonomy.cdm.io.common.ImportResult; |
| 30 | 30 |
import eu.etaxonomy.cdm.io.common.Source; |
| 31 |
import eu.etaxonomy.cdm.model.common.GrantedAuthorityImpl; |
|
| 32 |
import eu.etaxonomy.cdm.model.common.Group; |
|
| 33 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 34 | 31 |
import eu.etaxonomy.cdm.model.name.INonViralName; |
| 35 | 32 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 33 |
import eu.etaxonomy.cdm.model.permission.GrantedAuthorityImpl; |
|
| 34 |
import eu.etaxonomy.cdm.model.permission.Group; |
|
| 35 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 36 | 36 |
import eu.etaxonomy.cdm.persistence.hibernate.permission.Role; |
| 37 | 37 |
|
| 38 | 38 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
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| 41 | 41 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.common.Language; |
| 44 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 45 | 44 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 46 | 45 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 47 | 46 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| ... | ... | |
| 51 | 50 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 52 | 51 |
import eu.etaxonomy.cdm.model.occurrence.FieldUnit; |
| 53 | 52 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
| 53 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 54 | 54 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 55 | 55 |
import eu.etaxonomy.cdm.model.term.DefinedTerm; |
| 56 | 56 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportBase.java | ||
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| 34 | 34 |
import eu.etaxonomy.cdm.model.common.Language; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 36 | 36 |
import eu.etaxonomy.cdm.model.common.SourcedEntityBase; |
| 37 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 38 | 37 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 39 | 38 |
import eu.etaxonomy.cdm.model.location.Country; |
| 40 | 39 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 41 | 40 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| 41 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 42 | 42 |
import eu.etaxonomy.cdm.model.reference.ISourceable; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 44 | 44 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelUserImport.java | ||
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| 29 | 29 |
import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 32 |
import eu.etaxonomy.cdm.model.common.User;
|
|
| 32 |
import eu.etaxonomy.cdm.model.permission.User;
|
|
| 33 | 33 |
|
| 34 | 34 |
|
| 35 | 35 |
/** |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportBase.java | ||
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| 41 | 41 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 43 | 43 |
import eu.etaxonomy.cdm.model.common.Language; |
| 44 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 45 | 44 |
import eu.etaxonomy.cdm.model.location.Country; |
| 46 | 45 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 47 | 46 |
import eu.etaxonomy.cdm.model.name.IZoologicalName; |
| 47 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 48 | 48 |
import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException; |
| 49 | 49 |
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser; |
| 50 | 50 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| ... | ... | |
| 54 | 54 |
* @since 20.03.2008 |
| 55 | 55 |
*/ |
| 56 | 56 |
public abstract class GlobisImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<GlobisImportConfigurator, GlobisImportState> implements ICdmIO<GlobisImportState>, IPartitionedIO<GlobisImportState> {
|
| 57 |
private static final Logger logger = Logger.getLogger(GlobisImportBase.class); |
|
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|
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| 58 |
private static final long serialVersionUID = -7813164269152576841L; |
|
| 59 |
private static final Logger logger = Logger.getLogger(GlobisImportBase.class); |
|
| 58 | 60 |
|
| 59 | 61 |
public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");
|
| 60 | 62 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImportState.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
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|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 21 | 21 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 22 | 22 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 23 | 23 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 24 |
import eu.etaxonomy.cdm.model.common.User; |
|
| 25 | 24 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 25 |
import eu.etaxonomy.cdm.model.permission.User; |
|
| 26 | 26 |
import eu.etaxonomy.cdm.model.term.DefinedTermBase; |
| 27 | 27 |
|
| 28 | 28 |
/** |
| ... | ... | |
| 35 | 35 |
private static final Logger logger = Logger.getLogger(GlobisImportState.class); |
| 36 | 36 |
|
| 37 | 37 |
private Map<String, DefinedTermBase> dbCdmDefTermMap = new HashMap<String, DefinedTermBase>(); |
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| 39 | 39 |
private Map<String, User> usernameMap = new HashMap<String, User>(); |
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| 41 | 41 |
private Map<Integer, Map<Integer,Rank>> rankMap; |
| 42 | 42 |
|
| 43 | 43 |
private Map<String, Person> personMap = new HashMap<String, Person>(); |
| 44 |
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| 45 | 45 |
private Map<String, Team> teamMap = new HashMap<String, Team>(); |
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@Override |
| 50 | 50 |
public void initialize(GlobisImportConfigurator config) {
|
| 51 | 51 |
// super(config); |
| ... | ... | |
| 61 | 61 |
public Map<String, DefinedTermBase> getDbCdmDefinedTermMap(){
|
| 62 | 62 |
return this.dbCdmDefTermMap; |
| 63 | 63 |
} |
| 64 |
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| 64 |
|
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| 65 | 65 |
public void putDefinedTermToMap(String tableName, String id, DefinedTermBase term){
|
| 66 | 66 |
this.dbCdmDefTermMap.put(tableName + "_" + id, term); |
| 67 | 67 |
} |
| 68 |
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| 68 |
|
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| 69 | 69 |
public void putDefinedTermToMap(String tableName, int id, DefinedTermBase term){
|
| 70 | 70 |
putDefinedTermToMap(tableName, String.valueOf(id), term); |
| 71 | 71 |
} |
| 72 |
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public User getUser(String username){
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@Override |
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public User getUser(String username){
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| 74 | 75 |
return usernameMap.get(username); |
| 75 | 76 |
} |
| 76 | 77 |
|
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public void putUser(String username, User user){
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@Override |
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public void putUser(String username, User user){
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| 78 | 80 |
usernameMap.put(username, user); |
| 79 | 81 |
} |
| 80 | 82 |
|
| ... | ... | |
| 91 | 93 |
// public Map<Integer, Map<Integer,Rank>> getRankMap() {
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// return rankMap; |
| 93 | 95 |
// } |
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| 96 | 98 |
/** |
| 97 | 99 |
* Returns the CDM rank depending on the ERMS rankId and the ERMS kingdomId. Returns <code> |
| 98 | 100 |
* null</code> if the rank does not exist. |
| ... | ... | |
| 117 | 119 |
public void putPerson(String str, Person person){
|
| 118 | 120 |
personMap.put(str, person); |
| 119 | 121 |
} |
| 120 |
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| 121 | 123 |
|
| 122 | 124 |
public Person getPerson(String str){
|
| 123 | 125 |
return personMap.get(str); |
| ... | ... | |
| 127 | 129 |
public void putTeam(String str, Team team){
|
| 128 | 130 |
teamMap.put(str, team); |
| 129 | 131 |
} |
| 130 |
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| 131 | 133 |
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| 132 | 134 |
public Team getTeam(String str){
|
| 133 | 135 |
return teamMap.get(str); |
| 134 | 136 |
} |
| 135 |
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| 136 | 138 |
public Set<AgentBase> getAgents(){
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| 137 | 139 |
Set<AgentBase> result = new HashSet<AgentBase>(); |
| 138 | 140 |
result.addAll(personMap.values()); |
| 139 | 141 |
result.addAll(teamMap.values()); |
| 140 | 142 |
return result; |
| 141 | 143 |
} |
| 142 |
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| 144 |
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| 143 | 145 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java | ||
|---|---|---|
| 40 | 40 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 43 |
import eu.etaxonomy.cdm.model.term.FeatureNode; |
|
| 44 |
import eu.etaxonomy.cdm.model.term.FeatureTree; |
|
| 45 | 43 |
import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary; |
| 44 |
import eu.etaxonomy.cdm.model.term.TermNode; |
|
| 45 |
import eu.etaxonomy.cdm.model.term.TermTree; |
|
| 46 | 46 |
import eu.etaxonomy.cdm.model.term.TermType; |
| 47 | 47 |
|
| 48 | 48 |
/** |
| ... | ... | |
| 133 | 133 |
} |
| 134 | 134 |
|
| 135 | 135 |
if (doFeatureTree){
|
| 136 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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| 136 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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|
| 137 | 137 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 138 | 138 |
} |
| 139 | 139 |
|
| ... | ... | |
| 285 | 285 |
return result; |
| 286 | 286 |
} |
| 287 | 287 |
|
| 288 |
private FeatureTree makeFeatureNode(ITermService service){
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| 288 |
private TermTree<Feature> makeFeatureNode(ITermService service){
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| 289 | 289 |
CentralAfricaEricaceaeTransformer transformer = new CentralAfricaEricaceaeTransformer(); |
| 290 | 290 |
|
| 291 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
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| 291 |
TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid);
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| 292 | 292 |
result.setTitleCache("Central Africa Ericaceae Feature Tree", true);
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| 293 |
FeatureNode root = result.getRoot(); |
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| 294 |
FeatureNode newNode; |
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| 293 |
TermNode<Feature> root = result.getRoot(); |
|
| 295 | 294 |
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| 296 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 297 |
root.addChild(newNode); |
|
| 295 |
TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 298 | 296 |
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| 299 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
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| 297 |
addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 300 | 298 |
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| 301 |
addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service);
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|
| 299 |
addFeatureNodesByStringList(generellDescriptionsList, root, transformer, service); |
|
| 302 | 300 |
|
| 301 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 303 | 302 |
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| 304 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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| 305 |
root.addChild(newNode);
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| 303 |
newNode = root.addChild(Feature.ECOLOGY());
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| 304 |
addFeatureNodesByStringList(habitatEcologyList, root, transformer, service);
|
|
| 306 | 305 |
|
| 307 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 308 |
root.addChild(newNode); |
|
| 309 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 306 |
newNode = root.addChild(Feature.USES()); |
|
| 310 | 307 |
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| 311 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 312 |
root.addChild(newNode); |
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| 308 |
addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 313 | 309 |
|
| 314 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
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| 310 |
newNode = root.addChild(Feature.COMMON_NAME());
|
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| 315 | 311 |
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| 316 |
newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); |
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| 317 |
root.addChild(newNode); |
|
| 318 |
|
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| 319 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 320 |
root.addChild(newNode); |
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| 312 |
newNode = root.addChild(Feature.CITATION()); |
|
| 321 | 313 |
|
| 322 | 314 |
return result; |
| 323 | 315 |
} |
| ... | ... | |
| 439 | 431 |
|
| 440 | 432 |
}; |
| 441 | 433 |
|
| 442 |
public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 434 |
public void addFeatureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
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| 443 | 435 |
try {
|
| 444 | 436 |
for (String featureString : featureStringList){
|
| 445 | 437 |
UUID featureUuid; |
| 446 | 438 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 447 | 439 |
Feature feature = (Feature)termService.find(featureUuid); |
| 448 | 440 |
if (feature != null){
|
| 449 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 450 |
root.addChild(child); |
|
| 441 |
TermNode<Feature> child = root.addChild(feature); |
|
| 451 | 442 |
} |
| 452 | 443 |
} |
| 453 | 444 |
} catch (UndefinedTransformerMethodException e) {
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaFernsActivator.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 27 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
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| 28 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
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| 27 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
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| 28 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 29 | 29 |
|
| 30 | 30 |
/** |
| 31 | 31 |
* @author a.mueller |
| ... | ... | |
| 96 | 96 |
|
| 97 | 97 |
|
| 98 | 98 |
|
| 99 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 99 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 100 | 100 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 101 | 101 |
|
| 102 | 102 |
//check keys |
| ... | ... | |
| 118 | 118 |
return result; |
| 119 | 119 |
} |
| 120 | 120 |
|
| 121 |
private FeatureTree makeFeatureNode(ITermService service){
|
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| 121 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
|
| 122 | 122 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
| 123 | 123 |
|
| 124 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
|
|
| 124 |
TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid);
|
|
| 125 | 125 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree", true);
|
| 126 |
FeatureNode root = result.getRoot();
|
|
| 127 |
FeatureNode newNode;
|
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| 126 |
TermNode<Feature> root = result.getRoot();
|
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| 127 |
TermNode<Feature> newNode = root.addChild(Feature.CITATION());
|
|
| 128 | 128 |
|
| 129 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 130 |
root.addChild(newNode); |
|
| 131 |
|
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| 132 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 133 |
root.addChild(newNode); |
|
| 129 |
root.addChild(Feature.DESCRIPTION()); |
|
| 134 | 130 |
|
| 135 | 131 |
return result; |
| 136 | 132 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/EfloraActivatorBase.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 |
*
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| 2 |
* |
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| 3 | 3 |
*/ |
| 4 | 4 |
package eu.etaxonomy.cdm.app.eflora; |
| 5 | 5 |
|
| ... | ... | |
| 26 | 26 |
import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator; |
| 27 | 27 |
import eu.etaxonomy.cdm.io.markup.MarkupImportState; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 29 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
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| 30 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
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| 29 |
import eu.etaxonomy.cdm.model.term.TermNode;
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| 30 |
import eu.etaxonomy.cdm.model.term.TermTree;
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| 31 | 31 |
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| 32 | 32 |
/** |
| 33 | 33 |
* @author a.mueller |
| ... | ... | |
| 35 | 35 |
*/ |
| 36 | 36 |
public class EfloraActivatorBase {
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| 37 | 37 |
private static final Logger logger = Logger.getLogger(EfloraActivatorBase.class); |
| 38 |
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| 38 |
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| 39 | 39 |
protected MarkupImportConfigurator config; |
| 40 | 40 |
protected CdmDefaultImport<MarkupImportConfigurator> myImport; |
| 41 | 41 |
protected IIoObserver observer = new LoggingIoObserver(); |
| ... | ... | |
| 49 | 49 |
config = MarkupImportConfigurator.NewInstance(source, cdmDestination); |
| 50 | 50 |
config.setObservers(observerList); |
| 51 | 51 |
config.setCheck(check); |
| 52 |
|
|
| 53 |
myImport = new CdmDefaultImport<MarkupImportConfigurator>();
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| 54 |
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| 52 |
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| 53 |
myImport = new CdmDefaultImport<MarkupImportConfigurator>(); |
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| 54 |
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| 55 | 55 |
return config; |
| 56 | 56 |
} |
| 57 |
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| 58 |
protected FeatureTree makeAutomatedFeatureTree(ICdmRepository app,
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|
| 57 |
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| 58 |
protected TermTree<Feature> makeAutomatedFeatureTree(ICdmRepository app,
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| 59 | 59 |
MarkupImportState state, UUID featureTreeUuid, String featureTreeTitle){
|
| 60 | 60 |
System.out.println("Start creating automated Feature Tree");
|
| 61 |
FeatureTree tree = FeatureTree.NewInstance(featureTreeUuid);
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| 61 |
TermTree<Feature> tree = TermTree.NewFeatureInstance(featureTreeUuid);
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| 62 | 62 |
tree.setTitleCache(featureTreeTitle, true); |
| 63 |
FeatureNode root = tree.getRoot();
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|
| 64 |
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| 63 |
TermNode<Feature> root = tree.getRoot();
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| 64 |
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| 65 | 65 |
ITermService termService = app.getTermService(); |
| 66 | 66 |
FeatureSorter sorter = new FeatureSorter(); |
| 67 |
FeatureNode descriptionNode = null;
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|
| 68 |
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| 67 |
TermNode<Feature> descriptionNode = null;
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|
| 68 |
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| 69 | 69 |
//general features |
| 70 | 70 |
Map<String, List<FeatureSorterInfo>> generalList = state.getGeneralFeatureSorterListMap(); |
| 71 | 71 |
List<UUID> uuidList = sorter.getSortOrder(generalList); |
| 72 | 72 |
Map<UUID, Feature> map = makeUuidMap(uuidList, termService); |
| 73 | 73 |
for (UUID key : uuidList){
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| 74 | 74 |
Feature feature = map.get(key); |
| 75 |
FeatureNode node = FeatureNode.NewInstance(feature); |
|
| 76 |
root.addChild(node); |
|
| 75 |
TermNode<Feature> node = root.addChild(feature); |
|
| 77 | 76 |
if (feature.equals(Feature.DESCRIPTION())){
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| 78 | 77 |
descriptionNode = node; |
| 79 | 78 |
} |
| 80 | 79 |
} |
| 81 |
FeatureNode newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 82 |
root.addChild(newNode); |
|
| 83 |
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|
| 84 |
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|
| 80 |
TermNode<Feature> newNode = root.addChild(Feature.CITATION()); |
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| 81 |
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| 82 |
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| 85 | 83 |
//description features |
| 86 | 84 |
if (descriptionNode != null){
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| 87 | 85 |
Map<String, List<FeatureSorterInfo>> charList = state.getCharFeatureSorterListMap(); |
| ... | ... | |
| 89 | 87 |
map = makeUuidMap(uuidList, termService); |
| 90 | 88 |
for (UUID key : uuidList){
|
| 91 | 89 |
Feature feature = map.get(key); |
| 92 |
descriptionNode.addChild(FeatureNode.NewInstance(feature));
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| 90 |
descriptionNode.addChild(feature);
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| 93 | 91 |
} |
| 94 | 92 |
}else{
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| 95 | 93 |
logger.warn("No description node found. Could not create feature nodes for description features.");
|
| ... | ... | |
| 97 | 95 |
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| 98 | 96 |
//save tree |
| 99 | 97 |
app.getFeatureTreeService().saveOrUpdate(tree); |
| 100 |
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| 98 |
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| 101 | 99 |
System.out.println("End creating automated Feature Tree");
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| 102 |
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| 100 |
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| 103 | 101 |
return tree; |
| 104 | 102 |
} |
| 105 |
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| 103 |
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| 106 | 104 |
private Map<UUID,Feature> makeUuidMap(Collection<UUID> uuids, ITermService termService){
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| 107 | 105 |
HashSet<UUID> uuidSet = new HashSet<UUID>(); |
| 108 | 106 |
uuidSet.addAll(uuids); |
| 109 | 107 |
List<Feature> featureSet = (List)termService.find(uuidSet); |
| 110 |
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|
| 108 |
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| 111 | 109 |
Map<UUID,Feature> result = new HashMap<UUID, Feature>(); |
| 112 | 110 |
for (Feature feature : featureSet){
|
| 113 | 111 |
result.put(feature.getUuid(), feature); |
| 114 | 112 |
} |
| 115 | 113 |
return result; |
| 116 | 114 |
} |
| 117 |
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|
| 118 |
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| 115 |
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| 116 |
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| 119 | 117 |
/** |
| 120 | 118 |
* @param markupConfig |
| 121 | 119 |
* @param myImport |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java | ||
|---|---|---|
| 27 | 27 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 30 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 31 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 30 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 31 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 32 | 32 |
|
| 33 | 33 |
/** |
| 34 | 34 |
* Activator for Flora of the Guianas imports. |
| ... | ... | |
| 186 | 186 |
//Vol30 |
| 187 | 187 |
executeVolume(fotg30, includeFotg30 ^ inverseInclude); |
| 188 | 188 |
|
| 189 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 189 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
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| 190 | 190 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 191 | 191 |
|
| 192 | 192 |
//check keys |
| ... | ... | |
| 208 | 208 |
return result; |
| 209 | 209 |
} |
| 210 | 210 |
|
| 211 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 211 |
private TermTree<Feature> makeFeatureNode(ITermService service){
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| 212 | 212 |
MarkupTransformer transformer = new MarkupTransformer(); |
| 213 | 213 |
|
| 214 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
|
|
| 214 |
TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid);
|
|
| 215 | 215 |
result.setTitleCache(FEATURE_TREE_TITLE, true); |
| 216 |
FeatureNode root = result.getRoot(); |
|
| 217 |
FeatureNode newNode; |
|
| 216 |
TermNode<Feature> root = result.getRoot(); |
|
| 218 | 217 |
|
| 219 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 220 |
root.addChild(newNode); |
|
| 218 |
TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 221 | 219 |
|
| 222 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
|
|
| 220 |
addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 223 | 221 |
|
| 224 |
addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
|
|
| 225 |
newNode = FeatureNode.NewInstance(Feature.ANATOMY());
|
|
| 226 |
addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
|
|
| 222 |
addFeatureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
|
| 223 |
newNode = TermNode.NewInstance(Feature.ANATOMY());
|
|
| 224 |
addFeatureNodesByStringList(anatomySubfeatureList, newNode, transformer, service); |
|
| 227 | 225 |
|
| 228 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
|
|
| 229 |
addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
|
|
| 226 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service); |
|
| 227 |
addFeatureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service); |
|
| 230 | 228 |
|
| 231 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
|
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| 229 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); |
|
| 232 | 230 |
|
| 233 | 231 |
|
| 234 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 235 |
root.addChild(newNode); |
|
| 232 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 236 | 233 |
|
| 237 |
newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); |
|
| 238 |
root.addChild(newNode); |
|
| 234 |
newNode = root.addChild(Feature.COMMON_NAME()); |
|
| 239 | 235 |
|
| 240 |
newNode = FeatureNode.NewInstance(Feature.PHENOLOGY()); |
|
| 241 |
root.addChild(newNode); |
|
| 236 |
newNode = root.addChild(Feature.PHENOLOGY()); |
|
| 242 | 237 |
|
| 243 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 244 |
root.addChild(newNode); |
|
| 245 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 238 |
newNode = root.addChild(Feature.ECOLOGY()); |
|
| 239 |
addFeatureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 246 | 240 |
|
| 247 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 248 |
root.addChild(newNode); |
|
| 241 |
newNode = root.addChild(Feature.USES()); |
|
| 249 | 242 |
|
| 250 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
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| 243 |
addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 251 | 244 |
|
| 252 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 253 |
root.addChild(newNode); |
|
| 245 |
newNode = root.addChild(Feature.CITATION()); |
|
| 254 | 246 |
|
| 255 | 247 |
String sql = "\nSELECT feature.titleCache " + |
| 256 | 248 |
" FROM DescriptionElementBase deb INNER JOIN DefinedTermBase feature ON deb.feature_id = feature.id " + |
| ... | ... | |
| 417 | 409 |
|
| 418 | 410 |
}; |
| 419 | 411 |
|
| 420 |
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
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| 421 |
FeatureNode lastChild = null;
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| 412 |
public TermNode<Feature> addFeatureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
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| 413 |
TermNode<Feature> lastChild = null;
|
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| 422 | 414 |
try {
|
| 423 | 415 |
for (String featureString : featureStringList){
|
| 424 | 416 |
UUID featureUuid; |
| 425 | 417 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 426 | 418 |
Feature feature = (Feature)termService.find(featureUuid); |
| 427 | 419 |
if (feature != null){
|
| 428 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 429 |
root.addChild(child); |
|
| 420 |
root.addChild(feature); |
|
| 430 | 421 |
} |
| 431 | 422 |
} |
| 432 | 423 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.java | ||
|---|---|---|
| 33 | 33 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 35 | 35 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 36 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 37 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 36 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 37 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 38 | 38 |
|
| 39 | 39 |
/** |
| 40 | 40 |
* @author a.mueller |
| ... | ... | |
| 365 | 365 |
|
| 366 | 366 |
// makeGeoService(); |
| 367 | 367 |
|
| 368 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 368 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 369 | 369 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 370 | 370 |
|
| 371 | 371 |
//check keys |
| ... | ... | |
| 398 | 398 |
return result; |
| 399 | 399 |
} |
| 400 | 400 |
|
| 401 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 401 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
|
| 402 | 402 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
| 403 | 403 |
|
| 404 |
FeatureTree result = FeatureTree.NewInstance(UUID.randomUUID());
|
|
| 404 |
TermTree<Feature> result = TermTree.NewFeatureInstance(UUID.randomUUID());
|
|
| 405 | 405 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree - Old", true);
|
| 406 |
FeatureNode root = result.getRoot(); |
|
| 407 |
FeatureNode newNode; |
|
| 406 |
TermNode<Feature> root = result.getRoot(); |
|
| 408 | 407 |
|
| 409 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 410 |
root.addChild(newNode); |
|
| 408 |
TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 411 | 409 |
|
| 412 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
|
|
| 410 |
addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 413 | 411 |
|
| 414 |
addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
|
|
| 415 |
newNode = FeatureNode.NewInstance(Feature.ANATOMY());
|
|
| 416 |
addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
|
|
| 412 |
addFeatureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
|
| 413 |
newNode = TermNode.NewInstance(Feature.ANATOMY());
|
|
| 414 |
addFeatureNodesByStringList(anatomySubfeatureList, newNode, transformer, service); |
|
| 417 | 415 |
|
| 418 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
|
|
| 419 |
addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
|
|
| 416 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service); |
|
| 417 |
addFeatureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service); |
|
| 420 | 418 |
|
| 421 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
|
|
| 419 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); |
|
| 422 | 420 |
|
| 423 | 421 |
|
| 424 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 425 |
root.addChild(newNode); |
|
| 422 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 426 | 423 |
|
| 427 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 428 |
root.addChild(newNode); |
|
| 429 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 424 |
newNode = root.addChild(Feature.ECOLOGY()); |
|
| 425 |
addFeatureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 430 | 426 |
|
| 431 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 432 |
root.addChild(newNode); |
|
| 427 |
newNode = root.addChild(Feature.USES()); |
|
| 433 | 428 |
|
| 434 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
|
| 429 |
addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 435 | 430 |
|
| 436 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 437 |
root.addChild(newNode); |
|
| 431 |
newNode = root.addChild(Feature.CITATION()); |
|
| 438 | 432 |
|
| 439 | 433 |
return result; |
| 440 | 434 |
} |
| ... | ... | |
| 588 | 582 |
|
| 589 | 583 |
}; |
| 590 | 584 |
|
| 591 |
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 592 |
FeatureNode lastChild = null; |
|
| 585 |
public TermNode<Feature> addFeatureNodesByStringList(String[] featureStringList, |
|
| 586 |
TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
|
| 587 |
TermNode<Feature> lastChild = null; |
|
| 593 | 588 |
try {
|
| 594 | 589 |
for (String featureString : featureStringList){
|
| 595 | 590 |
UUID featureUuid; |
| 596 | 591 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 597 | 592 |
Feature feature = (Feature)termService.find(featureUuid); |
| 598 | 593 |
if (feature != null){
|
| 599 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 600 |
root.addChild(child); |
|
| 594 |
root.addChild(feature); |
|
| 601 | 595 |
} |
| 602 | 596 |
} |
| 603 | 597 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator_OLD.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 29 | 29 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 32 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 33 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 32 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 33 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 34 | 34 |
|
| 35 | 35 |
/** |
| 36 | 36 |
* @author a.mueller |
| ... | ... | |
| 39 | 39 |
*/ |
| 40 | 40 |
public class FloraMalesianaActivator_OLD {
|
| 41 | 41 |
private static final Logger logger = Logger.getLogger(FloraMalesianaActivator_OLD.class); |
| 42 |
|
|
| 42 |
|
|
| 43 | 43 |
//database validation status (create, update, validate ...) |
| 44 | 44 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| 45 | 45 |
static final URI fmSource1 = EfloraSources.fm_sapindaceae_local(); |
| 46 | 46 |
static final URI fmSource2 = EfloraSources.fm_sapindaceae2_local(); |
| 47 | 47 |
static final URI fmSource13_1 = EfloraSources.fm_13_1_local(); |
| 48 | 48 |
static final URI fmSource13_2 = EfloraSources.fm_13_2_local(); |
| 49 |
|
|
| 50 |
|
|
| 49 |
|
|
| 50 |
|
|
| 51 | 51 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
| 52 | 52 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview(); |
| 53 | 53 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production(); |
| 54 | 54 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 55 | 55 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
| 56 |
|
|
| 56 |
|
|
| 57 | 57 |
|
| 58 | 58 |
//feature tree uuid |
| 59 | 59 |
public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
|
| 60 |
|
|
| 60 |
|
|
| 61 | 61 |
//classification |
| 62 | 62 |
static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
|
| 63 |
|
|
| 63 |
|
|
| 64 | 64 |
//check - import |
| 65 | 65 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 66 |
|
|
| 66 |
|
|
| 67 | 67 |
static boolean doPrintKeys = false; |
| 68 |
|
|
| 68 |
|
|
| 69 | 69 |
//taxa |
| 70 | 70 |
static final boolean doTaxa = true; |
| 71 | 71 |
|
| ... | ... | |
| 74 | 74 |
private boolean includeVol13_1 = false; |
| 75 | 75 |
private boolean includeVol13_2 = false; |
| 76 | 76 |
|
| 77 |
|
|
| 77 |
|
|
| 78 | 78 |
private void doImport(ICdmDataSource cdmDestination){
|
| 79 |
|
|
| 79 |
|
|
| 80 | 80 |
//make Source |
| 81 | 81 |
URI source = fmSource1; |
| 82 | 82 |
EfloraImportConfigurator floraMalesianaConfig= EfloraImportConfigurator.NewInstance(source, cdmDestination); |
| ... | ... | |
| 85 | 85 |
floraMalesianaConfig.setCheck(check); |
| 86 | 86 |
floraMalesianaConfig.setDoPrintKeys(doPrintKeys); |
| 87 | 87 |
floraMalesianaConfig.setDbSchemaValidation(hbm2dll); |
| 88 |
|
|
| 88 |
|
|
| 89 | 89 |
CdmDefaultImport<EfloraImportConfigurator> myImport = new CdmDefaultImport<EfloraImportConfigurator>(); |
| 90 | 90 |
|
| 91 |
|
|
| 91 |
|
|
| 92 | 92 |
//Sapindaceae1 |
| 93 | 93 |
if (includeSapindaceae1){
|
| 94 | 94 |
System.out.println("Start import from ("+ fmSource1.toString() + ") ...");
|
| ... | ... | |
| 96 | 96 |
myImport.invoke(floraMalesianaConfig); |
| 97 | 97 |
System.out.println("End import from ("+ fmSource1.toString() + ")...");
|
| 98 | 98 |
} |
| 99 |
|
|
| 99 |
|
|
| 100 | 100 |
//Sapindaceae2 |
| 101 | 101 |
if (includeSapindaceae2){
|
| 102 | 102 |
System.out.println("\nStart import from ("+ fmSource2.toString() + ") ...");
|
| ... | ... | |
| 106 | 106 |
myImport.invoke(floraMalesianaConfig); |
| 107 | 107 |
System.out.println("End import from ("+ fmSource2.toString() + ")...");
|
| 108 | 108 |
} |
| 109 |
|
|
| 109 |
|
|
| 110 | 110 |
floraMalesianaConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
|
| 111 | 111 |
//Vol13_1 |
| 112 | 112 |
if (includeVol13_1){
|
| ... | ... | |
| 125 | 125 |
myImport.invoke(floraMalesianaConfig); |
| 126 | 126 |
System.out.println("End import from ("+ fmSource13_2.toString() + ")...");
|
| 127 | 127 |
} |
| 128 |
|
|
| 129 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 128 |
|
|
| 129 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 130 | 130 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 131 |
|
|
| 131 |
|
|
| 132 | 132 |
//check keys |
| 133 | 133 |
if (doPrintKeys){
|
| 134 | 134 |
TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
| ... | ... | |
| 139 | 139 |
} |
| 140 | 140 |
myImport.getCdmAppController().commitTransaction(tx); |
| 141 | 141 |
} |
| 142 |
|
|
| 142 |
|
|
| 143 | 143 |
} |
| 144 |
|
|
| 144 |
|
|
| 145 | 145 |
private Reference getSourceReference(String string) {
|
| 146 | 146 |
Reference result = ReferenceFactory.newGeneric(); |
| 147 | 147 |
result.setTitleCache(string); |
| 148 | 148 |
return result; |
| 149 | 149 |
} |
| 150 | 150 |
|
| 151 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 151 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
|
| 152 | 152 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
| 153 |
|
|
| 154 |
FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
|
| 155 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree");
|
|
| 156 |
FeatureNode root = result.getRoot(); |
|
| 157 |
FeatureNode newNode; |
|
| 158 |
|
|
| 159 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 160 |
root.addChild(newNode); |
|
| 161 |
|
|
| 162 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 163 |
|
|
| 164 |
addFeataureNodesByStringList(generellDescriptionsList, root, transformer, service); |
|
| 165 |
|
|
| 166 |
|
|
| 167 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 168 |
root.addChild(newNode); |
|
| 169 |
|
|
| 170 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 171 |
root.addChild(newNode); |
|
| 172 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 173 |
|
|
| 174 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 175 |
root.addChild(newNode); |
|
| 176 |
|
|
| 177 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 178 |
|
|
| 179 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 180 |
root.addChild(newNode); |
|
| 181 |
|
|
| 153 |
|
|
| 154 |
TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid); |
|
| 155 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree", true);
|
|
| 156 |
TermNode<Feature> root = result.getRoot(); |
|
| 157 |
|
|
| 158 |
TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 159 |
|
|
| 160 |
addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 161 |
|
|
| 162 |
addFeatureNodesByStringList(generellDescriptionsList, root, transformer, service); |
|
| 163 |
|
|
| 164 |
|
|
| 165 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 166 |
|
|
| 167 |
newNode = root.addChild(Feature.ECOLOGY()); |
|
| 168 |
addFeatureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 169 |
|
|
| 170 |
newNode = root.addChild(Feature.USES()); |
|
| 171 |
|
|
| 172 |
addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 173 |
|
|
| 174 |
newNode = root.addChild(Feature.CITATION()); |
|
| 175 |
|
|
| 182 | 176 |
return result; |
| 183 | 177 |
} |
| 184 |
|
|
| 178 |
|
|
| 185 | 179 |
private static String [] chomosomesList = new String[]{
|
| 186 |
"Chromosomes",
|
|
| 180 |
"Chromosomes", |
|
| 187 | 181 |
}; |
| 188 | 182 |
|
| 189 |
|
|
| 183 |
|
|
| 190 | 184 |
private static String [] habitatEcologyList = new String[]{
|
| 191 | 185 |
"Habitat", |
| 192 | 186 |
"Habitat & Ecology" |
| 193 | 187 |
}; |
| 194 |
|
|
| 195 |
|
|
| 188 |
|
|
| 189 |
|
|
| 196 | 190 |
private static String [] generellDescriptionsList = new String[]{
|
| 197 | 191 |
"Fossils", |
| 198 | 192 |
"Morphology and anatomy", |
| 199 |
"Morphology",
|
|
| 193 |
"Morphology", |
|
| 200 | 194 |
"Vegetative morphology and anatomy", |
| 201 | 195 |
"Flower morphology", |
| 202 |
"Palynology",
|
|
| 203 |
"Pollination",
|
|
| 196 |
"Palynology", |
|
| 197 |
"Pollination", |
|
| 204 | 198 |
"Pollen morphology", |
| 205 | 199 |
"Life cycle", |
| 206 | 200 |
"Fruits and embryology", |
| 207 | 201 |
"Dispersal", |
| 208 |
"Wood anatomy",
|
|
| 209 |
"Leaf anatomy",
|
|
| 210 |
"Chromosome numbers",
|
|
| 202 |
"Wood anatomy", |
|
| 203 |
"Leaf anatomy", |
|
| 204 |
"Chromosome numbers", |
|
| 211 | 205 |
"Phytochemistry and Chemotaxonomy", |
| 212 | 206 |
"Phytochemistry", |
| 213 |
"Taxonomy",
|
|
| 207 |
"Taxonomy", |
|
| 214 | 208 |
}; |
| 215 | 209 |
|
| 216 | 210 |
private static String [] descriptionFeatureList = new String[]{
|
| 217 |
"lifeform",
|
|
| 218 |
"Bark",
|
|
| 219 |
"Indumentum",
|
|
| 220 |
"endophytic body",
|
|
| 221 |
"flowering buds",
|
|
| 222 |
"Branchlets",
|
|
| 223 |
"Branches",
|
|
| 224 |
"Branch",
|
|
| 211 |
"lifeform", |
|
| 212 |
"Bark", |
|
| 213 |
"Indumentum", |
|
| 214 |
"endophytic body", |
|
| 215 |
"flowering buds", |
|
| 216 |
"Branchlets", |
|
| 217 |
"Branches", |
|
| 218 |
"Branch", |
|
| 225 | 219 |
"Flowering branchlets", |
| 226 |
"Trees",
|
|
| 227 |
"Twigs",
|
|
| 228 |
"stem",
|
|
| 229 |
"Stems",
|
|
| 230 |
"stem leaves",
|
|
| 220 |
"Trees", |
|
| 221 |
"Twigs", |
|
| 222 |
"stem", |
|
| 223 |
"Stems", |
|
| 224 |
"stem leaves", |
|
| 231 | 225 |
"Leaves", |
| 232 |
"flower-bearing stems",
|
|
| 233 |
"Petiole",
|
|
| 234 |
"Petiolules",
|
|
| 235 |
"Leaflets",
|
|
| 236 |
"Thyrsus",
|
|
| 237 |
"Thyrses",
|
|
| 238 |
"Inflorescences",
|
|
| 226 |
"flower-bearing stems", |
|
| 227 |
"Petiole", |
|
| 228 |
"Petiolules", |
|
| 229 |
"Leaflets", |
|
| 230 |
"Thyrsus", |
|
| 231 |
"Thyrses", |
|
| 232 |
"Inflorescences", |
|
| 239 | 233 |
"Inflorescence", |
| 240 |
"Young inflorescences",
|
|
| 241 |
"Bracts",
|
|
| 242 |
"Pedicels",
|
|
| 243 |
"flowering buds",
|
|
| 244 |
"scales",
|
|
| 245 |
"Buds",
|
|
| 246 |
"Flowers",
|
|
| 247 |
"Flower",
|
|
| 234 |
"Young inflorescences", |
|
| 235 |
"Bracts", |
|
| 236 |
"Pedicels", |
|
| 237 |
"flowering buds", |
|
| 238 |
"scales", |
|
| 239 |
"Buds", |
|
| 240 |
"Flowers", |
|
| 241 |
"Flower", |
|
| 248 | 242 |
"Flowering", |
| 249 |
"Stigma",
|
|
| 250 |
"perianth",
|
|
| 251 |
"Sepals",
|
|
| 252 |
"Sepal",
|
|
| 253 |
"Outer Sepals",
|
|
| 254 |
"Axillary",
|
|
| 255 |
"cymes",
|
|
| 256 |
"Calyx",
|
|
| 257 |
"Petal",
|
|
| 258 |
"Petals",
|
|
| 243 |
"Stigma", |
|
| 244 |
"perianth", |
|
| 245 |
"Sepals", |
|
| 246 |
"Sepal", |
|
| 247 |
"Outer Sepals", |
|
| 248 |
"Axillary", |
|
| 249 |
"cymes", |
|
| 250 |
"Calyx", |
|
| 251 |
"Petal", |
|
| 252 |
"Petals", |
|
| 259 | 253 |
"perigone tube", |
| 260 |
"Disc",
|
|
| 261 |
"corolla",
|
|
| 262 |
"Stamens",
|
|
| 263 |
"Staminodes",
|
|
| 264 |
"Ovary",
|
|
| 254 |
"Disc", |
|
| 255 |
"corolla", |
|
| 256 |
"Stamens", |
|
| 257 |
"Staminodes", |
|
| 258 |
"Ovary", |
|
| 265 | 259 |
"Anthers", |
| 266 |
"anther",
|
|
| 267 |
"Pistil",
|
|
| 268 |
"Pistillode",
|
|
| 269 |
"Ovules",
|
|
| 270 |
"androecium",
|
|
| 271 |
"gynoecium",
|
|
| 272 |
"Filaments",
|
|
| 273 |
"Style",
|
|
| 274 |
"annulus",
|
|
| 275 |
"female flowers",
|
|
| 276 |
"Male flowers",
|
|
| 277 |
"Female",
|
|
| 278 |
"Infructescences", //order not consistent (sometimes before "Flowers")
|
|
| 279 |
"Fruit",
|
|
| 280 |
"Fruits",
|
|
| 281 |
"fruiting axes",
|
|
| 282 |
"drupes",
|
|
| 283 |
"Arillode",
|
|
| 284 |
"seed",
|
|
| 285 |
"Seeds",
|
|
| 286 |
"Seedling",
|
|
| 287 |
"flower tube",
|
|
| 288 |
"nutlets",
|
|
| 289 |
"pollen",
|
|
| 290 |
"secondary xylem",
|
|
| 291 |
"chromosome number",
|
|
| 292 |
|
|
| 293 |
"figure",
|
|
| 294 |
"fig",
|
|
| 295 |
"figs",
|
|
| 296 |
|
|
| 297 |
|
|
| 298 |
|
|
| 299 |
|
|
| 260 |
"anther", |
|
| 261 |
"Pistil", |
|
| 262 |
"Pistillode", |
|
| 263 |
"Ovules", |
|
| 264 |
"androecium", |
|
| 265 |
"gynoecium", |
|
| 266 |
"Filaments", |
|
| 267 |
"Style", |
|
| 268 |
"annulus", |
|
| 269 |
"female flowers", |
|
| 270 |
"Male flowers", |
|
| 271 |
"Female", |
|
| 272 |
"Infructescences", //order not consistent (sometimes before "Flowers") |
|
| 273 |
"Fruit", |
|
| 274 |
"Fruits", |
|
| 275 |
"fruiting axes", |
|
| 276 |
"drupes", |
|
| 277 |
"Arillode", |
|
| 278 |
"seed", |
|
| 279 |
"Seeds", |
|
| 280 |
"Seedling", |
|
| 281 |
"flower tube", |
|
| 282 |
"nutlets", |
|
| 283 |
"pollen", |
|
| 284 |
"secondary xylem", |
|
| 285 |
"chromosome number", |
|
| 286 |
|
|
| 287 |
"figure", |
|
| 288 |
"fig", |
|
| 289 |
"figs", |
|
| 290 |
|
|
| 291 |
|
|
| 292 |
|
|
| 293 |
|
|
| 300 | 294 |
}; |
| 301 |
|
|
| 302 |
public void addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 295 |
|
|
| 296 |
public void addFeatureNodesByStringList(String[] featureStringList, TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
|
| 303 | 297 |
try {
|
| 304 | 298 |
for (String featureString : featureStringList){
|
| 305 | 299 |
UUID featureUuid; |
| 306 | 300 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 307 | 301 |
Feature feature = (Feature)termService.find(featureUuid); |
| 308 | 302 |
if (feature != null){
|
| 309 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 310 |
root.addChild(child); |
|
| 303 |
root.addChild(feature); |
|
| 311 | 304 |
} |
| 312 | 305 |
} |
| 313 | 306 |
} catch (UndefinedTransformerMethodException e) {
|
| 314 | 307 |
logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
|
| 315 | 308 |
} |
| 316 | 309 |
} |
| 317 |
|
|
| 310 |
|
|
| 318 | 311 |
|
| 319 | 312 |
|
| 320 | 313 |
/** |
| ... | ... | |
| 324 | 317 |
FloraMalesianaActivator_OLD me = new FloraMalesianaActivator_OLD(); |
| 325 | 318 |
me.doImport(cdmDestination); |
| 326 | 319 |
} |
| 327 |
|
|
| 320 |
|
|
| 328 | 321 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java | ||
|---|---|---|
| 27 | 27 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 30 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 31 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 30 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 31 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 32 | 32 |
|
| 33 | 33 |
/** |
| 34 | 34 |
* @author a.mueller |
| ... | ... | |
| 319 | 319 |
|
| 320 | 320 |
|
| 321 | 321 |
|
| 322 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 322 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 323 | 323 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 324 | 324 |
|
| 325 | 325 |
makeAutomatedFeatureTree(myImport.getCdmAppController(), config.getState(), |
| ... | ... | |
| 348 | 348 |
|
| 349 | 349 |
|
| 350 | 350 |
|
| 351 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 351 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
|
| 352 | 352 |
MarkupTransformer transformer = new MarkupTransformer(); |
| 353 | 353 |
|
| 354 |
FeatureTree result = FeatureTree.NewInstance();
|
|
| 354 |
TermTree<Feature> result = TermTree.NewInstance();
|
|
| 355 | 355 |
result.setTitleCache("Old feature tree", true);
|
| 356 |
FeatureNode root = result.getRoot(); |
|
| 357 |
FeatureNode newNode; |
|
| 356 |
TermNode<Feature> root = result.getRoot(); |
|
| 358 | 357 |
|
| 359 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 360 |
root.addChild(newNode); |
|
| 358 |
TermNode<Feature> newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 361 | 359 |
|
| 362 |
addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
|
|
| 360 |
addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 363 | 361 |
|
| 364 |
addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
|
|
| 365 |
newNode = FeatureNode.NewInstance(Feature.ANATOMY());
|
|
| 366 |
addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
|
|
| 362 |
addFeatureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
|
| 363 |
newNode = TermNode.NewInstance(Feature.ANATOMY());
|
|
| 364 |
addFeatureNodesByStringList(anatomySubfeatureList, newNode, transformer, service); |
|
| 367 | 365 |
|
| 368 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
|
|
| 369 |
addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
|
|
| 366 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service); |
|
| 367 |
addFeatureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service); |
|
| 370 | 368 |
|
| 371 |
newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
|
|
| 369 |
newNode = addFeatureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); |
|
| 372 | 370 |
|
| 373 |
newNode = FeatureNode.NewInstance(Feature.COMMON_NAME()); |
|
| 374 |
root.addChild(newNode); |
|
| 371 |
newNode = root.addChild(Feature.COMMON_NAME()); |
|
| 375 | 372 |
|
| 376 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 377 |
root.addChild(newNode); |
|
| 373 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 378 | 374 |
|
| 379 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 380 |
root.addChild(newNode); |
|
| 381 |
addFeataureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 375 |
newNode = root.addChild(Feature.ECOLOGY()); |
|
| 376 |
addFeatureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 382 | 377 |
|
| 383 |
newNode = FeatureNode.NewInstance(Feature.USES()); |
|
| 384 |
root.addChild(newNode); |
|
| 378 |
newNode = root.addChild(Feature.USES()); |
|
| 385 | 379 |
|
| 386 |
addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
|
| 380 |
addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 387 | 381 |
|
| 388 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 389 |
root.addChild(newNode); |
|
| 382 |
newNode = root.addChild(Feature.CITATION()); |
|
| 390 | 383 |
|
| 391 | 384 |
return result; |
| 392 | 385 |
} |
| ... | ... | |
| 552 | 545 |
|
| 553 | 546 |
}; |
| 554 | 547 |
|
| 555 |
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 556 |
FeatureNode lastChild = null; |
|
| 548 |
public TermNode<Feature> addFeatureNodesByStringList(String[] featureStringList, |
|
| 549 |
TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
|
| 550 |
|
|
| 551 |
TermNode<Feature> lastChild = null; |
|
| 557 | 552 |
try {
|
| 558 | 553 |
for (String featureString : featureStringList){
|
| 559 | 554 |
UUID featureUuid; |
| 560 | 555 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 561 | 556 |
Feature feature = (Feature)termService.find(featureUuid); |
| 562 | 557 |
if (feature != null){
|
| 563 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 564 |
root.addChild(child); |
|
| 558 |
root.addChild(feature); |
|
| 565 | 559 |
} |
| 566 | 560 |
} |
| 567 | 561 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/NepenthesActivator.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.description.PolytomousKey; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 41 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 42 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 41 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 42 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 43 | 43 |
|
| 44 | 44 |
/** |
| 45 | 45 |
* @author a.mueller |
| ... | ... | |
| 138 | 138 |
|
| 139 | 139 |
// makeGeoService(); |
| 140 | 140 |
|
| 141 |
FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 141 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
|
|
| 142 | 142 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
| 143 | 143 |
|
| 144 | 144 |
//check keys |
| ... | ... | |
| 196 | 196 |
return result; |
| 197 | 197 |
} |
| 198 | 198 |
|
| 199 |
private FeatureTree makeFeatureNode(ITermService service){
|
|
| 199 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
|
| 200 | 200 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
| 201 | 201 |
|
| 202 |
FeatureTree result = FeatureTree.NewInstance(UUID.randomUUID());
|
|
| 202 |
TermTree<Feature> result = TermTree.NewFeatureInstance(UUID.randomUUID());
|
|
| 203 | 203 |
result.setTitleCache("Flora Malesiana Nepenthaceae Simple Feature Tree", true);
|
| 204 |
FeatureNode root = result.getRoot(); |
|
| 205 |
FeatureNode newNode; |
|
| 204 |
TermNode<Feature> root = result.getRoot(); |
|
| 206 | 205 |
|
| 207 |
newNode = FeatureNode.NewInstance(Feature.CITATION()); |
|
| 208 |
root.addChild(newNode); |
|
| 206 |
TermNode<Feature> newNode = root.addChild(Feature.CITATION()); |
|
| 209 | 207 |
|
| 208 |
newNode = root.addChild(Feature.DESCRIPTION()); |
|
| 210 | 209 |
|
| 211 |
newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
|
| 212 |
root.addChild(newNode); |
|
| 210 |
newNode = root.addChild(Feature.DISTRIBUTION()); |
|
| 213 | 211 |
|
| 214 |
newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
|
| 215 |
root.addChild(newNode); |
|
| 212 |
newNode = root.addChild(Feature.ECOLOGY()); |
|
| 216 | 213 |
|
| 217 |
newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
|
| 218 |
root.addChild(newNode); |
|
| 214 |
newNode = root.addChild(Feature.SPECIMEN()); |
|
| 219 | 215 |
|
| 220 |
newNode = FeatureNode.NewInstance(Feature.SPECIMEN()); |
|
| 221 |
root.addChild(newNode); |
|
| 216 |
newNode = root.addChild(Feature.NOTES()); |
|
| 222 | 217 |
|
| 223 |
newNode = FeatureNode.NewInstance(Feature.NOTES()); |
|
| 224 |
root.addChild(newNode); |
|
| 218 |
// addFeatureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 225 | 219 |
|
| 226 |
// addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service); |
|
| 227 |
|
|
| 228 |
// addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
|
| 220 |
// addFeatureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service); |
|
| 229 | 221 |
// newNode = FeatureNode.NewInstance(Feature.ANATOMY()); |
| 230 |
// addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
|
|
| 222 |
// addFeatureNodesByStringList(anatomySubfeatureList, newNode, transformer, service); |
|
| 231 | 223 |
// |
| 232 |
// newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
|
|
| 233 |
// addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
|
|
| 224 |
// newNode = addFeatureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service); |
|
| 225 |
// addFeatureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service); |
|
| 234 | 226 |
// |
| 235 |
// newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
|
|
| 227 |
// newNode = addFeatureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service); |
|
| 236 | 228 |
// |
| 237 | 229 |
// |
| 238 | 230 |
|
| 239 | 231 |
// |
| 240 | 232 |
// newNode = FeatureNode.NewInstance(Feature.ECOLOGY()); |
| 241 | 233 |
// root.addChild(newNode); |
| 242 |
// addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
|
|
| 234 |
// addFeatureNodesByStringList(habitatEcologyList, root, transformer, service); |
|
| 243 | 235 |
// |
| 244 | 236 |
// newNode = FeatureNode.NewInstance(Feature.USES()); |
| 245 | 237 |
// root.addChild(newNode); |
| 246 | 238 |
// |
| 247 |
// addFeataureNodesByStringList(chomosomesList, root, transformer, service);
|
|
| 239 |
// addFeatureNodesByStringList(chomosomesList, root, transformer, service); |
|
| 248 | 240 |
|
| 249 | 241 |
|
| 250 | 242 |
return result; |
| ... | ... | |
| 399 | 391 |
|
| 400 | 392 |
}; |
| 401 | 393 |
|
| 402 |
public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
|
|
| 403 |
FeatureNode lastChild = null; |
|
| 394 |
public TermNode<Feature> addFeatureNodesByStringList(String[] featureStringList, |
|
| 395 |
TermNode<Feature> root, IInputTransformer transformer, ITermService termService){
|
|
| 396 |
|
|
| 397 |
TermNode<Feature> lastChild = null; |
|
| 404 | 398 |
try {
|
| 405 | 399 |
for (String featureString : featureStringList){
|
| 406 | 400 |
UUID featureUuid; |
| 407 | 401 |
featureUuid = transformer.getFeatureUuid(featureString); |
| 408 | 402 |
Feature feature = (Feature)termService.find(featureUuid); |
| 409 | 403 |
if (feature != null){
|
| 410 |
FeatureNode child = FeatureNode.NewInstance(feature); |
|
| 411 |
root.addChild(child); |
|
| 404 |
root.addChild(feature); |
|
| 412 | 405 |
} |
| 413 | 406 |
} |
| 414 | 407 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/testUpdate/EricaceaeTestUpdateActivator.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 28 | 28 |
import eu.etaxonomy.cdm.io.eflora.EfloraImportConfigurator; |
| 29 | 29 |
import eu.etaxonomy.cdm.io.eflora.centralAfrica.ericaceae.CentralAfricaEricaceaeImportConfigurator; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.common.Language; |
| 31 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 31 | 32 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 32 | 33 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 33 |
import eu.etaxonomy.cdm.model.term.FeatureNode;
|
|
| 34 |
import eu.etaxonomy.cdm.model.term.FeatureTree;
|
|
| 34 |
import eu.etaxonomy.cdm.model.term.TermNode;
|
|
| 35 |
import eu.etaxonomy.cdm.model.term.TermTree;
|
|
| 35 | 36 |
|
| 36 | 37 |
/** |
| 37 | 38 |
* @author a.mueller |
| ... | ... | |
| 41 | 42 |
public class EricaceaeTestUpdateActivator {
|
| 42 | 43 |
@SuppressWarnings("unused")
|
| 43 | 44 |
private static final Logger logger = Logger.getLogger(EricaceaeTestUpdateActivator.class); |
| 44 |
|
|
| 45 |
|
|
| 45 | 46 |
//database validation status (create, update, validate ...) |
| 46 | 47 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
| 47 | 48 |
static final URI source = EfloraSources.ericacea_local(); |
| 48 | 49 |
|
| 49 |
|
|
| 50 |
|
|
| 50 | 51 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM2(); |
| 51 | 52 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
| 52 | 53 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
| 53 | 54 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 54 | 55 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
| 55 |
|
|
| 56 |
|
|
| 56 | 57 |
|
| 57 | 58 |
//feature tree uuid |
| 58 | 59 |
public static final UUID featureTreeUuid = UUID.fromString("051d35ee-22f1-42d8-be07-9e9bfec5bcf7");
|
| 59 |
|
|
| 60 |
|
|
| 60 | 61 |
public static UUID defaultLanguageUuid = Language.uuidEnglish; |
| 61 |
|
|
| 62 |
|
|
| 62 | 63 |
//classification |
| 63 | 64 |
static final UUID classificationUuid = UUID.fromString("10e5efcc-6e13-4abc-ad42-e0b46e50cbe7");
|
| 64 |
|
|
| 65 |
|
|
| 65 | 66 |
//check - import |
| 66 | 67 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 67 |
|
|
| 68 |
|
|
| 68 | 69 |
static boolean doPrintKeys = false; |
| 69 |
|
|
Also available in: Unified diff
ref #6794 , ref #7099 adapt app-import, pesi, eflora to modelchanges