cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportStateBase.java

   1 /**
   2 * Copyright (C) 2016 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.specimen;
  10
  11 import java.util.ArrayList;
  12 import java.util.HashMap;
  13 import java.util.HashSet;
  14 import java.util.List;
  15 import java.util.Map;
  16 import java.util.Set;
  17 import java.util.UUID;
  18
  19 import org.springframework.transaction.TransactionStatus;
  20
  21 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  22 import eu.etaxonomy.cdm.common.URI;
  23 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  24 import eu.etaxonomy.cdm.io.common.ImportStateBase;
  25 import eu.etaxonomy.cdm.io.common.MapWrapper;
  26 import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
  27 import eu.etaxonomy.cdm.model.agent.Institution;
  28 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  29 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  30 import eu.etaxonomy.cdm.model.name.TaxonName;
  31 import eu.etaxonomy.cdm.model.occurrence.Collection;
  32 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  33 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  34 import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
  35 import eu.etaxonomy.cdm.model.reference.Reference;
  36 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  37 import eu.etaxonomy.cdm.model.taxon.Classification;
  38
  39 /**
  40  * @author k.luther
  41  * @since 15.07.2016
  42  */
  43 public class SpecimenImportStateBase<CONFIG extends SpecimenImportConfiguratorBase, STATE extends SpecimenImportStateBase>
  44         extends ImportStateBase<CONFIG , CdmImportBase<CONFIG , STATE >>{
  45
  46     public SpecimenImportStateBase(CONFIG config) {
  47         super(config);
  48     }
  49
  50     private TransactionStatus tx;
  51
  52     private ICdmRepository cdmRepository;
  53     private Classification classification = null;
  54     private Classification defaultClassification = null;
  55     private Reference ref = null;
  56
  57     private HashMap<UUID, TaxonDescription> individualsAssociationDescriptionPerTaxon = new HashMap<>();
  58     private DerivedUnit derivedUnitBase;
  59
  60     private SpecimenImportReport report;
  61
  62     protected SpecimenDataHolder dataHolder;
  63
  64     private List<OriginalSourceBase> associationRefs = new ArrayList<>();
  65     private boolean associationSourcesSet=false;
  66     private List<OriginalSourceBase> descriptionRefs = new ArrayList<>();
  67     private boolean descriptionSourcesSet=false;
  68     private List<OriginalSourceBase> derivedUnitSources = new ArrayList<>();
  69     private boolean derivedUnitSourcesSet=false;
  70     private boolean descriptionGroupSet = false;
  71     protected Map<String, Institution> institutions = new HashMap<>();
  72     protected Map<String, Collection> collections= new HashMap<>();
  73     protected Map<String, TaxonName> names= new HashMap<>();
  74     private Map<String,FieldUnit> fieldUnits = new HashMap<>();
  75
  76     private MapWrapper<TeamOrPersonBase<?>> personStore;
  77     private Map<String, Reference> importReferences = new HashMap<>();
  78     private URI actualAccessPoint;
  79     private Set<URI> allAccesPoints = new HashSet<>();
  80
  81 // ************************* Getter/Setter **************/
  82
  83     public MapWrapper<TeamOrPersonBase<?>> getPersonStore() {
  84         return personStore;
  85     }
  86     public void setPersonStore(MapWrapper<TeamOrPersonBase<?>> personStore) {
  87         this.personStore = personStore;
  88     }
  89
  90     public FieldUnit getFieldUnit(String fieldNumber) {
  91         return fieldUnits.get(fieldNumber);
  92     }
  93     public void setFieldUnit(FieldUnit fieldUnit) {
  94         this.fieldUnits.put(fieldUnit.getFieldNumber(), fieldUnit);
  95     }
  96
  97     @Override
  98     public CONFIG getConfig(){
  99         return super.getConfig();
 100     }
 101
 102     public List<OriginalSourceBase> getAssociationRefs() {
 103         return associationRefs;
 104     }
 105
 106     public void setAssociationRefs(List<OriginalSourceBase> associationRefs) {
 107         this.associationRefs = associationRefs;
 108     }
 109
 110     public boolean isAssociationSourcesSet() {
 111         return associationSourcesSet;
 112     }
 113
 114     public void setAssociationSourcesSet(boolean associationSourcesSet) {
 115         this.associationSourcesSet = associationSourcesSet;
 116     }
 117
 118     public List<OriginalSourceBase> getDescriptionRefs() {
 119         return descriptionRefs;
 120     }
 121
 122     public void setDescriptionRefs(List<OriginalSourceBase> descriptionRefs) {
 123         this.descriptionRefs = descriptionRefs;
 124     }
 125
 126     public boolean isDescriptionSourcesSet() {
 127         return descriptionSourcesSet;
 128     }
 129
 130     public void setDescriptionSourcesSet(boolean descriptionSourcesSet) {
 131         this.descriptionSourcesSet = descriptionSourcesSet;
 132     }
 133
 134     public List<OriginalSourceBase> getDerivedUnitSources() {
 135         return derivedUnitSources;
 136     }
 137
 138     public void setDerivedUnitSources(List<OriginalSourceBase> derivedUnitSources) {
 139         this.derivedUnitSources = derivedUnitSources;
 140     }
 141
 142     public boolean isDerivedUnitSourcesSet() {
 143         return derivedUnitSourcesSet;
 144     }
 145
 146     public void setDerivedUnitSourcesSet(boolean derivedUnitSourcesSet) {
 147         this.derivedUnitSourcesSet = derivedUnitSourcesSet;
 148     }
 149
 150     public boolean isDescriptionGroupSet() {
 151         return descriptionGroupSet;
 152     }
 153
 154     public void setDescriptionGroupSet(boolean descriptionGroupSet) {
 155         this.descriptionGroupSet = descriptionGroupSet;
 156     }
 157
 158     public TransactionStatus getTx() {
 159         return tx;
 160     }
 161
 162     public void setTx(TransactionStatus tx) {
 163         this.tx = tx;
 164     }
 165
 166     public ICdmRepository getCdmRepository() {
 167         return cdmRepository;
 168     }
 169
 170     public void setCdmRepository(ICdmRepository cdmRepository) {
 171         this.cdmRepository = cdmRepository;
 172     }
 173
 174     public Classification getClassification() {
 175         return classification;
 176     }
 177
 178     public void setClassification(Classification classification) {
 179         this.classification = classification;
 180     }
 181
 182     public Classification getDefaultClassification(boolean createIfNotExist) {
 183         if(defaultClassification==null && createIfNotExist){
 184             final String defaultClassificationAbcd = "Default Classification Specimen Import";
 185             for (Classification classif : cdmRepository.getClassificationService().list(Classification.class, null, null, null, null)){
 186                 if (classif.getTitleCache()!=null && classif.getTitleCache().equalsIgnoreCase(defaultClassificationAbcd)
 187                         && classif.getReference()!=null && classif.getReference().equals(getRef())) {
 188                     defaultClassification = classif;
 189                     break;
 190                 }
 191             }
 192             if(defaultClassification==null){
 193                 defaultClassification = Classification.NewInstance(defaultClassificationAbcd);
 194                 cdmRepository.getClassificationService().save(defaultClassification);
 195             }
 196         }
 197         return defaultClassification;
 198     }
 199
 200     public void setDefaultClassification(Classification defaultClassification) {
 201         this.defaultClassification = defaultClassification;
 202     }
 203
 204     public Reference getRef() {
 205         return ref;
 206     }
 207     public void setRef(Reference ref) {
 208         this.ref = ref;
 209     }
 210
 211     public TaxonDescription getIndividualsAssociationDescriptionPerTaxon(UUID taxonUUID) {
 212         return individualsAssociationDescriptionPerTaxon.get(taxonUUID);
 213     }
 214
 215     public void setIndividualsAssociationDescriptionPerTaxon(TaxonDescription description) {
 216         this.individualsAssociationDescriptionPerTaxon.put(description.getTaxon().getUuid(), description);
 217     }
 218
 219     public DerivedUnit getDerivedUnitBase() {
 220         return derivedUnitBase;
 221     }
 222     public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
 223         this.derivedUnitBase = derivedUnitBase;
 224     }
 225
 226     public URI getActualAccessPoint() {
 227         return actualAccessPoint;
 228     }
 229
 230     public Set<URI> getAllAccesPoint() {
 231         return allAccesPoints;
 232     }
 233
 234     public void addActualAccesPoint(URI actualAccesPoint) {
 235         this.allAccesPoints.add(actualAccesPoint);
 236     }
 237     public void setActualAccessPoint(URI actualAccessPoint) {
 238         this.addActualAccesPoint(actualAccessPoint);
 239         this.actualAccessPoint = actualAccessPoint;
 240     }
 241
 242     public SpecimenImportReport getReport() {
 243         if (report == null){
 244             report = new SpecimenImportReport();
 245         }
 246         return report;
 247     }
 248     public void setReport(SpecimenImportReport report) {
 249         this.report = report;
 250     }
 251
 252     public SpecimenDataHolder getDataHolder() {
 253         return dataHolder;
 254     }
 255     public void setDataHolder(SpecimenDataHolder dataHolder) {
 256         this.dataHolder = dataHolder;
 257     }
 258     public void reset() {
 259         getDataHolder().reset();
 260        // setDerivedUnitBase(null);
 261     }
 262
 263     public Reference getImportReference(URI accessPoint){
 264         if (accessPoint == null){
 265             return null;
 266         }
 267         if (importReferences == null){
 268             importReferences = new HashMap<>();
 269         }
 270         if (this.importReferences.containsKey(accessPoint.toString())){
 271             return this.importReferences.get(accessPoint.toString());
 272         }else{
 273             Reference ref = ReferenceFactory.newGeneric();
 274             ref.setUri(accessPoint);
 275             ref.setTitle(accessPoint.toString());
 276             this.importReferences.put(accessPoint.toString(), ref);
 277             return ref;
 278         }
 279     }
 280
 281     public void addImportReference(Reference ref) {
 282         if (ref.getUri() != null){
 283             this.importReferences.put(ref.getUri().toString(), ref);
 284         }
 285     }
 286 }