newest developments for specimen import (e.g. area levels)

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / specimen / excel / in / SpecimenRow.java

/**
* Copyright (C) 2009 EDIT
* European Distributed Institute of Taxonomy 
* http://www.e-taxonomy.eu
* 
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/

package eu.etaxonomy.cdm.io.specimen.excel.in;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenRow.LeveledArea;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
import eu.etaxonomy.cdm.model.reference.Reference;

/**
 * @author a.mueller
 * @created 08.04.2011
 * @version 1.0
 */
public class SpecimenRow {
        @SuppressWarnings("unused")
        private static final Logger logger = Logger.getLogger(SpecimenRow.class);

        private UUID uuid = null; 
        private String basisOfRecord;
        private String country;
        private String isoCountry;
        private String locality;
        private String latitude;
        private String longitude;
        private String fieldNotes;
        private String fieldNumber;
        private String accessionNumber;
        private String barcode;
//      private String author;
        private String absoluteElevation;
//      private String family;
//      private String genus;
//      private String specificEpithet;
        private String sex;
        private String ecology;
        private String plantDescription;
        private String collectionCode;
        private String collection;
        private String collectingDate;
        private String collectingDateEnd;
        private String collectorsNumber;
        private String referenceSystem;
        private String errorRadius;
        
        
        private TreeMap<Integer, IdentifiableSource> sources = new TreeMap<Integer, IdentifiableSource>();
        private TreeMap<Integer, String> collectors = new TreeMap<Integer, String>();
        private TreeMap<Integer, SpecimenTypeDesignation> types = new TreeMap<Integer, SpecimenTypeDesignation>();
        private TreeMap<Integer, DeterminationLight> determinations = new TreeMap<Integer, DeterminationLight>();
        private List<LeveledArea> levels  = new ArrayList<LeveledArea>(); 
        

        
        public SpecimenRow() {
        }
        
        protected class LeveledArea{
                String area;
                String areaLevel;
        }
        

        
        //      may be public if necessary
        protected class DeterminationLight{
                String family;
                String genus;
                String rank;
                String fullName;
                String speciesEpi;
                String infraSpeciesEpi;
                String author;
                String modifier;
                String determinedBy;
                String determinedWhen;
                String notes;
        }
        
        
// **************************** GETTER / SETTER *********************************/      
        

        public void setUuid(UUID uuid) {
                this.uuid = uuid;
        }


        public UUID getUuid() {
                return uuid;
        }


        public void setBasisOfRecord(String basisOfRecord) {
                this.basisOfRecord = basisOfRecord;
        }


        public String getBasisOfRecord() {
                return basisOfRecord;
        }


        public void setCountry(String country) {
                this.country = country;
        }


        public String getCountry() {
                return country;
        }


        public void setIsoCountry(String isoCountry) {
                this.isoCountry = isoCountry;
        }


        public String getIsoCountry() {
                return isoCountry;
        }


        public void setLocality(String locality) {
                this.locality = locality;
        }


        public String getLocality() {
                return locality;
        }


        public void setFieldNotes(String fieldNotes) {
                this.fieldNotes = fieldNotes;
        }


        public String getFieldNotes() {
                return fieldNotes;
        }


        public void setAccessionNumber(String accessionNumber) {
                this.accessionNumber = accessionNumber;
        }


        public String getAccessionNumber() {
                return accessionNumber;
        }


        public void setFieldNumber(String fieldNumber) {
                this.fieldNumber = fieldNumber;
        }


        public String getFieldNumber() {
                return fieldNumber;
        }


        public void setBarcode(String barcode) {
                this.barcode = barcode;
        }
//      
//      /**
//       * @return the author
//       */
//      public String getAuthor() {
//              return author;
//      }
//
//
//      /**
//       * @param author the author to set
//       */
//      public void setAuthor(String author) {
//              this.author = author;
//      }


        /**
         * @return the absoluteElevation
         */
        public String getAbsoluteElevation() {
                return absoluteElevation;
        }


        /**
         * @param absoluteElevation the absoluteElevation to set
         */
        public void setAbsoluteElevation(String absoluteElevation) {
                this.absoluteElevation = absoluteElevation;
        }



        /**
         * @return the ecology
         */
        public String getEcology() {
                return ecology;
        }


        /**
         * @param ecology the ecology to set
         */
        public void setEcology(String ecology) {
                this.ecology = ecology;
        }


        /**
         * @return the plantDescription
         */
        public String getPlantDescription() {
                return plantDescription;
        }


        /**
         * @param plantDescription the plantDescription to set
         */
        public void setPlantDescription(String plantDescription) {
                this.plantDescription = plantDescription;
        }


        /**
         * @return the collectionCode
         */
        public String getCollectionCode() {
                return collectionCode;
        }


        /**
         * @param collectionCode the collectionCode to set
         */
        public void setCollectionCode(String collectionCode) {
                this.collectionCode = collectionCode;
        }


        /**
         * @return the collectingDate
         */
        public String getCollectingDate() {
                return collectingDate;
        }


        /**
         * @param collectingDate the collectingDate to set
         */
        public void setCollectingDate(String collectingDate) {
                this.collectingDate = collectingDate;
        }


        /**
         * @return the collectorsNumber
         */
        public String getCollectorsNumber() {
                return collectorsNumber;
        }


        /**
         * @param collectorsNumber the collectorsNumber to set
         */
        public void setCollectorsNumber(String collectorsNumber) {
                this.collectorsNumber = collectorsNumber;
        }


        /**
         * @return the barcode
         */
        public String getBarcode() {
                return barcode;
        }


        /**
         * @return the collectingDateEnd
         */
        public String getCollectingDateEnd() {
                return collectingDateEnd;
        }


        /**
         * @param collectingDateEnd the collectingDateEnd to set
         */
        public void setCollectingDateEnd(String collectingDateEnd) {
                this.collectingDateEnd = collectingDateEnd;
        }


        /**
         * @return the latitude
         */
        public String getLatitude() {
                return latitude;
        }


        /**
         * @param latitude the latitude to set
         */
        public void setLatitude(String latitude) {
                this.latitude = latitude;
        }


        /**
         * @return the longitude
         */
        public String getLongitude() {
                return longitude;
        }


        /**
         * @param longitude the longitude to set
         */
        public void setLongitude(String longitude) {
                this.longitude = longitude;
        }


        public void putIdInSource(int key, String id){
                IdentifiableSource source = getOrMakeSource(key);
                source.setIdInSource(id);
        }
        public void putSourceReference(int key, Reference<?> reference){
                IdentifiableSource source = getOrMakeSource(key);
                source.setCitation(reference);
        }

        public List<IdentifiableSource> getSources() {
                return getOrdered(sources);
        }

        public void putCollector(int key, String collector){
                this.collectors.put(key, collector);
        }

        public List<String> getCollectors() {
                return getOrdered(collectors);
        }
        
        
        
        /**
         * @param key
         * @return
         */
        private IdentifiableSource getOrMakeSource(int key) {
                IdentifiableSource  source = sources.get(key);
                if (source == null){
                        source = IdentifiableSource.NewInstance();
                        sources.put(key, source);
                }
                return source;
        }
        

        public void putTypeCategory(int key, SpecimenTypeDesignationStatus status){
                SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
                designation.setTypeStatus(status);
        }
        public void putTypifiedName(int key, TaxonNameBase<?,?> name){
                if (name != null){
                        SpecimenTypeDesignation designation = getOrMakeTypeDesignation(key);
                        name.addTypeDesignation(designation, false);
                }
        }

        public List<SpecimenTypeDesignation> getTypeDesignations() {
                return getOrdered(types);
        }


        private SpecimenTypeDesignation getOrMakeTypeDesignation(int key) {
                SpecimenTypeDesignation designation = types.get(key);
                if (designation == null){
                        designation = SpecimenTypeDesignation.NewInstance();
                        types.put(key, designation);
                }
                return designation;
        }
        
        public void putDeterminationFamily(int key, String family){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.family = family;
        }

        public void putDeterminationFullName(int key, String fullName){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.fullName = fullName;
        }

        public void putDeterminationRank(int key, String rank){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.rank = rank;
        }

        public void putDeterminationGenus(int key, String genus){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.genus = genus;
        }
        
        public void putDeterminationSpeciesEpi(int key, String speciesEpi){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.speciesEpi = speciesEpi;
        }

        public void putDeterminationInfraSpeciesEpi(int key, String infraSpeciesEpi){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.infraSpeciesEpi = infraSpeciesEpi;
        }

        public void putDeterminationAuthor(int key, String author){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.author = author;
        }

        public void putDeterminationDeterminedBy(int key, String determinedBy){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.determinedBy = determinedBy;
        }

        public void putDeterminationDeterminedWhen(int key, String determinedWhen){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.determinedWhen = determinedWhen;
        }

        public void putDeterminationDeterminationNotes(int key, String notes){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.notes = notes;
        }
        
        public void putDeterminationDeterminationModifier(int key, String modifier){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.modifier = modifier;
        }
        
        public List<DeterminationLight> getDetermination() {
                return getOrdered(determinations);
        }
        
        
        
        private DeterminationLight getOrMakeDetermination(int key) {
                DeterminationLight determination = this.determinations.get(key);
                if (determination == null){
                        determination = new DeterminationLight();
                        this.determinations.put(key, determination);
                }
                return determination;
        }
        

        private<T extends Object> List<T> getOrdered(TreeMap<?, T> tree) {
                List<T> result = new ArrayList<T>();
                for (T value : tree.values()){
                        result.add(value);
                }
                return result;
        }
        
        public void setSex(String sex) {
                this.sex = sex;
        }


        public String getSex() {
                return sex;
        }


        /**
         * @return the referenceSystem
         */
        public String getReferenceSystem() {
                return referenceSystem;
        }


        /**
         * @param referenceSystem the referenceSystem to set
         */
        public void setReferenceSystem(String referenceSystem) {
                this.referenceSystem = referenceSystem;
        }


        /**
         * @return the errorRadius
         */
        public String getErrorRadius() {
                return errorRadius;
        }


        /**
         * @param errorRadius the errorRadius to set
         */
        public void setErrorRadius(String errorRadius) {
                this.errorRadius = errorRadius;
        }


        public void setCollection(String collection) {
                this.collection = collection;
        }


        public String getCollection() {
                return collection;
        }


        public void addLeveledArea(String levelPostfix, String value) {
                LeveledArea area = new LeveledArea();
                this.levels.add(area);
//              getOrMakeLeveledArea(level);
        }
        
        public List<LeveledArea> getLeveledAreas(){
                return levels;
        }
        
//      private NamedAreaLevel getOrMakeLeveledArea(String key) {
//              NamedAreaLevel level = this.levels.get(key);
//              if (level == null){
//                      level = new NamedAreaLevel();
//                      this.levels.put(key, level);
//              }
//              return level;
//      }
        
        
}