Latest updates to Specimen Excel import

[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.TreeMap;

import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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.reference.Reference;

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

        private String basisOfRecord;

        private String country;
        private String isoCountry;
        private String locality;
        private String latitude;
        private String longitude;
        private String referenceSystem;
        private String errorRadius;
        private String altitude;
        private String altitudeMax;
        private String fieldNotes;
        private String collectingDate;
        private String collectingDateEnd;
        private String collectorsNumber;
        private String primaryCollector;
        private String language;

        private String sex;

        private String accessionNumber;
        private String barcode;
        
        //      private String author;

//      private String family;
//      private String genus;
//      private String specificEpithet;
        private String collectionCode;
        private String collection;
        
        
        private TreeMap<Integer, IdentifiableSource> sources = new TreeMap<Integer, IdentifiableSource>();
        private TreeMap<Integer, String> collectors = new TreeMap<Integer, String>();
        private TreeMap<Integer, String> unitNotes = new TreeMap<Integer, String>();
        private TreeMap<Integer, SpecimenTypeDesignation> types = new TreeMap<Integer, SpecimenTypeDesignation>();
        private TreeMap<Integer, DeterminationLight> determinations = new TreeMap<Integer, DeterminationLight>();
        private List<PostfixTerm> levels  = new ArrayList<PostfixTerm>(); 
        

        
        public SpecimenRow() {
        }
        

        
        //      may be public if necessary
        protected class DeterminationLight{
                String taxonUuid;
                String family;
                String genus;
                String rank;
                String fullName;
                String speciesEpi;
                String infraSpeciesEpi;
                String author;
                String modifier;
                String determinedBy;
                String determinedWhen;
                String notes;
                
                public boolean hasTaxonInformation() {
                        boolean result = StringUtils.isNotBlank(taxonUuid) 
                                || StringUtils.isNotBlank(family)       
                                || StringUtils.isNotBlank(genus)
                                || StringUtils.isNotBlank(rank)
                                || StringUtils.isNotBlank(fullName)
                                || StringUtils.isNotBlank(speciesEpi)
                                || StringUtils.isNotBlank(author)
                                || StringUtils.isNotBlank(infraSpeciesEpi);
                        return result;
                }

        }
        
        
// **************************** GETTER / SETTER *********************************/      
        
        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 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 getAltitude() {
                return altitude;
        }


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


        /**
         * @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, OriginalSourceType.Import);
                source.setIdInSource(id);
        }
        public void putSourceReference(int key, Reference<?> reference){
                IdentifiableSource source = getOrMakeSource(key, OriginalSourceType.Unknown);
                source.setCitation(reference);
        }

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


        public void setCollectors(String value) {
                //TODO better parse somewhere else? Quick and dirty implementation
                List<String> authors = new ArrayList<String>();
                String[] splits = value.split("&");
                for (String split: splits){
                        split = split.trim();
                        authors.add(split);
                }
                int index = 1;
                for (int i = 0; i < authors.size() ; i++){
                        String author = authors.get(i);
                        if (i < authors.size()-1){
                                String[] internalSplits = author.split(",");
                                for (String internal : internalSplits){
                                        internal = internal.trim();
                                        this.collectors.put(index++, internal);
                                }
                        }else{
                                this.collectors.put(index++, author);
                        }
                }
        }
        
        public void putCollector(int key, String collector){
                this.collectors.put(key, collector);
        }

        public List<String> getCollectors() {
                return getOrdered(collectors);
        }
        
        public void putUnitNote(int key, String unitNote){
                this.unitNotes.put(key, unitNote);
        }

        public List<String> getUnitNotes() {
                return getOrdered(unitNotes);
        }
        
        
        
        /**
         * @param key
         * @return
         */
        private IdentifiableSource getOrMakeSource(int key, OriginalSourceType type) {
                IdentifiableSource  source = sources.get(key);
                if (source == null){
                        source = IdentifiableSource.NewInstance(type);
                        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 putDeterminationTaxonUuid(int key, String taxonUuid){
                DeterminationLight determinationEvent = getOrMakeDetermination(key);
                determinationEvent.taxonUuid = taxonUuid;
        }

        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() {
                List<DeterminationLight> result = getOrdered(determinations);
                if (determinations.size() > 1 && getCommonDetermination()!= null ){
                        result.remove(getCommonDetermination());
                }
                return result;
        }
        
        /**
         * Returns the determination with key "0".
         * @return
         */
        public DeterminationLight getCommonDetermination() {
                if (determinations.get(0) != null){
                        return determinations.get(0);
                }
                return null;
        }
        
        
        
        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) {
                PostfixTerm area = new PostfixTerm();
                area.term = value;
                area.postfix = levelPostfix;
                this.levels.add(area);
        }
        
        public List<PostfixTerm> getLeveledAreas(){
                return levels;
        }
        
        public void setAltitudeMax(String altitudeMax) {
                this.altitudeMax = altitudeMax;
        }


        public String getAltitudeMax() {
                return altitudeMax;
        }


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


        /**
         * @return the primaryCollector
         */
        public String getPrimaryCollector() {
                return primaryCollector;
        }


        public String getLanguage() {
                return language;
        }


        public void setLanguage(String language) {
                this.language = language;
        }
        
}