-// $Id$
-/**
-* Copyright (C) 2016 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;
-
-import java.util.HashMap;
-import java.util.List;
-
-/**
- * @author k.luther
- * @date 18.07.2016
- *
- */
-public class SpecimenDataHolder {
-
- private String nomenclatureCode;
- private List<HashMap<String, String>> atomisedIdentificationList;
-
-
-
- /**
- * @return the nomenclatureCode
- */
- public String getNomenclatureCode() {
- return nomenclatureCode;
- }
-
-
-
- /**
- * @param nomenclatureCode the nomenclatureCode to set
- */
- public void setNomenclatureCode(String nomenclatureCode) {
- this.nomenclatureCode = nomenclatureCode;
- }
-
-
-
- /**
- * @return the atomisedIdentificationList
- */
- public List<HashMap<String, String>> getAtomisedIdentificationList() {
- return atomisedIdentificationList;
- }
-
-
-
- /**
- * @param atomisedIdentificationList the atomisedIdentificationList to set
- */
- public void setAtomisedIdentificationList(List<HashMap<String, String>> atomisedIdentificationList) {
- this.atomisedIdentificationList = atomisedIdentificationList;
- }
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen;\r
+\r
+import java.util.HashMap;\r
+import java.util.List;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 18.07.2016\r
+ *\r
+ */\r
+public class SpecimenDataHolder {\r
+\r
+ private String nomenclatureCode;\r
+ private List<HashMap<String, String>> atomisedIdentificationList;\r
+\r
+\r
+\r
+ /**\r
+ * @return the nomenclatureCode\r
+ */\r
+ public String getNomenclatureCode() {\r
+ return nomenclatureCode;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param nomenclatureCode the nomenclatureCode to set\r
+ */\r
+ public void setNomenclatureCode(String nomenclatureCode) {\r
+ this.nomenclatureCode = nomenclatureCode;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the atomisedIdentificationList\r
+ */\r
+ public List<HashMap<String, String>> getAtomisedIdentificationList() {\r
+ return atomisedIdentificationList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param atomisedIdentificationList the atomisedIdentificationList to set\r
+ */\r
+ public void setAtomisedIdentificationList(List<HashMap<String, String>> atomisedIdentificationList) {\r
+ this.atomisedIdentificationList = atomisedIdentificationList;\r
+ }\r
+}\r
/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* 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;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Set;
+
import org.apache.log4j.Logger;
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
+import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
+import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.CdmImportBase;
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
+import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.agent.Team;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.common.LanguageString;
+import eu.etaxonomy.cdm.model.description.DescriptionBase;
+import eu.etaxonomy.cdm.model.name.BacterialName;
+import eu.etaxonomy.cdm.model.name.BotanicalName;
+import eu.etaxonomy.cdm.model.name.CultivarPlantName;
+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.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.ZoologicalName;
+import eu.etaxonomy.cdm.model.occurrence.Collection;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.persistence.query.MatchMode;
+import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
+import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
/**
* @author p.kelbert
* @created 20.10.2008
*/
-public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmImportBase<CONFIG, STATE> {
+public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends SpecimenImportStateBase> extends CdmImportBase<CONFIG, STATE> {
+
@SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
+ protected final boolean DEBUG = true;
+
+ @Override
+ protected abstract void doInvoke(STATE state);
+
+ /**
+ * Handle a single unit
+ * @param state
+ * @param item
+ */
+ @SuppressWarnings("rawtypes")
+ protected abstract void handleSingleUnit(STATE state, Object item) ;
+
+
+
+ protected TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
+ TaxonNameBase<?, ?> taxonName = null;
+ SpecimenImportConfiguratorBase config = (SpecimenImportConfiguratorBase) state.getConfig();
+
+ //check atomised name data for rank
+ //new name will be created
+ NonViralName<?> atomisedTaxonName = null;
+ if (rank==null && unitIndexInAbcdFile>=0 && (state.getDataHolder().getAtomisedIdentificationList() != null || state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
+ atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
+ if(atomisedTaxonName!=null){
+ rank = atomisedTaxonName.getRank();
+ }
+ }
+ if(config.isReuseExistingTaxaWhenPossible()){
+ NonViralName<?> parsedName = atomisedTaxonName;
+ if(parsedName==null){
+ parsedName = parseScientificName(scientificName, state, state.getReport());
+ }
+ if(config.isIgnoreAuthorship() && parsedName!=null && preferredFlag){
+ // do not ignore authorship for non-preferred names because they need
+ // to be created for the determination history
+ String nameCache = parsedName.getNameCache();
+ List<NonViralName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
+ taxonName = getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names), state);
+ }
+ else {
+ //search for existing names
+ List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(scientificName, names, state);
+ //still nothing found -> try with the atomised name full title cache
+ if(taxonName==null && atomisedTaxonName!=null){
+ names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
+ //still nothing found -> try with the atomised name title cache
+ if(taxonName==null){
+ names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
+ taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
+ }
+ }
+ }
+ }
+
+ if(taxonName==null && atomisedTaxonName!=null){
+ taxonName = atomisedTaxonName;
+ state.getReport().addName(taxonName);
+ logger.info("Created new taxon name "+taxonName);
+ if(taxonName.hasProblem()){
+ state.getReport().addInfoMessage(String.format("Created %s with parsing problems", taxonName));
+ }
+ if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
+ state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
+ }
+ }
+ else if(taxonName==null){
+ //create new taxon name
+ taxonName = NonViralName.NewInstance(rank);
+ taxonName.setFullTitleCache(scientificName,true);
+ taxonName.setTitleCache(scientificName, true);
+ state.getReport().addName(taxonName);
+ logger.info("Created new taxon name "+taxonName);
+ }
+ save(taxonName, state);
+ return taxonName;
+ }
+
+ protected TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names, STATE state){
+ List<TaxonNameBase> namesWithAcceptedTaxa = new ArrayList<TaxonNameBase>();
+ for (TaxonNameBase name : names) {
+ if(!name.getTaxa().isEmpty()){
+ namesWithAcceptedTaxa.add(name);
+ }
+ }
+ String message = "More than one taxon name was found for "+scientificName+"!";
+ //check for names with accepted taxa
+ if(namesWithAcceptedTaxa.size()>0){
+ if(namesWithAcceptedTaxa.size()>1){
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return namesWithAcceptedTaxa.iterator().next();
+ }
+ //no names with accepted taxa found -> check accepted taxa of synonyms
+ List<Taxon> taxaFromSynonyms = new ArrayList<Taxon>();
+ for (TaxonNameBase name : names) {
+ Set<TaxonBase> taxonBases = name.getTaxonBases();
+ for (TaxonBase taxonBase : taxonBases) {
+ if(taxonBase.isInstanceOf(Synonym.class)){
+ Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
+ taxaFromSynonyms.addAll(synonym.getAcceptedTaxa());
+ }
+ }
+ }
+ if(taxaFromSynonyms.size()>0){
+ if(taxaFromSynonyms.size()>1){
+ state.getReport().addInfoMessage(message);
+ logger.warn(message);
+ return null;
+ }
+ return taxaFromSynonyms.iterator().next().getName();
+ }
+ return null;
+ }
+ /**
+ * Parse automatically the scientific name
+ * @param scientificName the scientific name to parse
+ * @param state the current import state
+ * @param report the import report
+ * @return a parsed name
+ */
+ protected NonViralName<?> parseScientificName(String scientificName, STATE state, SpecimenImportReport report) {
+ NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
+ NonViralName<?> taxonName = null;
+ boolean problem = false;
+
+ if(DEBUG){
+ logger.info("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
+ }
+
+ if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
+ taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, null);
+ if (taxonName.hasProblem()) {
+ problem = true;
+ }
+ }
+ if (problem) {
+ String message = String.format("Parsing problems for %s", scientificName);
+ if(taxonName!=null){
+ for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
+ message += "\n\t- "+parserProblem;
+ }
+ }
+ report.addInfoMessage(message);
+ logger.info(message);
+ }
+ return taxonName;
+
+ }
+
+ /**
+ * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
+ * The name is built upon the ABCD fields
+ * @param atomisedMap : the ABCD atomised fields
+ * @param fullName : the full scientific name
+ * @param state
+ * @return the corresponding Botanical or Zoological or... name
+ */
+ protected NonViralName<?> setTaxonNameByType(
+ HashMap<String, String> atomisedMap, String fullName, STATE state) {
+ boolean problem = false;
+ if(DEBUG) {
+ logger.info("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
+ }
+
+ if (state.getDataHolder().getNomenclatureCode().equals("Zoological")) {
+ NonViralName<ZoologicalName> taxonName = ZoologicalName.NewInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
+
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+
+ if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+
+ if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ }
+ }
+ if (team != null) {
+ taxonName.setBasionymAuthorship(team);
+ }
+ else {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICZN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Botanical")) {
+ BotanicalName taxonName = (BotanicalName) parseScientificName(fullName, state, state.getReport());
+ if (taxonName != null){
+ return taxonName;
+ }
+ else{
+ taxonName = BotanicalName.NewInstance(null);
+ }
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
+ try {
+ taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
+ } catch (Exception e) {
+ if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ }
+ Team team = null;
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (team == null) {
+ if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
+ }
+ else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
+ taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
+ }
+ }
+ if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
+ team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICBN");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial")) {
+ NonViralName<BacterialName> taxonName = BacterialName.NewInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
+ taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
+ taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
+ taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
+
+ if (taxonName.getGenusOrUninomial() != null){
+ taxonName.setRank(Rank.GENUS());
+ }
+ else if (taxonName.getInfraGenericEpithet() != null){
+ taxonName.setRank(Rank.SUBGENUS());
+ }
+ else if (taxonName.getSpecificEpithet() != null){
+ taxonName.setRank(Rank.SPECIES());
+ }
+ else if (taxonName.getInfraSpecificEpithet() != null){
+ taxonName.setRank(Rank.SUBSPECIES());
+ }
+
+ if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
+ taxonName.setCombinationAuthorship(team);
+ }
+ if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
+ Team team = Team.NewInstance();
+ team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
+ taxonName.setBasionymAuthorship(team);
+ }
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNB");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ }
+ else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
+ CultivarPlantName taxonName = CultivarPlantName.NewInstance(null);
+
+ if (taxonName.hasProblem()) {
+ logger.info("pb ICNCP");
+ problem = true;
+ }
+ else {
+ return taxonName;
+ }
+ return taxonName;
+ }
+
+ if (problem) {
+ logger.info("Problem im setTaxonNameByType ");
+ NonViralName<?> taxonName = NonViralName.NewInstance(null);
+ taxonName.setFullTitleCache(fullName, true);
+ return taxonName;
+ }
+ NonViralName<?> tn = NonViralName.NewInstance(null);
+ return tn;
+ }
+
+ /**
+ * Get a formated string from a hashmap
+ * @param atomisedMap
+ * @param key
+ * @return
+ */
+ private String getFromMap(HashMap<String, String> atomisedMap, String key) {
+ String value = null;
+ if (atomisedMap.containsKey(key)) {
+ value = atomisedMap.get(key);
+ }
+
+ try {
+ if (value != null && key.matches(".*Year.*")) {
+ value = value.trim();
+ if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
+ String tmp = value.split("[0-9]{4}$")[0];
+ int year = Integer.parseInt(value.split(tmp)[1]);
+ if (year >= 1752) {
+ value = tmp;
+ }
+ else {
+ value = null;
+ }
+ }
+ else {
+ value = null;
+ }
+ }
+ }
+ catch (Exception e) {
+ value = null;
+ }
+ return value;
+ }
+
+ /**
+ * Very fast and dirty implementation to allow handling of transient objects as described in
+ * https://dev.e-taxonomy.eu/trac/ticket/3726
+ *
+ * Not yet complete.
+ *
+ * @param cdmBase
+ * @param state
+ */
+ protected void save(CdmBase cdmBase, SpecimenImportStateBase state) {
+ ICdmApplicationConfiguration cdmRepository = state.getConfig().getCdmAppController();
+ if (cdmRepository == null){
+ cdmRepository = this;
+ }
+
+ if (cdmBase.isInstanceOf(LanguageString.class)){
+ cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
+ }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
+ cdmRepository.getOccurrenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class));
+ }else if (cdmBase.isInstanceOf(Reference.class)){
+ cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
+ }else if (cdmBase.isInstanceOf(Classification.class)){
+ cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
+ }else if (cdmBase.isInstanceOf(AgentBase.class)){
+ cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
+ }else if (cdmBase.isInstanceOf(Collection.class)){
+ cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
+ }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
+ cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonBase.class)){
+ cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
+ }else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
+ cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
+ }else{
+ throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
+ }
+
+ }
+
+
+ protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
+ ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
+ if(cdmAppController==null){
+ cdmAppController = this;
+ }
+ FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
+ config.setSignificantIdentifier(unitId);
+ Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
+ if(!existingSpecimens.getRecords().isEmpty()){
+ if(existingSpecimens.getRecords().size()==1){
+ return existingSpecimens.getRecords().iterator().next();
+ }
+ }
+ return null;
+ }
+
+ protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
+
- protected abstract void doInvoke(STATE state);
}
\ No newline at end of file
-// $Id$
-/**
-* Copyright (C) 2016 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;
-
-import java.util.Map;
-
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
-import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
-import eu.etaxonomy.cdm.model.agent.Person;
-import eu.etaxonomy.cdm.model.agent.Team;
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public abstract class SpecimenImportConfiguratorBase<STATE extends SpecimenImportStateBase, InputStream> extends ImportConfiguratorBase<STATE, InputStream> {
-
- private boolean ignoreImportOfExistingSpecimen;
- private boolean reuseExistingTaxaWhenPossible;
- private Map<String, Team> teams;
- private Map<String, Person> persons;
- private boolean ignoreAuthorship;
- private boolean removeCountryFromLocalityText;
- private OccurenceQuery query ;
-
- /**
- * @param transformer
- */
- public SpecimenImportConfiguratorBase(IInputTransformer transformer) {
- super(transformer);
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @return
- */
- public boolean isReuseExistingTaxaWhenPossible() {
-
- return reuseExistingTaxaWhenPossible;
- }
-
- /**
- * @param titleCacheTeam
- */
- public void setTeams(Map<String, Team> titleCacheTeam) {
- this.teams = titleCacheTeam;
-
- }
-
- /**
- * @param titleCachePerson
- */
- public void setPersons(Map<String, Person> titleCachePerson) {
- this.persons = titleCachePerson;
- }
-
- /**
- * @return
- */
- public boolean isIgnoreAuthorship() {
- return ignoreAuthorship;
- }
-
- /**
- * @return
- */
- public boolean isRemoveCountryFromLocalityText() {
- return removeCountryFromLocalityText;
- }
-
- public boolean isIgnoreImportOfExistingSpecimens(){
- return ignoreImportOfExistingSpecimen;
- }
-
- public OccurenceQuery getOccurenceQuery(){
- return query;
- }
-
- public void setOccurenceQuery(OccurenceQuery query){
- this.query = query;
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen;\r
+\r
+import java.util.Map;\r
+\r
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;\r
+import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
+import eu.etaxonomy.cdm.model.agent.Person;\r
+import eu.etaxonomy.cdm.model.agent.Team;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public abstract class SpecimenImportConfiguratorBase<STATE extends SpecimenImportStateBase, InputStream> extends ImportConfiguratorBase<STATE, InputStream> {\r
+\r
+ private boolean ignoreImportOfExistingSpecimen;\r
+ private boolean reuseExistingTaxaWhenPossible;\r
+ private Map<String, Team> teams;\r
+ private Map<String, Person> persons;\r
+ private boolean ignoreAuthorship;\r
+ private boolean removeCountryFromLocalityText;\r
+ private OccurenceQuery query ;\r
+\r
+ /**\r
+ * @param transformer\r
+ */\r
+ public SpecimenImportConfiguratorBase(IInputTransformer transformer) {\r
+ super(transformer);\r
+ // TODO Auto-generated constructor stub\r
+ }\r
+\r
+ /**\r
+ * @return\r
+ */\r
+ public boolean isReuseExistingTaxaWhenPossible() {\r
+\r
+ return reuseExistingTaxaWhenPossible;\r
+ }\r
+\r
+ /**\r
+ * @param titleCacheTeam\r
+ */\r
+ public void setTeams(Map<String, Team> titleCacheTeam) {\r
+ this.teams = titleCacheTeam;\r
+\r
+ }\r
+\r
+ /**\r
+ * @param titleCachePerson\r
+ */\r
+ public void setPersons(Map<String, Person> titleCachePerson) {\r
+ this.persons = titleCachePerson;\r
+ }\r
+\r
+ /**\r
+ * @return\r
+ */\r
+ public boolean isIgnoreAuthorship() {\r
+ return ignoreAuthorship;\r
+ }\r
+\r
+ /**\r
+ * @return\r
+ */\r
+ public boolean isRemoveCountryFromLocalityText() {\r
+ return removeCountryFromLocalityText;\r
+ }\r
+\r
+ public boolean isIgnoreImportOfExistingSpecimens(){\r
+ return ignoreImportOfExistingSpecimen;\r
+ }\r
+\r
+ public OccurenceQuery getOccurenceQuery(){\r
+ return query;\r
+ }\r
+\r
+ public void setOccurenceQuery(OccurenceQuery query){\r
+ this.query = query;\r
+ }\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2016 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;
-
-import org.springframework.transaction.TransactionStatus;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.common.CdmImportBase;
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-
-/**
- * @author k.luther
- * @param <CONFIG>
- * @date 15.07.2016
- *
- */
-public abstract class SpecimenImportStateBase<CONFIG extends SpecimenImportConfiguratorBase, STATE extends SpecimenImportStateBase> extends ImportStateBase<CONFIG , CdmImportBase<CONFIG , STATE >>{
-
-
- private TransactionStatus tx;
-
- private ICdmApplicationConfiguration cdmRepository;
- private Classification classification = null;
- private Classification defaultClassification = null;
- private Reference ref = null;
-
- private TaxonDescription descriptionGroup = null;
- private DerivedUnit derivedUnitBase;
-
- private SpecimenImportReport report;
-
- private SpecimenDataHolder dataHolder;
-
-
- /**
- * @param config
- */
- protected SpecimenImportStateBase(CONFIG config) {
- super(config);
- // TODO Auto-generated constructor stub
- }
-
- /* -----Getter/Setter ---*/
-
- public TransactionStatus getTx() {
- return tx;
- }
-
- public void setTx(TransactionStatus tx) {
- this.tx = tx;
- }
-
- public ICdmApplicationConfiguration getCdmRepository() {
- return cdmRepository;
- }
-
- public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {
- this.cdmRepository = cdmRepository;
- }
-
- public Classification getClassification() {
- return classification;
- }
-
- public void setClassification(Classification classification) {
- this.classification = classification;
- }
-
- public Classification getDefaultClassification() {
- if(defaultClassification==null){
- final String defaultClassificationAbcd = "Default Classification ABCD";
- for (Classification classif : cdmRepository.getClassificationService().list(Classification.class, null, null, null, null)){
- if (classif.getTitleCache()!=null && classif.getTitleCache().equalsIgnoreCase(defaultClassificationAbcd)
- && classif.getCitation()!=null && classif.getCitation().equals(getRef())) {
- defaultClassification = classif;
- break;
- }
- }
- if(defaultClassification==null){
- defaultClassification = Classification.NewInstance(defaultClassificationAbcd);
- cdmRepository.getClassificationService().save(defaultClassification);
- }
- }
- return defaultClassification;
- }
-
- public void setDefaultClassification(Classification defaultClassification) {
- this.defaultClassification = defaultClassification;
- }
-
- public Reference getRef() {
- return ref;
- }
-
- public void setRef(Reference ref) {
- this.ref = ref;
- }
-
- public TaxonDescription getDescriptionGroup() {
- return descriptionGroup;
- }
-
- public void setDescriptionGroup(TaxonDescription descriptionGroup) {
- this.descriptionGroup = descriptionGroup;
- }
-
- public DerivedUnit getDerivedUnitBase() {
- return derivedUnitBase;
- }
-
- public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
- this.derivedUnitBase = derivedUnitBase;
- }
-
- /**
- * @return the report
- */
- public SpecimenImportReport getReport() {
- return report;
- }
-
- /**
- * @param report the report to set
- */
- public void setReport(SpecimenImportReport report) {
- this.report = report;
- }
-
- /**
- *
- */
- public abstract void reset() ;
-
- /**
- * @return the dataHolder
- */
- public SpecimenDataHolder getDataHolder() {
- return dataHolder;
- }
-
- /**
- * @param dataHolder the dataHolder to set
- */
- public void setDataHolder(SpecimenDataHolder dataHolder) {
- this.dataHolder = dataHolder;
- }
-
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen;\r
+\r
+import org.springframework.transaction.TransactionStatus;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.io.common.CdmImportBase;\r
+import eu.etaxonomy.cdm.io.common.ImportStateBase;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @param <CONFIG>\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public abstract class SpecimenImportStateBase<CONFIG extends SpecimenImportConfiguratorBase, STATE extends SpecimenImportStateBase> extends ImportStateBase<CONFIG , CdmImportBase<CONFIG , STATE >>{\r
+\r
+\r
+ private TransactionStatus tx;\r
+\r
+ private ICdmApplicationConfiguration cdmRepository;\r
+ private Classification classification = null;\r
+ private Classification defaultClassification = null;\r
+ private Reference ref = null;\r
+\r
+ private TaxonDescription descriptionGroup = null;\r
+ private DerivedUnit derivedUnitBase;\r
+\r
+ private SpecimenImportReport report;\r
+\r
+ private SpecimenDataHolder dataHolder;\r
+\r
+\r
+ /**\r
+ * @param config\r
+ */\r
+ protected SpecimenImportStateBase(CONFIG config) {\r
+ super(config);\r
+ // TODO Auto-generated constructor stub\r
+ }\r
+\r
+ /* -----Getter/Setter ---*/\r
+\r
+ public TransactionStatus getTx() {\r
+ return tx;\r
+ }\r
+\r
+ public void setTx(TransactionStatus tx) {\r
+ this.tx = tx;\r
+ }\r
+\r
+ public ICdmApplicationConfiguration getCdmRepository() {\r
+ return cdmRepository;\r
+ }\r
+\r
+ public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {\r
+ this.cdmRepository = cdmRepository;\r
+ }\r
+\r
+ public Classification getClassification() {\r
+ return classification;\r
+ }\r
+\r
+ public void setClassification(Classification classification) {\r
+ this.classification = classification;\r
+ }\r
+\r
+ public Classification getDefaultClassification() {\r
+ if(defaultClassification==null){\r
+ final String defaultClassificationAbcd = "Default Classification ABCD";\r
+ for (Classification classif : cdmRepository.getClassificationService().list(Classification.class, null, null, null, null)){\r
+ if (classif.getTitleCache()!=null && classif.getTitleCache().equalsIgnoreCase(defaultClassificationAbcd)\r
+ && classif.getCitation()!=null && classif.getCitation().equals(getRef())) {\r
+ defaultClassification = classif;\r
+ break;\r
+ }\r
+ }\r
+ if(defaultClassification==null){\r
+ defaultClassification = Classification.NewInstance(defaultClassificationAbcd);\r
+ cdmRepository.getClassificationService().save(defaultClassification);\r
+ }\r
+ }\r
+ return defaultClassification;\r
+ }\r
+\r
+ public void setDefaultClassification(Classification defaultClassification) {\r
+ this.defaultClassification = defaultClassification;\r
+ }\r
+\r
+ public Reference getRef() {\r
+ return ref;\r
+ }\r
+\r
+ public void setRef(Reference ref) {\r
+ this.ref = ref;\r
+ }\r
+\r
+ public TaxonDescription getDescriptionGroup() {\r
+ return descriptionGroup;\r
+ }\r
+\r
+ public void setDescriptionGroup(TaxonDescription descriptionGroup) {\r
+ this.descriptionGroup = descriptionGroup;\r
+ }\r
+\r
+ public DerivedUnit getDerivedUnitBase() {\r
+ return derivedUnitBase;\r
+ }\r
+\r
+ public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {\r
+ this.derivedUnitBase = derivedUnitBase;\r
+ }\r
+\r
+ /**\r
+ * @return the report\r
+ */\r
+ public SpecimenImportReport getReport() {\r
+ return report;\r
+ }\r
+\r
+ /**\r
+ * @param report the report to set\r
+ */\r
+ public void setReport(SpecimenImportReport report) {\r
+ this.report = report;\r
+ }\r
+\r
+ /**\r
+ *\r
+ */\r
+ public abstract void reset() ;\r
+\r
+ /**\r
+ * @return the dataHolder\r
+ */\r
+ public SpecimenDataHolder getDataHolder() {\r
+ return dataHolder;\r
+ }\r
+\r
+ /**\r
+ * @param dataHolder the dataHolder to set\r
+ */\r
+ public void setDataHolder(SpecimenDataHolder dataHolder) {\r
+ this.dataHolder = dataHolder;\r
+ }\r
+\r
+\r
+}\r
if (DEBUG) {
System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
}
- this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
+ // this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
}
/**
if (DEBUG) {
System.out.println("getteam:"+config.getTeams().get(t.getTitleCache()));
}
- this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
+ //this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
}
\r
import org.apache.log4j.Logger;\r
\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenDataHolder;\r
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;\r
\r
/**\r
* @date 16.06.2010\r
*\r
*/\r
-public class Abcd206DataHolder {\r
+public class Abcd206DataHolder extends SpecimenDataHolder{\r
@SuppressWarnings("unused")\r
private static final Logger logger = Logger.getLogger(Abcd206DataHolder.class);\r
\r
\r
//per unit\r
protected List<Identification> identificationList;\r
- protected List<HashMap<String, String>> atomisedIdentificationList;\r
+ private List<HashMap<String, String>> atomisedIdentificationList;\r
protected Map<String, String> namedAreaList;\r
protected List<String[]> referenceList;\r
protected List<String> multimediaObjects;\r
protected List<String> docSources;\r
protected List<String> associatedUnitIds;\r
\r
- protected String nomenclatureCode;\r
+ private String nomenclatureCode;\r
protected String institutionCode;\r
protected String collectionCode;\r
protected String unitID;\r
\r
public void reset() {\r
\r
- nomenclatureCode = null;\r
+ setNomenclatureCode(null);\r
institutionCode = null;\r
collectionCode = null;\r
unitID = null;\r
gatheringCoordinateErrorMethod = null;\r
\r
identificationList = new ArrayList<Identification>();\r
- atomisedIdentificationList = new ArrayList<HashMap<String, String>>();\r
+ setAtomisedIdentificationList(new ArrayList<HashMap<String, String>>());\r
namedAreaList = new HashMap<String, String>();\r
referenceList = new ArrayList<String[]>();\r
multimediaObjects = new ArrayList<String>();\r
associatedUnitIds = new ArrayList<String>();\r
}\r
\r
+\r
+\r
+\r
}\r
package eu.etaxonomy.cdm.io.specimen.abcd206.in;
+import java.io.InputStream;
import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashMap;
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
-import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
-import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.Language;
-import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
-import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.molecular.DnaSample;
-import eu.etaxonomy.cdm.model.name.BacterialName;
-import eu.etaxonomy.cdm.model.name.BotanicalName;
-import eu.etaxonomy.cdm.model.name.CultivarPlantName;
-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.name.ZoologicalName;
import eu.etaxonomy.cdm.model.occurrence.Collection;
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
import eu.etaxonomy.cdm.persistence.query.MatchMode;
-import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
-import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
/**
* @author p.kelbert
private static final Logger logger = Logger.getLogger(Abcd206Import.class);
- private final boolean DEBUG = true;
+
private static final String COLON = ":";
@Override
@SuppressWarnings("rawtypes")
public void doInvoke(Abcd206ImportState state) {
+ Abcd206ImportConfigurator config = state.getConfig();
try{
state.setTx(startTransaction());
logger.info("INVOKE Specimen Import from ABCD2.06 XML ");
-
+ InputStream response = null;
//init cd repository
if(state.getCdmRepository()==null){
state.setCdmRepository(this);
}
+ if (config.getOccurenceQuery() != null){
+ BioCaseQueryServiceWrapper queryService = new BioCaseQueryServiceWrapper();
+ try {
- SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
+ response = queryService.query(config.getOccurenceQuery(), config.getSourceUri());
- //init import reference
- List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
-
- if (state.getConfig().isInteractWithUser()){
- Map<String,Reference> refMap = new HashMap<String, Reference>();
- for (Reference reference : references) {
- if (! StringUtils.isBlank(reference.getTitleCache())) {
- refMap.put(reference.getTitleCache(),reference);
- }
+ }catch(Exception e){
+ logger.error("An error during ABCD import");
}
- state.setRef(sui.askForReference(refMap));
+ }
+ SpecimenUserInteraction sui = ((Abcd206ImportConfigurator)state.getConfig()).getSpecimenUserInteraction();
- if (state.getRef() == null){
- String cla = sui.createNewReference();
- if (refMap.get(cla)!= null) {
- state.setRef(refMap.get(cla));
- } else {
- state.setRef(ReferenceFactory.newGeneric());
- state.getRef().setTitle(cla);
- }
- }
- else{
- state.setRef(getReferenceService().find(state.getRef().getUuid()));
- }
- }else{
+ //init import reference
+ // List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
+ List<Reference> references = new ArrayList<Reference>();
+
+// if (state.getConfig().isInteractWithUser()){
+// Map<String,Reference> refMap = new HashMap<String, Reference>();
+// for (Reference reference : references) {
+// if (! StringUtils.isBlank(reference.getTitleCache())) {
+// refMap.put(reference.getTitleCache(),reference);
+// }
+// }
+// state.setRef(sui.askForReference(refMap));
+//
+// if (state.getRef() == null){
+// String cla = sui.createNewReference();
+// if (refMap.get(cla)!= null) {
+// state.setRef(refMap.get(cla));
+// } else {
+// state.setRef(ReferenceFactory.newGeneric());
+// state.getRef().setTitle(cla);
+// }
+// }
+// else{
+// state.setRef(getReferenceService().find(state.getRef().getUuid()));
+// }
+// }else{
if (state.getRef()==null){
- String name = NB(state.getConfig().getSourceReferenceTitle());
+ String name = NB(((Abcd206ImportConfigurator) state.getConfig()).getSourceReferenceTitle());
for (Reference reference : references) {
if (! StringUtils.isBlank(reference.getTitleCache())) {
if (reference.getTitleCache().equalsIgnoreCase(name)) {
state.getRef().setTitle("ABCD classic");
}
}
- }
+ //}
save(state.getRef(), state);
- state.getConfig().setSourceReference(state.getRef());
+ ((Abcd206ImportConfigurator) state.getConfig()).setSourceReference(state.getRef());
- if(state.getConfig().getClassificationUuid()!=null){
+ if(((Abcd206ImportConfigurator) state.getConfig()).getClassificationUuid()!=null){
//load classification from config if it exists
- state.setClassification(getClassificationService().load(state.getConfig().getClassificationUuid()));
+ state.setClassification(getClassificationService().load(((Abcd206ImportConfigurator) state.getConfig()).getClassificationUuid()));
}
if(state.getClassification()==null){//no existing classification was set in config
List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, null);
//get classification via user interaction
- if (state.getConfig().isUseClassification() && state.getConfig().isInteractWithUser()){
+ if (((Abcd206ImportConfigurator) state.getConfig()).isUseClassification() && ((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
Map<String,Classification> classMap = new HashMap<String, Classification>();
for (Classification tree : classificationList) {
if (! StringUtils.isBlank(tree.getTitleCache())) {
}
// use default classification as the classification to import into
if (state.getClassification() == null) {
- String name = NB(state.getConfig().getClassificationName());
+ String name = NB(((Abcd206ImportConfigurator) state.getConfig()).getClassificationName());
for (Classification classif : classificationList){
if (classif.getTitleCache() != null && classif.getTitleCache().equalsIgnoreCase(name)) {
state.setClassification(classif);
}
}
- UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(state.getConfig().getSource(), state.getReport());
+ if (response == null){
+ response =(InputStream) ((Abcd206ImportConfigurator) state.getConfig()).getSource();
+ }
+ UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(response, state.getReport());
NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
state.setPrefix(unitAssociationWrapper.getPrefix());
this.handleSingleUnit(state, item);
}
- if(state.getConfig().isDeduplicateReferences()){
+ if(((Abcd206ImportConfigurator)state.getConfig()).isDeduplicateReferences()){
getReferenceService().deduplicate(Reference.class, null, null);
}
- if(state.getConfig().isDeduplicateClassifications()){
+ if(((Abcd206ImportConfigurator)state.getConfig()).isDeduplicateClassifications()){
getClassificationService().deduplicate(Classification.class, null, null);
}
}
state.getReport().addException(errorDuringImport, e);
}
finally{
- state.getReport().printReport(state.getConfig().getReportUri());
+ state.getReport().printReport(((Abcd206ImportConfigurator)state.getConfig()).getReportUri());
}
return;
}
*/
@SuppressWarnings("rawtypes")
private void handleSingleUnit(Abcd206ImportState state, Element item) {
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
if (DEBUG) {
logger.info("handleSingleUnit "+state.getRef());
}
}
//check if unit already exists
DerivedUnitFacade derivedUnitFacade = null;
- if(state.getConfig().isIgnoreImportOfExistingSpecimens()){
+ if(((Abcd206ImportConfigurator)state.getConfig()).isIgnoreImportOfExistingSpecimens()){
SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(state.getDataHolder().unitID, state);
if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
state.setDerivedUnitBase(derivedUnit);
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
importAssociatedUnits(state, item, derivedUnitFacade);
- state.getReport().addAlreadyExistingSpecimen(AbcdImportUtility.getUnitID(derivedUnit, state.getConfig()), derivedUnit);
+ state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, config), derivedUnit);
return;
}
}
state.getDataHolder().gatheringElevationUnit, state.getDataHolder().gatheringDateText,
state.getDataHolder().gatheringNotes, state.getTransformer().getReferenceSystemByKey(
state.getDataHolder().gatheringSpatialDatum), state.getDataHolder().gatheringAgentList,
- state.getDataHolder().gatheringTeamList, state.getConfig());
+ state.getDataHolder().gatheringTeamList, (Abcd206ImportConfigurator)state.getConfig());
// country
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
- unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, state.getConfig(), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());
+ unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, ((Abcd206ImportConfigurator) state.getConfig()), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());
DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
// other areas
unitsGatheringArea = new UnitsGatheringArea();
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
- unitsGatheringArea.setAreas(state.getDataHolder().namedAreaList,state.getConfig(), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
+ unitsGatheringArea.setAreas(state.getDataHolder().namedAreaList,((Abcd206ImportConfigurator) state.getConfig()), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
for (DefinedTermBase namedArea : nas) {
unitsGatheringEvent.addArea(namedArea);
try {
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
derivedUnitFacade.addDerivedUnitMedia(media);
- if(state.getConfig().isAddMediaAsMediaSpecimen()){
+ if(((Abcd206ImportConfigurator)state.getConfig()).isAddMediaAsMediaSpecimen()){
//add media also as specimen scan
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.Media);
mediaSpecimen.setMediaSpecimen(media);
setCollectionData(state, derivedUnitFacade);
//Reference stuff
- SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
state.getDataHolder().docSources = new ArrayList<String>();
reference.addSource(sour);
save(reference, state);
}
-
- List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
- List<DescriptionElementSource> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+ List<IdentifiableSource> issTmp = new ArrayList<IdentifiableSource>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ List<DescriptionElementSource> issTmp2 = new ArrayList<DescriptionElementSource>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
if(issTmp2!=null) {
addToSourceMap(sourceMap, osbSet);
- if( state.getConfig().isInteractWithUser()){
+ if( ((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
List<OriginalSourceBase<?>>sources=null;
if(!state.isDerivedUnitSourcesSet()){
sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().docSources);
return;
}
- private void importAssociatedUnits(Abcd206ImportState state, Element item, DerivedUnitFacade derivedUnitFacade) {
+ @Override
+ protected void importAssociatedUnits(Abcd206ImportState state, Object itemObject, DerivedUnitFacade derivedUnitFacade) {
+
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator) state.getConfig();
//import associated units
FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
//TODO: push state (think of implementing stack architecture for state
DerivedUnit currentUnit = state.getDerivedUnitBase();
DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
String currentPrefix = state.getPrefix();
- NodeList unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
- for(int k=0;k<unitAssociationList.getLength();k++){
- if(unitAssociationList.item(k) instanceof Element){
- Element unitAssociation = (Element)unitAssociationList.item(k);
- UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());
- UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
- if(associationWrapper!=null){
- NodeList associatedUnits = associationWrapper.getAssociatedUnits();
- if(associatedUnits!=null){
- for(int m=0;m<associatedUnits.getLength();m++){
- if(associatedUnits.item(m) instanceof Element){
- state.reset();
- state.setPrefix(associationWrapper.getPrefix());
- this.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
- handleSingleUnit(state, (Element) associatedUnits.item(m));
-
- DerivedUnit associatedUnit = state.getDerivedUnitBase();
- FieldUnit associatedFieldUnit = null;
- java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
- //ignore field unit if associated unit has more than one
- if(associatedFieldUnits.size()>1){
- state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
- }
- else if(associatedFieldUnits.size()==1){
- associatedFieldUnit = associatedFieldUnits.iterator().next();
- }
-
- //attach current unit and associated unit depending on association type
-
- //parent-child relation:
- //copy derivation event and connect parent and sub derivative
- if(associationWrapper.getAssociationType().contains("individual")){
- if(currentDerivedFrom==null){
- state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",AbcdImportUtility.getUnitID(currentUnit, state.getConfig())));
- DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
- }
- else{
- DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
- updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
- updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
- updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
- updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
+ Element item = null;
+ if (item instanceof Element){
+ item = (Element)itemObject;
+ }
+ NodeList unitAssociationList = null;
+ if (item != null){
+ unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
+ for(int k=0;k<unitAssociationList.getLength();k++){
+ if(unitAssociationList.item(k) instanceof Element){
+ Element unitAssociation = (Element)unitAssociationList.item(k);
+ UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());
+ UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
+ if(associationWrapper!=null){
+ NodeList associatedUnits = associationWrapper.getAssociatedUnits();
+ if(associatedUnits!=null){
+ for(int m=0;m<associatedUnits.getLength();m++){
+ if(associatedUnits.item(m) instanceof Element){
+ state.reset();
+ state.setPrefix(associationWrapper.getPrefix());
+ this.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
+ handleSingleUnit(state, (Element) associatedUnits.item(m));
+
+ DerivedUnit associatedUnit = state.getDerivedUnitBase();
+ FieldUnit associatedFieldUnit = null;
+ java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
+ //ignore field unit if associated unit has more than one
+ if(associatedFieldUnits.size()>1){
+ state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
}
- state.getReport().addDerivate(associatedUnit, currentUnit, state.getConfig());
- }
- //siblings relation
- //connect current unit to field unit of associated unit
- else if(associationWrapper.getAssociationType().contains("population")){
- //no associated field unit -> using current one
- if(associatedFieldUnit==null){
- if(currentFieldUnit!=null){
- DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
- }
+ else if(associatedFieldUnits.size()==1){
+ associatedFieldUnit = associatedFieldUnits.iterator().next();
}
- else{
+
+ //attach current unit and associated unit depending on association type
+
+ //parent-child relation:
+ //copy derivation event and connect parent and sub derivative
+ if(associationWrapper.getAssociationType().contains("individual")){
if(currentDerivedFrom==null){
- state.getReport().addInfoMessage("No derivation event found for unit "+AbcdImportUtility.getUnitID(currentUnit, state.getConfig())+". Defaulting to ACCESIONING event.");
- DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
+ state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",SpecimenImportUtility.getUnitID(currentUnit, config)));
+ DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
}
- if(currentDerivedFrom!=null && associatedFieldUnit!=currentFieldUnit){
- DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
+ else{
+ DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
}
+ state.getReport().addDerivate(associatedUnit, currentUnit, config);
+ }
+ //siblings relation
+ //connect current unit to field unit of associated unit
+ else if(associationWrapper.getAssociationType().contains("population")){
+ //no associated field unit -> using current one
+ if(associatedFieldUnit==null){
+ if(currentFieldUnit!=null){
+ DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
+ }
+ }
+ else{
+ if(currentDerivedFrom==null){
+ state.getReport().addInfoMessage("No derivation event found for unit "+SpecimenImportUtility.getUnitID(currentUnit, config)+". Defaulting to ACCESIONING event.");
+ DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
+ }
+ if(currentDerivedFrom!=null && associatedFieldUnit!=currentFieldUnit){
+ DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
+ updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
+ updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
+ updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
+ updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
+ }
+ }
}
- }
- //delete current field unit if replaced
- if(currentFieldUnit!=null && currentDerivedFrom!=null
- && currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
- && currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
- && currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
- ){
- currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
- state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
- }
+ //delete current field unit if replaced
+ if(currentFieldUnit!=null && currentDerivedFrom!=null
+ && currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
+ && currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
+ && currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
+ ){
+ currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
+ state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
+ }
- save(associatedUnit, state);
+ save(associatedUnit, state);
+ }
}
}
}
state.setPrefix(currentPrefix);
}
- private SpecimenOrObservationBase findExistingSpecimen(String unitId, Abcd206ImportState state){
- ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
- if(cdmAppController==null){
- cdmAppController = this;
- }
- FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
- config.setSignificantIdentifier(unitId);
- Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
- if(!existingSpecimens.getRecords().isEmpty()){
- if(existingSpecimens.getRecords().size()==1){
- return existingSpecimens.getRecords().iterator().next();
- }
- }
- return null;
- }
+
/**
* @param sourceMap
// for our new source.
private IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
- List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ /* List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
if (reference != null){
e1.printStackTrace();
}
}
-
+*/
IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
return sour;
}
// }
- /**
- * Very fast and dirty implementation to allow handling of transient objects as described in
- * https://dev.e-taxonomy.eu/trac/ticket/3726
- *
- * Not yet complete.
- *
- * @param cdmBase
- * @param state
- */
- private void save(CdmBase cdmBase, Abcd206ImportState state) {
- ICdmApplicationConfiguration cdmRepository = state.getConfig().getCdmAppController();
- if (cdmRepository == null){
- cdmRepository = this;
- }
-
- if (cdmBase.isInstanceOf(LanguageString.class)){
- cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
- }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
- cdmRepository.getOccurrenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class));
- }else if (cdmBase.isInstanceOf(Reference.class)){
- cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
- }else if (cdmBase.isInstanceOf(Classification.class)){
- cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
- }else if (cdmBase.isInstanceOf(AgentBase.class)){
- cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
- }else if (cdmBase.isInstanceOf(Collection.class)){
- cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
- }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class));
- }else if (cdmBase.isInstanceOf(TaxonBase.class)){
- cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
- }else if (cdmBase.isInstanceOf(TaxonNameBase.class)){
- cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNameBase.class));
- }else{
- throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
- }
- }
/**
* setCollectionData : store the collection object into the
* @param state
*/
private void setCollectionData(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
- Abcd206ImportConfigurator config = state.getConfig();
- AbcdImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().unitID, config);
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
+ SpecimenImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().unitID, config);
if(!config.isMapUnitIdToAccessionNumber()){
derivedUnitFacade.setAccessionNumber(NB(state.getDataHolder().accessionNumber));
}
}
state.getDataHolder().identificationList = new ArrayList<Identification>();
state.getDataHolder().statusList = new ArrayList<SpecimenTypeDesignationStatus>();
- state.getDataHolder().atomisedIdentificationList = new ArrayList<HashMap<String, String>>();
+ state.getDataHolder().setAtomisedIdentificationList(new ArrayList<HashMap<String, String>>());
state.getDataHolder().referenceList = new ArrayList<String[]>();
state.getDataHolder().multimediaObjects = new ArrayList<String>();
* @return the Institution (existing or new)
*/
private Institution getInstitution(String institutionCode, Abcd206ImportState state) {
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
Institution institution=null;
List<Institution> institutions;
try {
institutions = new ArrayList<Institution>();
logger.warn(e);
}
- if (institutions.size() > 0 && state.getConfig().isReUseExistingMetadata()) {
+ if (institutions.size() > 0 && config.isReUseExistingMetadata()) {
for (Institution institut:institutions){
try{
if (institut.getCode().equalsIgnoreCase(institutionCode)) {
* @return the Collection (existing or new)
*/
private Collection getCollection(Institution institution, String collectionCode, Abcd206ImportState state) {
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
Collection collection = null;
List<Collection> collections;
try {
} catch (Exception e) {
collections = new ArrayList<Collection>();
}
- if (collections.size() > 0 && state.getConfig().isReUseExistingMetadata()) {
+ if (collections.size() > 0 && config.isReUseExistingMetadata()) {
for (Collection coll:collections){
if (coll.getCode() != null && coll.getInstitute() != null
&& coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
*/
@SuppressWarnings("rawtypes")
private void linkDeterminationEvent(Abcd206ImportState state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade) {
- Abcd206ImportConfigurator config = state.getConfig();
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
if(DEBUG){
logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
}
}
for (String[] fullReference : state.getDataHolder().referenceList) {
- List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
+
String strReference=fullReference[0];
String citationDetail = fullReference[1];
String citationURL = fullReference[2];
+ List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
- if (isNotBlank(strReference)){
+ if (!references.isEmpty()){
Reference reference = null;
for (Reference refe: references) {
if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
* @param determinationEvent:the determinationevent
*/
private void makeIndividualsAssociation(Abcd206ImportState state, Taxon taxon, DeterminationEvent determinationEvent) {
- SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
if (DEBUG) {
logger.info("MAKE INDIVIDUALS ASSOCIATION");
TaxonDescription taxonDescription = null;
Set<TaxonDescription> descriptions= taxon.getDescriptions();
- if (state.getConfig().isInteractWithUser()){
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
if(!state.isDescriptionGroupSet()){
taxonDescription = sui.askForDescriptionGroup(descriptions);
state.setDescriptionGroup(taxonDescription);
addToSourceMap(sourceMap, osbSet);
- if (state.getConfig().isInteractWithUser()){
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
List<OriginalSourceBase<?>> res = null;
if(!state.isDescriptionSourcesSet()){
res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
indAssociation.setFeature(feature);
- if (state.getConfig().isInteractWithUser()){
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
sourceMap = new HashMap<String, OriginalSourceBase<?>>();
issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
save(taxonDescription, state);
save(taxon, state);
- state.getReport().addDerivate(state.getDerivedUnitBase(), state.getConfig());
+ state.getReport().addDerivate(state.getDerivedUnitBase(), config);
state.getReport().addIndividualAssociation(taxon, state.getDataHolder().unitID, state.getDerivedUnitBase());
}
* @param derivedUnitFacade : the current derivedunitfacade
*/
private void handleIdentifications(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
- Abcd206ImportConfigurator config = state.getConfig();
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
String scientificName = "";
boolean preferredFlag = false;
- if (state.getDataHolder().nomenclatureCode == ""){
- state.getDataHolder().nomenclatureCode = config.getNomenclaturalCode().toString();
+ if (state.getDataHolder().getNomenclatureCode() == ""){
+ state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
}
for (int i = 0; i < state.getDataHolder().identificationList.size(); i++) {
}
if (identification.getCode().indexOf(':') != -1) {
- state.getDataHolder().nomenclatureCode = identification.getCode().split(COLON)[1];
+ state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
}
else{
- state.getDataHolder().nomenclatureCode = identification.getCode();
+ state.getDataHolder().setNomenclatureCode(identification.getCode());
}
TaxonNameBase<?,?> taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
Taxon taxon = getOrCreateTaxonForName(taxonName, state);
}
- private TaxonNameBase<?, ?> getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, Abcd206ImportState state, int unitIndexInAbcdFile){
- TaxonNameBase<?, ?> taxonName = null;
- Abcd206ImportConfigurator config = state.getConfig();
- //check atomised name data for rank
- //new name will be created
- NonViralName<?> atomisedTaxonName = null;
- if (rank==null && unitIndexInAbcdFile>=0 && (state.getDataHolder().atomisedIdentificationList != null || state.getDataHolder().atomisedIdentificationList.size() > 0)) {
- atomisedTaxonName = setTaxonNameByType(state.getDataHolder().atomisedIdentificationList.get(unitIndexInAbcdFile), scientificName, state);
- if(atomisedTaxonName!=null){
- rank = atomisedTaxonName.getRank();
- }
- }
- if(config.isReuseExistingTaxaWhenPossible()){
- NonViralName<?> parsedName = atomisedTaxonName;
- if(parsedName==null){
- parsedName = parseScientificName(scientificName, state, state.getReport());
- }
- if(config.isIgnoreAuthorship() && parsedName!=null && preferredFlag){
- // do not ignore authorship for non-preferred names because they need
- // to be created for the determination history
- String nameCache = parsedName.getNameCache();
- List<NonViralName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
- taxonName = getBestMatchingName(scientificName, new ArrayList<TaxonNameBase>(names), state);
- }
- else {
- //search for existing names
- List<TaxonNameBase> names = getNameService().listByTitle(TaxonNameBase.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
- taxonName = getBestMatchingName(scientificName, names, state);
- //still nothing found -> try with the atomised name full title cache
- if(taxonName==null && atomisedTaxonName!=null){
- names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
- taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
- //still nothing found -> try with the atomised name title cache
- if(taxonName==null){
- names = getNameService().listByTitle(TaxonNameBase.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
- taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
- }
- }
- }
- }
- if(taxonName==null && atomisedTaxonName!=null){
- taxonName = atomisedTaxonName;
- state.getReport().addName(taxonName);
- logger.info("Created new taxon name "+taxonName);
- if(taxonName.hasProblem()){
- state.getReport().addInfoMessage(String.format("Created %s with parsing problems", taxonName));
- }
- if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
- state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
- }
- }
- else if(taxonName==null){
- //create new taxon name
- taxonName = NonViralName.NewInstance(rank);
- taxonName.setFullTitleCache(scientificName,true);
- taxonName.setTitleCache(scientificName, true);
- state.getReport().addName(taxonName);
- logger.info("Created new taxon name "+taxonName);
- }
- save(taxonName, state);
- return taxonName;
- }
- private TaxonNameBase<?, ?> getBestMatchingName(String scientificName, java.util.Collection<TaxonNameBase> names, Abcd206ImportState state){
- List<TaxonNameBase> namesWithAcceptedTaxa = new ArrayList<TaxonNameBase>();
- for (TaxonNameBase name : names) {
- if(!name.getTaxa().isEmpty()){
- namesWithAcceptedTaxa.add(name);
- }
- }
- String message = "More than one taxon name was found for "+scientificName+"!";
- //check for names with accepted taxa
- if(namesWithAcceptedTaxa.size()>0){
- if(namesWithAcceptedTaxa.size()>1){
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
- return namesWithAcceptedTaxa.iterator().next();
- }
- //no names with accepted taxa found -> check accepted taxa of synonyms
- List<Taxon> taxaFromSynonyms = new ArrayList<Taxon>();
- for (TaxonNameBase name : names) {
- Set<TaxonBase> taxonBases = name.getTaxonBases();
- for (TaxonBase taxonBase : taxonBases) {
- if(taxonBase.isInstanceOf(Synonym.class)){
- Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
- taxaFromSynonyms.addAll(synonym.getAcceptedTaxa());
- }
- }
- }
- if(taxaFromSynonyms.size()>0){
- if(taxaFromSynonyms.size()>1){
- state.getReport().addInfoMessage(message);
- logger.warn(message);
- return null;
- }
- return taxaFromSynonyms.iterator().next().getName();
- }
- return null;
- }
private Taxon getOrCreateTaxonForName(TaxonNameBase<?, ?> taxonNameBase, Abcd206ImportState state){
Set<Taxon> acceptedTaxa = taxonNameBase.getTaxa();
* @param state : the ABCD import state
*/
private void addTaxonNode(Taxon taxon, Abcd206ImportState state, boolean preferredFlag) {
+ Abcd206ImportConfigurator config = (Abcd206ImportConfigurator)state.getConfig();
logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
//only add nodes if not already existing in current classification or default classification
//check if node exists in current classification
//NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
if (!existsInClassification(taxon, state.getClassification())){
- if(state.getConfig().isMoveNewTaxaToDefaultClassification()){
+ if(config.isMoveNewTaxaToDefaultClassification()){
//check if node exists in default classification
if(!existsInClassification(taxon, state.getDefaultClassification())){
addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification());
return null;
}
- /**
- * Parse automatically the scientific name
- * @param scientificName the scientific name to parse
- * @param state the current import state
- * @param report the import report
- * @return a parsed name
- */
- private NonViralName<?> parseScientificName(String scientificName, Abcd206ImportState state, Abcd206ImportReport report) {
- NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
- NonViralName<?> taxonName = null;
- boolean problem = false;
-
- if(DEBUG){
- logger.info("parseScientificName " + state.getDataHolder().nomenclatureCode.toString());
- }
-
- if (state.getDataHolder().nomenclatureCode.toString().equals("Zoological") || state.getDataHolder().nomenclatureCode.toString().contains("ICZN")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, null);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.toString().equals("Botanical") || state.getDataHolder().nomenclatureCode.toString().contains("ICBN")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, null);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.toString().equals("Bacterial") || state.getDataHolder().nomenclatureCode.toString().contains("ICBN")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, null);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.toString().equals("Cultivar") || state.getDataHolder().nomenclatureCode.toString().contains("ICNCP")) {
- taxonName = nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, null);
- if (taxonName.hasProblem()) {
- problem = true;
- }
- }
- if (problem) {
- String message = String.format("Parsing problems for %s", scientificName);
- if(taxonName!=null){
- for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
- message += "\n\t- "+parserProblem;
- }
- }
- report.addInfoMessage(message);
- logger.info(message);
- }
- return taxonName;
-
- }
-
- /**
- * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
- * The name is built upon the ABCD fields
- * @param atomisedMap : the ABCD atomised fields
- * @param fullName : the full scientific name
- * @param state
- * @return the corresponding Botanical or Zoological or... name
- */
- private NonViralName<?> setTaxonNameByType(
- HashMap<String, String> atomisedMap, String fullName, Abcd206ImportState state) {
- boolean problem = false;
- if(DEBUG) {
- logger.info("settaxonnamebytype " + state.getDataHolder().nomenclatureCode.toString());
- }
- if (state.getDataHolder().nomenclatureCode.equals("Zoological")) {
- NonViralName<ZoologicalName> taxonName = ZoologicalName.NewInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
- taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
- if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
- if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
- if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
- if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
- Team team = null;
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
- }
- else {
- if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
- }
- }
- if (team != null) {
- taxonName.setBasionymAuthorship(team);
- }
- else {
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
- }
- else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
- }
- }
- if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICZN");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.equals("Botanical")) {
- BotanicalName taxonName = (BotanicalName) parseScientificName(fullName, state, state.getReport());
- if (taxonName != null){
- return taxonName;
- }
- else{
- taxonName = BotanicalName.NewInstance(null);
- }
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
- try {
- taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
- } catch (Exception e) {
- if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
- else if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
- else if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
- else if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
- }
- Team team = null;
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
- taxonName.setBasionymAuthorship(team);
- }
- if (getFromMap(atomisedMap, "AuthorTeam") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (team == null) {
- if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
- }
- else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
- taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
- }
- }
- if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
- team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICBN");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.equals("Bacterial")) {
- NonViralName<BacterialName> taxonName = BacterialName.NewInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
- taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
- taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
- taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
-
- if (taxonName.getGenusOrUninomial() != null){
- taxonName.setRank(Rank.GENUS());
- }
- else if (taxonName.getInfraGenericEpithet() != null){
- taxonName.setRank(Rank.SUBGENUS());
- }
- else if (taxonName.getSpecificEpithet() != null){
- taxonName.setRank(Rank.SPECIES());
- }
- else if (taxonName.getInfraSpecificEpithet() != null){
- taxonName.setRank(Rank.SUBSPECIES());
- }
-
- if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
- Team team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
- taxonName.setCombinationAuthorship(team);
- }
- if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
- Team team = Team.NewInstance();
- team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
- taxonName.setBasionymAuthorship(team);
- }
- if (taxonName.hasProblem()) {
- logger.info("pb ICNB");
- problem = true;
- }
- else {
- return taxonName;
- }
- }
- else if (state.getDataHolder().nomenclatureCode.equals("Cultivar")) {
- CultivarPlantName taxonName = CultivarPlantName.NewInstance(null);
-
- if (taxonName.hasProblem()) {
- logger.info("pb ICNCP");
- problem = true;
- }
- else {
- return taxonName;
- }
- return taxonName;
- }
-
- if (problem) {
- logger.info("Problem im setTaxonNameByType ");
- NonViralName<?> taxonName = NonViralName.NewInstance(null);
- taxonName.setFullTitleCache(fullName, true);
- return taxonName;
- }
- NonViralName<?> tn = NonViralName.NewInstance(null);
- return tn;
- }
-
-
- /**
- * Get a formated string from a hashmap
- * @param atomisedMap
- * @param key
- * @return
- */
- private String getFromMap(HashMap<String, String> atomisedMap, String key) {
- String value = null;
- if (atomisedMap.containsKey(key)) {
- value = atomisedMap.get(key);
- }
-
- try {
- if (value != null && key.matches(".*Year.*")) {
- value = value.trim();
- if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
- String tmp = value.split("[0-9]{4}$")[0];
- int year = Integer.parseInt(value.split(tmp)[1]);
- if (year >= 1752) {
- value = tmp;
- }
- else {
- value = null;
- }
- }
- else {
- value = null;
- }
- }
- }
- catch (Exception e) {
- value = null;
- }
- return value;
- }
// private void compareABCDtoCDM(URI urlFileName, List<String> knownElts, Abcd206XMLFieldGetter abcdFieldGetter) {
// try {
//existing teams in DB
Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
- List<UuidAndTitleCache<Team>> hiberTeam = getAgentService().getTeamUuidAndTitleCache();
+ List<UuidAndTitleCache<Team>> hiberTeam = new ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
Set<UUID> uuids = new HashSet<UUID>();
for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
}
//existing persons in DB
- List<UuidAndTitleCache<Person>> hiberPersons = getAgentService().getPersonUuidAndTitleCache();
+ List<UuidAndTitleCache<Person>> hiberPersons = new ArrayList<UuidAndTitleCache<Person>>();//getAgentService().getPersonUuidAndTitleCache();
Map<String,Person> titleCachePerson = new HashMap<String, Person>();
uuids = new HashSet<UUID>();
for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
}
}
- state.getConfig().setTeams(titleCacheTeam);
- state.getConfig().setPersons(titleCachePerson);
+ ((Abcd206ImportConfigurator) state.getConfig()).setTeams(titleCacheTeam);
+ ((Abcd206ImportConfigurator) state.getConfig()).setPersons(titleCachePerson);
}
@Override
return false;
}
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.io.specimen.SpecimenImportBase#handleSingleUnit(eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase, java.lang.Object)
+ */
+ @Override
+ protected void handleSingleUnit(Abcd206ImportState state, Object item) {
+ // TODO Auto-generated method stub
+
+ }
+
}
\ No newline at end of file
package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
\r
\r
-import java.io.InputStream;\r
import java.net.URI;\r
import java.util.HashMap;\r
import java.util.Map;\r
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;\r
import eu.etaxonomy.cdm.io.common.IImportConfigurator;\r
import eu.etaxonomy.cdm.io.common.IMatchingImportConfigurator;\r
-import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;\r
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;\r
import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;\r
import eu.etaxonomy.cdm.model.agent.Person;\r
import eu.etaxonomy.cdm.model.agent.Team;\r
* @author p.kelbert\r
* @created 20.10.2008\r
* @version 1.0\r
+ * @param <SOURCE>\r
*/\r
-public class Abcd206ImportConfigurator extends ImportConfiguratorBase<Abcd206ImportState, InputStream> implements IImportConfigurator, IMatchingImportConfigurator {\r
+public class Abcd206ImportConfigurator<AbcdImportState, InputStream> extends SpecimenImportConfiguratorBase implements IImportConfigurator, IMatchingImportConfigurator {\r
private static final Logger logger = Logger.getLogger(Abcd206ImportConfigurator.class);\r
\r
private static String sourceReferenceTitle = null;\r
* @param object\r
* @param b\r
* @return\r
- */\r
+ *//*\r
public static Abcd206ImportConfigurator NewInstance(InputStream stream, ICdmDataSource destination, boolean interact) {\r
return new Abcd206ImportConfigurator(stream, null, destination, interact);\r
}\r
-\r
+*/\r
\r
\r
/**\r
@Override\r
public InputStream getSource(){\r
if (super.getSource() != null){\r
- return super.getSource();\r
+ return (InputStream)super.getSource();\r
}else if (this.sourceUri != null){\r
try {\r
- InputStream is = UriUtils.getInputStream(sourceUri);\r
+ InputStream is = (InputStream) UriUtils.getInputStream(sourceUri);\r
setSource(is);\r
return is;\r
} catch (Exception e) {\r
}\r
}\r
\r
- @Override\r
- public void setSource(InputStream is) {\r
- //this.sourceUri = null;\r
- super.setSource(is);\r
- }\r
+\r
\r
public URI getSourceUri(){\r
return this.sourceUri;\r
return titleCacheTeam;\r
}\r
\r
- public void setTeams(Map<String, Team> titleCacheTeam) {\r
- this.titleCacheTeam = titleCacheTeam;\r
- }\r
+\r
\r
public Map<String, Person> getPersons() {\r
return titleCachePerson;\r
}\r
\r
- public void setPersons(Map<String, Person> titleCachePerson) {\r
- this.titleCachePerson = titleCachePerson;\r
- }\r
+\r
\r
public void setDefaultAuthor(String string) {\r
defaultAuthor=string;\r
this.ignoreAuthorship = ignoreAuthorship;\r
}\r
\r
+ @Override\r
public boolean isIgnoreAuthorship() {\r
return ignoreAuthorship;\r
}\r
this.removeCountryFromLocalityText = removeCountryFromLocalityText;\r
}\r
\r
+ @Override\r
public boolean isRemoveCountryFromLocalityText() {\r
return removeCountryFromLocalityText;\r
}\r
this.overwriteExistingSpecimens = overwriteExistingSpecimens;\r
}\r
\r
+ @Override\r
public boolean isIgnoreImportOfExistingSpecimens() {\r
return ignoreImportOfExistingSpecimens;\r
}\r
this.ignoreImportOfExistingSpecimens = ignoreImportOfExistingSpecimens;\r
}\r
\r
+ @Override\r
public OccurenceQuery getOccurenceQuery(){\r
return query;\r
}\r
\r
+ @Override\r
public void setOccurenceQuery(OccurenceQuery query){\r
this.query = query;\r
}\r
+\r
+\r
+\r
}\r
* @date Jan 23, 2015
*
*/
-public class Abcd206ImportReport {
+public class Abcd206ImportReport extends SpecimenImportReport{
static private final Logger logger = Logger.getLogger(Abcd206ImportReport.class);
private final List<TaxonNode> createdTaxonNodes = new ArrayList<TaxonNode>();
private final List<String> infoMessages = new ArrayList<String>();
+ @Override
public void addTaxon(Taxon taxon){
createdTaxa.add(taxon);
}
+ @Override
public void addName(TaxonNameBase<?, ?> taxonName){
createdNames.add(taxonName);
}
+ @Override
public void addTaxonNode(TaxonNode taxonNode){
createdTaxonNodes.add(taxonNode);
}
+ @Override
public void addDerivate(DerivedUnit parent, Abcd206ImportConfigurator config){
addDerivate(parent, null, config);
}
+ @Override
public void addDerivate(DerivedUnit parent, DerivedUnit child, Abcd206ImportConfigurator config){
- UnitIdSpecimen parentUnitIdSpecimen = new UnitIdSpecimen(AbcdImportUtility.getUnitID(parent, config), parent);
+ UnitIdSpecimen parentUnitIdSpecimen = new UnitIdSpecimen(SpecimenImportUtility.getUnitID(parent, config), parent);
List<UnitIdSpecimen> children = derivateMap.get(parentUnitIdSpecimen);
if(children==null){
children = new ArrayList<UnitIdSpecimen>();
}
if(child!=null){
- children.add(new UnitIdSpecimen(AbcdImportUtility.getUnitID(child, config), child));
+ children.add(new UnitIdSpecimen(SpecimenImportUtility.getUnitID(child, config), child));
}
derivateMap.put(parentUnitIdSpecimen, children);
}
+ @Override
public void addIndividualAssociation(Taxon taxon, String derivedUnitId, DerivedUnit derivedUnitBase) {
UnitIdSpecimen derivedUnitIdSpecimen = new UnitIdSpecimen(derivedUnitId, derivedUnitBase);
List<UnitIdSpecimen> associatedSpecimens = taxonToAssociatedSpecimens.get(taxon);
taxonToAssociatedSpecimens.put(taxon, associatedSpecimens);
}
+ @Override
public void addAlreadyExistingSpecimen(String unitId, DerivedUnit derivedUnit){
alreadyExistingSpecimens.add(new UnitIdSpecimen(unitId, derivedUnit));
}
+ @Override
public void addException(String message, Exception e) {
StringWriter errors = new StringWriter();
e.printStackTrace(new PrintWriter(errors));
infoMessages.add(message+"\n"+e.getMessage()+"\n"+errors.toString());
}
+ @Override
public void addInfoMessage(String message) {
infoMessages.add(message);
}
+ @Override
public void printReport(URI reportUri) {
PrintStream out;
if(reportUri != null){
}
+ @Override
public void printReport(PrintStream out) {
out.println("++++++++Import Report+++++++++");
package eu.etaxonomy.cdm.io.specimen.abcd206.in;
import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
-import org.springframework.transaction.TransactionStatus;
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.common.CdmImportBase;
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase;
import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.Classification;
/**
* @author a.mueller
* @created 11.05.2009
* @version 1.0
*/
-public class Abcd206ImportState extends ImportStateBase<Abcd206ImportConfigurator, CdmImportBase<Abcd206ImportConfigurator,Abcd206ImportState>>{
+public class Abcd206ImportState extends SpecimenImportStateBase<Abcd206ImportConfigurator<Abcd206ImportState, InputStream>, Abcd206ImportState>{
@SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(Abcd206ImportState.class);
- private TransactionStatus tx;
-
- private ICdmApplicationConfiguration cdmRepository;
private String prefix;
- private Abcd206ImportReport report;
- private Classification classification = null;
- private Classification defaultClassification = null;
- private Reference ref = null;
+
+
private Abcd206DataHolder dataHolder;
- private DerivedUnit derivedUnitBase;
+
private List<OriginalSourceBase<?>> associationRefs = new ArrayList<OriginalSourceBase<?>>();
private boolean associationSourcesSet=false;
private List<OriginalSourceBase<?>> derivedUnitSources = new ArrayList<OriginalSourceBase<?>>();
private boolean derivedUnitSourcesSet=false;
private boolean descriptionGroupSet = false;
- private TaxonDescription descriptionGroup = null;
+
//****************** CONSTRUCTOR ***************************************************/
public Abcd206ImportState(Abcd206ImportConfigurator config) {
super(config);
- report = new Abcd206ImportReport();
+ setReport(new SpecimenImportReport());
setTransformer(new AbcdTransformer());
}
//************************ GETTER / SETTER *****************************************/
- public TransactionStatus getTx() {
- return tx;
- }
-
- public void setTx(TransactionStatus tx) {
- this.tx = tx;
- }
-
- public ICdmApplicationConfiguration getCdmRepository() {
- return cdmRepository;
- }
-
- public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {
- this.cdmRepository = cdmRepository;
- }
-
- public Classification getClassification() {
- return classification;
- }
-
- public void setClassification(Classification classification) {
- this.classification = classification;
- }
-
- public Classification getDefaultClassification() {
- if(defaultClassification==null){
- final String defaultClassificationAbcd = "Default Classification ABCD";
- for (Classification classif : cdmRepository.getClassificationService().list(Classification.class, null, null, null, null)){
- if (classif.getTitleCache()!=null && classif.getTitleCache().equalsIgnoreCase(defaultClassificationAbcd)
- && classif.getCitation()!=null && classif.getCitation().equals(getRef())) {
- defaultClassification = classif;
- break;
- }
- }
- if(defaultClassification==null){
- defaultClassification = Classification.NewInstance(defaultClassificationAbcd);
- cdmRepository.getClassificationService().save(defaultClassification);
- }
- }
- return defaultClassification;
- }
-
- public void setDefaultClassification(Classification defaultClassification) {
- this.defaultClassification = defaultClassification;
- }
-
- public Reference getRef() {
- return ref;
- }
- public void setRef(Reference ref) {
- this.ref = ref;
- }
+ @Override
public Abcd206DataHolder getDataHolder() {
return dataHolder;
}
this.dataHolder = dataHolder;
}
- public DerivedUnit getDerivedUnitBase() {
- return derivedUnitBase;
- }
- public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
- this.derivedUnitBase = derivedUnitBase;
- }
public List<OriginalSourceBase<?>> getAssociationRefs() {
return associationRefs;
this.descriptionGroupSet = descriptionGroupSet;
}
- public TaxonDescription getDescriptionGroup() {
- return descriptionGroup;
- }
- public void setDescriptionGroup(TaxonDescription descriptionGroup) {
- this.descriptionGroup = descriptionGroup;
- }
public void setPrefix(String prefix) {
this.prefix = prefix;
return prefix;
}
- public Abcd206ImportReport getReport(){
- return report;
- }
@Override
public byte[] getReportAsByteArray() {
ByteArrayOutputStream importStream = new ByteArrayOutputStream();
- report.printReport(new PrintStream(importStream));
+ getReport().printReport(new PrintStream(importStream));
return importStream.toByteArray();
}
+ @Override
public void reset() {
getDataHolder().reset();
- derivedUnitBase = null;
+ setDerivedUnitBase(null);
}
}
}
}
} else if (identifications.item(m).getNodeName().equals(prefix + "PreferredFlag")) {
- if (dataHolder.nomenclatureCode != null&& dataHolder.nomenclatureCode != "") {
+ if (dataHolder.getNomenclatureCode() != null&& dataHolder.getNomenclatureCode() != "") {
// logger.info("TMP NAME P" + tmpName);
- dataHolder.identificationList.add(new Identification(tmpName, identifications.item(m).getTextContent(), dataHolder.nomenclatureCode));
+ dataHolder.identificationList.add(new Identification(tmpName, identifications.item(m).getTextContent(), dataHolder.getNomenclatureCode()));
} else {
dataHolder.identificationList.add(new Identification(tmpName, identifications.item(m).getTextContent()));
}
boolean hasPref = false;
for (int j = 0; j < group.getLength(); j++) {
if (group.item(j).getNodeName().equals(prefix + "Identification")) {
- dataHolder.nomenclatureCode = "";
+ dataHolder.setNomenclatureCode("");
identifications = group.item(j).getChildNodes();
for (int m = 0; m < identifications.getLength(); m++) {
if (identifications.item(m).getNodeName().equals(prefix + "Result")) {
}
}
if (!hasPref && tmpName != null) {
- if (dataHolder.nomenclatureCode != null
- && dataHolder.nomenclatureCode != "") {
- dataHolder.identificationList.add(new Identification(tmpName, "0", dataHolder.nomenclatureCode));
+ if (dataHolder.getNomenclatureCode() != null
+ && dataHolder.getNomenclatureCode() != "") {
+ dataHolder.identificationList.add(new Identification(tmpName, "0", dataHolder.getNomenclatureCode()));
} else {
dataHolder.identificationList.add(new Identification(tmpName, "0"));
}
if (scnames.item(n).hasChildNodes()) {
String tmp = scnames.item(n).getChildNodes().item(1).getNodeName();
if (tmp.indexOf(prefix) != -1&& prefix.length() > 0) {
- dataHolder.nomenclatureCode = tmp.split(prefix)[1];
+ dataHolder.setNomenclatureCode(tmp.split(prefix)[1]);
}
else {
- dataHolder.nomenclatureCode = scnames.item(n).getChildNodes().item(1).getNodeName();
+ dataHolder.setNomenclatureCode(scnames.item(n).getChildNodes().item(1).getNodeName());
}
}
} catch (Exception e) {
if(DEBUG) {
logger.warn("PB nomenclaturecode");
}
- dataHolder.nomenclatureCode = "";
+ dataHolder.setNomenclatureCode("");
}
atomised = scnames.item(n).getChildNodes().item(1).getChildNodes();
- dataHolder.atomisedIdentificationList.add(this.getAtomisedNames(dataHolder.nomenclatureCode,atomised));
+ dataHolder.getAtomisedIdentificationList().add(this.getAtomisedNames(dataHolder.getNomenclatureCode(),atomised));
}
}
}
-// $Id$
-/**
-* Copyright (C) 2015 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.abcd206.in;
-
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-
-/**
- * @author pplitzner
- * @date 16.06.2015
- *
- */
-public class AbcdImportUtility {
-
- public static String getUnitID(DerivedUnit derivedUnit, Abcd206ImportConfigurator config){
- if(config.isMapUnitIdToAccessionNumber()){
- return derivedUnit.getAccessionNumber();
- }
- if(config.isMapUnitIdToBarcode()){
- return derivedUnit.getBarcode();
- }
- return derivedUnit.getCatalogNumber();
- }
-
- public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){
- if(config.isMapUnitIdToCatalogNumber()
- || !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){
- // set catalog number (default if nothing is set)
- derivedUnit.setCatalogNumber(unitId);
- }
- if(config.isMapUnitIdToAccessionNumber()){
- derivedUnit.setAccessionNumber(unitId);
- }
- if(config.isMapUnitIdToBarcode()){
- derivedUnit.setBarcode(unitId);
- }
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 16.06.2015\r
+ *\r
+ */\r
+public class AbcdImportUtility {\r
+\r
+ public static String getUnitID(DerivedUnit derivedUnit, Abcd206ImportConfigurator config){\r
+ if(config.isMapUnitIdToAccessionNumber()){\r
+ return derivedUnit.getAccessionNumber();\r
+ }\r
+ if(config.isMapUnitIdToBarcode()){\r
+ return derivedUnit.getBarcode();\r
+ }\r
+ return derivedUnit.getCatalogNumber();\r
+ }\r
+\r
+ public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){\r
+ if(config.isMapUnitIdToCatalogNumber()\r
+ || !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){\r
+ // set catalog number (default if nothing is set)\r
+ derivedUnit.setCatalogNumber(unitId);\r
+ }\r
+ if(config.isMapUnitIdToAccessionNumber()){\r
+ derivedUnit.setAccessionNumber(unitId);\r
+ }\r
+ if(config.isMapUnitIdToBarcode()){\r
+ derivedUnit.setBarcode(unitId);\r
+ }\r
+ }\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2015 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.abcd206.in;
-
-import java.io.InputStream;
-import java.net.URI;
-import java.util.Date;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.joda.time.DateTime;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
-import eu.etaxonomy.cdm.persistence.query.MatchMode;
-
-/**
- * @author pplitzner
- * @date 16.06.2015
- *
- */
-public class AbcdParseUtility {
-
- private static final Logger logger = Logger.getLogger(AbcdParseUtility.class);
-
-
- public static URI parseFirstUri(NodeList nodeList, Abcd206ImportReport report){
- URI uri = null;
- String textContent = parseFirstTextContent(nodeList);
- if(textContent!=null){
- try {
- uri = URI.create(textContent);
- } catch (IllegalArgumentException e) {
- if(report!=null){
- report.addException("Exception during URI parsing!", e);
- }
- }
- }
- return uri;
- }
-
- public static String parseFirstTextContent(NodeList nodeList){
- return parseFirstTextContent(nodeList, true);
- }
-
- public static String parseFirstTextContent(NodeList nodeList, boolean cleanUpWhiteSpaces){
- String string = null;
- if(nodeList.getLength()>0){
- string = nodeList.item(0).getTextContent();
- if(cleanUpWhiteSpaces){
- string = string.replace("\n", "").replaceAll("( )+", " ").trim();
- }
- }
- return string;
- }
-
- public static Double parseFirstDouble(NodeList nodeList, Abcd206ImportReport report){
- if(nodeList.getLength()>0){
- return parseDouble(nodeList.item(0), report);
- }
- return null;
- }
-
- public static Double parseDouble(Node node, Abcd206ImportReport report){
- String message = "Could not parse double value for node " + node.getNodeName();
- Double doubleValue = null;
- try{
- String textContent = node.getTextContent();
- //remove 1000 dots
- textContent = textContent.replace(".","");
- //convert commmas
- textContent = textContent.replace(",",".");
- doubleValue = Double.parseDouble(textContent);
- } catch (NullPointerException npe){
- logger.error(message, npe);
- if(report!=null){
- report.addException(message, npe);
- }
- } catch (NumberFormatException nfe){
- logger.error(message, nfe);
- if(report!=null){
- report.addException(message, nfe);
- }
- }
- return doubleValue;
- }
-
- public static DateTime parseFirstDateTime(NodeList nodeList) {
- DateTime dateTime = null;
- String textContent = parseFirstTextContent(nodeList);
- if(textContent!=null){
- dateTime = DateTime.parse(textContent);
- }
- return dateTime;
- }
-
- public static Date parseFirstDate(NodeList nodeList) {
- Date date = null;
- DateTime dateTime = parseFirstDateTime(nodeList);
- if(dateTime!=null){
- date = dateTime.toDate();
- }
- return date;
- }
-
- public static Reference parseFirstReference(NodeList referenceNodeList, ICdmApplicationConfiguration cdmAppController){
- String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);
- //check if reference already exists
- List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitle(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();
- Reference reference;
- if(matchingReferences.size()==1){
- reference = matchingReferences.iterator().next();
- }
- else{
- reference = ReferenceFactory.newGeneric();
- reference.setTitle(referenceCitation);
- cdmAppController.getReferenceService().saveOrUpdate(reference);
- }
- return reference;
- }
-
- /**
- * Return the wrapper with the list of root nodes for an ABCD XML file
- * @param fileName: the file's location
- * @return a wrapper with a list of root nodes ("Unit")
- */
- public static UnitAssociationWrapper parseUnitsNodeList(InputStream inputStream, Abcd206ImportReport report) {
- UnitAssociationWrapper unitAssociationWrapper = new UnitAssociationWrapper();
- NodeList unitList = null;
- try {
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
-
- Document document = builder.parse(inputStream);
- Element root = document.getDocumentElement();
- unitList = root.getElementsByTagName("Unit");
- if (unitList.getLength()>0) {
- unitAssociationWrapper.setPrefix("");
- unitAssociationWrapper.setAssociatedUnits(unitList);
- return unitAssociationWrapper;
- }
- unitList = root.getElementsByTagName("abcd:Unit");
- if (unitList.getLength()>0) {
- unitAssociationWrapper.setPrefix("abcd:");
- unitAssociationWrapper.setAssociatedUnits(unitList);
- return unitAssociationWrapper;
- }
- unitList = root.getElementsByTagName("abcd21:Unit");
- if (unitList.getLength()>0) {
- unitAssociationWrapper.setPrefix("abcd21:");
- unitAssociationWrapper.setAssociatedUnits(unitList);
- }
- } catch (Exception e) {
- logger.warn(e);
- if(report!=null){
- report.addException("Exception during parsing of nodeList!", e);
- }
- }
- return unitAssociationWrapper;
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import java.io.InputStream;\r
+import java.net.URI;\r
+import java.util.Date;\r
+import java.util.List;\r
+\r
+import javax.xml.parsers.DocumentBuilder;\r
+import javax.xml.parsers.DocumentBuilderFactory;\r
+\r
+import org.apache.log4j.Logger;\r
+import org.joda.time.DateTime;\r
+import org.w3c.dom.Document;\r
+import org.w3c.dom.Element;\r
+import org.w3c.dom.Node;\r
+import org.w3c.dom.NodeList;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 16.06.2015\r
+ *\r
+ */\r
+public class AbcdParseUtility {\r
+\r
+ private static final Logger logger = Logger.getLogger(AbcdParseUtility.class);\r
+\r
+\r
+ public static URI parseFirstUri(NodeList nodeList, SpecimenImportReport report){\r
+ URI uri = null;\r
+ String textContent = parseFirstTextContent(nodeList);\r
+ if(textContent!=null){\r
+ try {\r
+ uri = URI.create(textContent);\r
+ } catch (IllegalArgumentException e) {\r
+ if(report!=null){\r
+ report.addException("Exception during URI parsing!", e);\r
+ }\r
+ }\r
+ }\r
+ return uri;\r
+ }\r
+\r
+ public static String parseFirstTextContent(NodeList nodeList){\r
+ return parseFirstTextContent(nodeList, true);\r
+ }\r
+\r
+ public static String parseFirstTextContent(NodeList nodeList, boolean cleanUpWhiteSpaces){\r
+ String string = null;\r
+ if(nodeList.getLength()>0){\r
+ string = nodeList.item(0).getTextContent();\r
+ if(cleanUpWhiteSpaces){\r
+ string = string.replace("\n", "").replaceAll("( )+", " ").trim();\r
+ }\r
+ }\r
+ return string;\r
+ }\r
+\r
+ public static Double parseFirstDouble(NodeList nodeList, SpecimenImportReport report){\r
+ if(nodeList.getLength()>0){\r
+ return parseDouble(nodeList.item(0), report);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public static Double parseDouble(Node node, SpecimenImportReport report){\r
+ String message = "Could not parse double value for node " + node.getNodeName();\r
+ Double doubleValue = null;\r
+ try{\r
+ String textContent = node.getTextContent();\r
+ //remove 1000 dots\r
+ textContent = textContent.replace(".","");\r
+ //convert commmas\r
+ textContent = textContent.replace(",",".");\r
+ doubleValue = Double.parseDouble(textContent);\r
+ } catch (NullPointerException npe){\r
+ logger.error(message, npe);\r
+ if(report!=null){\r
+ report.addException(message, npe);\r
+ }\r
+ } catch (NumberFormatException nfe){\r
+ logger.error(message, nfe);\r
+ if(report!=null){\r
+ report.addException(message, nfe);\r
+ }\r
+ }\r
+ return doubleValue;\r
+ }\r
+\r
+ public static DateTime parseFirstDateTime(NodeList nodeList) {\r
+ DateTime dateTime = null;\r
+ String textContent = parseFirstTextContent(nodeList);\r
+ if(textContent!=null){\r
+ dateTime = DateTime.parse(textContent);\r
+ }\r
+ return dateTime;\r
+ }\r
+\r
+ public static Date parseFirstDate(NodeList nodeList) {\r
+ Date date = null;\r
+ DateTime dateTime = parseFirstDateTime(nodeList);\r
+ if(dateTime!=null){\r
+ date = dateTime.toDate();\r
+ }\r
+ return date;\r
+ }\r
+\r
+ public static Reference parseFirstReference(NodeList referenceNodeList, ICdmApplicationConfiguration cdmAppController){\r
+ String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);\r
+ //check if reference already exists\r
+ List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitle(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();\r
+ Reference reference;\r
+ if(matchingReferences.size()==1){\r
+ reference = matchingReferences.iterator().next();\r
+ }\r
+ else{\r
+ reference = ReferenceFactory.newGeneric();\r
+ reference.setTitle(referenceCitation);\r
+ cdmAppController.getReferenceService().saveOrUpdate(reference);\r
+ }\r
+ return reference;\r
+ }\r
+\r
+ /**\r
+ * Return the wrapper with the list of root nodes for an ABCD XML file\r
+ * @param fileName: the file's location\r
+ * @return a wrapper with a list of root nodes ("Unit")\r
+ */\r
+ public static UnitAssociationWrapper parseUnitsNodeList(InputStream inputStream, SpecimenImportReport report) {\r
+ UnitAssociationWrapper unitAssociationWrapper = new UnitAssociationWrapper();\r
+ NodeList unitList = null;\r
+ try {\r
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();\r
+ DocumentBuilder builder = factory.newDocumentBuilder();\r
+\r
+ Document document = builder.parse(inputStream);\r
+ Element root = document.getDocumentElement();\r
+ unitList = root.getElementsByTagName("Unit");\r
+ if (unitList.getLength()>0) {\r
+ unitAssociationWrapper.setPrefix("");\r
+ unitAssociationWrapper.setAssociatedUnits(unitList);\r
+ return unitAssociationWrapper;\r
+ }\r
+ unitList = root.getElementsByTagName("abcd:Unit");\r
+ if (unitList.getLength()>0) {\r
+ unitAssociationWrapper.setPrefix("abcd:");\r
+ unitAssociationWrapper.setAssociatedUnits(unitList);\r
+ return unitAssociationWrapper;\r
+ }\r
+ unitList = root.getElementsByTagName("abcd21:Unit");\r
+ if (unitList.getLength()>0) {\r
+ unitAssociationWrapper.setPrefix("abcd21:");\r
+ unitAssociationWrapper.setAssociatedUnits(unitList);\r
+ }\r
+ } catch (Exception e) {\r
+ logger.warn(e);\r
+ if(report!=null){\r
+ report.addException("Exception during parsing of nodeList!", e);\r
+ }\r
+ }\r
+ return unitAssociationWrapper;\r
+ }\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2015 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.abcd206.in;
-
-import java.util.List;
-
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.model.agent.AgentBase;
-import eu.etaxonomy.cdm.model.agent.Person;
-import eu.etaxonomy.cdm.persistence.query.MatchMode;
-
-/**
- * @author pplitzner
- * @date 16.06.2015
- *
- */
-public class AbcdPersonParser {
-
- private final String prefix;
-
- private final Abcd206ImportReport report;
-
- private final ICdmApplicationConfiguration cdmAppController;
-
-
- public AbcdPersonParser(String prefix, Abcd206ImportReport report, ICdmApplicationConfiguration cdmAppController) {
- this.prefix = prefix;
- this.report = report;
- this.cdmAppController = cdmAppController;
- }
-
-
- public AgentBase<?> parse(Element item) {
- AgentBase<?> agentBase = null;
- NodeList fullNameList = item.getElementsByTagName(prefix+"FullName");
- String fullName = AbcdParseUtility.parseFirstTextContent(fullNameList);
- if(fullName!=null){
- List<AgentBase> matchingAgents = cdmAppController.getAgentService().findByTitle(AgentBase.class, fullName, MatchMode.EXACT, null, null, null, null, null).getRecords();
- if(matchingAgents.size()==1){
- agentBase = matchingAgents.iterator().next();
- }
- else{
- agentBase = Person.NewTitledInstance(fullName);
- }
- }
- return agentBase;
- }
-
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import java.util.List;\r
+\r
+import org.w3c.dom.Element;\r
+import org.w3c.dom.NodeList;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.model.agent.AgentBase;\r
+import eu.etaxonomy.cdm.model.agent.Person;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 16.06.2015\r
+ *\r
+ */\r
+public class AbcdPersonParser {\r
+\r
+ private final String prefix;\r
+\r
+ private final SpecimenImportReport report;\r
+\r
+ private final ICdmApplicationConfiguration cdmAppController;\r
+\r
+\r
+ public AbcdPersonParser(String prefix, SpecimenImportReport report, ICdmApplicationConfiguration cdmAppController) {\r
+ this.prefix = prefix;\r
+ this.report = report;\r
+ this.cdmAppController = cdmAppController;\r
+ }\r
+\r
+\r
+ public AgentBase<?> parse(Element item) {\r
+ AgentBase<?> agentBase = null;\r
+ NodeList fullNameList = item.getElementsByTagName(prefix+"FullName");\r
+ String fullName = AbcdParseUtility.parseFirstTextContent(fullNameList);\r
+ if(fullName!=null){\r
+ List<AgentBase> matchingAgents = cdmAppController.getAgentService().findByTitle(AgentBase.class, fullName, MatchMode.EXACT, null, null, null, null, null).getRecords();\r
+ if(matchingAgents.size()==1){\r
+ agentBase = matchingAgents.iterator().next();\r
+ }\r
+ else{\r
+ agentBase = Person.NewTitledInstance(fullName);\r
+ }\r
+ }\r
+ return agentBase;\r
+ }\r
+\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2015 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.abcd206.in.molecular;
-
-import java.util.Date;
-import java.util.UUID;
-
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportReport;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdPersonParser;
-import eu.etaxonomy.cdm.model.agent.AgentBase;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
-import eu.etaxonomy.cdm.model.common.TimePeriod;
-import eu.etaxonomy.cdm.model.molecular.DnaSample;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
-import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
-import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
-
-/**
- * @author pplitzner
- * @date 15.06.2015
- *
- */
-public class AbcdDnaParser {
-
- private final String prefix;
-
- private final Abcd206ImportReport report;
-
- private final ICdmApplicationConfiguration cdmAppController;
-
- public AbcdDnaParser(String prefix, Abcd206ImportReport report, ICdmApplicationConfiguration cdmAppController) {
- this.prefix = prefix;
- this.report = report;
- this.cdmAppController = cdmAppController;
- }
-
- public DnaSample parse(Element item, Abcd206ImportState state) {
- FieldUnit fieldUnit = FieldUnit.NewInstance();
- DnaSample dnaSample = DnaSample.NewInstance();
- DerivationEvent.NewSimpleInstance(fieldUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
-
- //specimen unit
- NodeList specimenUnitList = item.getElementsByTagName(prefix+"SpecimenUnit");
- if(specimenUnitList.item(0)!=null && specimenUnitList.item(0) instanceof Element){
- parseSpecimenUnit((Element)specimenUnitList.item(0), dnaSample);
- }
- NodeList unitExtensions = item.getElementsByTagName(prefix+"UnitExtension");
- for(int i=0;i<unitExtensions.getLength();i++){
- if(unitExtensions.item(i) instanceof Element){
- Element unitExtension = (Element) unitExtensions.item(i);
- NodeList ggbn = unitExtension.getElementsByTagName("ggbn:GGBN");
- if(ggbn.getLength()>0){
- AbcdGgbnParser ggbnParser = new AbcdGgbnParser(report, cdmAppController);
- ggbnParser.parse(ggbn, dnaSample, state);
- }
- }
- }
- return dnaSample;
- }
-
- private void parseSpecimenUnit(Element item, DnaSample dnaSample) {
- NodeList preparationsList = item.getElementsByTagName(prefix+"Preparations");
- if(preparationsList.item(0)!=null && preparationsList.item(0) instanceof Element){
- parsePreparations((Element) preparationsList.item(0), dnaSample);
- }
- NodeList preservationsList = item.getElementsByTagName(prefix+"Preservations");
- if(preservationsList.item(0)!=null && preservationsList.item(0) instanceof Element){
- parsePreservations((Element) preservationsList.item(0), dnaSample);
- }
- }
-
- private void parsePreparations(Element item, DnaSample dnaSample) {
- NodeList preparationList = item.getElementsByTagName(prefix+"preparation");
- for(int i=0;i<preparationList.getLength();i++){
- Node node = preparationList.item(i);
- if(node instanceof Element){
- DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
-
- String preparationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationType"));
- //preparation materials
- String preparationMaterials = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationMaterials"));
- derivedFrom.setDescription(preparationMaterials);
- //preparation actor
- NodeList preparationAgentList = ((Element) node).getElementsByTagName(prefix+"preparationAgent");
- if(preparationAgentList.item(0)!=null && preparationAgentList.item(0) instanceof Element){
- AgentBase<?> preparationAgent = parsePreparationAgent((Element)preparationAgentList.item(0));
- derivedFrom.setActor(preparationAgent);
- }
- //preparation date
- Date preparationDate = AbcdParseUtility.parseFirstDate(((Element) node).getElementsByTagName(prefix+"preparationDate"));
- derivedFrom.setTimeperiod(TimePeriod.NewInstance(preparationDate, null));
- //sample designation
- NodeList sampleDesignationsList = ((Element) node).getElementsByTagName(prefix+"sampleDesignations");
- if(sampleDesignationsList.item(0)!=null && sampleDesignationsList.item(0) instanceof Element){
- parseSampleDesignations((Element)sampleDesignationsList.item(0), dnaSample);
- }
- }
- }
- }
-
- /**
- * @param item
- * @param dnaSample
- */
- private void parseSampleDesignations(Element item, DnaSample dnaSample) {
- NodeList sampleDesignationList = item.getElementsByTagName(prefix+"sampleDesignation");
- for(int i=0;i<sampleDesignationList.getLength();i++){
- dnaSample.addIdentifier(sampleDesignationList.item(i).getTextContent(), (DefinedTerm)cdmAppController.getTermService().find(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc")));
- }
-
- }
-
- private AgentBase<?> parsePreparationAgent(Element item) {
- AgentBase<?> agentBase = null;
- NodeList personList = item.getElementsByTagName(prefix+"Person");
- if(personList.item(0)!=null && personList.item(0) instanceof Element){
- agentBase = new AbcdPersonParser(prefix,report, cdmAppController).parse((Element)personList.item(0));
- }
- return agentBase;
- }
-
- private void parsePreservations(Element item, DnaSample dnaSample) {
- NodeList preservationList = item.getElementsByTagName(prefix+"preservation");
- for(int i=0;i<preservationList.getLength();i++){
- Node node = preservationList.item(i);
- if(node instanceof Element){
- PreservationMethod preservation = PreservationMethod.NewInstance();
- dnaSample.setPreservation(preservation);
-
- String preservationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preservationType"));
-
- Double preservationTemperature = AbcdParseUtility.parseFirstDouble(((Element) node).getElementsByTagName(prefix+"preservationTemperature"), report);
- preservation.setTemperature(preservationTemperature);
- }
- }
- }
-
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular;\r
+\r
+import java.util.Date;\r
+import java.util.UUID;\r
+\r
+import org.w3c.dom.Element;\r
+import org.w3c.dom.Node;\r
+import org.w3c.dom.NodeList;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdPersonParser;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;\r
+import eu.etaxonomy.cdm.model.agent.AgentBase;\r
+import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
+import eu.etaxonomy.cdm.model.common.TimePeriod;\r
+import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 15.06.2015\r
+ *\r
+ */\r
+public class AbcdDnaParser {\r
+\r
+ private final String prefix;\r
+\r
+ private final SpecimenImportReport report;\r
+\r
+ private final ICdmApplicationConfiguration cdmAppController;\r
+\r
+ public AbcdDnaParser(String prefix, SpecimenImportReport report, ICdmApplicationConfiguration cdmAppController) {\r
+ this.prefix = prefix;\r
+ this.report = report;\r
+ this.cdmAppController = cdmAppController;\r
+ }\r
+\r
+ public DnaSample parse(Element item, Abcd206ImportState state) {\r
+ FieldUnit fieldUnit = FieldUnit.NewInstance();\r
+ DnaSample dnaSample = DnaSample.NewInstance();\r
+ DerivationEvent.NewSimpleInstance(fieldUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());\r
+\r
+ //specimen unit\r
+ NodeList specimenUnitList = item.getElementsByTagName(prefix+"SpecimenUnit");\r
+ if(specimenUnitList.item(0)!=null && specimenUnitList.item(0) instanceof Element){\r
+ parseSpecimenUnit((Element)specimenUnitList.item(0), dnaSample);\r
+ }\r
+ NodeList unitExtensions = item.getElementsByTagName(prefix+"UnitExtension");\r
+ for(int i=0;i<unitExtensions.getLength();i++){\r
+ if(unitExtensions.item(i) instanceof Element){\r
+ Element unitExtension = (Element) unitExtensions.item(i);\r
+ NodeList ggbn = unitExtension.getElementsByTagName("ggbn:GGBN");\r
+ if(ggbn.getLength()>0){\r
+ AbcdGgbnParser ggbnParser = new AbcdGgbnParser(report, cdmAppController);\r
+ ggbnParser.parse(ggbn, dnaSample, state);\r
+ }\r
+ }\r
+ }\r
+ return dnaSample;\r
+ }\r
+\r
+ private void parseSpecimenUnit(Element item, DnaSample dnaSample) {\r
+ NodeList preparationsList = item.getElementsByTagName(prefix+"Preparations");\r
+ if(preparationsList.item(0)!=null && preparationsList.item(0) instanceof Element){\r
+ parsePreparations((Element) preparationsList.item(0), dnaSample);\r
+ }\r
+ NodeList preservationsList = item.getElementsByTagName(prefix+"Preservations");\r
+ if(preservationsList.item(0)!=null && preservationsList.item(0) instanceof Element){\r
+ parsePreservations((Element) preservationsList.item(0), dnaSample);\r
+ }\r
+ }\r
+\r
+ private void parsePreparations(Element item, DnaSample dnaSample) {\r
+ NodeList preparationList = item.getElementsByTagName(prefix+"preparation");\r
+ for(int i=0;i<preparationList.getLength();i++){\r
+ Node node = preparationList.item(i);\r
+ if(node instanceof Element){\r
+ DerivationEvent derivedFrom = dnaSample.getDerivedFrom();\r
+\r
+ String preparationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationType"));\r
+ //preparation materials\r
+ String preparationMaterials = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationMaterials"));\r
+ derivedFrom.setDescription(preparationMaterials);\r
+ //preparation actor\r
+ NodeList preparationAgentList = ((Element) node).getElementsByTagName(prefix+"preparationAgent");\r
+ if(preparationAgentList.item(0)!=null && preparationAgentList.item(0) instanceof Element){\r
+ AgentBase<?> preparationAgent = parsePreparationAgent((Element)preparationAgentList.item(0));\r
+ derivedFrom.setActor(preparationAgent);\r
+ }\r
+ //preparation date\r
+ Date preparationDate = AbcdParseUtility.parseFirstDate(((Element) node).getElementsByTagName(prefix+"preparationDate"));\r
+ derivedFrom.setTimeperiod(TimePeriod.NewInstance(preparationDate, null));\r
+ //sample designation\r
+ NodeList sampleDesignationsList = ((Element) node).getElementsByTagName(prefix+"sampleDesignations");\r
+ if(sampleDesignationsList.item(0)!=null && sampleDesignationsList.item(0) instanceof Element){\r
+ parseSampleDesignations((Element)sampleDesignationsList.item(0), dnaSample);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * @param item\r
+ * @param dnaSample\r
+ */\r
+ private void parseSampleDesignations(Element item, DnaSample dnaSample) {\r
+ NodeList sampleDesignationList = item.getElementsByTagName(prefix+"sampleDesignation");\r
+ for(int i=0;i<sampleDesignationList.getLength();i++){\r
+ dnaSample.addIdentifier(sampleDesignationList.item(i).getTextContent(), (DefinedTerm)cdmAppController.getTermService().find(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc")));\r
+ }\r
+\r
+ }\r
+\r
+ private AgentBase<?> parsePreparationAgent(Element item) {\r
+ AgentBase<?> agentBase = null;\r
+ NodeList personList = item.getElementsByTagName(prefix+"Person");\r
+ if(personList.item(0)!=null && personList.item(0) instanceof Element){\r
+ agentBase = new AbcdPersonParser(prefix,report, cdmAppController).parse((Element)personList.item(0));\r
+ }\r
+ return agentBase;\r
+ }\r
+\r
+ private void parsePreservations(Element item, DnaSample dnaSample) {\r
+ NodeList preservationList = item.getElementsByTagName(prefix+"preservation");\r
+ for(int i=0;i<preservationList.getLength();i++){\r
+ Node node = preservationList.item(i);\r
+ if(node instanceof Element){\r
+ PreservationMethod preservation = PreservationMethod.NewInstance();\r
+ dnaSample.setPreservation(preservation);\r
+\r
+ String preservationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preservationType"));\r
+\r
+ Double preservationTemperature = AbcdParseUtility.parseFirstDouble(((Element) node).getElementsByTagName(prefix+"preservationTemperature"), report);\r
+ preservation.setTemperature(preservationTemperature);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2015 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.abcd206.in.molecular;
-
-import java.net.URI;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportReport;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-import eu.etaxonomy.cdm.model.common.OrderedTerm;
-import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.molecular.Amplification;
-import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
-import eu.etaxonomy.cdm.model.molecular.DnaQuality;
-import eu.etaxonomy.cdm.model.molecular.DnaSample;
-import eu.etaxonomy.cdm.model.molecular.Primer;
-import eu.etaxonomy.cdm.model.molecular.Sequence;
-import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
-import eu.etaxonomy.cdm.model.molecular.SequenceString;
-import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.persistence.query.MatchMode;
-
-/**
- * @author pplitzner
- * @date Mar 4, 2015
- *
- */
-public class AbcdGgbnParser {
-
- //DNA Quality term
- private static final String HIGH = "high";
- private static final String MEDIUM = "medium";
- private static final String LOW = "low";
- private static final UUID HIGH_QUALITY_TERM = UUID.fromString("ec443c76-5987-4ec5-a66b-da207f70b47f");
- private static final UUID MEDIUM_QUALITY_TERM = UUID.fromString("2a174892-1246-4807-9022-71ce8639346b");
- private static final UUID LOW_QUALITY_TERM = UUID.fromString("a3bf12ff-b041-425f-bdaa-aa51da65eebc");
-
- private static final String FORWARD = "forward";
-
- private static final String REVERSE = "reverse";
-
- private static final Logger logger = Logger.getLogger(AbcdGgbnParser.class);
-
- private final String prefix = "ggbn:";
-
- private final Abcd206ImportReport report;
-
- private final ICdmApplicationConfiguration cdmAppController;
-
- public AbcdGgbnParser(Abcd206ImportReport report, ICdmApplicationConfiguration cdmAppController) {
- this.report = report;
- this.cdmAppController = cdmAppController;
- }
-
- public DnaSample parse(NodeList ggbn, DnaSample dnaSample, Abcd206ImportState state) {
-
- for(int i=0;i<ggbn.getLength();i++){
- Node item = ggbn.item(i);
- if(item instanceof Element){
- Element element = (Element) item;
- NodeList methodDeterminationConcentrationAndRatiosList = element.getElementsByTagName(prefix+"methodDeterminationConcentrationAndRatios");
- NodeList volumeList = element.getElementsByTagName(prefix+"volume");
- NodeList weightList = element.getElementsByTagName(prefix+"weight");
- NodeList methodDeterminationWeightList = element.getElementsByTagName(prefix+"methodDeterminationWeight");
- NodeList DNADNAHybridizationList = element.getElementsByTagName(prefix+"DNADNAHybridization");
- NodeList DNAMeltingPointList = element.getElementsByTagName(prefix+"DNAMeltingPoint");
- NodeList estimatedSizeList = element.getElementsByTagName(prefix+"estimated_size");
- NodeList poolDnaExtractsList = element.getElementsByTagName(prefix+"pool_dna_extracts");
- NodeList gelImageList = element.getElementsByTagName(prefix+"gelImage");
- NodeList amplificationsList = element.getElementsByTagName(prefix+"Amplifications");
-
- dnaSample.setDnaQuality(parseDnaQuality(element, state));
-
- parseGelImage(gelImageList, state);
- parseAmplifications(amplificationsList, dnaSample, state);
- }
- }
- return dnaSample;
- }
-
- private DnaQuality parseDnaQuality(Element element, Abcd206ImportState state) {
- DnaQuality dnaQuality = DnaQuality.NewInstance();
-
- NodeList purificationMethodList = element.getElementsByTagName(prefix+"purificationMethod");
- String purificationMethod = AbcdParseUtility.parseFirstTextContent(purificationMethodList);
- dnaQuality.setPurificationMethod(purificationMethod);
-
- NodeList concentrationList = element.getElementsByTagName(prefix+"concentration");
- if(concentrationList.getLength()==1){
- Node concentration = concentrationList.item(0);
- dnaQuality.setConcentration(AbcdParseUtility.parseDouble(concentration, report));
- if(concentration instanceof Element){
- String unit = ((Element) concentration).getAttribute("Unit");
- //TODO
-// dnaQuality.setConcentrationUnit(concentrationUnit)
- }
- }
-
- NodeList ratioOfAbsorbance260_280List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_280");
- dnaQuality.setRatioOfAbsorbance260_280(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_280List, report));
-
- NodeList ratioOfAbsorbance260_230List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_230");
- dnaQuality.setRatioOfAbsorbance260_230(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_230List, report));
-
- NodeList qualityCheckDateList = element.getElementsByTagName(prefix+"qualityCheckDate");
- if(qualityCheckDateList.item(0)!=null){
- dnaQuality.setQualityCheckDate(AbcdParseUtility.parseFirstDateTime(qualityCheckDateList));
- }
-
- NodeList qualityList = element.getElementsByTagName(prefix+"quality");
- String quality = AbcdParseUtility.parseFirstTextContent(qualityList);
- if(LOW.equals(quality)){
- dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(LOW_QUALITY_TERM));
- }
- else if(MEDIUM.equals(quality)){
- dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(MEDIUM_QUALITY_TERM));
- }
- else if(HIGH.equals(quality)){
- dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(HIGH_QUALITY_TERM));
- }
-
- NodeList qualityRemarksList = element.getElementsByTagName(prefix+"qualityRemarks");
-
-
- return dnaQuality;
- }
-
- private void parseGelImage(NodeList gelImageList, Abcd206ImportState state) {
- if(gelImageList.item(0)!=null && gelImageList.item(0) instanceof Element){
- Element gelImage = (Element)gelImageList.item(0);
- NodeList fileURIList = gelImage.getElementsByTagName("fileURI");
- NodeList gelVoltageList = gelImage.getElementsByTagName("gelVoltage");
- NodeList gelConcentrationList = gelImage.getElementsByTagName("gelConcentration");
- NodeList gelDurationList = gelImage.getElementsByTagName("gelDuration");
- NodeList gelLadderList = gelImage.getElementsByTagName("gelLadder");
- NodeList gelStainList = gelImage.getElementsByTagName("gelStain");
- NodeList gelRemarksList = gelImage.getElementsByTagName("gelRemarks");
-
- }
-
- }
-
- private void parseAmplifications(NodeList amplificationsList, DnaSample dnaSample, Abcd206ImportState state) {
- if(amplificationsList.item(0)!=null && amplificationsList.item(0) instanceof Element){
- AmplificationResult amplificationResult = AmplificationResult.NewInstance();
- Amplification amplification = Amplification.NewInstance();
- NodeList amplificationList = ((Element) amplificationsList.item(0)).getElementsByTagName(prefix+"amplification");
- for(int i=0;i<amplificationList.getLength();i++){
- if(amplificationList.item(i) instanceof Element){
- Element amplificationElement = (Element)amplificationList.item(i);
- NodeList amplificationDateList = amplificationElement.getElementsByTagName(prefix+"amplificationDate");
- NodeList amplificationStaffList = amplificationElement.getElementsByTagName(prefix+"amplificationStaff");
-
- //amplification dna marker
- NodeList markerList = amplificationElement.getElementsByTagName(prefix+"marker");
- if(markerList.item(0)!=null){
- String amplificationMarker = markerList.item(0).getTextContent();
- DefinedTerm dnaMarker = null;
- List<DefinedTermBase> markersFound = cdmAppController.getTermService().findByTitle(DefinedTerm.class, amplificationMarker, MatchMode.EXACT, null, null, null, null, null).getRecords();
- if(markersFound.size()==1){
- dnaMarker = (DefinedTerm) markersFound.get(0);
- }
- else{
- dnaMarker = DefinedTerm.NewDnaMarkerInstance(amplificationMarker, amplificationMarker, amplificationMarker);
- cdmAppController.getTermService().saveOrUpdate(dnaMarker);
- }
- amplification.setDnaMarker(dnaMarker);
- }
-
- NodeList markerSubfragmentList = amplificationElement.getElementsByTagName(prefix+"markerSubfragment");
- NodeList amplificationSuccessList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccess");
- NodeList amplificationSuccessDetailsList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccessDetails");
- NodeList amplificationMethodList = amplificationElement.getElementsByTagName(prefix+"amplificationMethod");
- NodeList purificationMethodList = amplificationElement.getElementsByTagName(prefix+"purificationMethod");
- NodeList libReadsSeqdList = amplificationElement.getElementsByTagName(prefix+"lib_reads_seqd");
- NodeList libScreenList = amplificationElement.getElementsByTagName(prefix+"lib_screen");
- NodeList libVectorList = amplificationElement.getElementsByTagName(prefix+"lib_vector");
- NodeList libConstMethList = amplificationElement.getElementsByTagName(prefix+"lib_const_meth");
- NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");
-
- //consensus sequence
- NodeList sequencingsList = amplificationElement.getElementsByTagName(prefix+"Sequencings");
- if(sequencingsList.item(0)!=null && sequencingsList.item(0) instanceof Element){
- parseAmplificationSequencings((Element)sequencingsList.item(0), amplification, amplificationResult, dnaSample, state);
- }
- parseAmplificationPrimers(amplificationElement.getElementsByTagName(prefix+"AmplificationPrimers"));
- }
- }
- //check if amplification already exists (can only be checked after all fields are initialized because comparison is done on the label cache))
- List<Amplification> matchingAmplifications = cdmAppController.getAmplificationService().findByLabelCache(amplification.getLabelCache(), MatchMode.EXACT, null, null, null, null, null).getRecords();
- if(matchingAmplifications.size()==1){
- amplification = matchingAmplifications.iterator().next();
- }
- cdmAppController.getAmplificationService().save(amplification);
- amplificationResult.setAmplification(amplification);
- dnaSample.addAmplificationResult(amplificationResult);
- }
- }
-
- private void parseAmplificationPrimers(NodeList elementsByTagName) {
- // TODO Auto-generated method stub
-
- }
-
- private void parseAmplificationSequencings(Element sequencings, Amplification amplification, AmplificationResult amplificationResult, DnaSample dnaSample, Abcd206ImportState state) {
- NodeList sequencingList = sequencings.getElementsByTagName(prefix+"sequencing");
- for(int i=0;i<sequencingList.getLength();i++){
- Sequence sequence = Sequence.NewInstance("");
- dnaSample.addSequence(sequence);
- sequence.setDnaMarker(amplification.getDnaMarker());
-
- if(sequencingList.item(i) instanceof Element){
- Element sequencing = (Element)sequencingList.item(i);
-
- //singleSequencings
- NodeList singleSequencingsList = sequencing.getElementsByTagName(prefix+"SingleSequencings");
- parseSingleSequencings(singleSequencingsList, amplification, amplificationResult, sequence);
- //Consensus sequence
- NodeList consensusSequencesList = sequencing.getElementsByTagName(prefix+"consensusSequence");
- sequence.setConsensusSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(consensusSequencesList)));
- //sequence length
- Double consensusSequenceLength = AbcdParseUtility.parseFirstDouble(sequencing.getElementsByTagName(prefix+"consensusSequenceLength"), report);
- if(sequence.getConsensusSequence()!=null && consensusSequenceLength!=null){
- //TODO: this can be different from the actual length in ABCD but not in CDM!
- sequence.getConsensusSequence().setLength(consensusSequenceLength.intValue());
- }
- //contig file URL
- NodeList consensusSequenceChromatogramFileURIList = sequencing.getElementsByTagName(prefix+"consensusSequenceChromatogramFileURI");
- URI uri = AbcdParseUtility.parseFirstUri(consensusSequenceChromatogramFileURIList, report);
- Media contigFile = Media.NewInstance(uri, null, null, null);
- sequence.setContigFile(contigFile);
-
- //genetic Accession
- NodeList geneticAccessionList = sequencing.getElementsByTagName(prefix+"geneticAccession");
- parseGeneticAccession(geneticAccessionList, sequence);
-
- //references
- NodeList referencesList = sequencing.getElementsByTagName(prefix+"References");
- if(referencesList.item(0)!=null && referencesList.item(0) instanceof Element){
- parseSequencingReferences((Element) referencesList.item(0), sequence);
- }
- }
- }
-// if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){
-// NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");
-
- }
-
- private void parseSequencingReferences(Element references, Sequence sequence) {
- NodeList referenceList = references.getElementsByTagName(prefix+"Reference");
- for(int i=0;i<referenceList.getLength();i++){
- if(referenceList.item(i) instanceof Element){
- Element element = (Element)referenceList.item(i);
- NodeList referenceCitationList = element.getElementsByTagName(prefix+"ReferenceCitation");
- Reference reference = AbcdParseUtility.parseFirstReference(referenceCitationList, cdmAppController);
- sequence.addCitation(reference);
- }
- }
- }
-
- private void parseSingleSequencings(NodeList singleSequencingsList, Amplification amplification, AmplificationResult amplificationResult, Sequence sequence) {
- if(singleSequencingsList.item(0)!=null && singleSequencingsList.item(0) instanceof Element){
- Element singleSequencings = (Element)singleSequencingsList.item(0);
- NodeList singleSequencingList = singleSequencings.getElementsByTagName(prefix+"singleSequencing");
- for(int i=0;i<singleSequencingList.getLength();i++){
- //single read
- SingleRead singleRead = SingleRead.NewInstance();
- SingleReadAlignment.NewInstance(sequence, singleRead);
- amplificationResult.addSingleRead(singleRead);
- if(singleSequencingList.item(i) instanceof Element){
- Element singleSequencing = (Element)singleSequencingList.item(i);
- NodeList sequencingDirectionList = singleSequencing.getElementsByTagName(prefix+"sequencingDirection");
- //read direction
- String singleReadDirection = AbcdParseUtility.parseFirstTextContent(sequencingDirectionList);
- if(singleReadDirection.equals(FORWARD)){
- singleRead.setDirection(SequenceDirection.Forward);
- }
- else if(singleReadDirection.equals(REVERSE)){
- singleRead.setDirection(SequenceDirection.Reverse);
- }
- //read pherogram URI
- NodeList chromatogramFileURIList = singleSequencing.getElementsByTagName(prefix+"chromatogramFileURI");
- singleRead.setPherogram(Media.NewInstance(AbcdParseUtility.parseFirstUri(chromatogramFileURIList, report), null, null, null));
- NodeList sequencingPrimersList = singleSequencing.getElementsByTagName(prefix+"SequencingPrimers");
- parseSequencingPrimers(sequencingPrimersList, singleRead, amplification);
- }
- }
- }
- }
-
- private void parseSequencingPrimers(NodeList sequencingPrimersList, SingleRead singleRead, Amplification amplification) {
- if(sequencingPrimersList.item(0)!=null && sequencingPrimersList.item(0) instanceof Element){
- Element sequencingPrimers = (Element)sequencingPrimersList.item(0);
- NodeList sequencingPrimerList = sequencingPrimers.getElementsByTagName(prefix+"sequencingPrimer");
- for(int i=0;i<sequencingPrimerList.getLength();i++){
- if(sequencingPrimerList.item(i) instanceof Element){
- Element sequencingPrimer = (Element)sequencingPrimerList.item(i);
- //primer name
- String primerName = AbcdParseUtility.parseFirstTextContent(sequencingPrimer.getElementsByTagName(prefix+"primerName"));
- //check if primer already exists
- List<Primer> matchingPrimers = cdmAppController.getPrimerService().findByLabel(primerName, MatchMode.EXACT, null, null, null, null, null).getRecords();
- Primer primer = null;
- if(matchingPrimers.size()==1){
- primer = matchingPrimers.iterator().next();
- return;
- }
- else{
- primer = Primer.NewInstance(null);
- primer.setLabel(primerName);
- }
- singleRead.setPrimer(primer);
- //primer sequence
- NodeList primerSequenceList = sequencingPrimer.getElementsByTagName(prefix+"primerSequence");
- primer.setSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(primerSequenceList)));
- //primer direction
- String direction = parseFirstAttribute("Direction", primerSequenceList);
- if(direction!=null){
- if(direction.equals(FORWARD)){
- amplification.setForwardPrimer(primer);
- }
- else if(direction.equals(REVERSE)){
- amplification.setReversePrimer(primer);
- }
- }
- //reference citation
- NodeList primerReferenceCitationList = sequencingPrimer.getElementsByTagName(prefix+"primerReferenceCitation");
- String primerReferenceCitation = AbcdParseUtility.parseFirstTextContent(primerReferenceCitationList);
- Reference reference = AbcdParseUtility.parseFirstReference(primerReferenceCitationList, cdmAppController);
- primer.setPublishedIn(reference);
-
- cdmAppController.getPrimerService().save(primer);
- }
- }
- }
- }
-
- private String parseFirstAttribute(String attributeName, NodeList nodeList) {
- String attribute = null;
- if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){
- Element element = (Element)nodeList.item(0);
- attribute = element.getAttribute(attributeName);
- }
- return attribute;
- }
-
- private void parseGeneticAccession(NodeList geneticAccessionList, Sequence sequence) {
- for(int i=0;i<geneticAccessionList.getLength();i++){
- if(geneticAccessionList.item(i) instanceof Element){
- //genetic accession number
- NodeList geneticAccessionNumberList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumber");
- sequence.setGeneticAccessionNumber(AbcdParseUtility.parseFirstTextContent(geneticAccessionNumberList));
-
- //genetic accession number uri
- NodeList geneticAccessionNumberUriList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumberURI");
- //TODO: this is different from the geneticAccessionNumber
-
- }
- }
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular;\r
+\r
+import java.net.URI;\r
+import java.util.List;\r
+import java.util.UUID;\r
+\r
+import org.apache.log4j.Logger;\r
+import org.w3c.dom.Element;\r
+import org.w3c.dom.Node;\r
+import org.w3c.dom.NodeList;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;\r
+import eu.etaxonomy.cdm.model.common.DefinedTerm;\r
+import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
+import eu.etaxonomy.cdm.model.common.OrderedTerm;\r
+import eu.etaxonomy.cdm.model.media.Media;\r
+import eu.etaxonomy.cdm.model.molecular.Amplification;\r
+import eu.etaxonomy.cdm.model.molecular.AmplificationResult;\r
+import eu.etaxonomy.cdm.model.molecular.DnaQuality;\r
+import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
+import eu.etaxonomy.cdm.model.molecular.Primer;\r
+import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+import eu.etaxonomy.cdm.model.molecular.SequenceDirection;\r
+import eu.etaxonomy.cdm.model.molecular.SequenceString;\r
+import eu.etaxonomy.cdm.model.molecular.SingleRead;\r
+import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date Mar 4, 2015\r
+ *\r
+ */\r
+public class AbcdGgbnParser {\r
+\r
+ //DNA Quality term\r
+ private static final String HIGH = "high";\r
+ private static final String MEDIUM = "medium";\r
+ private static final String LOW = "low";\r
+ private static final UUID HIGH_QUALITY_TERM = UUID.fromString("ec443c76-5987-4ec5-a66b-da207f70b47f");\r
+ private static final UUID MEDIUM_QUALITY_TERM = UUID.fromString("2a174892-1246-4807-9022-71ce8639346b");\r
+ private static final UUID LOW_QUALITY_TERM = UUID.fromString("a3bf12ff-b041-425f-bdaa-aa51da65eebc");\r
+\r
+ private static final String FORWARD = "forward";\r
+\r
+ private static final String REVERSE = "reverse";\r
+\r
+ private static final Logger logger = Logger.getLogger(AbcdGgbnParser.class);\r
+\r
+ private final String prefix = "ggbn:";\r
+\r
+ private final SpecimenImportReport report;\r
+\r
+ private final ICdmApplicationConfiguration cdmAppController;\r
+\r
+ public AbcdGgbnParser(SpecimenImportReport report, ICdmApplicationConfiguration cdmAppController) {\r
+ this.report = report;\r
+ this.cdmAppController = cdmAppController;\r
+ }\r
+\r
+ public DnaSample parse(NodeList ggbn, DnaSample dnaSample, Abcd206ImportState state) {\r
+\r
+ for(int i=0;i<ggbn.getLength();i++){\r
+ Node item = ggbn.item(i);\r
+ if(item instanceof Element){\r
+ Element element = (Element) item;\r
+ NodeList methodDeterminationConcentrationAndRatiosList = element.getElementsByTagName(prefix+"methodDeterminationConcentrationAndRatios");\r
+ NodeList volumeList = element.getElementsByTagName(prefix+"volume");\r
+ NodeList weightList = element.getElementsByTagName(prefix+"weight");\r
+ NodeList methodDeterminationWeightList = element.getElementsByTagName(prefix+"methodDeterminationWeight");\r
+ NodeList DNADNAHybridizationList = element.getElementsByTagName(prefix+"DNADNAHybridization");\r
+ NodeList DNAMeltingPointList = element.getElementsByTagName(prefix+"DNAMeltingPoint");\r
+ NodeList estimatedSizeList = element.getElementsByTagName(prefix+"estimated_size");\r
+ NodeList poolDnaExtractsList = element.getElementsByTagName(prefix+"pool_dna_extracts");\r
+ NodeList gelImageList = element.getElementsByTagName(prefix+"gelImage");\r
+ NodeList amplificationsList = element.getElementsByTagName(prefix+"Amplifications");\r
+\r
+ dnaSample.setDnaQuality(parseDnaQuality(element, state));\r
+\r
+ parseGelImage(gelImageList, state);\r
+ parseAmplifications(amplificationsList, dnaSample, state);\r
+ }\r
+ }\r
+ return dnaSample;\r
+ }\r
+\r
+ private DnaQuality parseDnaQuality(Element element, Abcd206ImportState state) {\r
+ DnaQuality dnaQuality = DnaQuality.NewInstance();\r
+\r
+ NodeList purificationMethodList = element.getElementsByTagName(prefix+"purificationMethod");\r
+ String purificationMethod = AbcdParseUtility.parseFirstTextContent(purificationMethodList);\r
+ dnaQuality.setPurificationMethod(purificationMethod);\r
+\r
+ NodeList concentrationList = element.getElementsByTagName(prefix+"concentration");\r
+ if(concentrationList.getLength()==1){\r
+ Node concentration = concentrationList.item(0);\r
+ dnaQuality.setConcentration(AbcdParseUtility.parseDouble(concentration, report));\r
+ if(concentration instanceof Element){\r
+ String unit = ((Element) concentration).getAttribute("Unit");\r
+ //TODO\r
+// dnaQuality.setConcentrationUnit(concentrationUnit)\r
+ }\r
+ }\r
+\r
+ NodeList ratioOfAbsorbance260_280List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_280");\r
+ dnaQuality.setRatioOfAbsorbance260_280(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_280List, report));\r
+\r
+ NodeList ratioOfAbsorbance260_230List = element.getElementsByTagName(prefix+"ratioOfAbsorbance260_230");\r
+ dnaQuality.setRatioOfAbsorbance260_230(AbcdParseUtility.parseFirstDouble(ratioOfAbsorbance260_230List, report));\r
+\r
+ NodeList qualityCheckDateList = element.getElementsByTagName(prefix+"qualityCheckDate");\r
+ if(qualityCheckDateList.item(0)!=null){\r
+ dnaQuality.setQualityCheckDate(AbcdParseUtility.parseFirstDateTime(qualityCheckDateList));\r
+ }\r
+\r
+ NodeList qualityList = element.getElementsByTagName(prefix+"quality");\r
+ String quality = AbcdParseUtility.parseFirstTextContent(qualityList);\r
+ if(LOW.equals(quality)){\r
+ dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(LOW_QUALITY_TERM));\r
+ }\r
+ else if(MEDIUM.equals(quality)){\r
+ dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(MEDIUM_QUALITY_TERM));\r
+ }\r
+ else if(HIGH.equals(quality)){\r
+ dnaQuality.setQualityTerm((OrderedTerm) state.getCdmRepository().getTermService().load(HIGH_QUALITY_TERM));\r
+ }\r
+\r
+ NodeList qualityRemarksList = element.getElementsByTagName(prefix+"qualityRemarks");\r
+\r
+\r
+ return dnaQuality;\r
+ }\r
+\r
+ private void parseGelImage(NodeList gelImageList, Abcd206ImportState state) {\r
+ if(gelImageList.item(0)!=null && gelImageList.item(0) instanceof Element){\r
+ Element gelImage = (Element)gelImageList.item(0);\r
+ NodeList fileURIList = gelImage.getElementsByTagName("fileURI");\r
+ NodeList gelVoltageList = gelImage.getElementsByTagName("gelVoltage");\r
+ NodeList gelConcentrationList = gelImage.getElementsByTagName("gelConcentration");\r
+ NodeList gelDurationList = gelImage.getElementsByTagName("gelDuration");\r
+ NodeList gelLadderList = gelImage.getElementsByTagName("gelLadder");\r
+ NodeList gelStainList = gelImage.getElementsByTagName("gelStain");\r
+ NodeList gelRemarksList = gelImage.getElementsByTagName("gelRemarks");\r
+\r
+ }\r
+\r
+ }\r
+\r
+ private void parseAmplifications(NodeList amplificationsList, DnaSample dnaSample, Abcd206ImportState state) {\r
+ if(amplificationsList.item(0)!=null && amplificationsList.item(0) instanceof Element){\r
+ AmplificationResult amplificationResult = AmplificationResult.NewInstance();\r
+ Amplification amplification = Amplification.NewInstance();\r
+ NodeList amplificationList = ((Element) amplificationsList.item(0)).getElementsByTagName(prefix+"amplification");\r
+ for(int i=0;i<amplificationList.getLength();i++){\r
+ if(amplificationList.item(i) instanceof Element){\r
+ Element amplificationElement = (Element)amplificationList.item(i);\r
+ NodeList amplificationDateList = amplificationElement.getElementsByTagName(prefix+"amplificationDate");\r
+ NodeList amplificationStaffList = amplificationElement.getElementsByTagName(prefix+"amplificationStaff");\r
+\r
+ //amplification dna marker\r
+ NodeList markerList = amplificationElement.getElementsByTagName(prefix+"marker");\r
+ if(markerList.item(0)!=null){\r
+ String amplificationMarker = markerList.item(0).getTextContent();\r
+ DefinedTerm dnaMarker = null;\r
+ List<DefinedTermBase> markersFound = cdmAppController.getTermService().findByTitle(DefinedTerm.class, amplificationMarker, MatchMode.EXACT, null, null, null, null, null).getRecords();\r
+ if(markersFound.size()==1){\r
+ dnaMarker = (DefinedTerm) markersFound.get(0);\r
+ }\r
+ else{\r
+ dnaMarker = DefinedTerm.NewDnaMarkerInstance(amplificationMarker, amplificationMarker, amplificationMarker);\r
+ cdmAppController.getTermService().saveOrUpdate(dnaMarker);\r
+ }\r
+ amplification.setDnaMarker(dnaMarker);\r
+ }\r
+\r
+ NodeList markerSubfragmentList = amplificationElement.getElementsByTagName(prefix+"markerSubfragment");\r
+ NodeList amplificationSuccessList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccess");\r
+ NodeList amplificationSuccessDetailsList = amplificationElement.getElementsByTagName(prefix+"amplificationSuccessDetails");\r
+ NodeList amplificationMethodList = amplificationElement.getElementsByTagName(prefix+"amplificationMethod");\r
+ NodeList purificationMethodList = amplificationElement.getElementsByTagName(prefix+"purificationMethod");\r
+ NodeList libReadsSeqdList = amplificationElement.getElementsByTagName(prefix+"lib_reads_seqd");\r
+ NodeList libScreenList = amplificationElement.getElementsByTagName(prefix+"lib_screen");\r
+ NodeList libVectorList = amplificationElement.getElementsByTagName(prefix+"lib_vector");\r
+ NodeList libConstMethList = amplificationElement.getElementsByTagName(prefix+"lib_const_meth");\r
+ NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");\r
+\r
+ //consensus sequence\r
+ NodeList sequencingsList = amplificationElement.getElementsByTagName(prefix+"Sequencings");\r
+ if(sequencingsList.item(0)!=null && sequencingsList.item(0) instanceof Element){\r
+ parseAmplificationSequencings((Element)sequencingsList.item(0), amplification, amplificationResult, dnaSample, state);\r
+ }\r
+ parseAmplificationPrimers(amplificationElement.getElementsByTagName(prefix+"AmplificationPrimers"));\r
+ }\r
+ }\r
+ //check if amplification already exists (can only be checked after all fields are initialized because comparison is done on the label cache))\r
+ List<Amplification> matchingAmplifications = cdmAppController.getAmplificationService().findByLabelCache(amplification.getLabelCache(), MatchMode.EXACT, null, null, null, null, null).getRecords();\r
+ if(matchingAmplifications.size()==1){\r
+ amplification = matchingAmplifications.iterator().next();\r
+ }\r
+ cdmAppController.getAmplificationService().save(amplification);\r
+ amplificationResult.setAmplification(amplification);\r
+ dnaSample.addAmplificationResult(amplificationResult);\r
+ }\r
+ }\r
+\r
+ private void parseAmplificationPrimers(NodeList elementsByTagName) {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+ private void parseAmplificationSequencings(Element sequencings, Amplification amplification, AmplificationResult amplificationResult, DnaSample dnaSample, Abcd206ImportState state) {\r
+ NodeList sequencingList = sequencings.getElementsByTagName(prefix+"sequencing");\r
+ for(int i=0;i<sequencingList.getLength();i++){\r
+ Sequence sequence = Sequence.NewInstance("");\r
+ dnaSample.addSequence(sequence);\r
+ sequence.setDnaMarker(amplification.getDnaMarker());\r
+\r
+ if(sequencingList.item(i) instanceof Element){\r
+ Element sequencing = (Element)sequencingList.item(i);\r
+\r
+ //singleSequencings\r
+ NodeList singleSequencingsList = sequencing.getElementsByTagName(prefix+"SingleSequencings");\r
+ parseSingleSequencings(singleSequencingsList, amplification, amplificationResult, sequence);\r
+ //Consensus sequence\r
+ NodeList consensusSequencesList = sequencing.getElementsByTagName(prefix+"consensusSequence");\r
+ sequence.setConsensusSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(consensusSequencesList)));\r
+ //sequence length\r
+ Double consensusSequenceLength = AbcdParseUtility.parseFirstDouble(sequencing.getElementsByTagName(prefix+"consensusSequenceLength"), report);\r
+ if(sequence.getConsensusSequence()!=null && consensusSequenceLength!=null){\r
+ //TODO: this can be different from the actual length in ABCD but not in CDM!\r
+ sequence.getConsensusSequence().setLength(consensusSequenceLength.intValue());\r
+ }\r
+ //contig file URL\r
+ NodeList consensusSequenceChromatogramFileURIList = sequencing.getElementsByTagName(prefix+"consensusSequenceChromatogramFileURI");\r
+ URI uri = AbcdParseUtility.parseFirstUri(consensusSequenceChromatogramFileURIList, report);\r
+ Media contigFile = Media.NewInstance(uri, null, null, null);\r
+ sequence.setContigFile(contigFile);\r
+\r
+ //genetic Accession\r
+ NodeList geneticAccessionList = sequencing.getElementsByTagName(prefix+"geneticAccession");\r
+ parseGeneticAccession(geneticAccessionList, sequence);\r
+\r
+ //references\r
+ NodeList referencesList = sequencing.getElementsByTagName(prefix+"References");\r
+ if(referencesList.item(0)!=null && referencesList.item(0) instanceof Element){\r
+ parseSequencingReferences((Element) referencesList.item(0), sequence);\r
+ }\r
+ }\r
+ }\r
+// if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){\r
+// NodeList plasmidList = amplificationElement.getElementsByTagName(prefix+"plasmid");\r
+\r
+ }\r
+\r
+ private void parseSequencingReferences(Element references, Sequence sequence) {\r
+ NodeList referenceList = references.getElementsByTagName(prefix+"Reference");\r
+ for(int i=0;i<referenceList.getLength();i++){\r
+ if(referenceList.item(i) instanceof Element){\r
+ Element element = (Element)referenceList.item(i);\r
+ NodeList referenceCitationList = element.getElementsByTagName(prefix+"ReferenceCitation");\r
+ Reference reference = AbcdParseUtility.parseFirstReference(referenceCitationList, cdmAppController);\r
+ sequence.addCitation(reference);\r
+ }\r
+ }\r
+ }\r
+\r
+ private void parseSingleSequencings(NodeList singleSequencingsList, Amplification amplification, AmplificationResult amplificationResult, Sequence sequence) {\r
+ if(singleSequencingsList.item(0)!=null && singleSequencingsList.item(0) instanceof Element){\r
+ Element singleSequencings = (Element)singleSequencingsList.item(0);\r
+ NodeList singleSequencingList = singleSequencings.getElementsByTagName(prefix+"singleSequencing");\r
+ for(int i=0;i<singleSequencingList.getLength();i++){\r
+ //single read\r
+ SingleRead singleRead = SingleRead.NewInstance();\r
+ SingleReadAlignment.NewInstance(sequence, singleRead);\r
+ amplificationResult.addSingleRead(singleRead);\r
+ if(singleSequencingList.item(i) instanceof Element){\r
+ Element singleSequencing = (Element)singleSequencingList.item(i);\r
+ NodeList sequencingDirectionList = singleSequencing.getElementsByTagName(prefix+"sequencingDirection");\r
+ //read direction\r
+ String singleReadDirection = AbcdParseUtility.parseFirstTextContent(sequencingDirectionList);\r
+ if(singleReadDirection.equals(FORWARD)){\r
+ singleRead.setDirection(SequenceDirection.Forward);\r
+ }\r
+ else if(singleReadDirection.equals(REVERSE)){\r
+ singleRead.setDirection(SequenceDirection.Reverse);\r
+ }\r
+ //read pherogram URI\r
+ NodeList chromatogramFileURIList = singleSequencing.getElementsByTagName(prefix+"chromatogramFileURI");\r
+ singleRead.setPherogram(Media.NewInstance(AbcdParseUtility.parseFirstUri(chromatogramFileURIList, report), null, null, null));\r
+ NodeList sequencingPrimersList = singleSequencing.getElementsByTagName(prefix+"SequencingPrimers");\r
+ parseSequencingPrimers(sequencingPrimersList, singleRead, amplification);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private void parseSequencingPrimers(NodeList sequencingPrimersList, SingleRead singleRead, Amplification amplification) {\r
+ if(sequencingPrimersList.item(0)!=null && sequencingPrimersList.item(0) instanceof Element){\r
+ Element sequencingPrimers = (Element)sequencingPrimersList.item(0);\r
+ NodeList sequencingPrimerList = sequencingPrimers.getElementsByTagName(prefix+"sequencingPrimer");\r
+ for(int i=0;i<sequencingPrimerList.getLength();i++){\r
+ if(sequencingPrimerList.item(i) instanceof Element){\r
+ Element sequencingPrimer = (Element)sequencingPrimerList.item(i);\r
+ //primer name\r
+ String primerName = AbcdParseUtility.parseFirstTextContent(sequencingPrimer.getElementsByTagName(prefix+"primerName"));\r
+ //check if primer already exists\r
+ List<Primer> matchingPrimers = cdmAppController.getPrimerService().findByLabel(primerName, MatchMode.EXACT, null, null, null, null, null).getRecords();\r
+ Primer primer = null;\r
+ if(matchingPrimers.size()==1){\r
+ primer = matchingPrimers.iterator().next();\r
+ return;\r
+ }\r
+ else{\r
+ primer = Primer.NewInstance(null);\r
+ primer.setLabel(primerName);\r
+ }\r
+ singleRead.setPrimer(primer);\r
+ //primer sequence\r
+ NodeList primerSequenceList = sequencingPrimer.getElementsByTagName(prefix+"primerSequence");\r
+ primer.setSequence(SequenceString.NewInstance(AbcdParseUtility.parseFirstTextContent(primerSequenceList)));\r
+ //primer direction\r
+ String direction = parseFirstAttribute("Direction", primerSequenceList);\r
+ if(direction!=null){\r
+ if(direction.equals(FORWARD)){\r
+ amplification.setForwardPrimer(primer);\r
+ }\r
+ else if(direction.equals(REVERSE)){\r
+ amplification.setReversePrimer(primer);\r
+ }\r
+ }\r
+ //reference citation\r
+ NodeList primerReferenceCitationList = sequencingPrimer.getElementsByTagName(prefix+"primerReferenceCitation");\r
+ String primerReferenceCitation = AbcdParseUtility.parseFirstTextContent(primerReferenceCitationList);\r
+ Reference reference = AbcdParseUtility.parseFirstReference(primerReferenceCitationList, cdmAppController);\r
+ primer.setPublishedIn(reference);\r
+\r
+ cdmAppController.getPrimerService().save(primer);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ private String parseFirstAttribute(String attributeName, NodeList nodeList) {\r
+ String attribute = null;\r
+ if(nodeList.item(0)!=null && nodeList.item(0) instanceof Element){\r
+ Element element = (Element)nodeList.item(0);\r
+ attribute = element.getAttribute(attributeName);\r
+ }\r
+ return attribute;\r
+ }\r
+\r
+ private void parseGeneticAccession(NodeList geneticAccessionList, Sequence sequence) {\r
+ for(int i=0;i<geneticAccessionList.getLength();i++){\r
+ if(geneticAccessionList.item(i) instanceof Element){\r
+ //genetic accession number\r
+ NodeList geneticAccessionNumberList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumber");\r
+ sequence.setGeneticAccessionNumber(AbcdParseUtility.parseFirstTextContent(geneticAccessionNumberList));\r
+\r
+ //genetic accession number uri\r
+ NodeList geneticAccessionNumberUriList = ((Element)geneticAccessionList.item(i)).getElementsByTagName(prefix+"geneticAccessionNumberURI");\r
+ //TODO: this is different from the geneticAccessionNumber\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2016 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.gbif.in;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import eu.etaxonomy.cdm.io.specimen.SpecimenDataHolder;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;
-import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public class GbifDataHolder extends SpecimenDataHolder{
- @SuppressWarnings("unused")
- private static final Logger logger = Logger.getLogger(Abcd206DataHolder.class);
-
- //per import
- protected List<SpecimenTypeDesignationStatus> statusList;
- protected List<String> knownGbifElements = new ArrayList<String>();
- protected HashMap<String,String> allGbifElements = new HashMap<String,String>();
- public List<String> gatheringAgentList;
- protected List<String> gatheringTeamList;
-
- /*per unit
- protected List<Identification> identificationList;
- private List<HashMap<String, String>> atomisedIdentificationList;
- protected Map<String, String> namedAreaList;
- protected List<String[]> referenceList;
- protected List<String> multimediaObjects;
- protected List<String> docSources;
- protected List<String> associatedUnitIds;
-
- private String nomenclatureCode;
- protected String institutionCode;
- protected String collectionCode;
- protected String unitID;
- protected String recordBasis;
- protected String kindOfUnit;
- protected String accessionNumber;
- protected String fieldNumber;
- protected Double longitude;
- protected Double latitude;
- protected String locality;
- protected String languageIso;
- protected String country;
- protected String isocountry;
- protected Integer depth;
- protected Integer altitude;
- protected String unitNotes;
- protected String gatheringNotes;
- protected String gatheringDateText;
- protected String gatheringElevationText;
- protected String gatheringElevation;
- protected String gatheringElevationMax;
- protected String gatheringElevationMin;
- protected String gatheringElevationUnit;
- protected String gatheringSpatialDatum;
- protected String gatheringCoordinateErrorMethod;
- */
-
-
- protected String key;
- protected String datasetKey;
- protected String publishingOrgKey;
- protected String publishingCountry;
- protected String protocol;
- protected String lastCrawled;
- protected String lastParsed;
- protected String extensions;
- protected String basisOfRecord;
- protected String individualCount;
- protected String taxonKey;
- protected String kingdomKey;
- protected String phylumKey;
- protected String classKey;
- protected String orderKey;
- protected String familyKey;
- protected String genusKey;
- protected String speciesKey;
- protected String scientificName;
- protected String kingdom;
- protected String phylum;
- protected String order;
- protected String family;
- protected String genus;
- protected String species;
- protected String genericName;
- protected String specificEpithet;
- protected String taxonRank;
- protected String dateIdentified;
- protected String decimalLongitude;
- protected String decimalLatitude;
- protected String elevation;
- protected String continent;
- protected String stateProvince;
- protected String year;
- protected String month;
- protected String day;
- protected String eventDate;
- protected String[] issues;
- protected String lastInterpreted;
- protected String identifiers;
- protected String[] facts;
- protected String[] relations;
- protected String geodeticDatum;
- protected String className;
- protected String countryCode;
- protected String country;
- protected String nomenclaturalStatus;
- protected String rightsHolder;
- protected String identifier;
- protected String recordNumber;
- protected String nomenclaturalCode;
- protected String county;
- protected String locality;
- protected String datasetName;
- protected String gbifID;
- protected String collectionCode;
- protected String occurrenceID;
- protected String type;
- protected String taxonID;
- protected String license;
- protected String catalogNumber;
- protected String recordedBy;
- protected String institutionCode;
- protected String ownerInstitutionCode;
- protected String bibliographicCitation;
- protected String identifiedBy;
- protected String collectionID;
-
-
- public void reset() {
-
- key = null;
- datasetKey = null;
- publishingOrgKey = null;
- publishingCountry = null;
- protocol = null;
- lastCrawled = null;
- lastParsed = null;
- extensions = null;
- basisOfRecord = null;
- individualCount = null;
- taxonKey = null;
- kingdomKey = null;
- phylumKey = null;
- classKey = null;
- orderKey = null;
- familyKey = null;
- genusKey = null;
- speciesKey = null;
- scientificName = null;
- kingdom = null;
- phylum = null;
- order = null;
- family = null;
- genus = null;
- species = null;
- genericName = null;
- specificEpithet = null;
- taxonRank = null;
- dateIdentified = null;
- decimalLongitude = null;
- decimalLatitude = null;
- elevation = null;
- continent = null;
- stateProvince = null;
- year = null;
- month = null;
- day = null;
- eventDate = null;
- issues = null;
- lastInterpreted = null;
- identifiers = null;
- facts = null;
- relations = null;
- geodeticDatum = null;
- className = null;
- countryCode = null;
- country = null;
- nomenclaturalStatus = null;
- rightsHolder = null;
- identifier = null;
- recordNumber = null;
- nomenclaturalCode = null;
- county = null;
- locality = null;
- datasetName = null;
- gbifID = null;
- collectionCode = null;
- occurrenceID = null;
- type = null;
- taxonID = null;
- license = null;
- catalogNumber = null;
- recordedBy = null;
- institutionCode = null;
- ownerInstitutionCode = null;
- bibliographicCitation = null;
- identifiedBy = null;
- collectionID = null;
- }
-
-
-
- /**
- * @return the nomenclatureCode
- */
- public String getNomenclatureCode() {
- return nomenclaturalCode;
- }
-
-
-
- /**
- * @param nomenclatureCode the nomenclatureCode to set
- */
- public void setNomenclatureCode(String nomenclatureCode) {
- this.nomenclaturalCode = nomenclatureCode;
- }
-
-
-
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.gbif.in;\r
+\r
+import java.util.ArrayList;\r
+import java.util.HashMap;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenDataHolder;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206DataHolder;\r
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public class GbifDataHolder extends SpecimenDataHolder{\r
+ @SuppressWarnings("unused")\r
+ private static final Logger logger = Logger.getLogger(Abcd206DataHolder.class);\r
+\r
+ //per import\r
+ protected List<SpecimenTypeDesignationStatus> statusList;\r
+ protected List<String> knownGbifElements = new ArrayList<String>();\r
+ protected HashMap<String,String> allGbifElements = new HashMap<String,String>();\r
+ public List<String> gatheringAgentList;\r
+ protected List<String> gatheringTeamList;\r
+\r
+ /*per unit\r
+ protected List<Identification> identificationList;\r
+ private List<HashMap<String, String>> atomisedIdentificationList;\r
+ protected Map<String, String> namedAreaList;\r
+ protected List<String[]> referenceList;\r
+ protected List<String> multimediaObjects;\r
+ protected List<String> docSources;\r
+ protected List<String> associatedUnitIds;\r
+\r
+ private String nomenclatureCode;\r
+ protected String institutionCode;\r
+ protected String collectionCode;\r
+ protected String unitID;\r
+ protected String recordBasis;\r
+ protected String kindOfUnit;\r
+ protected String accessionNumber;\r
+ protected String fieldNumber;\r
+ protected Double longitude;\r
+ protected Double latitude;\r
+ protected String locality;\r
+ protected String languageIso;\r
+ protected String country;\r
+ protected String isocountry;\r
+ protected Integer depth;\r
+ protected Integer altitude;\r
+ protected String unitNotes;\r
+ protected String gatheringNotes;\r
+ protected String gatheringDateText;\r
+ protected String gatheringElevationText;\r
+ protected String gatheringElevation;\r
+ protected String gatheringElevationMax;\r
+ protected String gatheringElevationMin;\r
+ protected String gatheringElevationUnit;\r
+ protected String gatheringSpatialDatum;\r
+ protected String gatheringCoordinateErrorMethod;\r
+ */\r
+\r
+\r
+ protected String key;\r
+ protected String datasetKey;\r
+ protected String publishingOrgKey;\r
+ protected String publishingCountry;\r
+ protected String protocol;\r
+ protected String lastCrawled;\r
+ protected String lastParsed;\r
+ protected String extensions;\r
+ protected String basisOfRecord;\r
+ protected String individualCount;\r
+ protected String taxonKey;\r
+ protected String kingdomKey;\r
+ protected String phylumKey;\r
+ protected String classKey;\r
+ protected String orderKey;\r
+ protected String familyKey;\r
+ protected String genusKey;\r
+ protected String speciesKey;\r
+ protected String scientificName;\r
+ protected String kingdom;\r
+ protected String phylum;\r
+ protected String order;\r
+ protected String family;\r
+ protected String genus;\r
+ protected String species;\r
+ protected String genericName;\r
+ protected String specificEpithet;\r
+ protected String taxonRank;\r
+ protected String dateIdentified;\r
+ protected String decimalLongitude;\r
+ protected String decimalLatitude;\r
+ protected String elevation;\r
+ protected String continent;\r
+ protected String stateProvince;\r
+ protected String year;\r
+ protected String month;\r
+ protected String day;\r
+ protected String eventDate;\r
+ protected String[] issues;\r
+ protected String lastInterpreted;\r
+ protected String identifiers;\r
+ protected String[] facts;\r
+ protected String[] relations;\r
+ protected String geodeticDatum;\r
+ protected String className;\r
+ protected String countryCode;\r
+ protected String country;\r
+ protected String nomenclaturalStatus;\r
+ protected String rightsHolder;\r
+ protected String identifier;\r
+ protected String recordNumber;\r
+ protected String nomenclaturalCode;\r
+ protected String county;\r
+ protected String locality;\r
+ protected String datasetName;\r
+ protected String gbifID;\r
+ protected String collectionCode;\r
+ protected String occurrenceID;\r
+ protected String type;\r
+ protected String taxonID;\r
+ protected String license;\r
+ protected String catalogNumber;\r
+ protected String recordedBy;\r
+ protected String institutionCode;\r
+ protected String ownerInstitutionCode;\r
+ protected String bibliographicCitation;\r
+ protected String identifiedBy;\r
+ protected String collectionID;\r
+\r
+\r
+ public void reset() {\r
+\r
+ key = null;\r
+ datasetKey = null;\r
+ publishingOrgKey = null;\r
+ publishingCountry = null;\r
+ protocol = null;\r
+ lastCrawled = null;\r
+ lastParsed = null;\r
+ extensions = null;\r
+ basisOfRecord = null;\r
+ individualCount = null;\r
+ taxonKey = null;\r
+ kingdomKey = null;\r
+ phylumKey = null;\r
+ classKey = null;\r
+ orderKey = null;\r
+ familyKey = null;\r
+ genusKey = null;\r
+ speciesKey = null;\r
+ scientificName = null;\r
+ kingdom = null;\r
+ phylum = null;\r
+ order = null;\r
+ family = null;\r
+ genus = null;\r
+ species = null;\r
+ genericName = null;\r
+ specificEpithet = null;\r
+ taxonRank = null;\r
+ dateIdentified = null;\r
+ decimalLongitude = null;\r
+ decimalLatitude = null;\r
+ elevation = null;\r
+ continent = null;\r
+ stateProvince = null;\r
+ year = null;\r
+ month = null;\r
+ day = null;\r
+ eventDate = null;\r
+ issues = null;\r
+ lastInterpreted = null;\r
+ identifiers = null;\r
+ facts = null;\r
+ relations = null;\r
+ geodeticDatum = null;\r
+ className = null;\r
+ countryCode = null;\r
+ country = null;\r
+ nomenclaturalStatus = null;\r
+ rightsHolder = null;\r
+ identifier = null;\r
+ recordNumber = null;\r
+ nomenclaturalCode = null;\r
+ county = null;\r
+ locality = null;\r
+ datasetName = null;\r
+ gbifID = null;\r
+ collectionCode = null;\r
+ occurrenceID = null;\r
+ type = null;\r
+ taxonID = null;\r
+ license = null;\r
+ catalogNumber = null;\r
+ recordedBy = null;\r
+ institutionCode = null;\r
+ ownerInstitutionCode = null;\r
+ bibliographicCitation = null;\r
+ identifiedBy = null;\r
+ collectionID = null;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the nomenclatureCode\r
+ */\r
+ public String getNomenclatureCode() {\r
+ return nomenclaturalCode;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param nomenclatureCode the nomenclatureCode to set\r
+ */\r
+ public void setNomenclatureCode(String nomenclatureCode) {\r
+ this.nomenclaturalCode = nomenclatureCode;\r
+ }\r
+\r
+\r
+\r
+\r
+}\r
-package eu.etaxonomy.cdm.io.specimen.gbif.in;
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.http.client.ClientProtocolException;
-import org.apache.log4j.Logger;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper;
-import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
-import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;
-import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportUtility;
-import eu.etaxonomy.cdm.model.common.Language;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-
-// $Id$
-/**
- * Copyright (C) 2016 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.
- */
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public class GbifImport extends SpecimenImportBase<DwcaImportConfigurator, GbifImportState> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- private static final Logger logger = Logger.getLogger(GbifImport.class);
-
- @Override
- protected boolean doCheck(GbifImportState state) {
- logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
- return true;
- }
-
-
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
- */
- @Override
- protected boolean isIgnore(GbifImportState state) {
- // TODO Auto-generated method stub
- return false;
- }
-
-
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.specimen.SpecimenImportBase#doInvoke(eu.etaxonomy.cdm.io.common.ImportStateBase)
- */
- @Override
- protected void doInvoke(GbifImportState state) {
- GbifImportState gbifImportState = state;
- GbifImportConfigurator config = state.getConfig();
-
- state.setTx(startTransaction());
- logger.info("INVOKE Specimen Import from ABCD2.06 XML ");
- Collection<GbifResponse> results = null;
- //init cd repository
- if(state.getCdmRepository()==null){
- state.setCdmRepository(this);
- }
- if (config.getOccurenceQuery() != null){
- try {
- results = new GbifQueryServiceWrapper().query(config.getOccurenceQuery());
- } catch (ClientProtocolException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (URISyntaxException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
-
- }
-
- if(state.getConfig().getClassificationUuid()!=null){
- //load classification from config if it exists
- state.setClassification(getClassificationService().load(state.getConfig().getClassificationUuid()));
- }
- if(state.getClassification()==null){//no existing classification was set in config
- List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, null);
- //get classification via user interaction
- if (state.getConfig().isUseClassification() && state.getConfig().isInteractWithUser()){
- Map<String,Classification> classMap = new HashMap<String, Classification>();
- for (Classification tree : classificationList) {
- if (! StringUtils.isBlank(tree.getTitleCache())) {
- classMap.put(tree.getTitleCache(),tree);
- }
- }
-
- }
- // use default classification as the classification to import into
- if (state.getClassification() == null) {
- String name = NB(state.getConfig().getClassificationName());
- for (Classification classif : classificationList){
- if (classif.getTitleCache() != null && classif.getTitleCache().equalsIgnoreCase(name)) {
- state.setClassification(classif);
- }
- }
- if (state.getClassification() == null){
- state.setClassification(Classification.NewInstance(name, state.getRef(), Language.DEFAULT()));
- //we do not need a default classification when creating an empty new one
- state.setDefaultClassification(state.getClassification());
-
- }
-
- }
- }
- String message = "nb units to insert: " + results.size();
- logger.info(message);
- state.getConfig().getProgressMonitor().beginTask("Importing ABCD file", results.size());
- updateProgress(state, message);
-
- state.setDataHolder(new GbifDataHolder());
- state.getDataHolder().reset();
-
- for (GbifResponse response:results) {
- if(state.getConfig().getProgressMonitor().isCanceled()){
- break;
- }
-
-
-
-
- //this.setUnitPropertiesXML( item, abcdFieldGetter, state);
- // updateProgress(state, "Importing data for unit "+state.getDataHolder().unitID+" ("+i+"/"+unitsList.getLength()+")");
-
- //import unit + field unit data
- this.handleSingleUnit(state, response);
-
- }
-
-
- commitTransaction(state.getTx());
-
-
-
- }
-
- @Override
- protected void importAssociatedUnits(GbifImportState state, Object item, DerivedUnitFacade derivedUnitFacade) {
-
- //import associated units
- FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
- //TODO: push state (think of implementing stack architecture for state
- DerivedUnit currentUnit = state.getDerivedUnitBase();
- DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
- String currentPrefix = state.getPrefix();
- /* NodeList unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
- for(int k=0;k<unitAssociationList.getLength();k++){
- if(unitAssociationList.item(k) instanceof Element){
- Element unitAssociation = (Element)unitAssociationList.item(k);
- UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());
- UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
- if(associationWrapper!=null){
- NodeList associatedUnits = associationWrapper.getAssociatedUnits();
- if(associatedUnits!=null){
- for(int m=0;m<associatedUnits.getLength();m++){
- if(associatedUnits.item(m) instanceof Element){
- state.reset();
- state.setPrefix(associationWrapper.getPrefix());
- this.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
- handleSingleUnit(state, associatedUnits.item(m));
-
- DerivedUnit associatedUnit = state.getDerivedUnitBase();
- FieldUnit associatedFieldUnit = null;
- java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
- //ignore field unit if associated unit has more than one
- if(associatedFieldUnits.size()>1){
- state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
- }
- else if(associatedFieldUnits.size()==1){
- associatedFieldUnit = associatedFieldUnits.iterator().next();
- }
-
- //attach current unit and associated unit depending on association type
-
- //parent-child relation:
- //copy derivation event and connect parent and sub derivative
- if(associationWrapper.getAssociationType().contains("individual")){
- if(currentDerivedFrom==null){
- state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",AbcdImportUtility.getUnitID(currentUnit, config)));
- DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
- }
- else{
- DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
- updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
- updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
- updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
- updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
- }
- state.getReport().addDerivate(associatedUnit, currentUnit, config);
- }
- //siblings relation
- //connect current unit to field unit of associated unit
- else if(associationWrapper.getAssociationType().contains("population")){
- //no associated field unit -> using current one
- if(associatedFieldUnit==null){
- if(currentFieldUnit!=null){
- DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
- }
- }
- else{
- if(currentDerivedFrom==null){
- state.getReport().addInfoMessage("No derivation event found for unit "+AbcdImportUtility.getUnitID(currentUnit, config)+". Defaulting to ACCESIONING event.");
- DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
- }
- if(currentDerivedFrom!=null && associatedFieldUnit!=currentFieldUnit){
- DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
- updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
- updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
- updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
- updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
- }
- }
- }
-
- //delete current field unit if replaced
- if(currentFieldUnit!=null && currentDerivedFrom!=null
- && currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
- && currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
- && currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
- ){
- currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
- state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
- }
-
- save(associatedUnit, state);
- }
- }
- }
- }
- }
- }*/
- //TODO: pop state
- state.reset();
- state.setDerivedUnitBase(currentUnit);
- state.setPrefix(currentPrefix);
- }
-@Override
-protected void handleSingleUnit(GbifImportState state, Object itemObject){
- GbifResponse item;
- if (itemObject instanceof GbifResponse){
- item = (GbifResponse) itemObject;
- } else{
- logger.error("For Gbif Import the item has to be of type GbifResponse.");
- return;
- }
- if (DEBUG) {
- logger.info("handleSingleUnit "+state.getRef());
- }
- try {
- ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();
- if(cdmAppController==null){
- cdmAppController = this;
- }
- //check if unit already exists
- DerivedUnitFacade derivedUnitFacade = null;
- if(state.getConfig().isIgnoreImportOfExistingSpecimens()){
- String[] tripleId = item.getTripleID();
- SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(tripleId[0], state);
- if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){
- DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
- state.setDerivedUnitBase(derivedUnit);
- derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
- importAssociatedUnits(state, item, derivedUnitFacade);
- state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, state.getConfig()), derivedUnit);
- return;
- }
- }
- // TODO: implement overwrite/merge specimen
-// else if(state.getConfig().isOverwriteExistingSpecimens()){
-// Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
-// if(!existingSpecimens.getRecords().isEmpty()){
-// derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit);
-// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
-// fieldUnit = derivedUnitFacade.getFieldUnit(true);
-// }
-// }
- //import new specimen
-
- // import DNA unit
- //TODO!!!!
-// if(state.getDataHolder().catalogNumber!=null && state.getDataHolder()..equalsIgnoreCase("dna")){
-// AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
-// DnaSample dnaSample = dnaParser.parse(item, state);
-// save(dnaSample, state);
-// //set dna as derived unit to avoid creating an extra specimen for this dna sample (instead just the field unit will be created)
-// state.setDerivedUnitBase(dnaSample);
-// derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
-// }
-// else{
-// // create facade
-// derivedUnitFacade = getFacade(state);
-// state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());
-// }
-
- /**
- * GATHERING EVENT
- */
- // gathering event
- /* UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),
- state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude,
- state.getDataHolder().latitude, state.getDataHolder().gatheringElevationText,
- state.getDataHolder().gatheringElevationMin, state.getDataHolder().gatheringElevationMax,
- state.getDataHolder().gatheringElevationUnit, state.getDataHolder().gatheringDateText,
- state.getDataHolder().gatheringNotes, state.getTransformer().getReferenceSystemByKey(
- state.getDataHolder().gatheringSpatialDatum), state.getDataHolder().gatheringAgentList,
- state.getDataHolder().gatheringTeamList, state.getConfig());
-
- // country
- UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
- // unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
- unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, state.getConfig(), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());
-
- DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
-
- // other areas
- unitsGatheringArea = new UnitsGatheringArea();
- // unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
- unitsGatheringArea.setAreas(state.getDataHolder().namedAreaList,state.getConfig(), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
- ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
- for (DefinedTermBase namedArea : nas) {
- unitsGatheringEvent.addArea(namedArea);
- }
-
- // copy gathering event to facade
- GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
- derivedUnitFacade.setLocality(gatheringEvent.getLocality());
- derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
- derivedUnitFacade.setCollector(gatheringEvent.getCollector());
- derivedUnitFacade.setCountry((NamedArea)areaCountry);
- derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
- derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
- derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
- derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
-
- for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
- derivedUnitFacade.addCollectingArea((NamedArea) area);
- }
- // derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
- // TODO exsiccatum
-
- // add fieldNumber
- derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().fieldNumber));
-
- // add unitNotes
- derivedUnitFacade.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().unitNotes)));
-
- // //add Multimedia URLs
- if (state.getDataHolder().multimediaObjects.size() != -1) {
- for (String multimediaObject : state.getDataHolder().multimediaObjects) {
- Media media;
- try {
- media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
- derivedUnitFacade.addDerivedUnitMedia(media);
- if(state.getConfig().isAddMediaAsMediaSpecimen()){
- //add media also as specimen scan
- MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.Media);
- mediaSpecimen.setMediaSpecimen(media);
- DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
- if(specimenScanTerm instanceof DefinedTerm){
- mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
- }
- DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.PREPARATION());
- derivationEvent.addDerivative(mediaSpecimen);
- derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);
- }
-
- } catch (MalformedURLException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- }
- }
-
- // /*
- // * merge AND STORE DATA
- // */
- // getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
- //
- // for (NamedArea area : otherAreas) {
- // getTermService().saveOrUpdate(area);// merge it sooner (foreach area)
- // }
-/*
- save(unitsGatheringEvent.getLocality(), state);
-
- // handle collection data
- setCollectionData(state, derivedUnitFacade);
-
- //Reference stuff
- SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
- Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
-
- state.getDataHolder().docSources = new ArrayList<String>();
- for (String[] fullReference : state.getDataHolder().referenceList) {
- String strReference=fullReference[0];
- String citationDetail = fullReference[1];
- String citationURL = fullReference[2];
-
- if (!citationURL.isEmpty()) {
- citationDetail+=", "+citationURL;
- }
-
- Reference reference;
- if(strReference.equals(state.getRef().getTitleCache())){
- reference = state.getRef();
- }
- else{
- reference = ReferenceFactory.newGeneric();
- reference.setTitle(strReference);
- }
-
- IdentifiableSource sour = getIdentifiableSource(reference,citationDetail);
-
- try{
- if (sour.getCitation() != null){
- if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
- state.getDataHolder().docSources.add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
- } else {
- state.getDataHolder().docSources.add(sour.getCitation().getTitleCache());
- }
- }
- }catch(Exception e){
- logger.warn("oups");
- }
- reference.addSource(sour);
- save(reference, state);
- }
- List<IdentifiableSource> issTmp = new ArrayList<IdentifiableSource>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
- List<DescriptionElementSource> issTmp2 = new ArrayList<DescriptionElementSource>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
-
- Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
- if(issTmp2!=null) {
- osbSet.addAll(issTmp2);
- }
- if(issTmp!=null) {
- osbSet.addAll(issTmp);
- }
-
- addToSourceMap(sourceMap, osbSet);
-
- if( state.getConfig().isInteractWithUser()){
- List<OriginalSourceBase<?>>sources=null;
- if(!state.isDerivedUnitSourcesSet()){
- sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().docSources);
- state.setDerivedUnitSources(sources);
- state.setDerivedUnitSourcesSet(true);
- }
- else{
- sources=state.getDerivedUnitSources();
- }
-// System.out.println("nb sources: "+sources.size());
-// System.out.println("derivedunitfacade : "+derivedUnitFacade.getTitleCache());
- for (OriginalSourceBase<?> sour:sources){
- if(sour.isInstanceOf(IdentifiableSource.class)){
- if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
-// System.out.println("add source to derivedunitfacade1 "+derivedUnitFacade.getTitleCache());
- derivedUnitFacade.addSource((IdentifiableSource)sour.clone());
- }
- }else{
- if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
-// System.out.println("add source to derivedunitfacade2 "+derivedUnitFacade.getTitleCache());
- derivedUnitFacade.addSource(OriginalSourceType.Import,sour.getCitation(),sour.getCitationMicroReference(), ioName);
- }
- }
- }
- }else{
- for (OriginalSourceBase<?> sr : sourceMap.values()){
- if(sr.isInstanceOf(IdentifiableSource.class)){
- if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
-// System.out.println("add source to derivedunitfacade3 "+derivedUnitFacade.getTitleCache());
- derivedUnitFacade.addSource((IdentifiableSource)sr.clone());
- }
- }else{
- if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
-// System.out.println("add source to derivedunitfacade4 "+derivedUnitFacade.getTitleCache());
- derivedUnitFacade.addSource(OriginalSourceType.Import,sr.getCitation(),sr.getCitationMicroReference(), ioName);
- }
- }
- }
- }
-
- save(state.getDerivedUnitBase(), state);
-
- if(DEBUG) {
- logger.info("saved ABCD specimen ...");
- }
-
- // handle identifications
- handleIdentifications(state, derivedUnitFacade);
-
- //associatedUnits
- importAssociatedUnits(state, item, derivedUnitFacade);
-
-*/
-
- } catch (Exception e) {
- String message = "Error when reading record!";
- logger.warn(message);
- state.getReport().addException(message, e);
- e.printStackTrace();
- state.setUnsuccessfull();
- }
-
- return;
-}
-
-
-
-
-
-
-
-
-
-
- /*
- * "key": 1257570425,
-"datasetKey": "7bd65a7a-f762-11e1-a439-00145eb45e9a",
-"publishingOrgKey": "90fd6680-349f-11d8-aa2d-b8a03c50a862",
-"publishingCountry": "US",
-"protocol": "DWC_ARCHIVE",
-"lastCrawled": "2016-06-06T11:11:35.800+0000",
-"lastParsed": "2016-03-21T14:11:42.224+0000",
-"extensions": { },
-"basisOfRecord": "PRESERVED_SPECIMEN",
-"individualCount": 1,
-"taxonKey": 5338762,
-"kingdomKey": 6,
-"phylumKey": 7707728,
-"classKey": 220,
-"orderKey": 412,
-"familyKey": 8798,
-"genusKey": 2907867,
-"speciesKey": 5338762,
-"scientificName": "Mitchella repens L.",
-"kingdom": "Plantae",
-"phylum": "Tracheophyta",
-"order": "Gentianales",
-"family": "Rubiaceae",
-"genus": "Mitchella",
-"species": "Mitchella repens",
-"genericName": "Mitchella",
-"specificEpithet": "repens",
-"taxonRank": "SPECIES",
-"dateIdentified": "2005-12-31T23:00:00.000+0000",
-"decimalLongitude": -98.70693,
-"decimalLatitude": 20.77805,
-"elevation": 1524.0,
-"continent": "NORTH_AMERICA",
-"stateProvince": "Hidalgo",
-"year": 2006,
-"month": 6,
-"day": 11,
-"eventDate": "2006-06-10T22:00:00.000+0000",
-"issues": [
-
- "COORDINATE_ROUNDED",
- "GEODETIC_DATUM_ASSUMED_WGS84"
-
-],
-"lastInterpreted": "2016-04-17T13:34:52.325+0000",
-"identifiers": [ ],
-"facts": [ ],
-"relations": [ ],
-"geodeticDatum": "WGS84",
-"class": "Magnoliopsida",
-"countryCode": "MX",
-"country": "Mexico",
-"nomenclaturalStatus": "No opinion",
-"rightsHolder": "Missouri Botanical Garden",
-"identifier": "urn:catalog:MO:Tropicos:100217973",
-"recordNumber": "Oberle 274",
-"nomenclaturalCode": "ICNafp",
-"county": "Metztitlán",
-"locality": "Along trail downslope of road between Molango and Zacualtipan.",
-"datasetName": "Tropicos",
-"gbifID": "1257570425",
-"collectionCode": "MO",
-"occurrenceID": "urn:catalog:MO:Tropicos:100217973",
-"type": "PhysicalObject",
-"taxonID": "27902971",
-"license": "http://creativecommons.org/licenses/by/4.0/legalcode",
-"catalogNumber": "100217973",
-"recordedBy": "Brad Oberle",
-"institutionCode": "MO",
-"ownerInstitutionCode": "MOBOT",
-"bibliographicCitation": "http://www.tropicos.org/Specimen/100217973",
-"identifiedBy": "B. Oberle",
-"collectionID": "http://biocol.org/urn:lsid:biocol.org:col:15859
- *
- */
-
-
-
-}
+package eu.etaxonomy.cdm.io.specimen.gbif.in;\r
+import java.io.IOException;\r
+import java.net.URISyntaxException;\r
+import java.util.Collection;\r
+import java.util.HashMap;\r
+import java.util.List;\r
+import java.util.Map;\r
+\r
+import org.apache.commons.lang.StringUtils;\r
+import org.apache.http.client.ClientProtocolException;\r
+import org.apache.log4j.Logger;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
+import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifQueryServiceWrapper;\r
+import eu.etaxonomy.cdm.ext.occurrence.gbif.GbifResponse;\r
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;\r
+import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportUtility;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\r
+\r
+// $Id$\r
+/**\r
+ * Copyright (C) 2016 EDIT\r
+ * European Distributed Institute of Taxonomy\r
+ * http://www.e-taxonomy.eu\r
+ *\r
+ * The contents of this file are subject to the Mozilla Public License Version 1.1\r
+ * See LICENSE.TXT at the top of this package for the full license terms.\r
+ */\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public class GbifImport extends SpecimenImportBase<DwcaImportConfigurator, GbifImportState> {\r
+ /**\r
+ *\r
+ */\r
+ private static final long serialVersionUID = 1L;\r
+ private static final Logger logger = Logger.getLogger(GbifImport.class);\r
+\r
+ @Override\r
+ protected boolean doCheck(GbifImportState state) {\r
+ logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());\r
+ return true;\r
+ }\r
+\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)\r
+ */\r
+ @Override\r
+ protected boolean isIgnore(GbifImportState state) {\r
+ // TODO Auto-generated method stub\r
+ return false;\r
+ }\r
+\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.specimen.SpecimenImportBase#doInvoke(eu.etaxonomy.cdm.io.common.ImportStateBase)\r
+ */\r
+ @Override\r
+ protected void doInvoke(GbifImportState state) {\r
+ GbifImportState gbifImportState = state;\r
+ GbifImportConfigurator config = state.getConfig();\r
+\r
+ state.setTx(startTransaction());\r
+ logger.info("INVOKE Specimen Import from ABCD2.06 XML ");\r
+ Collection<GbifResponse> results = null;\r
+ //init cd repository\r
+ if(state.getCdmRepository()==null){\r
+ state.setCdmRepository(this);\r
+ }\r
+ if (config.getOccurenceQuery() != null){\r
+ try {\r
+ results = new GbifQueryServiceWrapper().query(config.getOccurenceQuery());\r
+ } catch (ClientProtocolException e) {\r
+ // TODO Auto-generated catch block\r
+ e.printStackTrace();\r
+ } catch (IOException e) {\r
+ // TODO Auto-generated catch block\r
+ e.printStackTrace();\r
+ } catch (URISyntaxException e) {\r
+ // TODO Auto-generated catch block\r
+ e.printStackTrace();\r
+ }\r
+\r
+\r
+ }\r
+\r
+ if(state.getConfig().getClassificationUuid()!=null){\r
+ //load classification from config if it exists\r
+ state.setClassification(getClassificationService().load(state.getConfig().getClassificationUuid()));\r
+ }\r
+ if(state.getClassification()==null){//no existing classification was set in config\r
+ List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, null);\r
+ //get classification via user interaction\r
+ if (state.getConfig().isUseClassification() && state.getConfig().isInteractWithUser()){\r
+ Map<String,Classification> classMap = new HashMap<String, Classification>();\r
+ for (Classification tree : classificationList) {\r
+ if (! StringUtils.isBlank(tree.getTitleCache())) {\r
+ classMap.put(tree.getTitleCache(),tree);\r
+ }\r
+ }\r
+\r
+ }\r
+ // use default classification as the classification to import into\r
+ if (state.getClassification() == null) {\r
+ String name = NB(state.getConfig().getClassificationName());\r
+ for (Classification classif : classificationList){\r
+ if (classif.getTitleCache() != null && classif.getTitleCache().equalsIgnoreCase(name)) {\r
+ state.setClassification(classif);\r
+ }\r
+ }\r
+ if (state.getClassification() == null){\r
+ state.setClassification(Classification.NewInstance(name, state.getRef(), Language.DEFAULT()));\r
+ //we do not need a default classification when creating an empty new one\r
+ state.setDefaultClassification(state.getClassification());\r
+\r
+ }\r
+\r
+ }\r
+ }\r
+ String message = "nb units to insert: " + results.size();\r
+ logger.info(message);\r
+ state.getConfig().getProgressMonitor().beginTask("Importing ABCD file", results.size());\r
+ updateProgress(state, message);\r
+\r
+ state.setDataHolder(new GbifDataHolder());\r
+ state.getDataHolder().reset();\r
+\r
+ for (GbifResponse response:results) {\r
+ if(state.getConfig().getProgressMonitor().isCanceled()){\r
+ break;\r
+ }\r
+\r
+\r
+\r
+\r
+ //this.setUnitPropertiesXML( item, abcdFieldGetter, state);\r
+ // updateProgress(state, "Importing data for unit "+state.getDataHolder().unitID+" ("+i+"/"+unitsList.getLength()+")");\r
+\r
+ //import unit + field unit data\r
+ this.handleSingleUnit(state, response);\r
+\r
+ }\r
+\r
+\r
+ commitTransaction(state.getTx());\r
+\r
+\r
+\r
+ }\r
+\r
+ @Override\r
+ protected void importAssociatedUnits(GbifImportState state, Object item, DerivedUnitFacade derivedUnitFacade) {\r
+\r
+ //import associated units\r
+ FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();\r
+ //TODO: push state (think of implementing stack architecture for state\r
+ DerivedUnit currentUnit = state.getDerivedUnitBase();\r
+ DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();\r
+ String currentPrefix = state.getPrefix();\r
+ /* NodeList unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");\r
+ for(int k=0;k<unitAssociationList.getLength();k++){\r
+ if(unitAssociationList.item(k) instanceof Element){\r
+ Element unitAssociation = (Element)unitAssociationList.item(k);\r
+ UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());\r
+ UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);\r
+ if(associationWrapper!=null){\r
+ NodeList associatedUnits = associationWrapper.getAssociatedUnits();\r
+ if(associatedUnits!=null){\r
+ for(int m=0;m<associatedUnits.getLength();m++){\r
+ if(associatedUnits.item(m) instanceof Element){\r
+ state.reset();\r
+ state.setPrefix(associationWrapper.getPrefix());\r
+ this.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);\r
+ handleSingleUnit(state, associatedUnits.item(m));\r
+\r
+ DerivedUnit associatedUnit = state.getDerivedUnitBase();\r
+ FieldUnit associatedFieldUnit = null;\r
+ java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());\r
+ //ignore field unit if associated unit has more than one\r
+ if(associatedFieldUnits.size()>1){\r
+ state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));\r
+ }\r
+ else if(associatedFieldUnits.size()==1){\r
+ associatedFieldUnit = associatedFieldUnits.iterator().next();\r
+ }\r
+\r
+ //attach current unit and associated unit depending on association type\r
+\r
+ //parent-child relation:\r
+ //copy derivation event and connect parent and sub derivative\r
+ if(associationWrapper.getAssociationType().contains("individual")){\r
+ if(currentDerivedFrom==null){\r
+ state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",AbcdImportUtility.getUnitID(currentUnit, config)));\r
+ DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());\r
+ }\r
+ else{\r
+ DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());\r
+ updatedDerivationEvent.setActor(currentDerivedFrom.getActor());\r
+ updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());\r
+ updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());\r
+ updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());\r
+ }\r
+ state.getReport().addDerivate(associatedUnit, currentUnit, config);\r
+ }\r
+ //siblings relation\r
+ //connect current unit to field unit of associated unit\r
+ else if(associationWrapper.getAssociationType().contains("population")){\r
+ //no associated field unit -> using current one\r
+ if(associatedFieldUnit==null){\r
+ if(currentFieldUnit!=null){\r
+ DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());\r
+ }\r
+ }\r
+ else{\r
+ if(currentDerivedFrom==null){\r
+ state.getReport().addInfoMessage("No derivation event found for unit "+AbcdImportUtility.getUnitID(currentUnit, config)+". Defaulting to ACCESIONING event.");\r
+ DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());\r
+ }\r
+ if(currentDerivedFrom!=null && associatedFieldUnit!=currentFieldUnit){\r
+ DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());\r
+ updatedDerivationEvent.setActor(currentDerivedFrom.getActor());\r
+ updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());\r
+ updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());\r
+ updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());\r
+ }\r
+ }\r
+ }\r
+\r
+ //delete current field unit if replaced\r
+ if(currentFieldUnit!=null && currentDerivedFrom!=null\r
+ && currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit\r
+ && currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units\r
+ && currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted\r
+ ){\r
+ currentFieldUnit.removeDerivationEvent(currentDerivedFrom);\r
+ state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);\r
+ }\r
+\r
+ save(associatedUnit, state);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }*/\r
+ //TODO: pop state\r
+ state.reset();\r
+ state.setDerivedUnitBase(currentUnit);\r
+ state.setPrefix(currentPrefix);\r
+ }\r
+@Override\r
+protected void handleSingleUnit(GbifImportState state, Object itemObject){\r
+ GbifResponse item;\r
+ if (itemObject instanceof GbifResponse){\r
+ item = (GbifResponse) itemObject;\r
+ } else{\r
+ logger.error("For Gbif Import the item has to be of type GbifResponse.");\r
+ return;\r
+ }\r
+ if (DEBUG) {\r
+ logger.info("handleSingleUnit "+state.getRef());\r
+ }\r
+ try {\r
+ ICdmApplicationConfiguration cdmAppController = state.getConfig().getCdmAppController();\r
+ if(cdmAppController==null){\r
+ cdmAppController = this;\r
+ }\r
+ //check if unit already exists\r
+ DerivedUnitFacade derivedUnitFacade = null;\r
+ if(state.getConfig().isIgnoreImportOfExistingSpecimens()){\r
+ String[] tripleId = item.getTripleID();\r
+ SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(tripleId[0], state);\r
+ if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){\r
+ DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);\r
+ state.setDerivedUnitBase(derivedUnit);\r
+ derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());\r
+ importAssociatedUnits(state, item, derivedUnitFacade);\r
+ state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, state.getConfig()), derivedUnit);\r
+ return;\r
+ }\r
+ }\r
+ // TODO: implement overwrite/merge specimen\r
+// else if(state.getConfig().isOverwriteExistingSpecimens()){\r
+// Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);\r
+// if(!existingSpecimens.getRecords().isEmpty()){\r
+// derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit);\r
+// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();\r
+// fieldUnit = derivedUnitFacade.getFieldUnit(true);\r
+// }\r
+// }\r
+ //import new specimen\r
+\r
+ // import DNA unit\r
+ //TODO!!!!\r
+// if(state.getDataHolder().catalogNumber!=null && state.getDataHolder()..equalsIgnoreCase("dna")){\r
+// AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), state.getReport(), state.getCdmRepository());\r
+// DnaSample dnaSample = dnaParser.parse(item, state);\r
+// save(dnaSample, state);\r
+// //set dna as derived unit to avoid creating an extra specimen for this dna sample (instead just the field unit will be created)\r
+// state.setDerivedUnitBase(dnaSample);\r
+// derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());\r
+// }\r
+// else{\r
+// // create facade\r
+// derivedUnitFacade = getFacade(state);\r
+// state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());\r
+// }\r
+\r
+ /**\r
+ * GATHERING EVENT\r
+ */\r
+ // gathering event\r
+ /* UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),\r
+ state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude,\r
+ state.getDataHolder().latitude, state.getDataHolder().gatheringElevationText,\r
+ state.getDataHolder().gatheringElevationMin, state.getDataHolder().gatheringElevationMax,\r
+ state.getDataHolder().gatheringElevationUnit, state.getDataHolder().gatheringDateText,\r
+ state.getDataHolder().gatheringNotes, state.getTransformer().getReferenceSystemByKey(\r
+ state.getDataHolder().gatheringSpatialDatum), state.getDataHolder().gatheringAgentList,\r
+ state.getDataHolder().gatheringTeamList, state.getConfig());\r
+\r
+ // country\r
+ UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();\r
+ // unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());\r
+ unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, state.getConfig(), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());\r
+\r
+ DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();\r
+\r
+ // other areas\r
+ unitsGatheringArea = new UnitsGatheringArea();\r
+ // unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());\r
+ unitsGatheringArea.setAreas(state.getDataHolder().namedAreaList,state.getConfig(), cdmAppController.getTermService(), cdmAppController.getVocabularyService());\r
+ ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();\r
+ for (DefinedTermBase namedArea : nas) {\r
+ unitsGatheringEvent.addArea(namedArea);\r
+ }\r
+\r
+ // copy gathering event to facade\r
+ GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();\r
+ derivedUnitFacade.setLocality(gatheringEvent.getLocality());\r
+ derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());\r
+ derivedUnitFacade.setCollector(gatheringEvent.getCollector());\r
+ derivedUnitFacade.setCountry((NamedArea)areaCountry);\r
+ derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());\r
+ derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());\r
+ derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());\r
+ derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());\r
+\r
+ for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){\r
+ derivedUnitFacade.addCollectingArea((NamedArea) area);\r
+ }\r
+ // derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());\r
+ // TODO exsiccatum\r
+\r
+ // add fieldNumber\r
+ derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().fieldNumber));\r
+\r
+ // add unitNotes\r
+ derivedUnitFacade.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().unitNotes)));\r
+\r
+ // //add Multimedia URLs\r
+ if (state.getDataHolder().multimediaObjects.size() != -1) {\r
+ for (String multimediaObject : state.getDataHolder().multimediaObjects) {\r
+ Media media;\r
+ try {\r
+ media = getImageMedia(multimediaObject, READ_MEDIA_DATA);\r
+ derivedUnitFacade.addDerivedUnitMedia(media);\r
+ if(state.getConfig().isAddMediaAsMediaSpecimen()){\r
+ //add media also as specimen scan\r
+ MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.Media);\r
+ mediaSpecimen.setMediaSpecimen(media);\r
+ DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);\r
+ if(specimenScanTerm instanceof DefinedTerm){\r
+ mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);\r
+ }\r
+ DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.PREPARATION());\r
+ derivationEvent.addDerivative(mediaSpecimen);\r
+ derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);\r
+ }\r
+\r
+ } catch (MalformedURLException e) {\r
+ // TODO Auto-generated catch block\r
+ e.printStackTrace();\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ // /*\r
+ // * merge AND STORE DATA\r
+ // */\r
+ // getTermService().saveOrUpdate(areaCountry);// TODO save area sooner\r
+ //\r
+ // for (NamedArea area : otherAreas) {\r
+ // getTermService().saveOrUpdate(area);// merge it sooner (foreach area)\r
+ // }\r
+/*\r
+ save(unitsGatheringEvent.getLocality(), state);\r
+\r
+ // handle collection data\r
+ setCollectionData(state, derivedUnitFacade);\r
+\r
+ //Reference stuff\r
+ SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();\r
+ Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();\r
+\r
+ state.getDataHolder().docSources = new ArrayList<String>();\r
+ for (String[] fullReference : state.getDataHolder().referenceList) {\r
+ String strReference=fullReference[0];\r
+ String citationDetail = fullReference[1];\r
+ String citationURL = fullReference[2];\r
+\r
+ if (!citationURL.isEmpty()) {\r
+ citationDetail+=", "+citationURL;\r
+ }\r
+\r
+ Reference reference;\r
+ if(strReference.equals(state.getRef().getTitleCache())){\r
+ reference = state.getRef();\r
+ }\r
+ else{\r
+ reference = ReferenceFactory.newGeneric();\r
+ reference.setTitle(strReference);\r
+ }\r
+\r
+ IdentifiableSource sour = getIdentifiableSource(reference,citationDetail);\r
+\r
+ try{\r
+ if (sour.getCitation() != null){\r
+ if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {\r
+ state.getDataHolder().docSources.add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());\r
+ } else {\r
+ state.getDataHolder().docSources.add(sour.getCitation().getTitleCache());\r
+ }\r
+ }\r
+ }catch(Exception e){\r
+ logger.warn("oups");\r
+ }\r
+ reference.addSource(sour);\r
+ save(reference, state);\r
+ }\r
+ List<IdentifiableSource> issTmp = new ArrayList<IdentifiableSource>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);\r
+ List<DescriptionElementSource> issTmp2 = new ArrayList<DescriptionElementSource>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);\r
+\r
+ Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();\r
+ if(issTmp2!=null) {\r
+ osbSet.addAll(issTmp2);\r
+ }\r
+ if(issTmp!=null) {\r
+ osbSet.addAll(issTmp);\r
+ }\r
+\r
+ addToSourceMap(sourceMap, osbSet);\r
+\r
+ if( state.getConfig().isInteractWithUser()){\r
+ List<OriginalSourceBase<?>>sources=null;\r
+ if(!state.isDerivedUnitSourcesSet()){\r
+ sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().docSources);\r
+ state.setDerivedUnitSources(sources);\r
+ state.setDerivedUnitSourcesSet(true);\r
+ }\r
+ else{\r
+ sources=state.getDerivedUnitSources();\r
+ }\r
+// System.out.println("nb sources: "+sources.size());\r
+// System.out.println("derivedunitfacade : "+derivedUnitFacade.getTitleCache());\r
+ for (OriginalSourceBase<?> sour:sources){\r
+ if(sour.isInstanceOf(IdentifiableSource.class)){\r
+ if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {\r
+// System.out.println("add source to derivedunitfacade1 "+derivedUnitFacade.getTitleCache());\r
+ derivedUnitFacade.addSource((IdentifiableSource)sour.clone());\r
+ }\r
+ }else{\r
+ if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {\r
+// System.out.println("add source to derivedunitfacade2 "+derivedUnitFacade.getTitleCache());\r
+ derivedUnitFacade.addSource(OriginalSourceType.Import,sour.getCitation(),sour.getCitationMicroReference(), ioName);\r
+ }\r
+ }\r
+ }\r
+ }else{\r
+ for (OriginalSourceBase<?> sr : sourceMap.values()){\r
+ if(sr.isInstanceOf(IdentifiableSource.class)){\r
+ if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {\r
+// System.out.println("add source to derivedunitfacade3 "+derivedUnitFacade.getTitleCache());\r
+ derivedUnitFacade.addSource((IdentifiableSource)sr.clone());\r
+ }\r
+ }else{\r
+ if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {\r
+// System.out.println("add source to derivedunitfacade4 "+derivedUnitFacade.getTitleCache());\r
+ derivedUnitFacade.addSource(OriginalSourceType.Import,sr.getCitation(),sr.getCitationMicroReference(), ioName);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ save(state.getDerivedUnitBase(), state);\r
+\r
+ if(DEBUG) {\r
+ logger.info("saved ABCD specimen ...");\r
+ }\r
+\r
+ // handle identifications\r
+ handleIdentifications(state, derivedUnitFacade);\r
+\r
+ //associatedUnits\r
+ importAssociatedUnits(state, item, derivedUnitFacade);\r
+\r
+*/\r
+\r
+ } catch (Exception e) {\r
+ String message = "Error when reading record!";\r
+ logger.warn(message);\r
+ state.getReport().addException(message, e);\r
+ e.printStackTrace();\r
+ state.setUnsuccessfull();\r
+ }\r
+\r
+ return;\r
+}\r
+\r
+\r
+\r
+\r
+\r
+\r
+\r
+\r
+\r
+\r
+ /*\r
+ * "key": 1257570425,\r
+"datasetKey": "7bd65a7a-f762-11e1-a439-00145eb45e9a",\r
+"publishingOrgKey": "90fd6680-349f-11d8-aa2d-b8a03c50a862",\r
+"publishingCountry": "US",\r
+"protocol": "DWC_ARCHIVE",\r
+"lastCrawled": "2016-06-06T11:11:35.800+0000",\r
+"lastParsed": "2016-03-21T14:11:42.224+0000",\r
+"extensions": { },\r
+"basisOfRecord": "PRESERVED_SPECIMEN",\r
+"individualCount": 1,\r
+"taxonKey": 5338762,\r
+"kingdomKey": 6,\r
+"phylumKey": 7707728,\r
+"classKey": 220,\r
+"orderKey": 412,\r
+"familyKey": 8798,\r
+"genusKey": 2907867,\r
+"speciesKey": 5338762,\r
+"scientificName": "Mitchella repens L.",\r
+"kingdom": "Plantae",\r
+"phylum": "Tracheophyta",\r
+"order": "Gentianales",\r
+"family": "Rubiaceae",\r
+"genus": "Mitchella",\r
+"species": "Mitchella repens",\r
+"genericName": "Mitchella",\r
+"specificEpithet": "repens",\r
+"taxonRank": "SPECIES",\r
+"dateIdentified": "2005-12-31T23:00:00.000+0000",\r
+"decimalLongitude": -98.70693,\r
+"decimalLatitude": 20.77805,\r
+"elevation": 1524.0,\r
+"continent": "NORTH_AMERICA",\r
+"stateProvince": "Hidalgo",\r
+"year": 2006,\r
+"month": 6,\r
+"day": 11,\r
+"eventDate": "2006-06-10T22:00:00.000+0000",\r
+"issues": [\r
+\r
+ "COORDINATE_ROUNDED",\r
+ "GEODETIC_DATUM_ASSUMED_WGS84"\r
+\r
+],\r
+"lastInterpreted": "2016-04-17T13:34:52.325+0000",\r
+"identifiers": [ ],\r
+"facts": [ ],\r
+"relations": [ ],\r
+"geodeticDatum": "WGS84",\r
+"class": "Magnoliopsida",\r
+"countryCode": "MX",\r
+"country": "Mexico",\r
+"nomenclaturalStatus": "No opinion",\r
+"rightsHolder": "Missouri Botanical Garden",\r
+"identifier": "urn:catalog:MO:Tropicos:100217973",\r
+"recordNumber": "Oberle 274",\r
+"nomenclaturalCode": "ICNafp",\r
+"county": "Metztitlán",\r
+"locality": "Along trail downslope of road between Molango and Zacualtipan.",\r
+"datasetName": "Tropicos",\r
+"gbifID": "1257570425",\r
+"collectionCode": "MO",\r
+"occurrenceID": "urn:catalog:MO:Tropicos:100217973",\r
+"type": "PhysicalObject",\r
+"taxonID": "27902971",\r
+"license": "http://creativecommons.org/licenses/by/4.0/legalcode",\r
+"catalogNumber": "100217973",\r
+"recordedBy": "Brad Oberle",\r
+"institutionCode": "MO",\r
+"ownerInstitutionCode": "MOBOT",\r
+"bibliographicCitation": "http://www.tropicos.org/Specimen/100217973",\r
+"identifiedBy": "B. Oberle",\r
+"collectionID": "http://biocol.org/urn:lsid:biocol.org:col:15859\r
+ *\r
+ */\r
+\r
+\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2016 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.gbif.in;
-
-import eu.etaxonomy.cdm.io.common.ImportStateBase;
-import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
-import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;
-import eu.etaxonomy.cdm.model.reference.Reference;
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public class GbifImportConfigurator<GbifImportState> extends SpecimenImportConfiguratorBase{
-
- /**
- * @param transformer
- */
- public GbifImportConfigurator(IInputTransformer transformer) {
- super(transformer);
- // TODO Auto-generated constructor stub
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#makeIoClassList()
- */
- @Override
- protected void makeIoClassList() {
- System.out.println("makeIOClassList");
- ioClassList = new Class[]{
- GbifImport.class,
- };
-
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference()
- */
- @Override
- public Reference getSourceReference() {
- // TODO Auto-generated method stub
- return null;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
- */
- @Override
- public <STATE extends ImportStateBase> STATE getNewState() {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.gbif.in;\r
+\r
+import eu.etaxonomy.cdm.io.common.ImportStateBase;\r
+import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public class GbifImportConfigurator<GbifImportState> extends SpecimenImportConfiguratorBase{\r
+\r
+ /**\r
+ * @param transformer\r
+ */\r
+ public GbifImportConfigurator(IInputTransformer transformer) {\r
+ super(transformer);\r
+ // TODO Auto-generated constructor stub\r
+ }\r
+\r
+ /**\r
+ *\r
+ */\r
+ private static final long serialVersionUID = 1L;\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#makeIoClassList()\r
+ */\r
+ @Override\r
+ protected void makeIoClassList() {\r
+ System.out.println("makeIOClassList");\r
+ ioClassList = new Class[]{\r
+ GbifImport.class,\r
+ };\r
+\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference()\r
+ */\r
+ @Override\r
+ public Reference getSourceReference() {\r
+ // TODO Auto-generated method stub\r
+ return null;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()\r
+ */\r
+ @Override\r
+ public <STATE extends ImportStateBase> STATE getNewState() {\r
+ // TODO Auto-generated method stub\r
+ return null;\r
+ }\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2016 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.gbif.in;
-
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public class GbifImportReport extends SpecimenImportReport{
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.gbif.in;\r
+\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public class GbifImportReport extends SpecimenImportReport{\r
+\r
+}\r
-// $Id$
-/**
-* Copyright (C) 2016 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.gbif.in;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.springframework.transaction.TransactionStatus;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdTransformer;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
-import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-
-/**
- * @author k.luther
- * @date 15.07.2016
- *
- */
-public class GbifImportState extends SpecimenImportStateBase<GbifImportConfigurator, GbifImportState> {
-
- private TransactionStatus tx;
-
-
-
-
- private ICdmApplicationConfiguration cdmRepository;
-
- private String prefix;
-
- private GbifImportReport report;
-
- private Classification classification = null;
- private Classification defaultClassification = null;
- private Reference ref = null;
-
- private GbifDataHolder dataHolder;
- private DerivedUnit derivedUnitBase;
-
- private List<OriginalSourceBase<?>> associationRefs = new ArrayList<OriginalSourceBase<?>>();
- private boolean associationSourcesSet=false;
- private List<OriginalSourceBase<?>> descriptionRefs = new ArrayList<OriginalSourceBase<?>>();
- private boolean descriptionSourcesSet=false;
- private List<OriginalSourceBase<?>> derivedUnitSources = new ArrayList<OriginalSourceBase<?>>();
- private boolean derivedUnitSourcesSet=false;
- private boolean descriptionGroupSet = false;
- private TaxonDescription descriptionGroup = null;
-
-
- /**
- * @param config
- */
- protected GbifImportState(GbifImportConfigurator config) {
- super(config);
- report = new GbifImportReport();
- setTransformer(new AbcdTransformer());
- }
-
- /* ------Getter/Setter -----*/
-
- @Override
- public TransactionStatus getTx() {
- return tx;
- }
-
-
- @Override
- public void setTx(TransactionStatus tx) {
- this.tx = tx;
- }
-
-
- @Override
- public ICdmApplicationConfiguration getCdmRepository() {
- return cdmRepository;
- }
-
-
- @Override
- public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {
- this.cdmRepository = cdmRepository;
- }
-
-
- public String getPrefix() {
- return prefix;
- }
-
-
- public void setPrefix(String prefix) {
- this.prefix = prefix;
- }
-
-
- @Override
- public SpecimenImportReport getReport() {
- return report;
- }
-
-
- public void setReport(GbifImportReport report) {
- this.report = report;
- }
-
-
- @Override
- public Classification getClassification() {
- return classification;
- }
-
-
- @Override
- public void setClassification(Classification classification) {
- this.classification = classification;
- }
-
-
- @Override
- public Classification getDefaultClassification() {
- return defaultClassification;
- }
-
-
- @Override
- public void setDefaultClassification(Classification defaultClassification) {
- this.defaultClassification = defaultClassification;
- }
-
-
- @Override
- public Reference getRef() {
- return ref;
- }
-
-
- @Override
- public void setRef(Reference ref) {
- this.ref = ref;
- }
-
-
- @Override
- public GbifDataHolder getDataHolder() {
- return dataHolder;
- }
-
-
- public void setDataHolder(GbifDataHolder dataHolder) {
- this.dataHolder = dataHolder;
- }
-
-
- @Override
- public DerivedUnit getDerivedUnitBase() {
- return derivedUnitBase;
- }
-
-
- @Override
- public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {
- this.derivedUnitBase = derivedUnitBase;
- }
-
-
- public List<OriginalSourceBase<?>> getAssociationRefs() {
- return associationRefs;
- }
-
-
- public void setAssociationRefs(List<OriginalSourceBase<?>> associationRefs) {
- this.associationRefs = associationRefs;
- }
-
-
- public boolean isAssociationSourcesSet() {
- return associationSourcesSet;
- }
-
-
- public void setAssociationSourcesSet(boolean associationSourcesSet) {
- this.associationSourcesSet = associationSourcesSet;
- }
-
-
- public List<OriginalSourceBase<?>> getDescriptionRefs() {
- return descriptionRefs;
- }
-
-
- public void setDescriptionRefs(List<OriginalSourceBase<?>> descriptionRefs) {
- this.descriptionRefs = descriptionRefs;
- }
-
-
- public boolean isDescriptionSourcesSet() {
- return descriptionSourcesSet;
- }
-
-
- public void setDescriptionSourcesSet(boolean descriptionSourcesSet) {
- this.descriptionSourcesSet = descriptionSourcesSet;
- }
-
-
- public List<OriginalSourceBase<?>> getDerivedUnitSources() {
- return derivedUnitSources;
- }
-
-
- public void setDerivedUnitSources(List<OriginalSourceBase<?>> derivedUnitSources) {
- this.derivedUnitSources = derivedUnitSources;
- }
-
-
- public boolean isDerivedUnitSourcesSet() {
- return derivedUnitSourcesSet;
- }
-
-
- public void setDerivedUnitSourcesSet(boolean derivedUnitSourcesSet) {
- this.derivedUnitSourcesSet = derivedUnitSourcesSet;
- }
-
-
- public boolean isDescriptionGroupSet() {
- return descriptionGroupSet;
- }
-
-
- public void setDescriptionGroupSet(boolean descriptionGroupSet) {
- this.descriptionGroupSet = descriptionGroupSet;
- }
-
-
- @Override
- public TaxonDescription getDescriptionGroup() {
- return descriptionGroup;
- }
-
-
- @Override
- public void setDescriptionGroup(TaxonDescription descriptionGroup) {
- this.descriptionGroup = descriptionGroup;
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase#reset()
- */
- @Override
- public void reset() {
- // TODO Auto-generated method stub
-
- }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2016 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.gbif.in;\r
+\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import org.springframework.transaction.TransactionStatus;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdTransformer;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;\r
+import eu.etaxonomy.cdm.model.common.OriginalSourceBase;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
+import eu.etaxonomy.cdm.model.taxon.Classification;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 15.07.2016\r
+ *\r
+ */\r
+public class GbifImportState extends SpecimenImportStateBase<GbifImportConfigurator, GbifImportState> {\r
+\r
+ private TransactionStatus tx;\r
+\r
+\r
+\r
+\r
+ private ICdmApplicationConfiguration cdmRepository;\r
+\r
+ private String prefix;\r
+\r
+ private GbifImportReport report;\r
+\r
+ private Classification classification = null;\r
+ private Classification defaultClassification = null;\r
+ private Reference ref = null;\r
+\r
+ private GbifDataHolder dataHolder;\r
+ private DerivedUnit derivedUnitBase;\r
+\r
+ private List<OriginalSourceBase<?>> associationRefs = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean associationSourcesSet=false;\r
+ private List<OriginalSourceBase<?>> descriptionRefs = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean descriptionSourcesSet=false;\r
+ private List<OriginalSourceBase<?>> derivedUnitSources = new ArrayList<OriginalSourceBase<?>>();\r
+ private boolean derivedUnitSourcesSet=false;\r
+ private boolean descriptionGroupSet = false;\r
+ private TaxonDescription descriptionGroup = null;\r
+\r
+\r
+ /**\r
+ * @param config\r
+ */\r
+ protected GbifImportState(GbifImportConfigurator config) {\r
+ super(config);\r
+ report = new GbifImportReport();\r
+ setTransformer(new AbcdTransformer());\r
+ }\r
+\r
+ /* ------Getter/Setter -----*/\r
+\r
+ @Override\r
+ public TransactionStatus getTx() {\r
+ return tx;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setTx(TransactionStatus tx) {\r
+ this.tx = tx;\r
+ }\r
+\r
+\r
+ @Override\r
+ public ICdmApplicationConfiguration getCdmRepository() {\r
+ return cdmRepository;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setCdmRepository(ICdmApplicationConfiguration cdmRepository) {\r
+ this.cdmRepository = cdmRepository;\r
+ }\r
+\r
+\r
+ public String getPrefix() {\r
+ return prefix;\r
+ }\r
+\r
+\r
+ public void setPrefix(String prefix) {\r
+ this.prefix = prefix;\r
+ }\r
+\r
+\r
+ @Override\r
+ public SpecimenImportReport getReport() {\r
+ return report;\r
+ }\r
+\r
+\r
+ public void setReport(GbifImportReport report) {\r
+ this.report = report;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Classification getClassification() {\r
+ return classification;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setClassification(Classification classification) {\r
+ this.classification = classification;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Classification getDefaultClassification() {\r
+ return defaultClassification;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setDefaultClassification(Classification defaultClassification) {\r
+ this.defaultClassification = defaultClassification;\r
+ }\r
+\r
+\r
+ @Override\r
+ public Reference getRef() {\r
+ return ref;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setRef(Reference ref) {\r
+ this.ref = ref;\r
+ }\r
+\r
+\r
+ @Override\r
+ public GbifDataHolder getDataHolder() {\r
+ return dataHolder;\r
+ }\r
+\r
+\r
+ public void setDataHolder(GbifDataHolder dataHolder) {\r
+ this.dataHolder = dataHolder;\r
+ }\r
+\r
+\r
+ @Override\r
+ public DerivedUnit getDerivedUnitBase() {\r
+ return derivedUnitBase;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setDerivedUnitBase(DerivedUnit derivedUnitBase) {\r
+ this.derivedUnitBase = derivedUnitBase;\r
+ }\r
+\r
+\r
+ public List<OriginalSourceBase<?>> getAssociationRefs() {\r
+ return associationRefs;\r
+ }\r
+\r
+\r
+ public void setAssociationRefs(List<OriginalSourceBase<?>> associationRefs) {\r
+ this.associationRefs = associationRefs;\r
+ }\r
+\r
+\r
+ public boolean isAssociationSourcesSet() {\r
+ return associationSourcesSet;\r
+ }\r
+\r
+\r
+ public void setAssociationSourcesSet(boolean associationSourcesSet) {\r
+ this.associationSourcesSet = associationSourcesSet;\r
+ }\r
+\r
+\r
+ public List<OriginalSourceBase<?>> getDescriptionRefs() {\r
+ return descriptionRefs;\r
+ }\r
+\r
+\r
+ public void setDescriptionRefs(List<OriginalSourceBase<?>> descriptionRefs) {\r
+ this.descriptionRefs = descriptionRefs;\r
+ }\r
+\r
+\r
+ public boolean isDescriptionSourcesSet() {\r
+ return descriptionSourcesSet;\r
+ }\r
+\r
+\r
+ public void setDescriptionSourcesSet(boolean descriptionSourcesSet) {\r
+ this.descriptionSourcesSet = descriptionSourcesSet;\r
+ }\r
+\r
+\r
+ public List<OriginalSourceBase<?>> getDerivedUnitSources() {\r
+ return derivedUnitSources;\r
+ }\r
+\r
+\r
+ public void setDerivedUnitSources(List<OriginalSourceBase<?>> derivedUnitSources) {\r
+ this.derivedUnitSources = derivedUnitSources;\r
+ }\r
+\r
+\r
+ public boolean isDerivedUnitSourcesSet() {\r
+ return derivedUnitSourcesSet;\r
+ }\r
+\r
+\r
+ public void setDerivedUnitSourcesSet(boolean derivedUnitSourcesSet) {\r
+ this.derivedUnitSourcesSet = derivedUnitSourcesSet;\r
+ }\r
+\r
+\r
+ public boolean isDescriptionGroupSet() {\r
+ return descriptionGroupSet;\r
+ }\r
+\r
+\r
+ public void setDescriptionGroupSet(boolean descriptionGroupSet) {\r
+ this.descriptionGroupSet = descriptionGroupSet;\r
+ }\r
+\r
+\r
+ @Override\r
+ public TaxonDescription getDescriptionGroup() {\r
+ return descriptionGroup;\r
+ }\r
+\r
+\r
+ @Override\r
+ public void setDescriptionGroup(TaxonDescription descriptionGroup) {\r
+ this.descriptionGroup = descriptionGroup;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase#reset()\r
+ */\r
+ @Override\r
+ public void reset() {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+}\r
BGBM BDI Projects / cdmlib.git / commitdiff