}
}
if(query.accessionNumber!=null && !query.accessionNumber.trim().isEmpty()){
- addLikeFilter(elAnd, query.accessionNumber, ACCESSION_NUMBER_PATH_ABCD_2_0);
+ Element elOr = new Element(OR);
+ addLikeFilter(elOr, query.accessionNumber, ACCESSION_NUMBER_PATH_ABCD_2_0);
+ addLikeFilter(elOr, query.accessionNumber, CAT_PATH_ABCD_2_0);
+ addLikeFilter(elOr, query.accessionNumber, UNIT_ID_PATH_ABCD_2_0);
+ elAnd.addContent(elOr);
}
if(query.collector!=null && !query.collector.trim().isEmpty()){
addLikeFilter(elAnd, query.collector, COLLECTOR_PATH_ABCD_2_0);
import net.sf.json.JSONObject;
import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpException;
import org.apache.log4j.Logger;
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
import eu.etaxonomy.cdm.common.UriUtils;
+import eu.etaxonomy.cdm.common.media.ImageInfo;
import eu.etaxonomy.cdm.model.agent.Institution;
import eu.etaxonomy.cdm.model.agent.Person;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.location.Country;
import eu.etaxonomy.cdm.model.location.Point;
import eu.etaxonomy.cdm.model.location.ReferenceSystem;
+import eu.etaxonomy.cdm.model.media.ImageFile;
+import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.media.MediaRepresentation;
import eu.etaxonomy.cdm.model.name.BacterialName;
import eu.etaxonomy.cdm.model.name.BotanicalName;
import eu.etaxonomy.cdm.model.name.CultivarPlantName;
private static final String BACTERIA = "Bacteria";
+ private static final String MULTIMEDIA = "media";
+
+
derivedUnitFacade.addSource(source);
}
+ if (record.has(MULTIMEDIA)){
+ //http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
+ JSONArray multimediaArray = record.getJSONArray(MULTIMEDIA);
+ JSONObject mediaRecord;
+ Media media;
+ URI uri = null;
+ ImageInfo imageInf = null;
+ MediaRepresentation representation = null;
+ SpecimenOrObservationType type = null;
+ for(Object object:multimediaArray){
+ //parse every record
+ media = Media.NewInstance();
+ uri = null;
+ imageInf = null;
+
+ if(object instanceof JSONObject){
+ mediaRecord = (JSONObject) object;
+
+ if (mediaRecord.has("identifier")){
+ try {
+ uri = new URI(mediaRecord.getString("identifier"));
+ imageInf = ImageInfo.NewInstance(uri, 0);
+
+ } catch (URISyntaxException |IOException | HttpException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ // media.addIdentifier(mediaRecord.getString("identifier"), null);
+ }
+ if (mediaRecord.has("references")){
+
+
+ }
+ if (mediaRecord.has("format")){
+
+ }
+ if (mediaRecord.has("type")){
+ if (mediaRecord.get("type").equals("StillImage")){
+ type = SpecimenOrObservationType.StillImage;
+ }
+ }
+
+ }
+ ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInf);
+ representation = MediaRepresentation.NewInstance();
+
+ representation.addRepresentationPart(imageFile);
+ media.addRepresentation(representation);
+
+ derivedUnitFacade.addDerivedUnitMedia(media);
+ }
+ //identifier=http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
+ //references=http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=136628
+ //format=image/jpeg
+ //type=StillImage
+
+ }
+
// create dataset URL
URI uri = null;
try {
// only look for preserved specimens
if (checkForValidQuery(query)) {
- ServiceWrapperBase.addNameValuePairTo(queryParamsGET, "basisOfRecord", "PRESERVED_SPECIMEN");
+ //ServiceWrapperBase.addNameValuePairTo(queryParamsGET, "basisOfRecord", "PRESERVED_SPECIMEN");
ServiceWrapperBase.addNameValuePairTo(queryParamsGET, "limit", "100");
if (query.tripleIds != null){
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+import eu.etaxonomy.cdm.model.reference.ReferenceType;
import eu.etaxonomy.cdm.model.taxon.Classification;
import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
ref.setAuthorship(taxonNameBase.getCombinationAuthorship());
}
- ref.setProtectedAbbrevTitleCache(false);
- ref.setProtectedTitleCache(false);
+ if (ref.getAbbrevTitle() == null && !ref.isOfType(ReferenceType.Article)) {
+ ref.setAbbrevTitle(reference);
+ ref.setProtectedAbbrevTitleCache(false);
+ }
+
+ ref.setProtectedTitleCache(false);
taxonNameBase.setNomenclaturalReference(ref);
}
-// $Id$
-/**
- * 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.service;
-
-import java.io.ByteArrayInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.Serializable;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.List;
-import java.util.UUID;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-import eu.etaxonomy.cdm.api.service.IProgressMonitorService;
-import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
-import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;
-import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;
-import eu.etaxonomy.cdm.io.common.ExportResult;
-import eu.etaxonomy.cdm.io.common.IExportConfigurator;
-import eu.etaxonomy.cdm.io.common.IExportConfigurator.TARGET;
-import eu.etaxonomy.cdm.io.common.IImportConfigurator;
-import eu.etaxonomy.cdm.io.common.IImportConfigurator.SOURCE_TYPE;
-import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
-import eu.etaxonomy.cdm.io.common.ImportResult;
-import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
-
-/**
- * @author cmathew
- * @date 31 Jul 2015
- *
- */
-@Service
-@Transactional(readOnly = false)
-public class IOServiceImpl implements IIOService {
-
- @Autowired
- CdmApplicationAwareDefaultExport cdmExport;
-
- @Autowired
- @Qualifier("defaultImport")
- CdmApplicationAwareDefaultImport cdmImport;
-
- @Autowired
- IProgressMonitorService progressMonitorService;
-
-
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.io.service.IExportService#export(eu.etaxonomy.cdm.io.common.IExportConfigurator)
- */
- @Override
- public ExportResult export(IExportConfigurator config) {
- config.setTarget(TARGET.EXPORT_DATA);
- return cdmExport.execute(config);
- }
-
-
- @Override
- public UUID monitImportData(final IImportConfigurator configurator, final byte[] importData, final SOURCE_TYPE type) {
- RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {
- @Override
- public Serializable doRun(IRemotingProgressMonitor monitor) {
- configurator.setProgressMonitor(monitor);
- ImportResult result = importData(configurator, importData, type);
- for(byte[] report : result.getReports()) {
- monitor.addReport(new String(report));
- }
- return result;
- }
- };
- UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);
- monitorThread.setPriority(3);
- monitorThread.start();
- return uuid;
- }
-
- @Override
- public ImportResult importData(IImportConfigurator configurator, byte[] importData, SOURCE_TYPE type) {
- ImportResult result;
- switch(type) {
- case URI:
- return importDataFromUri(configurator, importData);
- case INPUTSTREAM:
- return importDataFromInputStream(configurator,importData);
- default :
- throw new RuntimeException("Source type is not recongnised");
- }
- }
-
- @Override
- public ImportResult importDataFromUri(IImportConfigurator configurator, byte[] importData) {
- ImportResult result;
-
- ImportConfiguratorBase config = (ImportConfiguratorBase)configurator;
- String suffix = ".import";
- String prefix = "cdm-";
- FileOutputStream stream = null;
-
- try {
- Path tempFilePath = Files.createTempFile(prefix, suffix);
- stream = new FileOutputStream(tempFilePath.toFile());
- stream.write(importData);
- config.setSource(tempFilePath.toUri());
- result = cdmImport.execute(config);
- Files.delete(tempFilePath);
- } catch (Exception e) {
- throw new RuntimeException(e);
- } finally {
- if(stream != null) {
- try {
- stream.close();
- } catch (IOException e) {
- throw new RuntimeException(e);
- }
- }
- }
- return result;
- }
-
- @Override
- public ImportResult importDataFromInputStream(IImportConfigurator configurator, byte[] importData) {
- ImportConfiguratorBase config = (ImportConfiguratorBase)configurator;
- ImportResult result;
- try {
- config.setSource(new ByteArrayInputStream(importData));
- result = cdmImport.execute(config);
- } catch (Exception e) {
- throw new RuntimeException(e);
- }
- return result;
- }
-
-
- @Override
- public ImportResult importDataFromStream(SpecimenImportConfiguratorBase configurator) {
- ImportResult result = new ImportResult();
-
- OccurenceQuery query;
- result = cdmImport.execute(configurator);
- return result;
- }
-
- @Override
- public ImportResult importDataFromStream(List<Abcd206ImportConfigurator> configurators) {
- ImportResult result = new ImportResult();
-
- OccurenceQuery query;
- for (SpecimenImportConfiguratorBase configurator:configurators){
- result = cdmImport.execute(configurator);
- }
- return result;
- }
-
-
-
-
-
-}
+// $Id$\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.service;\r
+\r
+import java.io.ByteArrayInputStream;\r
+import java.io.FileOutputStream;\r
+import java.io.IOException;\r
+import java.io.Serializable;\r
+import java.nio.file.Files;\r
+import java.nio.file.Path;\r
+import java.util.List;\r
+import java.util.UUID;\r
+\r
+import org.springframework.beans.factory.annotation.Autowired;\r
+import org.springframework.beans.factory.annotation.Qualifier;\r
+import org.springframework.stereotype.Service;\r
+import org.springframework.transaction.annotation.Transactional;\r
+\r
+import eu.etaxonomy.cdm.api.service.IProgressMonitorService;\r
+import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;\r
+import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;\r
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;\r
+import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultExport;\r
+import eu.etaxonomy.cdm.io.common.CdmApplicationAwareDefaultImport;\r
+import eu.etaxonomy.cdm.io.common.ExportResult;\r
+import eu.etaxonomy.cdm.io.common.IExportConfigurator;\r
+import eu.etaxonomy.cdm.io.common.IExportConfigurator.TARGET;\r
+import eu.etaxonomy.cdm.io.common.IImportConfigurator;\r
+import eu.etaxonomy.cdm.io.common.IImportConfigurator.SOURCE_TYPE;\r
+import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.io.common.ImportResult;\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;\r
+\r
+/**\r
+ * @author cmathew\r
+ * @date 31 Jul 2015\r
+ *\r
+ */\r
+@Service\r
+@Transactional(readOnly = false)\r
+public class IOServiceImpl implements IIOService {\r
+\r
+ @Autowired\r
+ CdmApplicationAwareDefaultExport cdmExport;\r
+\r
+ @Autowired\r
+ @Qualifier("defaultImport")\r
+ CdmApplicationAwareDefaultImport cdmImport;\r
+\r
+ @Autowired\r
+ IProgressMonitorService progressMonitorService;\r
+\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.io.service.IExportService#export(eu.etaxonomy.cdm.io.common.IExportConfigurator)\r
+ */\r
+ @Override\r
+ public ExportResult export(IExportConfigurator config) {\r
+ config.setTarget(TARGET.EXPORT_DATA);\r
+ return cdmExport.execute(config);\r
+ }\r
+\r
+\r
+ @Override\r
+ public UUID monitImportData(final IImportConfigurator configurator, final byte[] importData, final SOURCE_TYPE type) {\r
+ RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {\r
+ @Override\r
+ public Serializable doRun(IRemotingProgressMonitor monitor) {\r
+ configurator.setProgressMonitor(monitor);\r
+ ImportResult result = importData(configurator, importData, type);\r
+ for(byte[] report : result.getReports()) {\r
+ monitor.addReport(new String(report));\r
+ }\r
+ return result;\r
+ }\r
+ };\r
+ UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);\r
+ monitorThread.setPriority(3);\r
+ monitorThread.start();\r
+ return uuid;\r
+ }\r
+\r
+ @Override\r
+ public ImportResult importData(IImportConfigurator configurator, byte[] importData, SOURCE_TYPE type) {\r
+ ImportResult result;\r
+ switch(type) {\r
+ case URI:\r
+ return importDataFromUri(configurator, importData);\r
+ case INPUTSTREAM:\r
+ return importDataFromInputStream(configurator,importData);\r
+ default :\r
+ throw new RuntimeException("Source type is not recongnised");\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public ImportResult importDataFromUri(IImportConfigurator configurator, byte[] importData) {\r
+ ImportResult result;\r
+\r
+ ImportConfiguratorBase config = (ImportConfiguratorBase)configurator;\r
+ String suffix = ".import";\r
+ String prefix = "cdm-";\r
+ FileOutputStream stream = null;\r
+\r
+ try {\r
+ Path tempFilePath = Files.createTempFile(prefix, suffix);\r
+ stream = new FileOutputStream(tempFilePath.toFile());\r
+ stream.write(importData);\r
+ config.setSource(tempFilePath.toUri());\r
+ result = cdmImport.execute(config);\r
+ // Files.delete(tempFilePath);\r
+ } catch (Exception e) {\r
+ throw new RuntimeException(e);\r
+ } finally {\r
+ if(stream != null) {\r
+ try {\r
+ stream.close();\r
+ } catch (IOException e) {\r
+ throw new RuntimeException(e);\r
+ }\r
+ }\r
+ }\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public ImportResult importDataFromInputStream(IImportConfigurator configurator, byte[] importData) {\r
+ ImportConfiguratorBase config = (ImportConfiguratorBase)configurator;\r
+ ImportResult result;\r
+ try {\r
+ config.setSource(new ByteArrayInputStream(importData));\r
+ result = cdmImport.execute(config);\r
+ } catch (Exception e) {\r
+ throw new RuntimeException(e);\r
+ }\r
+ return result;\r
+ }\r
+\r
+\r
+ @Override\r
+ public ImportResult importDataFromStream(SpecimenImportConfiguratorBase configurator) {\r
+ ImportResult result = new ImportResult();\r
+\r
+ OccurenceQuery query;\r
+ result = cdmImport.execute(configurator);\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public ImportResult importDataFromStream(List<Abcd206ImportConfigurator> configurators) {\r
+ ImportResult result = new ImportResult();\r
+\r
+ OccurenceQuery query;\r
+ for (SpecimenImportConfiguratorBase configurator:configurators){\r
+ result = cdmImport.execute(configurator);\r
+ }\r
+ return result;\r
+ }\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;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
-import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
-
-/**
- * @author k.luther
- * @date 18.07.2016
- *
- */
-public class SpecimenDataHolder {
-
- protected String nomenclatureCode;
- protected List<HashMap<String, String>> atomisedIdentificationList;
- private String recordBasis;
- protected String gatheringElevationText;
- private String gatheringElevationMin;
- private String gatheringElevationMax;
- private String gatheringNotes;
- private String gatheringDateText;
-
- protected String gatheringElevation;
-
- private String gatheringElevationUnit;
- private String gatheringSpatialDatum;
- private String gatheringCoordinateErrorMethod;
- private String kindOfUnit;
-
- private Map<String, String> namedAreaList;
- private String fieldNumber;
- private String unitNotes; // occurenceRemarks(DwCA)
-
- private List<String> multimediaObjects;
- private List<Identification> identificationList;
-
- private List<SpecimenTypeDesignationStatus> statusList;
-
- private List<String[]> referenceList;
- private List<String> docSources;
- private String unitID;
-
-
-
-
-
- /**
- * @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;
- }
-
-
-
- /**
- * @return the gatheringElevationText
- */
- public String getGatheringElevationText() {
- return gatheringElevationText;
- }
-
-
-
- /**
- * @param gatheringElevationText the gatheringElevationText to set
- */
- public void setGatheringElevationText(String gatheringElevationText) {
- this.gatheringElevationText = gatheringElevationText;
- }
-
-
-
- /**
- * @return the gatheringElevationMax
- */
- public String getGatheringElevationMax() {
- return gatheringElevationMax;
- }
-
-
-
- /**
- * @param gatheringElevationMax the gatheringElevationMax to set
- */
- public void setGatheringElevationMax(String gatheringElevationMax) {
- this.gatheringElevationMax = gatheringElevationMax;
- }
-
-
-
- /**
- * @return the gatheringElevationMin
- */
- public String getGatheringElevationMin() {
- return gatheringElevationMin;
- }
-
-
-
- /**
- * @param gatheringElevationMin the gatheringElevationMin to set
- */
- public void setGatheringElevationMin(String gatheringElevationMin) {
- this.gatheringElevationMin = gatheringElevationMin;
- }
-
-
-
- /**
- * @return the kindOfUnit
- */
- public String getKindOfUnit() {
- return kindOfUnit;
- }
-
-
-
- /**
- * @param kindOfUnit the kindOfUnit to set
- */
- public void setKindOfUnit(String kindOfUnit) {
- this.kindOfUnit = kindOfUnit;
- }
-
-
-
- /**
- * @return the gatheringElevationUnit
- */
- public String getGatheringElevationUnit() {
- return gatheringElevationUnit;
- }
-
-
-
- /**
- * @param gatheringElevationUnit the gatheringElevationUnit to set
- */
- public void setGatheringElevationUnit(String gatheringElevationUnit) {
- this.gatheringElevationUnit = gatheringElevationUnit;
- }
-
-
-
- /**
- * @return the gatheringDateText
- */
- public String getGatheringDateText() {
- return gatheringDateText;
- }
-
-
-
- /**
- * @param gatheringDateText the gatheringDateText to set
- */
- public void setGatheringDateText(String gatheringDateText) {
- this.gatheringDateText = gatheringDateText;
- }
-
-
-
- /**
- * @return the gatheringNotes
- */
- public String getGatheringNotes() {
- return gatheringNotes;
- }
-
-
-
- /**
- * @param gatheringNotes the gatheringNotes to set
- */
- public void setGatheringNotes(String gatheringNotes) {
- this.gatheringNotes = gatheringNotes;
- }
-
-
-
- /**
- * @return the gatheringSpatialDatum
- */
- public String getGatheringSpatialDatum() {
- return gatheringSpatialDatum;
- }
-
-
-
- /**
- * @param gatheringSpatialDatum the gatheringSpatialDatum to set
- */
- public void setGatheringSpatialDatum(String gatheringSpatialDatum) {
- this.gatheringSpatialDatum = gatheringSpatialDatum;
- }
-
-
-
- /**
- * @return the namedAreaList
- */
- public Map<String, String> getNamedAreaList() {
- return namedAreaList;
- }
-
-
-
- /**
- * @param namedAreaList the namedAreaList to set
- */
- public void setNamedAreaList(Map<String, String> namedAreaList) {
- this.namedAreaList = namedAreaList;
- }
-
-
-
- /**
- * @return the gatheringCoordinateErrorMethod
- */
- public String getGatheringCoordinateErrorMethod() {
- return gatheringCoordinateErrorMethod;
- }
-
-
-
- /**
- * @param gatheringCoordinateErrorMethod the gatheringCoordinateErrorMethod to set
- */
- public void setGatheringCoordinateErrorMethod(String gatheringCoordinateErrorMethod) {
- this.gatheringCoordinateErrorMethod = gatheringCoordinateErrorMethod;
- }
-
-
-
- /**
- *
- */
- public void reset() {
- nomenclatureCode = null;
- atomisedIdentificationList = new ArrayList<HashMap<String,String>>();
- gatheringDateText = null;
- gatheringNotes = null;
- kindOfUnit = null;
-
- setRecordBasis(null);
- gatheringElevationText = null;
- gatheringElevationMin = null;
- gatheringElevationMax = null;
- gatheringNotes = null;
- gatheringDateText = null;
-
- gatheringElevation = null;
-
- gatheringElevationUnit = null;
- gatheringSpatialDatum = null;
- gatheringCoordinateErrorMethod = null;
-
-
- }
-
-
-
- /**
- * @return the fieldNumber
- */
- public String getFieldNumber() {
- return fieldNumber;
- }
-
-
-
- /**
- * @param fieldNumber the fieldNumber to set
- */
- public void setFieldNumber(String fieldNumber) {
- this.fieldNumber = fieldNumber;
- }
-
-
-
- /**
- * @return the unitNotes
- */
- public String getUnitNotes() {
- return unitNotes;
- }
-
-
-
- /**
- * @param unitNotes the unitNotes to set
- */
- public void setUnitNotes(String unitNotes) {
- this.unitNotes = unitNotes;
- }
-
-
-
- /**
- * @return the multimediaObjects
- */
- public List<String> getMultimediaObjects() {
- return multimediaObjects;
- }
-
-
-
- /**
- * @param multimediaObjects the multimediaObjects to set
- */
- public void setMultimediaObjects(List<String> multimediaObjects) {
- this.multimediaObjects = multimediaObjects;
- }
-
-
-
- /**
- * @return the identificationList
- */
- public List<Identification> getIdentificationList() {
- return identificationList;
- }
-
-
-
- /**
- * @param identificationList the identificationList to set
- */
- public void setIdentificationList(List<Identification> identificationList) {
- this.identificationList = identificationList;
- }
-
-
-
- /**
- * @return the statusList
- */
- public List<SpecimenTypeDesignationStatus> getStatusList() {
- return statusList;
- }
-
-
-
- /**
- * @param statusList the statusList to set
- */
- public void setStatusList(List<SpecimenTypeDesignationStatus> statusList) {
- this.statusList = statusList;
- }
-
-
-
- /**
- * @return the referenceList
- */
- public List<String[]> getReferenceList() {
- return referenceList;
- }
-
-
-
- /**
- * @param referenceList the referenceList to set
- */
- public void setReferenceList(List<String[]> referenceList) {
- this.referenceList = referenceList;
- }
-
-
-
- /**
- * @return the docSources
- */
- public List<String> getDocSources() {
- return docSources;
- }
-
-
-
- /**
- * @param docSources the docSources to set
- */
- public void setDocSources(List<String> docSources) {
- this.docSources = docSources;
- }
-
-
-
- /**
- * @return the unitID
- */
- public String getUnitID() {
- return unitID;
- }
-
-
-
- /**
- * @param unitID the unitID to set
- */
- public void setUnitID(String unitID) {
- this.unitID = unitID;
- }
-
-
-
- /**
- * @return the recordBasis
- */
- public String getRecordBasis() {
- return recordBasis;
- }
-
-
-
- /**
- * @param recordBasis the recordBasis to set
- */
- public void setRecordBasis(String recordBasis) {
- this.recordBasis = recordBasis;
- }
-}
+// $Id$\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.ArrayList;\r
+import java.util.HashMap;\r
+import java.util.List;\r
+import java.util.Map;\r
+\r
+import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;\r
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;\r
+\r
+/**\r
+ * @author k.luther\r
+ * @date 18.07.2016\r
+ *\r
+ */\r
+public class SpecimenDataHolder {\r
+\r
+ protected String nomenclatureCode;\r
+ protected List<HashMap<String, String>> atomisedIdentificationList;\r
+ private String recordBasis;\r
+ protected String gatheringElevationText;\r
+ private String gatheringElevationMin;\r
+ private String gatheringElevationMax;\r
+ private String gatheringNotes;\r
+ private String gatheringDateText;\r
+\r
+ protected String gatheringElevation;\r
+\r
+ private String gatheringElevationUnit;\r
+ protected Double depth;\r
+ /**\r
+ * @return the depth\r
+ */\r
+ public Double getDepth() {\r
+ return depth;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param depth the depth to set\r
+ */\r
+ public void setDepth(Double depth) {\r
+ this.depth = depth;\r
+ }\r
+\r
+\r
+\r
+ private String gatheringSpatialDatum;\r
+ private String gatheringCoordinateErrorMethod;\r
+ private String kindOfUnit;\r
+\r
+ private Map<String, String> namedAreaList;\r
+ private String fieldNumber;\r
+ private String unitNotes; // occurenceRemarks(DwCA)\r
+\r
+ private HashMap<String, Map<String,String>> multimediaObjects;\r
+ private HashMap<String, Map<String,String>> gatheringMultimediaObjects;\r
+ private List<Identification> identificationList;\r
+\r
+ private List<SpecimenTypeDesignationStatus> statusList;\r
+\r
+ private List<String[]> referenceList;\r
+ private List<String> docSources;\r
+ private String unitID;\r
+\r
+\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
+\r
+\r
+ /**\r
+ * @return the gatheringElevationText\r
+ */\r
+ public String getGatheringElevationText() {\r
+ return gatheringElevationText;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringElevationText the gatheringElevationText to set\r
+ */\r
+ public void setGatheringElevationText(String gatheringElevationText) {\r
+ this.gatheringElevationText = gatheringElevationText;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringElevationMax\r
+ */\r
+ public String getGatheringElevationMax() {\r
+ return gatheringElevationMax;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringElevationMax the gatheringElevationMax to set\r
+ */\r
+ public void setGatheringElevationMax(String gatheringElevationMax) {\r
+ this.gatheringElevationMax = gatheringElevationMax;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringElevationMin\r
+ */\r
+ public String getGatheringElevationMin() {\r
+ return gatheringElevationMin;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringElevationMin the gatheringElevationMin to set\r
+ */\r
+ public void setGatheringElevationMin(String gatheringElevationMin) {\r
+ this.gatheringElevationMin = gatheringElevationMin;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the kindOfUnit\r
+ */\r
+ public String getKindOfUnit() {\r
+ return kindOfUnit;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param kindOfUnit the kindOfUnit to set\r
+ */\r
+ public void setKindOfUnit(String kindOfUnit) {\r
+ this.kindOfUnit = kindOfUnit;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringElevationUnit\r
+ */\r
+ public String getGatheringElevationUnit() {\r
+ return gatheringElevationUnit;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringElevationUnit the gatheringElevationUnit to set\r
+ */\r
+ public void setGatheringElevationUnit(String gatheringElevationUnit) {\r
+ this.gatheringElevationUnit = gatheringElevationUnit;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringDateText\r
+ */\r
+ public String getGatheringDateText() {\r
+ return gatheringDateText;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringDateText the gatheringDateText to set\r
+ */\r
+ public void setGatheringDateText(String gatheringDateText) {\r
+ this.gatheringDateText = gatheringDateText;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringNotes\r
+ */\r
+ public String getGatheringNotes() {\r
+ return gatheringNotes;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringNotes the gatheringNotes to set\r
+ */\r
+ public void setGatheringNotes(String gatheringNotes) {\r
+ this.gatheringNotes = gatheringNotes;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringSpatialDatum\r
+ */\r
+ public String getGatheringSpatialDatum() {\r
+ return gatheringSpatialDatum;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringSpatialDatum the gatheringSpatialDatum to set\r
+ */\r
+ public void setGatheringSpatialDatum(String gatheringSpatialDatum) {\r
+ this.gatheringSpatialDatum = gatheringSpatialDatum;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the namedAreaList\r
+ */\r
+ public Map<String, String> getNamedAreaList() {\r
+ return namedAreaList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param namedAreaList the namedAreaList to set\r
+ */\r
+ public void setNamedAreaList(Map<String, String> namedAreaList) {\r
+ this.namedAreaList = namedAreaList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringCoordinateErrorMethod\r
+ */\r
+ public String getGatheringCoordinateErrorMethod() {\r
+ return gatheringCoordinateErrorMethod;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringCoordinateErrorMethod the gatheringCoordinateErrorMethod to set\r
+ */\r
+ public void setGatheringCoordinateErrorMethod(String gatheringCoordinateErrorMethod) {\r
+ this.gatheringCoordinateErrorMethod = gatheringCoordinateErrorMethod;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ *\r
+ */\r
+ public void reset() {\r
+ nomenclatureCode = null;\r
+ atomisedIdentificationList = new ArrayList<HashMap<String,String>>();\r
+ gatheringDateText = null;\r
+ gatheringNotes = null;\r
+ kindOfUnit = null;\r
+\r
+ setRecordBasis(null);\r
+ gatheringElevationText = null;\r
+ gatheringElevationMin = null;\r
+ gatheringElevationMax = null;\r
+ gatheringNotes = null;\r
+ gatheringDateText = null;\r
+\r
+ gatheringElevation = null;\r
+\r
+ gatheringElevationUnit = null;\r
+ gatheringSpatialDatum = null;\r
+ gatheringCoordinateErrorMethod = null;\r
+ depth = null;\r
+\r
+\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the fieldNumber\r
+ */\r
+ public String getFieldNumber() {\r
+ return fieldNumber;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param fieldNumber the fieldNumber to set\r
+ */\r
+ public void setFieldNumber(String fieldNumber) {\r
+ this.fieldNumber = fieldNumber;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the unitNotes\r
+ */\r
+ public String getUnitNotes() {\r
+ return unitNotes;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param unitNotes the unitNotes to set\r
+ */\r
+ public void setUnitNotes(String unitNotes) {\r
+ this.unitNotes = unitNotes;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the multimediaObjects\r
+ */\r
+ public HashMap<String,Map<String, String>> getMultimediaObjects() {\r
+ return multimediaObjects;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param multimediaObjects the multimediaObjects to set\r
+ */\r
+ public void setMultimediaObjects(HashMap<String,Map<String, String>> multimediaObjects) {\r
+ this.multimediaObjects = multimediaObjects;\r
+ }\r
+\r
+ public void putMultiMediaObject(String uri, Map<String, String> attributes){\r
+ this.multimediaObjects.put(uri, attributes);\r
+ }\r
+\r
+ /**\r
+ * @return the multimediaObjects\r
+ */\r
+ public HashMap<String,Map<String, String>> getGatheringMultimediaObjects() {\r
+ return gatheringMultimediaObjects;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param multimediaObjects the multimediaObjects to set\r
+ */\r
+ public void setGatheringMultimediaObjects(HashMap<String,Map<String, String>> multimediaObjects) {\r
+ this.gatheringMultimediaObjects = multimediaObjects;\r
+ }\r
+\r
+ public void putGatheringMultiMediaObject(String uri, Map<String, String> attributes){\r
+ this.gatheringMultimediaObjects.put(uri, attributes);\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the identificationList\r
+ */\r
+ public List<Identification> getIdentificationList() {\r
+ return identificationList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param identificationList the identificationList to set\r
+ */\r
+ public void setIdentificationList(List<Identification> identificationList) {\r
+ this.identificationList = identificationList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the statusList\r
+ */\r
+ public List<SpecimenTypeDesignationStatus> getStatusList() {\r
+ return statusList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param statusList the statusList to set\r
+ */\r
+ public void setStatusList(List<SpecimenTypeDesignationStatus> statusList) {\r
+ this.statusList = statusList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the referenceList\r
+ */\r
+ public List<String[]> getReferenceList() {\r
+ return referenceList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param referenceList the referenceList to set\r
+ */\r
+ public void setReferenceList(List<String[]> referenceList) {\r
+ this.referenceList = referenceList;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the docSources\r
+ */\r
+ public List<String> getDocSources() {\r
+ return docSources;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param docSources the docSources to set\r
+ */\r
+ public void setDocSources(List<String> docSources) {\r
+ this.docSources = docSources;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the unitID\r
+ */\r
+ public String getUnitID() {\r
+ return unitID;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param unitID the unitID to set\r
+ */\r
+ public void setUnitID(String unitID) {\r
+ this.unitID = unitID;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the recordBasis\r
+ */\r
+ public String getRecordBasis() {\r
+ return recordBasis;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param recordBasis the recordBasis to set\r
+ */\r
+ public void setRecordBasis(String recordBasis) {\r
+ this.recordBasis = recordBasis;\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 java.net.URI;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.UUID;
-
-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> {
-
- /**
- * @param transformer
- */
- public SpecimenImportConfiguratorBase(IInputTransformer transformer) {
- super(transformer);
-
- }
-
- private boolean ignoreImportOfExistingSpecimen = true;
- private boolean reuseExistingTaxaWhenPossible = true;
- private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();
-
- private Map<String, Team> titleCacheTeam;
- private Map<String, Person> titleCachePerson;
- private boolean ignoreAuthorship = false;
- private boolean removeCountryFromLocalityText = false;
- protected OccurenceQuery query ;
-
- private boolean addMediaAsMediaSpecimen = false;
- private boolean reuseExistingMetaData = true;
-
- private static String sourceReferenceTitle = null;
-
- private String taxonReference = null;
- private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;
- private boolean reuseExistingDescriptiveGroups = false;
-
-
- private String defaultAuthor="";
- private boolean allowReuseOtherClassifications =true;
-
- private boolean deduplicateReferences = false;
- private boolean deduplicateClassifications = false;
-
- private boolean moveNewTaxaToDefaultClassification = true;
-
- private boolean mapUnitIdToCatalogNumber = true;
- private boolean mapUnitIdToAccessionNumber = false;
- private boolean mapUnitIdToBarcode = false;
-
- private boolean overwriteExistingSpecimens = false;
-
-
- private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();
-
- protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();
-
- private URI reportUri;
-
-
- public boolean isIgnoreImportOfExistingSpecimen() {
- return ignoreImportOfExistingSpecimen;
- }
-
- public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {
- this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;
- }
-
- public Map<String, Team> getTitleCacheTeam() {
- return titleCacheTeam;
- }
-
- public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {
- this.titleCacheTeam = titleCacheTeam;
- }
-
- public Map<String, Person> getTitleCachePerson() {
- return titleCachePerson;
- }
-
- public void setTitleCachePerson(Map<String, Person> titleCachePerson) {
- this.titleCachePerson = titleCachePerson;
- }
-
- public OccurenceQuery getQuery() {
- return query;
- }
-
- public void setQuery(OccurenceQuery query) {
- this.query = query;
- }
-
-
-
-
-
- public String getTaxonReference() {
- return taxonReference;
- }
-
- public void setTaxonReference(String taxonReference) {
- this.taxonReference = taxonReference;
- }
-
- public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {
- return addIndividualsAssociationsSuchAsSpecimenAndObservations;
- }
-
- public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(
- boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {
- this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;
- }
-
- public boolean isReuseExistingDescriptiveGroups() {
- return reuseExistingDescriptiveGroups;
- }
-
- public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {
- this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;
- }
-
- public String getDefaultAuthor() {
- return defaultAuthor;
- }
-
- public void setDefaultAuthor(String defaultAuthor) {
- this.defaultAuthor = defaultAuthor;
- }
-
- public boolean isAllowReuseOtherClassifications() {
- return allowReuseOtherClassifications;
- }
-
- public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {
- this.allowReuseOtherClassifications = allowReuseOtherClassifications;
- }
-
- public boolean isDeduplicateReferences() {
- return deduplicateReferences;
- }
-
- public void setDeduplicateReferences(boolean deduplicateReferences) {
- this.deduplicateReferences = deduplicateReferences;
- }
-
- public boolean isDeduplicateClassifications() {
- return deduplicateClassifications;
- }
-
- public void setDeduplicateClassifications(boolean deduplicateClassifications) {
- this.deduplicateClassifications = deduplicateClassifications;
- }
-
- public boolean isMoveNewTaxaToDefaultClassification() {
- return moveNewTaxaToDefaultClassification;
- }
-
- public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {
- this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;
- }
-
- public boolean isMapUnitIdToCatalogNumber() {
- return mapUnitIdToCatalogNumber;
- }
-
- public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {
- this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;
- }
-
- public boolean isMapUnitIdToAccessionNumber() {
- return mapUnitIdToAccessionNumber;
- }
-
- public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {
- this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;
- }
-
- public boolean isMapUnitIdToBarcode() {
- return mapUnitIdToBarcode;
- }
-
- public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {
- this.mapUnitIdToBarcode = mapUnitIdToBarcode;
- }
-
- public Map<String, UUID> getNamedAreaDecisions() {
- return namedAreaDecisions;
- }
-
-
- public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {
- this.namedAreaDecisions = namedAreaDecisions;
- }
-
- public void putNamedAreaDecision(String areaStr,UUID uuid){
- this.namedAreaDecisions.put(areaStr,uuid);
- }
-
- public UUID getNamedAreaDecision(String areaStr){
- return namedAreaDecisions.get(areaStr);
- }
-
- public Map<UUID, UUID> getTaxonToDescriptionMap() {
- return taxonToDescriptionMap;
- }
-
-
-
- public SpecimenUserInteraction getSpecimenUserInteraction() {
- return specimenUserInteraction;
- }
-
- public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {
- this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;
- }
-
- public void setIgnoreAuthorship(boolean ignoreAuthorship) {
- this.ignoreAuthorship = ignoreAuthorship;
- }
-
- public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {
- this.removeCountryFromLocalityText = removeCountryFromLocalityText;
- }
-
- public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {
- this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
- }
-
- public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {
- this.overwriteExistingSpecimens = overwriteExistingSpecimens;
- }
-
- public boolean isOverwriteExistingSpecimens(){
- return overwriteExistingSpecimens;
- }
-
-
-
-
- /**
- * @return
- */
- public boolean isReuseExistingTaxaWhenPossible() {
-
- return reuseExistingTaxaWhenPossible;
- }
-
- /**
- * @param titleCacheTeam
- */
- public void setTeams(Map<String, Team> titleCacheTeam) {
- this.titleCacheTeam = titleCacheTeam;
-
- }
-
- public Team getTeam(String titleCache){
- return titleCacheTeam.get(titleCache);
- }
-
- public Map<String, Team> getTeams(){
- return titleCacheTeam;
- }
- /**
- * @param titleCachePerson
- */
- public void setPersons(Map<String, Person> titleCachePerson) {
- this.titleCachePerson = titleCachePerson;
- }
-
- public Map<String, Person> getPersons(){
- return titleCachePerson;
- }
-
- public Person getPerson(String titleCache){
- return titleCachePerson.get(titleCache);
- }
-
- public boolean isAddMediaAsMediaSpecimen(){
- return addMediaAsMediaSpecimen;
- }
-
- public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){
- this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;
- }
-
-
- /**
- * @return
- */
- public boolean isIgnoreAuthorship() {
- return ignoreAuthorship;
- }
-
- /**
- * @return
- */
- public boolean isRemoveCountryFromLocalityText() {
- return removeCountryFromLocalityText;
- }
-
- public OccurenceQuery getOccurenceQuery(){
- return query;
- }
-
- public void setOccurenceQuery(OccurenceQuery query){
- this.query = query;
- }
-
-
-
- /**
- * @return the reuseExistingMetaData
- */
- public boolean isReuseExistingMetaData() {
- return reuseExistingMetaData;
- }
-
- /**
- * @param reuseExistingMetaData the reuseExistingMetaData to set
- */
- public void setReuseExistingMetaData(boolean reuseExistingMetaData) {
- this.reuseExistingMetaData = reuseExistingMetaData;
- }
-
- public void setReportUri(URI reportUri) {
- this.reportUri = reportUri;
- }
-
- public URI getReportUri() {
- return reportUri;
- }
-
- @Override
- public String getSourceReferenceTitle(){
- return this.sourceReferenceTitle;
- }
-
- @Override
- public void setSourceReferenceTitle(String name){
- this.sourceReferenceTitle=name;
- }
-
- @Override
- public boolean isValid(){
- return true;
- }
-
-
-
-}
+// $Id$\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.net.URI;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+import java.util.UUID;\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
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\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
+ /**\r
+ * @param transformer\r
+ */\r
+ public SpecimenImportConfiguratorBase(IInputTransformer transformer) {\r
+ super(transformer);\r
+\r
+ }\r
+\r
+ private boolean ignoreImportOfExistingSpecimen = true;\r
+ private boolean reuseExistingTaxaWhenPossible = true;\r
+ private final Map<UUID, UUID> taxonToDescriptionMap = new HashMap<UUID, UUID>();\r
+\r
+ private Map<String, Team> titleCacheTeam;\r
+ private Map<String, Person> titleCachePerson;\r
+ private boolean ignoreAuthorship = false;\r
+ private boolean removeCountryFromLocalityText = false;\r
+ protected OccurenceQuery query ;\r
+\r
+ private boolean addMediaAsMediaSpecimen = false;\r
+ private boolean reuseExistingMetaData = true;\r
+\r
+ private static String sourceReferenceTitle = null;\r
+\r
+ private String taxonReference = null;\r
+ private boolean addIndividualsAssociationsSuchAsSpecimenAndObservations = true;\r
+ private boolean reuseExistingDescriptiveGroups = false;\r
+\r
+\r
+ private String defaultAuthor="";\r
+ private boolean allowReuseOtherClassifications =true;\r
+\r
+ private boolean deduplicateReferences = false;\r
+ private boolean deduplicateClassifications = false;\r
+\r
+ private boolean moveNewTaxaToDefaultClassification = true;\r
+\r
+ private boolean mapUnitIdToCatalogNumber = true;\r
+ private boolean mapUnitIdToAccessionNumber = false;\r
+ private boolean mapUnitIdToBarcode = false;\r
+\r
+ private boolean overwriteExistingSpecimens = false;\r
+\r
+ private SpecimenOrObservationType type;\r
+\r
+\r
+ /**\r
+ * @return the type\r
+ */\r
+ public SpecimenOrObservationType getType() {\r
+ return type;\r
+ }\r
+\r
+ /**\r
+ * @param type the type to set\r
+ */\r
+ public void setType(SpecimenOrObservationType type) {\r
+ this.type = type;\r
+ }\r
+\r
+ private final SpecimenUserInteraction specimenUserInteraction = new SpecimenUserInteraction();\r
+\r
+ protected Map<String,UUID> namedAreaDecisions = new HashMap<String,UUID>();\r
+\r
+ private URI reportUri;\r
+\r
+\r
+ public boolean isIgnoreImportOfExistingSpecimen() {\r
+ return ignoreImportOfExistingSpecimen;\r
+ }\r
+\r
+ public void setIgnoreImportOfExistingSpecimen(boolean ignoreImportOfExistingSpecimen) {\r
+ this.ignoreImportOfExistingSpecimen = ignoreImportOfExistingSpecimen;\r
+ }\r
+\r
+ public Map<String, Team> getTitleCacheTeam() {\r
+ return titleCacheTeam;\r
+ }\r
+\r
+ public void setTitleCacheTeam(Map<String, Team> titleCacheTeam) {\r
+ this.titleCacheTeam = titleCacheTeam;\r
+ }\r
+\r
+ public Map<String, Person> getTitleCachePerson() {\r
+ return titleCachePerson;\r
+ }\r
+\r
+ public void setTitleCachePerson(Map<String, Person> titleCachePerson) {\r
+ this.titleCachePerson = titleCachePerson;\r
+ }\r
+\r
+ public OccurenceQuery getQuery() {\r
+ return query;\r
+ }\r
+\r
+ public void setQuery(OccurenceQuery query) {\r
+ this.query = query;\r
+ }\r
+\r
+\r
+\r
+\r
+\r
+ public String getTaxonReference() {\r
+ return taxonReference;\r
+ }\r
+\r
+ public void setTaxonReference(String taxonReference) {\r
+ this.taxonReference = taxonReference;\r
+ }\r
+\r
+ public boolean isAddIndividualsAssociationsSuchAsSpecimenAndObservations() {\r
+ return addIndividualsAssociationsSuchAsSpecimenAndObservations;\r
+ }\r
+\r
+ public void setAddIndividualsAssociationsSuchAsSpecimenAndObservations(\r
+ boolean addIndividualsAssociationsSuchAsSpecimenAndObservations) {\r
+ this.addIndividualsAssociationsSuchAsSpecimenAndObservations = addIndividualsAssociationsSuchAsSpecimenAndObservations;\r
+ }\r
+\r
+ public boolean isReuseExistingDescriptiveGroups() {\r
+ return reuseExistingDescriptiveGroups;\r
+ }\r
+\r
+ public void setReuseExistingDescriptiveGroups(boolean reuseExistingDescriptiveGroups) {\r
+ this.reuseExistingDescriptiveGroups = reuseExistingDescriptiveGroups;\r
+ }\r
+\r
+ public String getDefaultAuthor() {\r
+ return defaultAuthor;\r
+ }\r
+\r
+ public void setDefaultAuthor(String defaultAuthor) {\r
+ this.defaultAuthor = defaultAuthor;\r
+ }\r
+\r
+ public boolean isAllowReuseOtherClassifications() {\r
+ return allowReuseOtherClassifications;\r
+ }\r
+\r
+ public void setAllowReuseOtherClassifications(boolean allowReuseOtherClassifications) {\r
+ this.allowReuseOtherClassifications = allowReuseOtherClassifications;\r
+ }\r
+\r
+ public boolean isDeduplicateReferences() {\r
+ return deduplicateReferences;\r
+ }\r
+\r
+ public void setDeduplicateReferences(boolean deduplicateReferences) {\r
+ this.deduplicateReferences = deduplicateReferences;\r
+ }\r
+\r
+ public boolean isDeduplicateClassifications() {\r
+ return deduplicateClassifications;\r
+ }\r
+\r
+ public void setDeduplicateClassifications(boolean deduplicateClassifications) {\r
+ this.deduplicateClassifications = deduplicateClassifications;\r
+ }\r
+\r
+ public boolean isMoveNewTaxaToDefaultClassification() {\r
+ return moveNewTaxaToDefaultClassification;\r
+ }\r
+\r
+ public void setMoveNewTaxaToDefaultClassification(boolean moveNewTaxaToDefaultClassification) {\r
+ this.moveNewTaxaToDefaultClassification = moveNewTaxaToDefaultClassification;\r
+ }\r
+\r
+ public boolean isMapUnitIdToCatalogNumber() {\r
+ return mapUnitIdToCatalogNumber;\r
+ }\r
+\r
+ public void setMapUnitIdToCatalogNumber(boolean mapUnitIdToCatalogNumber) {\r
+ this.mapUnitIdToCatalogNumber = mapUnitIdToCatalogNumber;\r
+ }\r
+\r
+ public boolean isMapUnitIdToAccessionNumber() {\r
+ return mapUnitIdToAccessionNumber;\r
+ }\r
+\r
+ public void setMapUnitIdToAccessionNumber(boolean mapUnitIdToAccessionNumber) {\r
+ this.mapUnitIdToAccessionNumber = mapUnitIdToAccessionNumber;\r
+ }\r
+\r
+ public boolean isMapUnitIdToBarcode() {\r
+ return mapUnitIdToBarcode;\r
+ }\r
+\r
+ public void setMapUnitIdToBarcode(boolean mapUnitIdToBarcode) {\r
+ this.mapUnitIdToBarcode = mapUnitIdToBarcode;\r
+ }\r
+\r
+ public Map<String, UUID> getNamedAreaDecisions() {\r
+ return namedAreaDecisions;\r
+ }\r
+\r
+\r
+ public void setNamedAreaDecisions(Map<String,UUID> namedAreaDecisions) {\r
+ this.namedAreaDecisions = namedAreaDecisions;\r
+ }\r
+\r
+ public void putNamedAreaDecision(String areaStr,UUID uuid){\r
+ this.namedAreaDecisions.put(areaStr,uuid);\r
+ }\r
+\r
+ public UUID getNamedAreaDecision(String areaStr){\r
+ return namedAreaDecisions.get(areaStr);\r
+ }\r
+\r
+ public Map<UUID, UUID> getTaxonToDescriptionMap() {\r
+ return taxonToDescriptionMap;\r
+ }\r
+\r
+\r
+\r
+ public SpecimenUserInteraction getSpecimenUserInteraction() {\r
+ return specimenUserInteraction;\r
+ }\r
+\r
+ public void setReuseExistingTaxaWhenPossible(boolean reuseExistingTaxaWhenPossible) {\r
+ this.reuseExistingTaxaWhenPossible = reuseExistingTaxaWhenPossible;\r
+ }\r
+\r
+ public void setIgnoreAuthorship(boolean ignoreAuthorship) {\r
+ this.ignoreAuthorship = ignoreAuthorship;\r
+ }\r
+\r
+ public void setRemoveCountryFromLocalityText(boolean removeCountryFromLocalityText) {\r
+ this.removeCountryFromLocalityText = removeCountryFromLocalityText;\r
+ }\r
+\r
+ public void setAddMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen) {\r
+ this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;\r
+ }\r
+\r
+ public void setOverwriteExistingSpecimens(boolean overwriteExistingSpecimens) {\r
+ this.overwriteExistingSpecimens = overwriteExistingSpecimens;\r
+ }\r
+\r
+ public boolean isOverwriteExistingSpecimens(){\r
+ return overwriteExistingSpecimens;\r
+ }\r
+\r
+\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.titleCacheTeam = titleCacheTeam;\r
+\r
+ }\r
+\r
+ public Team getTeam(String titleCache){\r
+ return titleCacheTeam.get(titleCache);\r
+ }\r
+\r
+ public Map<String, Team> getTeams(){\r
+ return titleCacheTeam;\r
+ }\r
+ /**\r
+ * @param titleCachePerson\r
+ */\r
+ public void setPersons(Map<String, Person> titleCachePerson) {\r
+ this.titleCachePerson = titleCachePerson;\r
+ }\r
+\r
+ public Map<String, Person> getPersons(){\r
+ return titleCachePerson;\r
+ }\r
+\r
+ public Person getPerson(String titleCache){\r
+ return titleCachePerson.get(titleCache);\r
+ }\r
+\r
+ public boolean isAddMediaAsMediaSpecimen(){\r
+ return addMediaAsMediaSpecimen;\r
+ }\r
+\r
+ public void addMediaAsMediaSpecimen(boolean addMediaAsMediaSpecimen){\r
+ this.addMediaAsMediaSpecimen = addMediaAsMediaSpecimen;\r
+ }\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 OccurenceQuery getOccurenceQuery(){\r
+ return query;\r
+ }\r
+\r
+ public void setOccurenceQuery(OccurenceQuery query){\r
+ this.query = query;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @return the reuseExistingMetaData\r
+ */\r
+ public boolean isReuseExistingMetaData() {\r
+ return reuseExistingMetaData;\r
+ }\r
+\r
+ /**\r
+ * @param reuseExistingMetaData the reuseExistingMetaData to set\r
+ */\r
+ public void setReuseExistingMetaData(boolean reuseExistingMetaData) {\r
+ this.reuseExistingMetaData = reuseExistingMetaData;\r
+ }\r
+\r
+ public void setReportUri(URI reportUri) {\r
+ this.reportUri = reportUri;\r
+ }\r
+\r
+ public URI getReportUri() {\r
+ return reportUri;\r
+ }\r
+\r
+ @Override\r
+ public String getSourceReferenceTitle(){\r
+ return this.sourceReferenceTitle;\r
+ }\r
+\r
+ @Override\r
+ public void setSourceReferenceTitle(String name){\r
+ this.sourceReferenceTitle=name;\r
+ }\r
+\r
+ @Override\r
+ public boolean isValid(){\r
+ return true;\r
+ }\r
+\r
+\r
+\r
+}\r
package eu.etaxonomy.cdm.io.specimen;
-import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.UUID;
import org.apache.commons.lang.StringUtils;
import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;
import eu.etaxonomy.cdm.model.agent.Person;
import eu.etaxonomy.cdm.model.agent.Team;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.model.common.Annotation;
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
import eu.etaxonomy.cdm.model.common.Language;
*/
public UnitsGatheringEvent(ITermService termService, String locality, String languageIso, Double longitude,
Double latitude, String elevationText, String elevationMin, String elevationMax, String elevationUnit,
- String date, String gatheringNotes, ReferenceSystem referenceSystem, List<String> collectorName,
- List<String> team, Abcd206ImportConfigurator config) {
+ String date, String gatheringNotes, ReferenceSystem referenceSystem,
+ Abcd206ImportConfigurator config) {
this.setLocality(termService, locality, languageIso);
this.setCoordinates(longitude, latitude, referenceSystem);
this.setDate(date);
this.setNotes(gatheringNotes);
this.setElevation(elevationText, elevationMin, elevationMax, elevationUnit);
- if (!collectorName.isEmpty()) {
- List<String> tmp = new ArrayList<String>(new HashSet<String>(collectorName));
- this.setCollector(tmp.get(0), config);
- }
- if (!team.isEmpty()) {
- List<String> tmpTeam = new ArrayList<String>(new HashSet<String>(team));
- this.setTeam(StringUtils.join(tmpTeam," & "), config);
- }
+
+
+
+
+
}
+ /**
+ * @param gatheringImages
+ */
+ public void setGatheringImages(HashMap<String, Map<String, String>> gatheringImages) {
+
+
+ }
public GatheringEvent getGatheringEvent(){
return this.gatheringEvent;
}
}
}
+ public void setHeight(String heightText, String heightMin, String heightMax, String heightUnit){
+ if(heightText!=null){
+ this.gatheringEvent.setAbsoluteElevationText(heightText);
+ }
+ else{
+ //TODO check for unit at string end
+ String pattern = "\\D";// regex for non-digits
+ if(heightMin!=null){
+ Double min = Double.parseDouble(heightMin.replaceAll(pattern, ""));
+ this.gatheringEvent.setDistanceToGround(min);
+ }
+ if(heightMax!=null){
+ Double max = Double.parseDouble(heightMax.replaceAll(pattern, ""));
+ this.gatheringEvent.setDistanceToGroundMax(max);
+ }
+ if(heightUnit!=null){
+ if (!heightUnit.equals("m")){
+ logger.debug("The unit " + heightUnit + " of the distance to ground is not meter.");
+ }
+ }
+ }
+ }
+
+ public void setGatheringDepth(String depthText, Double depthMin, Double depthMax, String depthUnit){
+ if(depthText!=null){
+ this.gatheringEvent.setDistanceToWaterSurfaceText(depthText);
+ }
+ else{
+
+ if(depthMin!=null){
+ this.gatheringEvent.setDistanceToWaterSurface(depthMin);
+ }
+ if(depthMax!=null){
+ this.gatheringEvent.setDistanceToWaterSurfaceMax(depthMax);
+ }
+ if(depthUnit!=null){
+ if (!depthUnit.equals("m")){
+ logger.debug("The unit " + depthUnit + " of the distance to ground is not meter.");
+ }
+ }
+ }
+ }
+
/*
* Add a NamedArea to the GatheringEvent
* @param area: the NamedArea to add
* @param: collectorNames: the list of names to add as collector/collectorTeam
* USED - create each time a new Collector
*/
- public void setCollector(String collectorName, Abcd206ImportConfigurator config){
+ public void setCollector(TeamOrPersonBase collector, Abcd206ImportConfigurator config){
// System.out.println("collectors : "+collectorNames.toString());
- Person collector;
- collector = Person.NewInstance();
- collector.setTitleCache(collectorName, true);
+
if (DEBUG) {
System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
}
- // this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
+ this.gatheringEvent.setCollector(collector);
}
/**
import java.util.ArrayList;\r
import java.util.HashMap;\r
import java.util.List;\r
+import java.util.Map;\r
\r
import org.apache.log4j.Logger;\r
\r
\r
protected List<String> knownABCDelements = new ArrayList<String>();\r
protected HashMap<String,String> allABCDelements = new HashMap<String,String>();\r
- public List<String> gatheringAgentList;\r
- protected List<String> gatheringTeamList;\r
+ public String gatheringAgents ="";\r
+\r
\r
//per unit\r
\r
protected String languageIso;\r
protected String country;\r
protected String isocountry;\r
- protected Integer depth;\r
+\r
+\r
protected Integer altitude;\r
\r
+ private String gatheringDepthUnit;\r
+\r
+ private Double gatheringDepthMax;\r
+\r
+ private Double gatheringDepthMin;\r
+ private String gatheringDepthText;\r
+\r
\r
\r
\r
languageIso = null;\r
country = null;\r
isocountry = null;\r
- depth = null;\r
+\r
altitude = null;\r
\r
gatheringElevationText = null;\r
\r
\r
setReferenceList(new ArrayList<String[]>());\r
- setMultimediaObjects(new ArrayList<String>());\r
+ setMultimediaObjects(new HashMap<String,Map<String, String>>());\r
+ setGatheringMultimediaObjects(new HashMap<String,Map<String, String>>());\r
setDocSources(new ArrayList<String>());\r
associatedUnitIds = new ArrayList<String>();\r
}\r
\r
\r
\r
+ /**\r
+ * @param textContent\r
+ */\r
+ public void setGatheringDepthMin(Double gatheringDepthMin) {\r
+ this.gatheringDepthMin = gatheringDepthMin;\r
+\r
+ }\r
+\r
+ public Double getGatheringDepthMin() {\r
+ return gatheringDepthMin;\r
+\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param textContent\r
+ */\r
+ public void setGatheringDepthMax(Double gatheringDepthMax) {\r
+ this.gatheringDepthMax = gatheringDepthMax;\r
+\r
+ }\r
+\r
+ public Double getGatheringDepthMax() {\r
+ return gatheringDepthMax;\r
+\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * @param textContent\r
+ */\r
+ public void setGatheringDepthUnit(String gatheringDepthUnit) {\r
+ this.gatheringDepthUnit = gatheringDepthUnit;\r
+\r
+ }\r
+\r
+ public String getGatheringDepthUnit() {\r
+ return gatheringDepthUnit;\r
+\r
+ }\r
+\r
+\r
+\r
+\r
+\r
+ /**\r
+ * @return the gatheringDepthText\r
+ */\r
+ public String getGatheringDepthText() {\r
+ return gatheringDepthText;\r
+ }\r
+\r
+\r
+\r
+\r
+ /**\r
+ * @param gatheringDepthText the gatheringDepthText to set\r
+ */\r
+ public void setGatheringDepthText(String gatheringDepthText) {\r
+ this.gatheringDepthText = gatheringDepthText;\r
+ }\r
+\r
+\r
}\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
+import eu.etaxonomy.cdm.io.common.ICdmIO;
+import eu.etaxonomy.cdm.io.common.MapWrapper;
import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;
import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
import eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular.AbcdDnaParser;
-import eu.etaxonomy.cdm.model.agent.AgentBase;
import eu.etaxonomy.cdm.model.agent.Institution;
import eu.etaxonomy.cdm.model.agent.Person;
import eu.etaxonomy.cdm.model.agent.Team;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.model.common.Annotation;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
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.DescriptionElementSource;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
import eu.etaxonomy.cdm.model.taxon.Classification;
-import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
/**
* @author p.kelbert
@SuppressWarnings("rawtypes")
public void doInvoke(Abcd206ImportState state) {
Abcd206ImportConfigurator config = state.getConfig();
+ Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
+ MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
+ state.setPersonStore(authorStore);
+ MapWrapper<Reference> referenceStore = (MapWrapper<Reference>)stores.get(ICdmIO.REFERENCE_STORE);
+ MapWrapper<TaxonBase> taxonBaseStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
try{
state.setTx(startTransaction());
logger.info("INVOKE Specimen Import from ABCD2.06 XML ");
//init import reference
// List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
- List<Reference> references = new ArrayList<Reference>();
+ // List<Reference> references = new ArrayList<Reference>();
// if (state.getConfig().isInteractWithUser()){
// Map<String,Reference> refMap = new HashMap<String, Reference>();
// }else{
if (state.getRef()==null){
String name = NB(((Abcd206ImportConfigurator) state.getConfig()).getSourceReferenceTitle());
- for (Reference reference : references) {
+ for (Reference reference : referenceStore.getAllValues()) {
if (! StringUtils.isBlank(reference.getTitleCache())) {
if (reference.getTitleCache().equalsIgnoreCase(name)) {
state.setRef(reference);
prepareCollectors(state, unitsList, abcdFieldGetter);
+
+ // save authors
+ getAgentService().saveOrUpdate((java.util.Collection)state.getPersonStore().objects());
+
+ commitTransaction(state.getTx());
+ state.setTx(startTransaction());
+
state.setAssociationRefs(new ArrayList<OriginalSourceBase<?>>());
state.setDescriptionRefs(new ArrayList<OriginalSourceBase<?>>());
state.setDerivedUnitSources(new ArrayList<OriginalSourceBase<?>>());
state.getDataHolder().getGatheringElevationMin(), state.getDataHolder().getGatheringElevationMax(),
state.getDataHolder().getGatheringElevationUnit(), state.getDataHolder().getGatheringDateText(),
state.getDataHolder().getGatheringNotes(), state.getTransformer().getReferenceSystemByKey(
- state.getDataHolder().getGatheringSpatialDatum()), state.getDataHolder().gatheringAgentList,
- state.getDataHolder().gatheringTeamList, state.getConfig());
+ state.getDataHolder().getGatheringSpatialDatum()),
+ state.getConfig());
- // country
+ unitsGatheringEvent.setGatheringDepth(state.getDataHolder().getGatheringDepthText(),state.getDataHolder().getGatheringDepthMin(), state.getDataHolder().getGatheringDepthMax(), state.getDataHolder().getGatheringDepthUnit());
+ //unitsGatheringEvent.setHeight(heightText, heightMin, heightMax, heightUnit);
+ unitsGatheringEvent.setCollector(state.getPersonStore().get(state.getDataHolder().gatheringAgents), config);
+ // count
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, (state.getConfig()), cdmAppController.getTermService(), cdmAppController.getOccurrenceService());
derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
+ derivedUnitFacade.setDistanceToGroundText(gatheringEvent.getDistanceToGroundText());
+ derivedUnitFacade.setDistanceToGroundMax(gatheringEvent.getDistanceToGroundMax());
+ derivedUnitFacade.setDistanceToGround(gatheringEvent.getDistanceToGround());
+ derivedUnitFacade.setDistanceToWaterSurfaceText(gatheringEvent.getDistanceToWaterSurfaceText());
+ derivedUnitFacade.setDistanceToWaterSurfaceMax(gatheringEvent.getDistanceToWaterSurfaceMax());
+ derivedUnitFacade.setDistanceToWaterSurface(gatheringEvent.getDistanceToWaterSurface());
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
// add unitNotes
derivedUnitFacade.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().getUnitNotes())));
+
+
// //add Multimedia URLs
if (state.getDataHolder().getMultimediaObjects().size() != -1) {
- for (String multimediaObject : state.getDataHolder().getMultimediaObjects()) {
+ for (String multimediaObject : state.getDataHolder().getMultimediaObjects().keySet()) {
Media media;
try {
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
+ Map<String, String> attributes = state.getDataHolder().getMultimediaObjects().get(multimediaObject);
+ if (attributes.containsKey("Context")){
+ LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
+ media.addDescription(description);
+ }
+ if (attributes.containsKey("Comment")){
+ LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
+ media.addDescription(description);
+ }
+ if (attributes.containsKey("Creators")){
+ String creators = attributes.get("Creators");
+ Person artist;
+ Team artistTeam;
+ String[] artists;
+ if (creators != null){
+ if (creators.contains("&")){
+ artists = creators.split("&");
+ artistTeam = new Team();
+ for (String creator:artists){
+ artist = Person.NewTitledInstance(creator);
+ artistTeam.addTeamMember(artist);
+ }
+ media.setArtist(artistTeam);
+ } else{
+
+ artist = Person.NewTitledInstance(creators);
+ media.setArtist(artist);
+ }
+ }
+
+
+
+ }
+
derivedUnitFacade.addDerivedUnitMedia(media);
if(((Abcd206ImportConfigurator)state.getConfig()).isAddMediaAsMediaSpecimen()){
//add media also as specimen scan
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
mediaSpecimen.setMediaSpecimen(media);
+ //do it only once!!
DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
if(specimenScanTerm instanceof DefinedTerm){
mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
}
}
+ //multimedia for fieldUnit
+ if (state.getDataHolder().getGatheringMultimediaObjects().size() != -1) {
+ for (String multimediaObject : state.getDataHolder().getGatheringMultimediaObjects().keySet()) {
+ Media media;
+ try {
+ media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
+ Map<String, String> attributes = state.getDataHolder().getGatheringMultimediaObjects().get(multimediaObject);
+ if (attributes.containsKey("Context")){
+ LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
+ media.addDescription(description);
+ }
+ if (attributes.containsKey("Comment")){
+ LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
+ media.addDescription(description);
+ }
+ if (attributes.containsKey("Creators")){
+ String creators = attributes.get("Creators");
+ Person artist;
+ Team artistTeam;
+ String[] artists;
+ if (creators != null){
+ if (creators.contains("&")){
+ artists = creators.split("&");
+ artistTeam = new Team();
+ for (String creator:artists){
+ artist = Person.NewTitledInstance(creator);
+ artistTeam.addTeamMember(artist);
+ }
+ media.setArtist(artistTeam);
+ } else{
+
+ artist = Person.NewTitledInstance(creators);
+ media.setArtist(artist);
+ }
+ }
+
+
+
+ }
+
+ derivedUnitFacade.addFieldObjectMedia(media);
+
+
+ } catch (MalformedURLException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+ }
// /*
// * merge AND STORE DATA
// for (NamedArea area : otherAreas) {
// getTermService().saveOrUpdate(area);// merge it sooner (foreach area)
// }
-
+ save(derivedUnitFacade.getFieldUnit(false), state);
save(unitsGatheringEvent.getLocality(), state);
// handle collection data
break;
}
}
- state.getDataHolder().gatheringAgentList = new ArrayList<String>();
- state.getDataHolder().gatheringTeamList = new ArrayList<String>();
+ //state.getDataHolder().gatheringAgents = "";
+
abcdFieldGetter.getType(root);
abcdFieldGetter.getGatheringPeople(root);
}
state.getDataHolder().setStatusList(new ArrayList<SpecimenTypeDesignationStatus>());
state.getDataHolder().setAtomisedIdentificationList(new ArrayList<HashMap<String, String>>());
state.getDataHolder().setReferenceList(new ArrayList<String[]>());
- state.getDataHolder().setMultimediaObjects(new ArrayList<String>());
+ state.getDataHolder().setMultimediaObjects(new HashMap<String,Map<String, String>>());
+ state.getDataHolder().setGatheringMultimediaObjects(new HashMap<String,Map<String, String>>());
abcdFieldGetter.getScientificNames(group);
abcdFieldGetter.getType(root);
abcdFieldGetter.getGatheringDate(root);
abcdFieldGetter.getGatheringElevation(root);
abcdFieldGetter.getGatheringNotes(root);
+ abcdFieldGetter.getGatheringImages(root);
abcdFieldGetter.getAssociatedUnitIds(root);
abcdFieldGetter.getUnitNotes(root);
boolean referencefound = abcdFieldGetter.getReferences(root);
* @param abcdFieldGetter : the ABCD parser
*/
private void prepareCollectors(Abcd206ImportState state, NodeList unitsList, Abcd206XMLFieldGetter abcdFieldGetter) {
- List<String> collectors = new ArrayList<String>();
- List<String> teams = new ArrayList<String>();
- List<List<String>> collectorinteams = new ArrayList<List<String>>();
+ TeamOrPersonBase teamOrPerson = null;
+
+ //ImportHelper.setOriginalSource(teamOrPerson, state.getConfig().getSourceReference(), collector, "Collector");
for (int i = 0; i < unitsList.getLength(); i++) {
this.getCollectorsFromXML((Element) unitsList.item(i), abcdFieldGetter, state);
- for (String agent : state.getDataHolder().gatheringAgentList) {
- collectors.add(agent);
- }
- List<String> tmpTeam = new ArrayList<String>(new HashSet<String>(state.getDataHolder().gatheringTeamList));
- if(!tmpTeam.isEmpty()) {
- teams.add(StringUtils.join(tmpTeam.toArray()," & "));
- }
- for (String agent:tmpTeam) {
- collectors.add(agent);
- }
- }
-
- List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
- List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
-
-
- //existing teams in DB
- Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
- List<UuidAndTitleCache<Team>> hiberTeam = new ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
-
- Set<UUID> uuids = new HashSet<UUID>();
- for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
- uuids.add(hibernateT.getUuid());
- }
- if (!uuids.isEmpty()){
- List<AgentBase> existingTeams = getAgentService().find(uuids);
- for (AgentBase<?> existingP:existingTeams){
- titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
+ if (!StringUtils.isBlank(state.getDataHolder().gatheringAgents)){
+ teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgents);
+ if (!state.getPersonStore().containsId(state.getDataHolder().gatheringAgents)) {
+ state.getPersonStore().put(state.getDataHolder().gatheringAgents, teamOrPerson);
+ if (logger.isDebugEnabled()) { logger.debug("Stored author " + state.getDataHolder().gatheringAgents ); }
+ } else {
+ logger.warn("Not imported author with duplicated aut_id " + state.getDataHolder().gatheringAgents );
+ }
}
- }
-
- Map<String,UUID> teamMap = new HashMap<String, UUID>();
- for (UuidAndTitleCache<Team> uuidt:hiberTeam){
- teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
}
- //existing persons in DB
- 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){
- uuids.add(hibernateP.getUuid());
- }
- if (!uuids.isEmpty()){
- List<AgentBase> existingPersons = getAgentService().find(uuids);
- for (AgentBase<?> existingP:existingPersons){
- titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
- }
- }
- Map<String,UUID> personMap = new HashMap<String, UUID>();
- for (UuidAndTitleCache<Person> person:hiberPersons){
- personMap.put(person.getTitleCache(), person.getUuid());
- }
- java.util.Collection<Person> personToadd = new ArrayList<Person>();
- java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
+// List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
+// List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
+//
+//
+// //existing teams in DB
+// Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
+ // List<UuidAndTitleCache<Team>> hiberTeam = new ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
+
+// Set<UUID> uuids = new HashSet<UUID>();
+// for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
+// uuids.add(hibernateT.getUuid());
+// }
+// if (!uuids.isEmpty()){
+// List<AgentBase> existingTeams = getAgentService().find(uuids);
+// for (AgentBase<?> existingP:existingTeams){
+// titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
+// }
+// }
- for (String collector:collectorsU){
- Person p = Person.NewInstance();
- p.setTitleCache(collector,true);
- if (!personMap.containsKey(p.getTitleCache())){
- personToadd.add(p);
- }
- }
- for (String team:teamsU){
- Team p = Team.NewInstance();
- p.setTitleCache(team,true);
- if (!teamMap.containsKey(p.getTitleCache())){
- teamToAdd.add(p);
- }
- }
- if(!personToadd.isEmpty()){
- for (Person agent: personToadd){
- save(agent, state);
- titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent, Person.class) );
- }
- }
+// Map<String,UUID> teamMap = new HashMap<String, UUID>();
+// for (UuidAndTitleCache<Team> uuidt:hiberTeam){
+// teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
+// }
- Person ptmp ;
- Map <String,Integer>teamdone = new HashMap<String, Integer>();
- for (List<String> collteam: collectorinteams){
- if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
- Team team = new Team();
- boolean em =true;
- for (String collector:collteam){
- ptmp = Person.NewInstance();
- ptmp.setTitleCache(collector,true);
- Person p2 = titleCachePerson.get(ptmp.getTitleCache());
- team.addTeamMember(p2);
- em=false;
- }
- if (!em) {
- teamToAdd.add(team);
- }
- teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
- }
- }
-
- if(!teamToAdd.isEmpty()){
- for (Team agent: teamToAdd){
- save(agent, state);
- titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy( agent,Team.class) );
- }
- }
+ //existing persons in DB
+// 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){
+// uuids.add(hibernateP.getUuid());
+// }
+//
+// if (!uuids.isEmpty()){
+// List<AgentBase> existingPersons = getAgentService().find(uuids);
+// for (AgentBase<?> existingP:existingPersons){
+// titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
+// }
+// }
+//
+// Map<String,UUID> personMap = new HashMap<String, UUID>();
+// for (UuidAndTitleCache<Person> person:hiberPersons){
+// personMap.put(person.getTitleCache(), person.getUuid());
+// }
+//
+// java.util.Collection<Person> personToadd = new ArrayList<Person>();
+// java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
+//
+// for (String collector:collectorsU){
+// Person p = Person.NewInstance();
+// p.setTitleCache(collector,true);
+// if (!personMap.containsKey(p.getTitleCache())){
+// personToadd.add(p);
+// }
+// }
+// for (String team:teamsU){
+// Team p = Team.NewInstance();
+// p.setTitleCache(team,true);
+// if (!teamMap.containsKey(p.getTitleCache())){
+// teamToAdd.add(p);
+// }
+// }
+//
+// if(!personToadd.isEmpty()){
+// for (Person agent: personToadd){
+// save(agent, state);
+// titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent, Person.class) );
+// }
+// }
+//
+// Person ptmp ;
+// Map <String,Integer>teamdone = new HashMap<String, Integer>();
+// for (List<String> collteam: collectorinteams){
+// if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
+// Team team = new Team();
+// boolean em =true;
+// for (String collector:collteam){
+// ptmp = Person.NewInstance();
+// ptmp.setTitleCache(collector,true);
+// Person p2 = titleCachePerson.get(ptmp.getTitleCache());
+// team.addTeamMember(p2);
+// em=false;
+// }
+// if (!em) {
+// teamToAdd.add(team);
+// }
+// teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
+// }
+// }
+//
+// if(!teamToAdd.isEmpty()){
+// for (Team agent: teamToAdd){
+// save(agent, state);
+// titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy( agent,Team.class) );
+// }
+// }
- ((Abcd206ImportConfigurator) state.getConfig()).setTeams(titleCacheTeam);
- ((Abcd206ImportConfigurator) state.getConfig()).setPersons(titleCachePerson);
+// ((Abcd206ImportConfigurator) state.getConfig()).setTeams(titleCacheTeam);
+// ((Abcd206ImportConfigurator) state.getConfig()).setPersons(titleCachePerson);
}
@Override
import org.apache.log4j.Logger;
+import eu.etaxonomy.cdm.io.common.MapWrapper;
import eu.etaxonomy.cdm.io.specimen.SpecimenImportStateBase;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
/**
* @author a.mueller
private String prefix;
-
+ MapWrapper<TeamOrPersonBase<?>> personStore;
//****************** CONSTRUCTOR ***************************************************/
- public Abcd206ImportState(Abcd206ImportConfigurator config) {
+ /**
+ * @return the personStore
+ */
+ public MapWrapper<TeamOrPersonBase<?>> getPersonStore() {
+ return personStore;
+ }
+
+ /**
+ * @param personStore the personStore to set
+ */
+ public void setPersonStore(MapWrapper<TeamOrPersonBase<?>> personStore) {
+ this.personStore = personStore;
+ }
+
+ public Abcd206ImportState(Abcd206ImportConfigurator config) {
super(config);
setReport(new SpecimenImportReport());
setTransformer(new AbcdTransformer());
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Map;
import org.apache.log4j.Logger;
import org.w3c.dom.Element;
protected void getScientificNames(NodeList group) {
NodeList identifications, results;
String tmpName = null;
-
+ //TODO: add the identifier!!
+// abcd:Identification>
+// <abcd:Result>
+// <abcd:TaxonIdentified>
+// <abcd:ScientificName>
+// <abcd:FullScientificNameString>Melosira varians C. Agardh</abcd:FullScientificNameString>
+// <abcd:NameAtomised><abcd:Botanical><abcd:GenusOrMonomial>Melosira</abcd:GenusOrMonomial><abcd:FirstEpithet>varians</abcd:FirstEpithet><abcd:Rank>sp.</abcd:Rank><abcd:AuthorTeam>C.Agardh</abcd:AuthorTeam></abcd:Botanical></abcd:NameAtomised>
+// </abcd:ScientificName>
+// </abcd:TaxonIdentified>
+// </abcd:Result>
+// <abcd:PreferredFlag>true</abcd:PreferredFlag>
+// <abcd:Identifiers>
+// <abcd:Identifier>
+// <abcd:PersonName><abcd:FullName>W.-H. Kusber</abcd:FullName></abcd:PersonName>
+// </abcd:Identifier>
+// </abcd:Identifiers>
+// <abcd:Date>
+// <abcd:DateText>2014-07-11T00:00:00</abcd:DateText></abcd:Date>
+// </abcd:Identification>
for (int j = 0; j < group.getLength(); j++) {
if (group.item(j).getNodeName().equals(prefix + "Identification")) {
identifications = group.item(j).getChildNodes();
dataHolder.altitude = -9999;
}
- try {
- group = root.getElementsByTagName(prefix + "Depth");
- path = group.item(0).getNodeName();
- getHierarchie(group.item(0));
- dataHolder.knownABCDelements.add(path);
- path = "";
- dataHolder.depth = Integer.valueOf(group.item(0).getTextContent());
- } catch (NullPointerException e) {
- dataHolder.depth = -9999;
- }
+ getGatheringDepth(root);
try {
group = root.getElementsByTagName(prefix + "NamedArea");
}
}
+
+ /**
+ * @param root
+ */
+ private void getGatheringDepth(Element root) {
+ NodeList group;
+ try {
+ group = root.getElementsByTagName(prefix + "Gathering");
+ for (int i = 0; i < group.getLength(); i++) {
+ NodeList children = group.item(i).getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item(j).getNodeName().equals(prefix + "Depth")) {
+ NodeList altitudes = children.item(j).getChildNodes();
+ for (int k = 0; k < altitudes.getLength(); k++) {
+ if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactText")) {
+ path = altitudes.item(k).getNodeName();
+ getHierarchie(altitudes.item(k));
+ dataHolder.knownABCDelements.add(path);
+ path = "";
+ try{
+ dataHolder.setGatheringDepthText(altitudes.item(k).getTextContent());
+ }catch(NumberFormatException e){
+ logger.debug("Gathering depth value is not parsable to double: " + altitudes.item(k).getTextContent());
+ }
+ }
+ }
+ }
+ }
+ }
+ } catch (NullPointerException e) {
+ dataHolder.setDepth( -9999.0);
+ }
+ if(dataHolder.getDepth()==null){
+ group = root.getElementsByTagName(prefix + "Gathering");
+ for (int i = 0; i < group.getLength(); i++) {
+ NodeList children = group.item(i).getChildNodes();
+ for (int j = 0; j < children.getLength(); j++) {
+ if (children.item(j).getNodeName().equals(prefix + "Depth")) {
+ NodeList altitudes = children.item(j).getChildNodes();
+ for (int k = 0; k < altitudes.getLength(); k++) {
+ if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactAtomised")) {
+ NodeList facts = altitudes.item(k).getChildNodes();
+ for (int l = 0; l < facts.getLength(); l++) {
+ if (facts.item(l).getNodeName().equalsIgnoreCase(prefix + "LowerValue")) {
+ path = facts.item(l).getNodeName();
+ getHierarchie(facts.item(l));
+ dataHolder.knownABCDelements.add(path);
+ path = "";
+ try{
+ dataHolder.setGatheringDepthMin(Double.parseDouble(facts.item(l).getTextContent()));
+ } catch(NumberFormatException e){
+ logger.debug("Gathering depth min is not numeric. " + facts.item(l).getTextContent());
+ }
+ }
+ else if (facts.item(l).getNodeName().equalsIgnoreCase(prefix + "UpperValue")) {
+ path = facts.item(l).getNodeName();
+ getHierarchie(facts.item(l));
+ dataHolder.knownABCDelements.add(path);
+ path = "";
+ try{
+ dataHolder.setGatheringDepthMax(Double.parseDouble(facts.item(l).getTextContent()));
+ }catch(NumberFormatException e){
+ logger.debug("Gathering depth max is not numeric. " + facts.item(l).getTextContent());
+ }
+ }
+ else if (facts.item(l).getNodeName().equals(prefix + "UnitOfMeasurement")) {
+ path = facts.item(l).getNodeName();
+ getHierarchie(facts.item(l));
+ dataHolder.knownABCDelements.add(path);
+ path = "";
+ dataHolder.setGatheringDepthUnit(facts.item(l).getTextContent());
+ } else{
+ System.out.println(facts.item(l).getNodeName() + " " + facts.item(l).getTextContent());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
/**
* getMultimedia: get the FileURI objects
* @param root
*/
protected void getMultimedia(Element root) {
- NodeList group, multimedias, multimedia;
+ NodeList group, multimedias, multimedia, creators, creator, copyRightNodes, iprNodes, textNodes, licences, copyrights;
try {
group = root.getElementsByTagName(prefix + "MultiMediaObjects");
for (int i = 0; i < group.getLength(); i++) {
for (int j = 0; j < multimedias.getLength(); j++) {
if (multimedias.item(j).getNodeName().equals(prefix + "MultiMediaObject")) {
multimedia = multimedias.item(j).getChildNodes();
+ Map<String,String> mediaObjectMap = new HashMap<String, String>();
+ String fileUri = "";
for (int k = 0; k < multimedia.getLength(); k++) {
- if (multimedia.item(k).getNodeName().equals(prefix + "FileURI")) {
- dataHolder.getMultimediaObjects().add(multimedia.item(k).getTextContent());
+ if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "fileURI")) {
+ fileUri = multimedia.item(k).getTextContent();
+ mediaObjectMap.put("fileUri", fileUri);
path = multimedia.item(k).getNodeName();
getHierarchie(multimedia.item(k));
dataHolder.knownABCDelements.add(path);
path = "";
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "context")) {
+ mediaObjectMap.put("Context", multimedia.item(k).getTextContent());
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creators")){
+ String creatorString = "";
+ creators = multimedia.item(k).getChildNodes();
+ for (int l = 0; l < creators.getLength(); l++) {
+
+ if (creators.item(l).getNodeName().equalsIgnoreCase(prefix + "Creator")){
+ if (creatorString != ""){
+ creatorString += ", ";
+ }
+ creatorString += creators.item(l).getTextContent();
+ }
+ }
+ mediaObjectMap.put("Creators",creatorString);
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creator")){
+ mediaObjectMap.put("Creators",multimedia.item(k).getTextContent());
+ } else if (multimedia.item(k).getNodeName().equals("CreatedDate")){
+ mediaObjectMap.put("CreatedDate",multimedia.item(k).getTextContent());
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "comment")){
+ mediaObjectMap.put("Comment",multimedia.item(k).getTextContent());
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "IPR")){
+ String copyRightString = "";
+ iprNodes = multimedia.item(k).getChildNodes();
+ for (int l = 0; l < iprNodes.getLength(); l++) {
+ if (iprNodes.item(l).getNodeName().equalsIgnoreCase(prefix + "Copyrights")){
+ copyRightNodes = iprNodes.item(l).getChildNodes();
+ for (int m = 0; m < copyRightNodes.getLength(); m++) {
+ if (copyRightNodes.item(l).getNodeName().equalsIgnoreCase(prefix + "Copyright")){
+ copyrights = copyRightNodes.item(l).getChildNodes();
+ for (int n = 0; n < copyrights.getLength(); n++){
+ if (copyrights.item(n).getNodeName().equalsIgnoreCase(prefix + "text")){
+ //TODO: decide whether this is the copyright owner or a description text
+ }
+ }
+ }
+ }
+ }
+ }
+
+
+
+ // TODO: mediaObjectMap.put("IPR",multimedia.item(k).getTextContent());
+ } else{
+ System.out.println(multimedia.item(k).getNodeName() + " " + multimedia.item(k).getTextContent());
}
+
+ }
+ if (fileUri != ""){
+ dataHolder.putMultiMediaObject(fileUri,mediaObjectMap);
}
}
}
*/
protected void getGatheringPeople(Element root) {
try {
- dataHolder.gatheringAgentList = new ArrayList<String>();
+ dataHolder.gatheringAgents = "";
NodeList group = root.getElementsByTagName(prefix + "GatheringAgent");
for (int i = 0; i < group.getLength(); i++) {
dataHolder.knownABCDelements.add(path);
path = "";
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
- dataHolder.gatheringAgentList.add(persons.item(k).getTextContent());
+
+ dataHolder.gatheringAgents += persons.item(k).getTextContent();
}
}
}
dataHolder.knownABCDelements.add(path);
path = "";
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
- dataHolder.gatheringAgentList.add(persons.item(k).getTextContent());
+ dataHolder.gatheringAgents+=persons.item(k).getTextContent();
}
}
}
}
} catch (NullPointerException e) {
- dataHolder.gatheringAgentList = new ArrayList<String>();
- }
- if (dataHolder.gatheringAgentList.size() > 1){
- dataHolder.gatheringTeamList.addAll(dataHolder.gatheringAgentList);
- dataHolder.gatheringAgentList = new ArrayList<String>();
+ dataHolder.gatheringAgents = "";
}
+
}
/*PARSING METHODS*/
return atomisedMap;
}
+
+ /**
+ * @param root
+ */
+ public void getGatheringImages(Element root) {
+ NodeList group, multimedias, multimedia, creators, creator;
+ try {
+ group = root.getElementsByTagName(prefix + "SiteImages");
+ for (int i = 0; i < group.getLength(); i++) {
+ multimedias = group.item(i).getChildNodes();
+ for (int j = 0; j < multimedias.getLength(); j++) {
+ if (multimedias.item(j).getNodeName().equals(prefix + "SiteImage")) {
+ multimedia = multimedias.item(j).getChildNodes();
+ Map<String,String> mediaObjectMap = new HashMap<String, String>();
+ String fileUri = "";
+ for (int k = 0; k < multimedia.getLength(); k++) {
+
+
+ if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "fileURI")) {
+ fileUri = multimedia.item(k).getTextContent();
+ mediaObjectMap.put("fileUri", fileUri);
+ path = multimedia.item(k).getNodeName();
+ getHierarchie(multimedia.item(k));
+ dataHolder.knownABCDelements.add(path);
+ path = "";
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Context")) {
+ mediaObjectMap.put("Context", multimedia.item(k).getTextContent());
+ }else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Comment")) {
+ mediaObjectMap.put("Comment", multimedia.item(k).getTextContent());
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creators")){
+ String creatorString = "";
+ creators = multimedia.item(k).getChildNodes();
+ for (int l = 0; l < creators.getLength(); l++) {
+
+ if (creators.item(l).getNodeName().equalsIgnoreCase(prefix + "Creator")){
+ if (creatorString != ""){
+ creatorString += ", ";
+ }
+ creatorString += creators.item(l).getTextContent();
+ }
+ }
+ mediaObjectMap.put("Creators",creatorString);
+ } else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creator")){
+ mediaObjectMap.put("Creators",multimedia.item(k).getTextContent());
+ }
+ }
+ if (fileUri != ""){
+ dataHolder.putGatheringMultiMediaObject(fileUri,mediaObjectMap);
+ }
+ }
+ }
+ }
+ } catch (NullPointerException e) {
+ logger.info(e);
+ }
+
+ }
+
}
-// $Id$
-/**
-* 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.File;
-import java.io.FileNotFoundException;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
-import eu.etaxonomy.cdm.model.taxon.Taxon;
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;
-
-/**
- * Gathers information about the ABCD import and presents them in a suitable way.
- * @author pplitzner
- * @date Jan 23, 2015
- *
- */
-public class SpecimenImportReport {
-
- static private final Logger logger = Logger.getLogger(SpecimenImportReport.class);
-
-
- private final List<Taxon> createdTaxa = new ArrayList<Taxon>();
- private final Map<Taxon, List<UnitIdSpecimen>> taxonToAssociatedSpecimens = new HashMap<Taxon, List<UnitIdSpecimen>>();
- private final Map<UnitIdSpecimen, List<UnitIdSpecimen>> derivateMap = new HashMap<UnitIdSpecimen, List<UnitIdSpecimen>>();
- private final List<UnitIdSpecimen> alreadyExistingSpecimens = new ArrayList<UnitIdSpecimen>();
- private final List<TaxonNameBase<?, ?>> createdNames = new ArrayList<TaxonNameBase<?,?>>();
- private final List<TaxonNode> createdTaxonNodes = new ArrayList<TaxonNode>();
- private final List<String> infoMessages = new ArrayList<String>();
-
- public void addTaxon(Taxon taxon){
- createdTaxa.add(taxon);
- }
-
- public void addName(TaxonNameBase<?, ?> taxonName){
- createdNames.add(taxonName);
- }
-
- public void addTaxonNode(TaxonNode taxonNode){
- createdTaxonNodes.add(taxonNode);
- }
-
- public void addDerivate(DerivedUnit parent, SpecimenImportConfiguratorBase config){
- addDerivate(parent, null, config);
- }
-
- public void addDerivate(DerivedUnit parent, DerivedUnit child, SpecimenImportConfiguratorBase config){
- 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(SpecimenImportUtility.getUnitID(child, config), child));
- }
- derivateMap.put(parentUnitIdSpecimen, children);
- }
-
- public void addIndividualAssociation(Taxon taxon, String derivedUnitId, DerivedUnit derivedUnitBase) {
- UnitIdSpecimen derivedUnitIdSpecimen = new UnitIdSpecimen(derivedUnitId, derivedUnitBase);
- List<UnitIdSpecimen> associatedSpecimens = taxonToAssociatedSpecimens.get(taxon);
- if(associatedSpecimens==null){
- associatedSpecimens = new ArrayList<UnitIdSpecimen>();
- }
- associatedSpecimens.add(derivedUnitIdSpecimen);
- taxonToAssociatedSpecimens.put(taxon, associatedSpecimens);
- }
-
- public void addAlreadyExistingSpecimen(String unitId, DerivedUnit derivedUnit){
- alreadyExistingSpecimens.add(new UnitIdSpecimen(unitId, derivedUnit));
- }
-
- 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());
- }
-
- public void addInfoMessage(String message) {
- infoMessages.add(message);
- }
-
- public void printReport(URI reportUri) {
- PrintStream out;
- if(reportUri != null){
- try {
- out = new PrintStream(new File(reportUri));
- } catch (FileNotFoundException e) {
- logger.warn("Report file could not be found.");
- out = System.out;
- }
- }
- else{
- out = System.out;
- }
- printReport(out);
- }
-
-
- public void printReport(PrintStream out) {
-
- out.println("++++++++Import Report+++++++++");
- //all specimens
- Set<UnitIdSpecimen> allSpecimens = new HashSet<UnitIdSpecimen>();
- for (Entry<UnitIdSpecimen, List<UnitIdSpecimen>> entry : derivateMap.entrySet()) {
- UnitIdSpecimen parentSpecimen = entry.getKey();
- allSpecimens.add(parentSpecimen);
- for (UnitIdSpecimen childSpecimen : entry.getValue()) {
- allSpecimens.add(childSpecimen);
- }
- }
- out.println("Specimens created: "+allSpecimens.size());
- Map<SpecimenOrObservationType, Integer> specimenTypeToCount = new HashMap<SpecimenOrObservationType, Integer>();
- for (UnitIdSpecimen unitIdSpecimen : allSpecimens) {
- incrementSpecimenTypeCount(specimenTypeToCount, unitIdSpecimen);
- }
- for(Entry<SpecimenOrObservationType, Integer> entry:specimenTypeToCount.entrySet()){
- SpecimenOrObservationType type = entry.getKey();
- out.println(type+": "+entry.getValue());
- }
- //not imported
- out.println("Skipped/not imported: "+alreadyExistingSpecimens.size());
- out.println("\n");
-
- out.println("Imported unit ids");
- for (UnitIdSpecimen unitIdSpecimen : allSpecimens) {
- out.print(unitIdSpecimen.unitId+", ");
- }
- out.println("\n");
-
- out.println("Ignored unit ids");
- for (UnitIdSpecimen unitIdSpecimen : alreadyExistingSpecimens) {
- out.print(unitIdSpecimen.unitId+", ");
- }
- out.println("\n");
-
- //taxon name
- out.println("---Created Taxon Names ("+createdNames.size()+")---");
- for (TaxonNameBase<?, ?> taxonName : createdNames) {
- out.println(taxonName.getTitleCache());
- }
- out.println("\n");
-
- //taxa
- out.println("---Created Taxa ("+createdTaxa.size()+")---");
- for (Taxon taxon : createdTaxa) {
- out.println(taxon.getTitleCache());
- }
- out.println("\n");
-
- //taxon nodes
- out.println("---Created Taxon Nodes ("+createdTaxonNodes.size()+")---");
- for (TaxonNode taxonNode : createdTaxonNodes) {
- String nodeString = taxonNode.toString();
- if(taxonNode.getTaxon()!=null){
- nodeString += " ("+taxonNode.getTaxon().getTitleCache()+")";
- }
- if(taxonNode.getParent()!=null){
- nodeString += " with parent "+taxonNode.getParent();
- if(taxonNode.getParent().getTaxon()!=null){
- nodeString += " ("+taxonNode.getParent().getTaxon().getTitleCache()+")";
- }
- }
- out.println(nodeString);
- }
- out.println("\n");
-
- //not imported
- out.println("---Already existing specimen/not imported ("+alreadyExistingSpecimens.size()+")---");
- for(UnitIdSpecimen specimen:alreadyExistingSpecimens){
- out.println(formatSpecimen(specimen));
- }
- out.println("\n");
-
- //taxa with associated specimens
- out.println("---Taxa with associated specimens ("+taxonToAssociatedSpecimens.size()+")---");
- for(Entry<Taxon, List<UnitIdSpecimen>> entry:taxonToAssociatedSpecimens.entrySet()){
- Taxon taxon = entry.getKey();
- List<UnitIdSpecimen> specimens = entry.getValue();
- out.println(taxon.getTitleCache() + " ("+specimens.size()+")");
- for (UnitIdSpecimen derivedUnit : specimens) {
- out.println("\t- "+formatSpecimen(derivedUnit));
- //check for derivatives
- List<UnitIdSpecimen> list = derivateMap.get(derivedUnit);
- for (UnitIdSpecimen derivate : list) {
- out.println("\t\t- "+formatSpecimen(derivate));
- }
- }
- }
- out.println("\n");
- out.println("\n");
- //info messages
- out.println("---Info messages---");
- for(String message:infoMessages){
- out.println(message);
- out.println("---");
- }
- if(out!=System.out){
- out.close();
- }
- }
-
- private void incrementSpecimenTypeCount(Map<SpecimenOrObservationType, Integer> specimenTypeToCount,
- UnitIdSpecimen specimen) {
- SpecimenOrObservationType specimenType = specimen.getSpecimen().getRecordBasis();
- Integer count = specimenTypeToCount.get(specimenType);
- if(count==null){
- count = 1;
- }
- else{
- count++;
- }
- specimenTypeToCount.put(specimenType, count);
- }
-
- private String formatSpecimen(UnitIdSpecimen specimen){
- return "("+specimen.getUnitId()+") ["+specimen.getSpecimen().getRecordBasis()+"] "+specimen.getSpecimen().getTitleCache();
- }
-
- private class UnitIdSpecimen{
- private final String unitId;
- private final SpecimenOrObservationBase<?> specimen;
-
-
- public UnitIdSpecimen(String unitId, SpecimenOrObservationBase<?> specimen) {
- super();
- this.unitId = unitId;
- this.specimen = specimen;
- }
- public String getUnitId() {
- return unitId;
- }
- public SpecimenOrObservationBase<?> getSpecimen() {
- return specimen;
- }
- @Override
- public int hashCode() {
- final int prime = 31;
- int result = 1;
- result = prime * result + ((specimen == null) ? 0 : specimen.hashCode());
- result = prime * result + ((unitId == null) ? 0 : unitId.hashCode());
- return result;
- }
- @Override
- public boolean equals(Object obj) {
- if (this == obj) {
- return true;
- }
- if (obj == null) {
- return false;
- }
- if (getClass() != obj.getClass()) {
- return false;
- }
- UnitIdSpecimen other = (UnitIdSpecimen) obj;
- if (specimen == null) {
- if (other.specimen != null) {
- return false;
- }
- } else if (!specimen.equals(other.specimen)) {
- return false;
- }
- if (unitId == null) {
- if (other.unitId != null) {
- return false;
- }
- } else if (!unitId.equals(other.unitId)) {
- return false;
- }
- return true;
- }
-
- }
-
-}
+// $Id$\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.File;\r
+import java.io.FileNotFoundException;\r
+import java.io.PrintStream;\r
+import java.io.PrintWriter;\r
+import java.io.StringWriter;\r
+import java.net.URI;\r
+import java.util.ArrayList;\r
+import java.util.HashMap;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Map.Entry;\r
+import java.util.Set;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
+import eu.etaxonomy.cdm.model.taxon.Taxon;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
+\r
+/**\r
+ * Gathers information about the ABCD import and presents them in a suitable way.\r
+ * @author pplitzner\r
+ * @date Jan 23, 2015\r
+ *\r
+ */\r
+public class SpecimenImportReport {\r
+\r
+ static private final Logger logger = Logger.getLogger(SpecimenImportReport.class);\r
+\r
+\r
+ private final List<Taxon> createdTaxa = new ArrayList<Taxon>();\r
+ private final Map<Taxon, List<UnitIdSpecimen>> taxonToAssociatedSpecimens = new HashMap<Taxon, List<UnitIdSpecimen>>();\r
+ private final Map<UnitIdSpecimen, List<UnitIdSpecimen>> derivateMap = new HashMap<UnitIdSpecimen, List<UnitIdSpecimen>>();\r
+ private final List<UnitIdSpecimen> alreadyExistingSpecimens = new ArrayList<UnitIdSpecimen>();\r
+ private final List<TaxonNameBase<?, ?>> createdNames = new ArrayList<TaxonNameBase<?,?>>();\r
+ private final List<TaxonNode> createdTaxonNodes = new ArrayList<TaxonNode>();\r
+ private final List<String> infoMessages = new ArrayList<String>();\r
+\r
+ public void addTaxon(Taxon taxon){\r
+ createdTaxa.add(taxon);\r
+ }\r
+\r
+ public void addName(TaxonNameBase<?, ?> taxonName){\r
+ createdNames.add(taxonName);\r
+ }\r
+\r
+ public void addTaxonNode(TaxonNode taxonNode){\r
+ createdTaxonNodes.add(taxonNode);\r
+ }\r
+\r
+ public void addDerivate(DerivedUnit parent, SpecimenImportConfiguratorBase config){\r
+ addDerivate(parent, null, config);\r
+ }\r
+\r
+ public void addDerivate(DerivedUnit parent, DerivedUnit child, SpecimenImportConfiguratorBase config){\r
+ UnitIdSpecimen parentUnitIdSpecimen = new UnitIdSpecimen(SpecimenImportUtility.getUnitID(parent, config), parent);\r
+ List<UnitIdSpecimen> children = derivateMap.get(parentUnitIdSpecimen);\r
+ if(children==null){\r
+ children = new ArrayList<UnitIdSpecimen>();\r
+ }\r
+ if(child!=null){\r
+ children.add(new UnitIdSpecimen(SpecimenImportUtility.getUnitID(child, config), child));\r
+ }\r
+ derivateMap.put(parentUnitIdSpecimen, children);\r
+ }\r
+\r
+ public void addIndividualAssociation(Taxon taxon, String derivedUnitId, DerivedUnit derivedUnitBase) {\r
+ UnitIdSpecimen derivedUnitIdSpecimen = new UnitIdSpecimen(derivedUnitId, derivedUnitBase);\r
+ List<UnitIdSpecimen> associatedSpecimens = taxonToAssociatedSpecimens.get(taxon);\r
+ if(associatedSpecimens==null){\r
+ associatedSpecimens = new ArrayList<UnitIdSpecimen>();\r
+ }\r
+ associatedSpecimens.add(derivedUnitIdSpecimen);\r
+ taxonToAssociatedSpecimens.put(taxon, associatedSpecimens);\r
+ }\r
+\r
+ public void addAlreadyExistingSpecimen(String unitId, DerivedUnit derivedUnit){\r
+ alreadyExistingSpecimens.add(new UnitIdSpecimen(unitId, derivedUnit));\r
+ }\r
+\r
+ public void addException(String message, Exception e) {\r
+ StringWriter errors = new StringWriter();\r
+ e.printStackTrace(new PrintWriter(errors));\r
+ infoMessages.add(message+"\n"+e.getMessage()+"\n"+errors.toString());\r
+ }\r
+\r
+ public void addInfoMessage(String message) {\r
+ infoMessages.add(message);\r
+ }\r
+\r
+ public void printReport(URI reportUri) {\r
+ PrintStream out;\r
+ if(reportUri != null){\r
+ try {\r
+ out = new PrintStream(new File(reportUri));\r
+ } catch (FileNotFoundException e) {\r
+ logger.warn("Report file could not be found.");\r
+ out = System.out;\r
+ }\r
+ }\r
+ else{\r
+ out = System.out;\r
+ }\r
+ printReport(out);\r
+ }\r
+\r
+\r
+ public void printReport(PrintStream out) {\r
+\r
+ out.println("++++++++Import Report+++++++++");\r
+ //all specimens\r
+ Set<UnitIdSpecimen> allSpecimens = new HashSet<UnitIdSpecimen>();\r
+ for (Entry<UnitIdSpecimen, List<UnitIdSpecimen>> entry : derivateMap.entrySet()) {\r
+ UnitIdSpecimen parentSpecimen = entry.getKey();\r
+ allSpecimens.add(parentSpecimen);\r
+ for (UnitIdSpecimen childSpecimen : entry.getValue()) {\r
+ allSpecimens.add(childSpecimen);\r
+ }\r
+ }\r
+ out.println("Specimens created: "+allSpecimens.size());\r
+ Map<SpecimenOrObservationType, Integer> specimenTypeToCount = new HashMap<SpecimenOrObservationType, Integer>();\r
+ for (UnitIdSpecimen unitIdSpecimen : allSpecimens) {\r
+ incrementSpecimenTypeCount(specimenTypeToCount, unitIdSpecimen);\r
+ }\r
+ for(Entry<SpecimenOrObservationType, Integer> entry:specimenTypeToCount.entrySet()){\r
+ SpecimenOrObservationType type = entry.getKey();\r
+ out.println(type+": "+entry.getValue());\r
+ }\r
+ //not imported\r
+ out.println("Skipped/not imported: "+alreadyExistingSpecimens.size());\r
+ out.println("\n");\r
+\r
+ out.println("Imported unit ids");\r
+ for (UnitIdSpecimen unitIdSpecimen : allSpecimens) {\r
+ out.print(unitIdSpecimen.unitId+", ");\r
+ }\r
+ out.println("\n");\r
+\r
+ out.println("Ignored unit ids");\r
+ for (UnitIdSpecimen unitIdSpecimen : alreadyExistingSpecimens) {\r
+ out.print(unitIdSpecimen.unitId+", ");\r
+ }\r
+ out.println("\n");\r
+\r
+ //taxon name\r
+ out.println("---Created Taxon Names ("+createdNames.size()+")---");\r
+ for (TaxonNameBase<?, ?> taxonName : createdNames) {\r
+ out.println(taxonName.getTitleCache());\r
+ }\r
+ out.println("\n");\r
+\r
+ //taxa\r
+ out.println("---Created Taxa ("+createdTaxa.size()+")---");\r
+ for (Taxon taxon : createdTaxa) {\r
+ out.println(taxon.getTitleCache());\r
+ }\r
+ out.println("\n");\r
+\r
+ //taxon nodes\r
+ out.println("---Created Taxon Nodes ("+createdTaxonNodes.size()+")---");\r
+ for (TaxonNode taxonNode : createdTaxonNodes) {\r
+ String nodeString = taxonNode.toString();\r
+ if(taxonNode.getTaxon()!=null){\r
+ nodeString += " ("+taxonNode.getTaxon().getTitleCache()+")";\r
+ }\r
+ if(taxonNode.getParent()!=null){\r
+ nodeString += " with parent "+taxonNode.getParent();\r
+ if(taxonNode.getParent().getTaxon()!=null){\r
+ nodeString += " ("+taxonNode.getParent().getTaxon().getTitleCache()+")";\r
+ }\r
+ }\r
+ out.println(nodeString);\r
+ }\r
+ out.println("\n");\r
+\r
+ //not imported\r
+ out.println("---Already existing specimen/not imported ("+alreadyExistingSpecimens.size()+")---");\r
+ for(UnitIdSpecimen specimen:alreadyExistingSpecimens){\r
+ out.println(formatSpecimen(specimen));\r
+ }\r
+ out.println("\n");\r
+\r
+ //taxa with associated specimens\r
+ out.println("---Taxa with associated specimens ("+taxonToAssociatedSpecimens.size()+")---");\r
+ for(Entry<Taxon, List<UnitIdSpecimen>> entry:taxonToAssociatedSpecimens.entrySet()){\r
+ Taxon taxon = entry.getKey();\r
+ List<UnitIdSpecimen> specimens = entry.getValue();\r
+ out.println(taxon.getTitleCache() + " ("+specimens.size()+")");\r
+ for (UnitIdSpecimen derivedUnit : specimens) {\r
+ out.println("\t- "+formatSpecimen(derivedUnit));\r
+ //check for derivatives\r
+ List<UnitIdSpecimen> list = derivateMap.get(derivedUnit);\r
+ for (UnitIdSpecimen derivate : list) {\r
+ out.println("\t\t- "+formatSpecimen(derivate));\r
+ }\r
+ }\r
+ }\r
+ out.println("\n");\r
+ out.println("\n");\r
+ //info messages\r
+ out.println("---Info messages---");\r
+ for(String message:infoMessages){\r
+ out.println(message);\r
+ out.println("---");\r
+ }\r
+ if(out!=System.out){\r
+ out.close();\r
+ }\r
+ }\r
+\r
+ private void incrementSpecimenTypeCount(Map<SpecimenOrObservationType, Integer> specimenTypeToCount,\r
+ UnitIdSpecimen specimen) {\r
+ SpecimenOrObservationType specimenType = specimen.getSpecimen().getRecordBasis();\r
+ Integer count = specimenTypeToCount.get(specimenType);\r
+ if(count==null){\r
+ count = 1;\r
+ }\r
+ else{\r
+ count++;\r
+ }\r
+ specimenTypeToCount.put(specimenType, count);\r
+ }\r
+\r
+ private String formatSpecimen(UnitIdSpecimen specimen){\r
+ return "("+specimen.getUnitId()+") ["+specimen.getSpecimen().getRecordBasis()+"] "+specimen.getSpecimen().getTitleCache();\r
+ }\r
+\r
+ private class UnitIdSpecimen{\r
+ private final String unitId;\r
+ private final SpecimenOrObservationBase<?> specimen;\r
+\r
+\r
+ public UnitIdSpecimen(String unitId, SpecimenOrObservationBase<?> specimen) {\r
+ super();\r
+ this.unitId = unitId;\r
+ this.specimen = specimen;\r
+ }\r
+ public String getUnitId() {\r
+ return unitId;\r
+ }\r
+ public SpecimenOrObservationBase<?> getSpecimen() {\r
+ return specimen;\r
+ }\r
+ @Override\r
+ public int hashCode() {\r
+ final int prime = 31;\r
+ int result = 1;\r
+ result = prime * result + ((specimen == null) ? 0 : specimen.hashCode());\r
+ result = prime * result + ((unitId == null) ? 0 : unitId.hashCode());\r
+ return result;\r
+ }\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ if (this == obj) {\r
+ return true;\r
+ }\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+ if (getClass() != obj.getClass()) {\r
+ return false;\r
+ }\r
+ UnitIdSpecimen other = (UnitIdSpecimen) obj;\r
+ if (specimen == null) {\r
+ if (other.specimen != null) {\r
+ return false;\r
+ }\r
+ } else if (!specimen.equals(other.specimen)) {\r
+ return false;\r
+ }\r
+ if (unitId == null) {\r
+ if (other.unitId != null) {\r
+ return false;\r
+ }\r
+ } else if (!unitId.equals(other.unitId)) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ }\r
+\r
+}\r
boolean result = defaultImport.invoke(importConfigurator).isSuccess();
assertTrue("Return value for import.invoke should be true", result);
- assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));
List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);
+ for (DerivedUnit derivedUnit:derivedUnits){
+ System.out.println(derivedUnit.getTitleCache());
+ }
+ assertEquals("Number of derived units is incorrect", 2, occurrenceService.count(DerivedUnit.class));
+ // List<DerivedUnit> derivedUnits = occurrenceService.list(DerivedUnit.class, null, null, null, null);
List<FieldUnit> fieldUnitsTemp = occurrenceService.list(FieldUnit.class, null, null, null, null);
assertEquals("Number of derived units is incorrect", 2, derivedUnits.size());
-// $Id$
-/**
-* 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.hibernate;
-
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.hibernate.LazyInitializationException;
-
-
-/**
- * Helper class to remove null values from collections which are left over artifacts due to
- * https://hibernate.atlassian.net/browse/HHH-9751
- *
- * @author a.kohlbecker
- * @date Jun 13, 2016
- *
- */
-public class HHH_9751_Util {
-
- private static final Logger logger = Logger.getLogger(HHH_9751_Util.class);
-
- /**
- *
- * @param collection
- * @return the number of null values removed from the collection
- */
- static public int removeAllNull(Collection collection) {
-
- int cnt = 0;
- try {
- if (collection.contains(null)){
- while(collection.contains(null)){
- cnt++;
- collection.remove(null);
- }
- }
- } catch (LazyInitializationException e) {
- logger.info("Cannot clean up uninitialized children without a session, skipping.");
- }
- return cnt;
- }
-
-}
+// $Id$\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.hibernate;\r
+\r
+import java.util.Collection;\r
+\r
+import org.apache.log4j.Logger;\r
+import org.hibernate.Hibernate;\r
+import org.hibernate.LazyInitializationException;\r
+\r
+\r
+/**\r
+ * Helper class to remove null values from collections which are left over artifacts due to\r
+ * https://hibernate.atlassian.net/browse/HHH-9751\r
+ *\r
+ * @author a.kohlbecker\r
+ * @date Jun 13, 2016\r
+ *\r
+ */\r
+public class HHH_9751_Util {\r
+\r
+ private static final Logger logger = Logger.getLogger(HHH_9751_Util.class);\r
+\r
+ /**\r
+ *\r
+ * @param collection\r
+ * @return the number of null values removed from the collection\r
+ */\r
+ static public int removeAllNull(Collection collection) {\r
+\r
+ int cnt = 0;\r
+ try {\r
+ if (Hibernate.isInitialized(collection)){\r
+ if (collection.contains(null)){\r
+ while(collection.contains(null)){\r
+ cnt++;\r
+ collection.remove(null);\r
+ }\r
+ }\r
+ }\r
+ } catch (LazyInitializationException e) {\r
+ logger.info("Cannot clean up uninitialized children without a session, skipping.");\r
+ }\r
+ return cnt;\r
+ }\r
+\r
+}\r
</property>\r
</bean>\r
\r
- <bean id="httpPreferenceService"\r
- class="org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter">\r
- <property name="service">\r
- <ref bean="preferenceServiceImpl" />\r
- </property>\r
- <property name="serviceInterface">\r
- <value>eu.etaxonomy.cdm.api.service.IPreferenceService</value>\r
- </property>\r
- </bean>\r
-\r
+ \r
<bean id="httpDescriptionService"\r
class="org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter">\r
<property name="service">\r
</property>\r
</bean>\r
\r
+ <bean id="httpPreferenceService"\r
+ class="org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter">\r
+ <property name="service">\r
+ <ref bean="preferenceServiceImpl" />\r
+ </property>\r
+ <property name="serviceInterface">\r
+ <value>eu.etaxonomy.cdm.api.service.IPreferenceService</value>\r
+ </property>\r
+ </bean>\r
+ \r
<bean id="httpProgressMonitorService"\r
class="org.springframework.remoting.httpinvoker.HttpInvokerServiceExporter">\r
<property name="service">\r
<prop key="/remoting/primer.service">httpPrimerService</prop>
<prop key="/remoting/progressmonitor.service">httpProgressMonitorService</prop>
<prop key="/remoting/reference.service">httpReferenceService</prop>
-
<prop key="/remoting/preference.service">httpPreferenceService</prop>
+ <prop key="/remoting/preference.service">httpPreferenceService</prop>
<prop key="/remoting/sequence.service">httpSequenceService</prop>
<prop key="/remoting/eventbase.service">httpEventBaseService</prop>
<prop key="/remoting/taxonnode.service">httpTaxonNodeService</prop>
BGBM BDI Projects / cdmlib.git / commitdiff