--- /dev/null
+/**
+* Copyright (C) 2017 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.app.greece;
+
+import java.net.URI;
+import java.util.UUID;
+
+import org.apache.log4j.Logger;
+
+import eu.etaxonomy.cdm.app.common.CdmDestinations;
+import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
+import eu.etaxonomy.cdm.database.DbSchemaValidation;
+import eu.etaxonomy.cdm.database.ICdmDataSource;
+import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
+import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
+import eu.etaxonomy.cdm.io.common.ImportResult;
+import eu.etaxonomy.cdm.io.greece.GreeceStatusUpdaterConfigurator;
+import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
+
+/**
+ * @author a.mueller
+ * @since 08.12.2017
+ */
+public class GreeceStatusUpdaterActivator {
+
+ @SuppressWarnings("unused")
+ private static final Logger logger = Logger.getLogger(GreeceStatusUpdaterActivator.class);
+
+ static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
+// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_greece_checklist();
+
+ private static final UUID sourceUuid = UUID.fromString("7f898cf8-5eef-4321-ba17-64983cf7ea26");
+ private static final String fileName = "xxx.xlsx";
+
+
+ //check - import
+ static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
+
+ private void doImport(ICdmDataSource cdmDestination){
+
+ DbSchemaValidation schemaVal = cdmDestination.getDatabaseType() == DatabaseTypeEnum.H2 ? DbSchemaValidation.CREATE : DbSchemaValidation.VALIDATE;
+ URI source = greekChecklist(); //just any
+ //make Source
+ GreeceStatusUpdaterConfigurator config = GreeceStatusUpdaterConfigurator.NewInstance(source, cdmDestination);
+ config.setCheck(check);
+ config.setDbSchemaValidation(schemaVal);
+ config.setSourceReference(getSourceReference());
+ config.setNomenclaturalCode(NomenclaturalCode.ICNAFP);
+
+ CdmDefaultImport<GreeceStatusUpdaterConfigurator> myImport = new CdmDefaultImport<>();
+ ImportResult result = myImport.invoke(config);
+ System.out.println(result.createReport());
+
+ }
+
+ private URI greekChecklist(){
+ return URI.create("file:////BGBM-PESIHPC/Greece/" + fileName);
+ }
+
+ private Reference getSourceReference(){
+ Reference result = ReferenceFactory.newDatabase();
+ result.setTitle(fileName);
+ result.setUuid(sourceUuid);
+
+ return result;
+ }
+
+ public static void main(String[] args) {
+ GreeceStatusUpdaterActivator me = new GreeceStatusUpdaterActivator();
+ me.doImport(cdmDestination);
+ System.exit(0);
+ }
+}
--- /dev/null
+/**
+* Copyright (C) 2017 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.greece;
+
+import java.util.Map;
+import java.util.Set;
+import java.util.UUID;
+
+import org.apache.log4j.Logger;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
+import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
+import eu.etaxonomy.cdm.model.common.CdmBase;
+import eu.etaxonomy.cdm.model.description.CategoricalData;
+import eu.etaxonomy.cdm.model.description.Distribution;
+import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
+import eu.etaxonomy.cdm.model.description.State;
+import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+
+/**
+ * @author a.mueller
+ * @since 08.12.2017
+ */
+@Component
+public class GreeceStatusUpdaterImport
+ extends SimpleExcelTaxonImport<GreeceStatusUpdaterConfigurator>{
+
+ private static final UUID UUID_STATE_ALIEN_ESTABLISHED = UUID.fromString("0df082b1-d38a-455e-9406-8d5ca58c1df9");
+ private static final UUID UUID_STATE_ALIEN_NON_ESTABLISHED = UUID.fromString("0642289d-3f7a-408f-b84f-335fb720d952");
+ private static final UUID UUID_STATE_DOUBT_ALIEN_ESTABLISHEMENT_UNKNOWN = UUID.fromString("d2ff3b0c-d8b2-4f0c-9ed9-12455e22fb17");
+ private static final UUID UUID_STATE_NATIVE_RANGE_RESTRICTED = UUID.fromString("6a646be7-df29-4594-93bb-af3fa1c83c72");
+ private static final UUID UUID_STATE_NATIVE_NON_RANGE_RESTRICTED = UUID.fromString("fbfa2d04-5d3b-4e22-8c6e-6d1cb9902141");
+ private static final UUID UUID_STATE_NATIVE_RANGE_RESTRICTION_UNKNWON = UUID.fromString("711d62a8-0763-4cd1-902a-f340612f8e8b");
+ private static final UUID UUID_STATE_DOUBT_NATIVE_NON_RANGE_RESTRICTED = UUID.fromString("7291a253-3020-4207-807c-4dacae486b4e");
+
+ private static final UUID UUID_IUCN_FEATURE = UUID.fromString("fc2b07a7-febe-4f8a-8713-da198e19bd69");
+ private static final UUID UUID_IUCN_EXTINCT = UUID.fromString("4e2244ca-5858-4efb-9a24-57d18a24f1ef");
+ private static final UUID UUID_IUCN_CRITICALLY_ENDANGERED = UUID.fromString("cbbde993-1acc-4dfb-bc3c-4f3a11592d3d");
+ private static final UUID UUID_IUCN_ENDANGERED = UUID.fromString("39b0d998-9e4b-4ee6-990a-0b8b334f1c4d");
+ private static final UUID UUID_IUCN_VULNERABLE = UUID.fromString("bd116f8d-2b1f-489b-9ba6-690fed6088aa");
+ private static final UUID UUID_IUCN_NEAR_THREATENED = UUID.fromString("acb4f244-9fe0-4bcb-91e2-e9237c4f8165");
+ private static final UUID UUID_IUCN_LEAST_CONCERN = UUID.fromString("40656435-0749-4ea6-ad10-071d8eddc332");
+ private static final UUID UUID_IUCN_DATA_DEFICIENT = UUID.fromString("43518936-4bae-4fbc-a69b-5ccde7849bb3");
+ private static final UUID UUID_IUCN_NOT_EVALUATED = UUID.fromString("ac0f2fe8-a7c9-4724-9d2e-cbe3d213d5d4");
+
+
+ private static final UUID UUID_PD_FEATURE = UUID.fromString("3b08be3b-e3cc-41f2-8784-87414679f87d");
+ private static final UUID UUID_PD_NO = UUID.fromString("7ba99117-fadc-40fe-8961-3f805ec8035a");
+ private static final UUID UUID_PD_YES = UUID.fromString("60a5b995-b497-4813-9e7f-c1a49333b84f");
+ private static final String PRESIDENTIAL_DECREE_67_81 = "Presidential Decree 67/81";
+ private static final String STATUS = "Status";
+ private static final String ESTABLISHMENT = "Establishment";
+ private static final String RANGE_RESTRICTION = "Range-restriction";
+ private static final String REDLIST_CATEGORY = "IUCN RedlistCategory";
+ private static final String SCIENTIFIC_NAME = "scientificName";
+ private static final String TAXON_UUID = "taxon uid";
+ private static final long serialVersionUID = 1017757693469612631L;
+ private static final Logger logger = Logger.getLogger(GreeceStatusUpdaterImport.class);
+
+ @Override
+ protected void firstPass(SimpleExcelTaxonImportState<GreeceStatusUpdaterConfigurator> state) {
+
+ Map<String, String> record = state.getOriginalRecord();
+ String line = "line" + state.getCurrentLine() + ": ";
+
+ UUID taxonUuid = UUID.fromString(getValue(record, TAXON_UUID));
+ TaxonBase<?> taxonBase = getTaxonService().find(taxonUuid);
+ if (taxonBase == null) {
+ logger.warn(line+"no taxon " + taxonUuid);
+ return;
+ }else if (!taxonBase.isInstanceOf(Taxon.class)) {
+ logger.warn(line + "is not accepted " + taxonUuid);
+ return;
+ }
+ if(!checkTaxonName(state, taxonBase, line)) {
+ return;
+ }
+ Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
+
+ //delete absent distribution status
+ Set<Distribution> distributions = taxon.getDescriptionItems(Feature.DISTRIBUTION(), Distribution.class);
+ for (Distribution distribution : distributions) {
+ if (PresenceAbsenceTerm.ABSENT().equals(distribution.getStatus())) {
+ logger.info("Remove distribution");
+ distribution.getInDescription().removeElement(distribution);
+ }
+ }
+
+ //delete old status
+ Set<CategoricalData> statuss = taxon.getDescriptionItems(Feature.STATUS(), CategoricalData.class);
+ for (CategoricalData status : statuss) {
+ if (Feature.uuidStatus.equals(status.getFeature().getUuid())) {
+ logger.info("Remove status");
+ status.getInDescription().removeElement(status);
+ }
+ }
+
+ //new data
+ TaxonDescription newDescription = TaxonDescription.NewInstance(taxon);
+ String redListCategoryStr = getValue(record, REDLIST_CATEGORY);
+ String presidentialDecreeStr = getValue(record, PRESIDENTIAL_DECREE_67_81);
+ String statusStr = getValue(record, STATUS);
+ String establishmentStr = getValue(record, ESTABLISHMENT);
+ String rangeRestrictionStr = getValue(record, RANGE_RESTRICTION);
+
+ CategoricalData presidentialDecree = getPresidentialDecree(state, line, presidentialDecreeStr);
+ CategoricalData redListCategory = getRedListCategory(state, line, redListCategoryStr);
+ CategoricalData newStatus = getNewStatus(state, line, statusStr, establishmentStr, rangeRestrictionStr);
+ newDescription.addElement(presidentialDecree);
+ newDescription.addElement(redListCategory);
+ newDescription.addElement(newStatus);
+ }
+
+ private CategoricalData getNewStatus(SimpleExcelTaxonImportState<GreeceStatusUpdaterConfigurator> state,
+ String line, String statusStr, String establishmentStr, String rangeRestrictionStr) {
+
+ CategoricalData result;
+ State state2;
+ Feature stateFeature = Feature.STATUS();
+ if ("Alien".equalsIgnoreCase(statusStr) || "? Alien".equalsIgnoreCase(statusStr)) {
+ if("Established".equalsIgnoreCase(establishmentStr)) {
+ state2 = getStateTerm(state, UUID_STATE_ALIEN_ESTABLISHED);
+ }else if("Non-established".equalsIgnoreCase(establishmentStr)) {
+ state2 = getStateTerm(state, UUID_STATE_ALIEN_NON_ESTABLISHED);
+ }else if("Establishment unknown".equalsIgnoreCase(establishmentStr)) {
+ state2 = getStateTerm(state, UUID_STATE_DOUBT_ALIEN_ESTABLISHEMENT_UNKNOWN);
+ }else{
+ logger.warn(line+"Establishement not recognized: " + establishmentStr);
+ state2 = null;
+ }
+ }else if ("Native".equalsIgnoreCase(statusStr)) {
+ if("Range-Restricted".equalsIgnoreCase(rangeRestrictionStr)) {
+ state2 = getStateTerm(state, UUID_STATE_NATIVE_RANGE_RESTRICTED);
+ }else if("Non Range-Restricted".equalsIgnoreCase(rangeRestrictionStr)) {
+ state2 = getStateTerm(state, UUID_STATE_NATIVE_NON_RANGE_RESTRICTED);
+ }else if("Range-Restriction unknown".equalsIgnoreCase(rangeRestrictionStr)) {
+ state2 = getStateTerm(state, UUID_STATE_NATIVE_RANGE_RESTRICTION_UNKNWON);
+ }else{
+ logger.warn(line+"Range restricted not recognized: " + rangeRestrictionStr);
+ state2 = null;
+ }
+ }else if ("? Native".equalsIgnoreCase(statusStr)) {
+ if("Non Range-Restricted".equalsIgnoreCase(rangeRestrictionStr)) {
+ state2 = getStateTerm(state, UUID_STATE_DOUBT_NATIVE_NON_RANGE_RESTRICTED);
+ }else{
+ logger.warn(line+"Range restricted for doubtful native not recognized: " + rangeRestrictionStr);
+ state2 = null;
+ }
+ }else {
+ logger.warn(line+"Red list category not recognized: " + statusStr);
+ state2 = null;
+ }
+ result = CategoricalData.NewInstance(state2, stateFeature);
+ return result;
+ }
+
+ private CategoricalData getRedListCategory(SimpleExcelTaxonImportState<GreeceStatusUpdaterConfigurator> state,
+ String line, String redListCategoryStr) {
+ CategoricalData result;
+ State state2;
+ Feature redListCategoryFeature = getFeature(state, UUID_IUCN_FEATURE);
+ if ("Extinct".equals(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_EXTINCT);
+ }else if ("Critically Endangered".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_CRITICALLY_ENDANGERED);
+ }else if ("Endangered".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_ENDANGERED);
+ }else if ("Vulnerable".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_VULNERABLE);
+ }else if ("Near Threatened".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_NEAR_THREATENED);
+ }else if ("Least Concern".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_LEAST_CONCERN);
+ }else if ("Data Deficient".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_DATA_DEFICIENT);
+ }else if ("Not Evaluated".equalsIgnoreCase(redListCategoryStr)) {
+ state2 = getStateTerm(state, UUID_IUCN_NOT_EVALUATED);
+ }else {
+ logger.warn(line+"Red list category not recognized: " + redListCategoryStr);
+ state2 = null;
+ }
+ result = CategoricalData.NewInstance(state2, redListCategoryFeature);
+ return result;
+ }
+
+ private CategoricalData getPresidentialDecree(SimpleExcelTaxonImportState<GreeceStatusUpdaterConfigurator> state,
+ String line, String presidentialDecreeStr) {
+ CategoricalData result;
+ State state2;
+ Feature presidentialDecreeFature = getFeature(state, UUID_PD_FEATURE);
+ if ("No".equals(presidentialDecreeStr)) {
+ state2 = getStateTerm(state, UUID_PD_NO);
+ }else if ("Yes".equalsIgnoreCase(presidentialDecreeStr)) {
+ state2 = getStateTerm(state, UUID_PD_YES);
+ }else {
+ logger.warn(line+"PresidentialDegree not recognized: " + presidentialDecreeStr);
+ state2 = null;
+ }
+ result = CategoricalData.NewInstance(state2, presidentialDecreeFature);
+ return result;
+ }
+
+ private boolean checkTaxonName(SimpleExcelTaxonImportState<GreeceStatusUpdaterConfigurator> state,
+ TaxonBase<?> taxonBase, String line) {
+ String nameStr = getValue(state.getOriginalRecord(), SCIENTIFIC_NAME);
+ boolean equals = (nameStr.equals(taxonBase.getName().getTitleCache()));
+ if (!equals) {
+ logger.warn(line + "Name does not match: " + nameStr + "<->" + taxonBase.getName().getTitleCache());
+ }
+ return true;
+ }
+}
BGBM BDI Projects / cdmlib-apps.git / commitdiff