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package eu.etaxonomy.cdm.app.vibrant;
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import java.lang.reflect.Method;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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*
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*/
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public class IopiActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(IopiActivator.class);
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//database validation status (create, update, validate ...)
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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static final ICdmDataSource cdmDestination = cdm_test_local_iopi();
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static final boolean useSingleClassification = false;
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static final Integer sourceSecId = null; //7000000;
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static final boolean useSingleClassification = true;
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static final Integer sourceSecId = 1892; //7000000;
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static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
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static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
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static boolean useClassification = true;
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//filter
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static String taxonTable = "v_cdm_exp_taxaAll";
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static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
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static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
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" FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
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static String nameIdTable = " v_cdm_exp_namesAll ";
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static String referenceIdTable = " v_cdm_exp_refAll ";
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static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
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static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
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static String authorFilter = null; // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
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//not used
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static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
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// **************** ALL *********************
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//authors
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config.setNomenclaturalCode(nomenclaturalCode);
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try {
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Method makeUrlMethod = MclActivator.class.getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);
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config.setMakeUrlForTaxon(makeUrlMethod);
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} catch (Exception e) {
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e.printStackTrace();
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return;
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}
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config.setIgnoreNull(ignoreNull);
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config.setDoAuthors(doAuthors);
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config.setDoReferences(doReferences);
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config.setCheck(check);
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config.setEditor(editor);
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config.setRecordsPerTransaction(partitionSize);
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// filter
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config.setTaxonTable(taxonTable);
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config.setClassificationQuery(classificationQuery);
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config.setRelTaxaIdQuery(relPTaxonIdQuery);
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config.setNameIdTable(nameIdTable);
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config.setReferenceIdTable(referenceIdTable);
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config.setAuthorTeamFilter(authorTeamFilter);
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config.setAuthorFilter(authorFilter);
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config.setFactFilter(factFilter);
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config.setCommonNameFilter(commonNameFilter);
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config.setOccurrenceFilter(occurrenceFilter);
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config.setOccurrenceSourceFilter(occurrenceSourceFilter);
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config.setUseSingleClassification(useSingleClassification);
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// invoke import
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return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
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}
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//for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)
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private static final String URLbase = "http://rbg-web2.rbge.org.uk/cgi-bin/nph-readbtree.pl/feout?FAMILY_XREF=%s&GENUS_XREF=%s&SPECIES_XREF=%s&TAXON_NAME_XREF=%s&RANK=%s";
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public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){
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Method result = null;
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ExtensionType urlExtensionType = ExtensionType.URL();
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String family = "";
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String genus = "";
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String species = "";
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String taxonName = "";
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String rankStr = "";
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NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class);
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Rank rank = name.getRank();
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rankStr = transformFeRanks(rank);
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if (rank.equals(Rank.FAMILY())){
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family = name.getGenusOrUninomial();
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taxonName = name.getGenusOrUninomial();
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}else if (rank.isHigher(Rank.GENUS())){
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taxonName = name.getGenusOrUninomial();
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}else if (rank.isGenus()){
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genus = name.getGenusOrUninomial();
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rankStr = "genus";
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}else if (rank.isInfraGeneric()){
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genus = name.getGenusOrUninomial();
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taxonName = name.getInfraGenericEpithet();
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}else if (rank.isSpecies()){
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genus = name.getGenusOrUninomial();
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species = name.getSpecificEpithet();
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rankStr = "species";
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}else if (rank.isInfraSpecific()){
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genus = name.getGenusOrUninomial();
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species = name.getSpecificEpithet();
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taxonName = name.getInfraSpecificEpithet();
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}
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String url = String.format(URLbase ,family, genus, species, taxonName, rankStr);
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taxon.addExtension(url, urlExtensionType);
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return result;
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}
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private static String transformFeRanks(Rank rank){
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if (rank.equals(Rank.SPECIESAGGREGATE())){ return "agg.";
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}else if (rank.equals(Rank.CLASS())){ return "Class";
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}else if (rank.equals(Rank.DIVISION())){ return "Division";
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}else if (rank.equals(Rank.FAMILY())){ return "family";
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}else if (rank.equals(Rank.FORM())){ return "forma";
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}else if (rank.equals(Rank.GENUS())){ return "genus";
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}else if (rank.equals(Rank.GREX())){ return "grex";
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}else if (rank.equals(Rank.SPECIESGROUP())){ return "group";
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}else if (rank.equals(Rank.ORDER())){ return "Order";
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// }else if (rank.equals(Rank.PROL())){ return "proles";
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//-- }else if (rank.equals(Rank.RACE())){ return "race";
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}else if (rank.equals(Rank.SECTION_BOTANY())){ return "Sect.";
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}else if (rank.equals(Rank.SERIES())){ return "Ser.";
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}else if (rank.equals(Rank.SPECIES())){ return "species";
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}else if (rank.equals(Rank.SUBCLASS())){ return "Subclass";
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}else if (rank.equals(Rank.SUBDIVISION())){ return "Subdivision";
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}else if (rank.equals(Rank.SUBFORM())){ return "Subf.";
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}else if (rank.equals(Rank.SUBGENUS())){ return "Subgen.";
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}else if (rank.equals(Rank.SUBORDER())){ return "Suborder";
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}else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return "Subsect.";
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}else if (rank.equals(Rank.SUBSERIES())){ return "Subser.";
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}else if (rank.equals(Rank.SUBSPECIES())){ return "subsp";
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}else if (rank.equals(Rank.SUBVARIETY())){ return "subvar.";
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}else if (rank.equals(Rank.SUPERORDER())){ return "Superorder";
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}else if (rank.equals(Rank.TRIBE())){ return "Tribe";
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}else if (rank.equals(Rank.VARIETY())){ return "var.";
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}else{
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logger.debug("Rank not found: " + rank.getTitleCache());
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return "";
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}
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}
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}
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latest for vibrant