Revision 7c0a9421
Added by Andreas Müller about 6 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java | ||
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
|
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import eu.etaxonomy.cdm.model.common.Representation; |
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import eu.etaxonomy.cdm.model.name.IZoologicalName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.RankClass; |
|
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
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|
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@Override |
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protected String getRecordQuery(EdaphobaseImportConfigurator config) {
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String result = " SELECT DISTINCT t.*, r.value_summary as rankStr, pr.value_summary as parentRankStr, ppr.value_summary as grandParentRankStr, " |
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+ " pt.name as parentName, ppt.name as grandParentName " |
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String result = " SELECT DISTINCT t.*, r.value_summary as rankStr, pr.value_summary as parentRankStr, ppr.value_summary as grandParentRankStr, pppr.value_summary as grandGrandParentRankStr, "
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+ " pt.name as parentName, ppt.name as grandParentName, pppt.name as grandGrandParentName "
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+ " FROM tax_taxon t " |
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+ " LEFT JOIN tax_taxon pt ON t.parent_taxon_fk = pt.taxon_id " |
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+ " LEFT JOIN tax_taxon ppt ON pt.parent_taxon_fk = ppt.taxon_id" |
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+ " LEFT JOIN tax_taxon ppt ON pt.parent_taxon_fk = ppt.taxon_id " |
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+ " LEFT JOIN tax_taxon pppt ON ppt.parent_taxon_fk = pppt.taxon_id " |
|
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+ " LEFT OUTER JOIN selective_list.element r ON r.element_id = t.tax_rank_fk " |
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+ " LEFT OUTER JOIN selective_list.element pr ON pr.element_id = pt.tax_rank_fk " |
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+ " LEFT OUTER JOIN selective_list.element ppr ON ppr.element_id = ppt.tax_rank_fk " |
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+ " LEFT OUTER JOIN selective_list.element pppr ON pppr.element_id = pppt.tax_rank_fk " |
|
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+ " WHERE t.taxon_id IN (@IDSET)"; |
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result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
|
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return result; |
| ... | ... | |
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String rankStr = rs.getString("rankStr");
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String parentRankStr = rs.getString("parentRankStr");
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String grandParentRankStr = rs.getString("grandParentRankStr");
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String grandGrandParentRankStr = rs.getString("grandGrandParentRankStr");
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String parentNameStr = rs.getString("parentName");
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String grandParentNameStr = rs.getString("grandParentName");
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String grandGrandParentNameStr = rs.getString("grandGrandParentName");
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TaxonBase<?> taxonBase; |
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rankStr= extractEnglish(rankStr); |
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parentRankStr= extractEnglish(parentRankStr); |
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grandParentRankStr= extractEnglish(grandParentRankStr); |
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grandGrandParentRankStr= extractEnglish(grandGrandParentRankStr); |
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//Name etc. |
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Rank rank = makeRank(state, rankStr); |
| ... | ... | |
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setNamePart(parentNameStr, parentRank, name); |
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Rank parentParentRank = makeRank(state, grandParentRankStr); |
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setNamePart(grandParentNameStr, parentParentRank, name); |
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if (parentParentRank != null && parentParentRank.isLower(Rank.GENUS()) || isBlank(name.getGenusOrUninomial()) ){
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logger.warn("Grandparent rank is lower than genus for " + name.getTitleCache() + " (edapho-id: " + id + "; cdm-id: " + name.getId());
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Rank grandParentParentRank = makeRank(state, grandGrandParentRankStr); |
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setNamePart(grandGrandParentNameStr, grandParentParentRank, name); |
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if (grandParentParentRank != null && grandParentParentRank.isLower(Rank.GENUS()) || isBlank(name.getGenusOrUninomial()) ){
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logger.warn("Grand-Grandparent rank is lower than genus for " +
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name.getTitleCache() + " (edapho-id: " + id + "; cdm-id: " + name.getId() + ")"); |
|
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} |
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|
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//Authors |
| ... | ... | |
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|
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if (rank != null){
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Set<Marker> markers = rank.getMarkers(); |
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if ( markers.size() == 0){ //we assume that no markers exist. at least not for markers of unused ranks
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if ( markers.size() == 0){ //we assume that no markers exist, at least not for markers of unused ranks
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UUID edaphoRankMarkerTypeUuid = state.getTransformer().getMarkerTypeUuid("EdaphoRankMarker");
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MarkerType marker = getMarkerType(state, edaphoRankMarkerTypeUuid, "Edaphobase rank", "Rank used in Edaphobase", "EdaRk" ); |
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Representation rep = Representation.NewInstance("Rang, verwendet in Edaphobase", "Edaphobase Rang", "EdaRg", Language.GERMAN());
|
| ... | ... | |
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getTermService().saveOrUpdate(rank); |
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} |
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}else{
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logger.warn("Rank is null and marker can not be set");
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logger.info("Rank is null and marker can not be set");
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} |
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} |
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|
| ... | ... | |
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private void setNamePart(String nameStr, Rank rank, IZoologicalName name) {
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if (rank != null){
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if (rank.isSupraGeneric() || rank.isGenus()){
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if (StringUtils.isBlank(name.getGenusOrUninomial())){
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if (isBlank(name.getGenusOrUninomial())){
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name.setGenusOrUninomial(nameStr); |
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} |
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}else if (rank.isInfraGenericButNotSpeciesGroup()){
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if (StringUtils.isBlank(name.getInfraGenericEpithet())){
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if (isBlank(name.getInfraGenericEpithet())){
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name.setInfraGenericEpithet(nameStr); |
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} |
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}else if (rank.isSpeciesAggregate() || rank.isSpecies()){
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if (StringUtils.isBlank(name.getSpecificEpithet())){
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if (isBlank(name.getSpecificEpithet())){
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name.setSpecificEpithet(nameStr); |
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} |
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}else if (rank.isInfraSpecific()){
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if (StringUtils.isBlank(name.getInfraSpecificEpithet())){
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if (isBlank(name.getInfraSpecificEpithet())){
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name.setInfraSpecificEpithet(nameStr); |
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} |
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} |
| ... | ... | |
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Rank rank = null; |
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try {
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rank = state.getTransformer().getRankByKey(rankStr); |
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if (rank == null && rankStr != null){
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if (rankStr.equals("Cohort")){
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//position not really clear #7285 |
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Rank lowerRank = Rank.SUPERORDER(); |
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rank = this.getRank(state, Rank.uuidCohort, "Cohort", "Cohort", null, |
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(OrderedTermVocabulary<Rank>)Rank.GENUS().getVocabulary(), |
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lowerRank, RankClass.Suprageneric); |
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}else if (rankStr.equals("Hyporder")){
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rank = this.getRank(state, Rank.uuidHyporder, "Hyporder", "Hyporder", null, |
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(OrderedTermVocabulary<Rank>)Rank.GENUS().getVocabulary(), |
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Rank.SUBORDER(), RankClass.Suprageneric); |
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} |
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} |
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace(); |
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} |
Also available in: Unified diff
ref #5499 latest changes to edaphobase import