Revision 030ad7c6
Added by Andreas Müller over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmImportSources.java | ||
|---|---|---|
| 128 | 128 |
return makeSource(dbms, strServer, strDB, port, userName, null); |
| 129 | 129 |
} |
| 130 | 130 |
|
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public static Source EDAPHOBASE2(){
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|
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String dbms = Source.POSTGRESQL9; |
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String strServer = "130.133.70.26"; //BGBM-PESISQL |
|
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String strDB = "edaphobase2"; |
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int port = 5432; |
|
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String userName = "postgres"; |
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return makeSource(dbms, strServer, strDB, port, userName, null); |
|
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} |
|
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|
|
| 131 | 140 |
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| 132 | 141 |
|
| 133 | 142 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/edaphobase/EdaphobaseActivator.java | ||
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| 38 | 38 |
//database validation status (create, update, validate ...) |
| 39 | 39 |
static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
| 40 | 40 |
|
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static final Source edaphoSource = CdmImportSources.EDAPHOBASE(); |
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static final Source edaphoSource = CdmImportSources.EDAPHOBASE2();
|
|
| 42 | 42 |
|
| 43 | 43 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 44 | 44 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_edaphobase(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseImportConfigurator.java | ||
|---|---|---|
| 13 | 13 |
|
| 14 | 14 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 15 | 15 |
import eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
| 17 | 16 |
import eu.etaxonomy.cdm.io.common.Source; |
| 18 | 17 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 19 | 18 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 26 | 25 |
*/ |
| 27 | 26 |
public class EdaphobaseImportConfigurator |
| 28 | 27 |
extends DbImportConfiguratorBase<EdaphobaseImportState> |
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implements IImportConfigurator |
|
| 30 | 28 |
{
|
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private static final long serialVersionUID = 5397992611211404553L; |
| 32 | 30 |
@SuppressWarnings("unused")
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseImportTransformer.java | ||
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| 9 | 9 |
*/ |
| 10 | 10 |
package eu.etaxonomy.cdm.io.edaphobase; |
| 11 | 11 |
|
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import java.util.UUID; |
|
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|
|
| 12 | 14 |
import org.apache.log4j.Logger; |
| 13 | 15 |
|
| 14 | 16 |
import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase; |
| ... | ... | |
| 25 | 27 |
@SuppressWarnings("unused")
|
| 26 | 28 |
private static final Logger logger = Logger.getLogger(EdaphobaseImportTransformer.class); |
| 27 | 29 |
|
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private static final UUID uuidTaxGrossgruppeMarker = UUID.fromString("71f22f44-5131-4d54-8362-1c77ac5c567a");
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private static final UUID uuidEdaphoRankMarker = UUID.fromString("6eaeffd2-b89b-436b-b0ee-75af5f0a9b81");
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|
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| 28 | 33 |
@Override |
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public Rank getRankByKey(String key) throws UndefinedTransformerMethodException {
|
| 30 | 35 |
if (key == null){return null;}
|
| ... | ... | |
| 55 | 60 |
return null; |
| 56 | 61 |
} |
| 57 | 62 |
|
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// @Override |
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// public UUID getRankUuid(String key) throws UndefinedTransformerMethodException {
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// // TODO Auto-generated method stub |
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// return super.getRankUuid(key); |
|
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// } |
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@Override |
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public UUID getMarkerTypeUuid(String key) throws UndefinedTransformerMethodException {
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if (key == null){
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return null; |
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}else if (key.equals("TaxGrossgruppe")){
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return uuidTaxGrossgruppeMarker; |
|
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}else if (key.equals("EdaphoRankMarker")){
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return uuidEdaphoRankMarker; |
|
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} |
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return null; |
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} |
|
| 63 | 74 |
|
| 64 | 75 |
|
| 65 | 76 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseTaxonImport.java | ||
|---|---|---|
| 28 | 28 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
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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.Representation; |
|
| 31 | 35 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 32 | 36 |
import eu.etaxonomy.cdm.model.name.ZoologicalName; |
| 33 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 75 | 79 |
+ " LEFT JOIN tax_taxon ppt ON pt.parent_taxon_fk = ppt.taxon_id" |
| 76 | 80 |
+ " LEFT OUTER JOIN tax_rank_en r ON r.element_id = t.tax_rank_fk " |
| 77 | 81 |
+ " LEFT OUTER JOIN tax_rank_en pr ON pr.element_id = pt.tax_rank_fk " |
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+ " LEFT OUTER JOIN tax_rank_en ppr ON pr.element_id = ppt.tax_rank_fk " |
|
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+ " LEFT OUTER JOIN tax_rank_en ppr ON ppr.element_id = ppt.tax_rank_fk "
|
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| 79 | 83 |
+ " WHERE t.taxon_id IN (@IDSET)"; |
| 80 | 84 |
result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
|
| 81 | 85 |
return result; |
| ... | ... | |
| 94 | 98 |
try {
|
| 95 | 99 |
while (rs.next()){
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makeSingleTaxon(state, rs, taxaToSave); |
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|
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| 98 | 101 |
} |
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} catch (SQLException e) {
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} catch (SQLException | UndefinedTransformerMethodException e) {
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e.printStackTrace(); |
|
| 102 | 104 |
} |
| 103 | 105 |
|
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getTaxonService().saveOrUpdate(taxaToSave); |
| ... | ... | |
| 110 | 112 |
* @param rs |
| 111 | 113 |
* @param taxaToSave |
| 112 | 114 |
* @throws SQLException |
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* @throws UndefinedTransformerMethodException |
|
| 113 | 116 |
*/ |
| 114 | 117 |
private void makeSingleTaxon(EdaphobaseImportState state, ResultSet rs, Set<TaxonBase> taxaToSave) |
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throws SQLException {
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throws SQLException, UndefinedTransformerMethodException {
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| 116 | 119 |
Integer id = nullSafeInt(rs, "taxon_id"); |
| 117 | 120 |
Integer year = nullSafeInt(rs, "tax_year"); |
| 118 | 121 |
boolean isBrackets = rs.getBoolean("tax_brackets");
|
| ... | ... | |
| 142 | 145 |
|
| 143 | 146 |
//Name etc. |
| 144 | 147 |
Rank rank = makeRank(state, rankStr); |
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checkRankMarker(state, rank); |
|
| 145 | 149 |
ZoologicalName name = ZoologicalName.NewInstance(rank); |
| 146 | 150 |
setNamePart(nameStr, rank, name); |
| 147 | 151 |
Rank parentRank = makeRank(state, parentRankStr); |
| 148 | 152 |
setNamePart(parentNameStr, parentRank, name); |
| 149 | 153 |
Rank parentParentRank = makeRank(state, grandParentRankStr); |
| 150 | 154 |
setNamePart(grandParentNameStr, parentParentRank, name); |
| 155 |
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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} |
|
| 151 | 158 |
|
| 152 | 159 |
//Authors |
| 153 | 160 |
if (StringUtils.isNotBlank(authorName)){
|
| ... | ... | |
| 175 | 182 |
} |
| 176 | 183 |
name.setNomenclaturalMicroReference(StringUtils.isBlank(pages)? null : pages); |
| 177 | 184 |
|
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|
|
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//taxon |
|
| 179 | 186 |
Reference secRef = state.getRelatedObject(REFERENCE_NAMESPACE, state.getConfig().getSecUuid().toString(), Reference.class); |
| 180 | 187 |
if (secRef == null){
|
| 181 | 188 |
secRef = makeSecRef(state); |
| ... | ... | |
| 185 | 192 |
}else{
|
| 186 | 193 |
taxonBase = Synonym.NewInstance(name, secRef); |
| 187 | 194 |
} |
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handleTaxonomicGroupMarker(state, taxonBase, isGroup); |
|
| 188 | 196 |
taxaToSave.add(taxonBase); |
| 189 | 197 |
|
| 190 | 198 |
//remarks |
| ... | ... | |
| 196 | 204 |
} |
| 197 | 205 |
|
| 198 | 206 |
|
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/** |
|
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* @param state |
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* @param rank |
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* @throws UndefinedTransformerMethodException |
|
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*/ |
|
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private void checkRankMarker(EdaphobaseImportState state, Rank rank) throws UndefinedTransformerMethodException {
|
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|
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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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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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marker.addRepresentation(rep); |
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rank.addMarker(Marker.NewInstance(marker, true)); |
|
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getTermService().saveOrUpdate(rank); |
|
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} |
|
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} |
|
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|
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/** |
|
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* @param state |
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* @param isGroup |
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* @param taxonBase |
|
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*/ |
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private void handleTaxonomicGroupMarker(EdaphobaseImportState state, TaxonBase<?> taxonBase, boolean isGroup) {
|
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if (! isGroup){
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return; |
|
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}else{
|
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try {
|
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MarkerType markerType = getMarkerType(state, state.getTransformer().getMarkerTypeUuid("TaxGrossgruppe"), "Tax. Gruppe", "Taxonomische Grossgruppe", "TGG", null, Language.GERMAN());
|
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if (taxonBase.isInstanceOf(Synonym.class)){
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logger.warn("Syonym is marked as 'taxonomische Grossgruppe'");
|
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} |
|
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taxonBase.addMarker(Marker.NewInstance(markerType, true)); |
|
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} catch (UndefinedTransformerMethodException e) {
|
|
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} |
|
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} |
|
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} |
|
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|
|
| 199 | 245 |
/** |
| 200 | 246 |
* @param state |
| 201 | 247 |
* @return |
Also available in: Unified diff
ref #5499 latest changes to Edaphobase import