ref #10242 synonym cleanup for Sileneae

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportConfigurator.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportConfigurator.java
index 76fda9ff777a3ed07c6e99b70752ccb091feac32..7cd0869883b6061c6eb2f945ff190c22587afb98 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportConfigurator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportConfigurator.java
@@ -54,10 +54,12 @@ public class CaryoSileneaeImportConfigurator extends ExcelImportConfiguratorBase
     @Override
     protected void makeIoClassList() {
         ioClassList = new Class[]{
-                CaryoSileneaeNameImport.class,
-                CaryoSileneaeNomRefImport.class,
-                CaryoSileneaeTaxonImport.class,
-                CaryoSileneaeSynonymImport.class
+//                CaryoSileneaeNameImport.class,
+//                CaryoSileneaeNomRefImport.class,
+//                CaryoSileneaeTaxonImport.class,
+//                CaryoSileneaeSynonymImport.class
+                CaryoSileneaeTaxonSynonymCleanupImport.class,
+                CaryoSileneaeSynonymSynonymCleanupImport.class
         };
     }
 

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeSynonymSynonymCleanupImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeSynonymSynonymCleanupImport.java
new file mode 100644 (file)
index 0000000..cc099f8
--- /dev/null
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeSynonymSynonymCleanupImport.java
@@ -0,0 +1,167 @@
+/**
+* Copyright (C) 2020 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.caryo;
+
+import java.util.Map;
+import java.util.UUID;
+import java.util.stream.Collectors;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.api.service.dto.IdentifiedEntityDTO;
+import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
+import eu.etaxonomy.cdm.model.name.TaxonName;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
+import eu.etaxonomy.cdm.model.taxon.SynonymType;
+import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.persistence.query.MatchMode;
+
+/**
+ * @author a.mueller
+ * @since 02.02.2023
+ */
+@Component
+public class CaryoSileneaeSynonymSynonymCleanupImport extends CaryoSileneaeImportBase {
+
+    private static final long serialVersionUID = -3721982716275962061L;
+    private static final Logger logger = LogManager.getLogger();
+
+    private static final UUID uuidSileneaeInfoNameIdType = UUID.fromString("95ecbf6d-521d-447f-bae5-d82585ff3617");
+
+    private static final String NOMTAX_ID = "NomTax_ID";
+    private static final String NOMEN_LINK = "Nomen_link";
+    private static final String TAXON_LINK = "Taxon_link";
+
+    @Override
+    protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
+        return "Synonyms";
+    }
+
+    @Override
+    protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
+        int line = state.getCurrentLine();
+        if ((line % 500) == 0){
+//            newTransaction(state);
+            System.out.println(line);
+        }
+
+        Map<String, String> record = state.getOriginalRecord();
+
+        Integer nomTaxId = Integer.valueOf(getValue(record, NOMTAX_ID));
+        Integer nameLinkID = Integer.valueOf(getValue(record, NOMEN_LINK));
+        Integer taxonLinkId = Integer.valueOf(getValue(record, TAXON_LINK));
+
+
+        String row = String.valueOf(line) + "("+nomTaxId+"): ";
+
+        //find synonym name
+        TaxonName synonymName = getNameFromDb(state, nameLinkID, row);
+        if (synonymName == null) {
+            logger.warn(row + "Name does not exist");
+            return;
+        }
+
+        Integer accNameId = accIdMap.get(taxonLinkId);
+        if (accNameId == null) {
+            logger.warn(row + "Taxon not found in taxon map: " + taxonLinkId);
+            return;
+        }
+        TaxonName accName = getNameFromDb(state, accNameId, row);
+        if (accName == null) {
+            logger.warn(row + "Accepeted taxon name for synonym " + synonymName.getTitleCache() + " not found. Keep as unresolved.");
+            return;
+        }
+
+        Taxon newAccTaxon;
+        //add as synonym
+        if (accName.getTaxa().size() != 1) {
+            if (accName.getTaxa().isEmpty()){
+                logger.warn(row + "Accepted taxon name "+accName.getTitleCache()+" has no taxon attached. Keep synonynm " + synonymName.getTitleCache() + "as unresolved");
+                return;
+            }else {
+                String names = accName.getTaxa().stream().map(t->t.getTitleCache()).collect(Collectors.toList()).toString();
+                logger.warn(row + "Acc taxon name has "+accName.getTaxa().size()+" taxa attached: n=" + accName.getTaxa().size() + " (" + names +")" );
+                newAccTaxon = accName.getTaxa().iterator().next();
+                logger.warn(row + " used: " + newAccTaxon.getTitleCache());
+            }
+        }else {
+            newAccTaxon = accName.getTaxa().iterator().next();
+        }
+
+        Synonym synonym = Synonym.NewInstance(synonymName, getSecRef(state));
+        newAccTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF);
+
+        getTaxonService().saveOrUpdate(newAccTaxon);
+
+
+        //remove from parent
+        if (synonymName.getTaxa().size() != 1) {
+            logger.warn(row + "syn taxon name "+ synonymName.getTitleCache() + " has "+synonymName.getTaxa().size()+"  taxa attached");
+            return;
+        }
+        Taxon accTaxon = synonymName.getTaxa().iterator().next();
+        if (accTaxon.getTaxonNodes().size() != 1) {
+            logger.warn(row + "syn taxon has "+accTaxon.getTaxonNodes().size()+" taxon nodes attached");
+            return;
+        }
+        TaxonNode node = accTaxon.getTaxonNodes().iterator().next();
+
+        //boolean success = node.getParent().deleteChildNode(node);
+        node.setTaxon(null);
+//        if (!success) {
+//            logger.warn(row + "deleteChildNode not successful");
+//        }
+
+        accTaxon.setName(null);
+        getTaxonService().delete(accTaxon);
+//        getTaxonNodeService().delete(node);
+    }
+
+
+    private TaxonName getNameFromDb(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state, Integer nameId, String row) {
+        try {
+            DefinedTerm sileneaeInfoNameIdType = getIdentiferType(state,
+                    uuidSileneaeInfoNameIdType, null, null, null, null);
+            Pager<IdentifiedEntityDTO<TaxonName>> list = getNameService().findByIdentifier(TaxonName.class, nameId.toString(),
+                    sileneaeInfoNameIdType, MatchMode.EXACT, true, null, null, null);
+            return list.getRecords().get(0).getCdmEntity().getEntity();
+        } catch (Exception e) {
+            logger.warn(row + "Error when getting name from DB. nameID = " + nameId);
+            e.printStackTrace();
+            return null;
+        }
+    }
+
+    boolean first = true;
+    @Override
+    protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
+//        if (first) {
+//            for (TaxonName taxonName : orphanedNameMap.values()) {
+//                Taxon taxon = Taxon.NewInstance(taxonName, getSecRef(state));
+//                TaxonNode node = getUnresolvedNode(state).addChildTaxon(taxon, null);
+//                getTaxonNodeService().saveOrUpdate(node);
+//            }
+//            first = false;
+//        }
+    }
+//
+//    private TaxonNode unresolvedNode;
+//    private TaxonNode getUnresolvedNode(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
+//        if (unresolvedNode == null) {
+//            unresolvedNode = getTaxonNodeService().find(state.getConfig().getUnresolvedNodeUuid());
+//        }
+//        return unresolvedNode;
+//    }
+
+}
\ No newline at end of file

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeTaxonSynonymCleanupImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeTaxonSynonymCleanupImport.java
new file mode 100644 (file)
index 0000000..0129f3a
--- /dev/null
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeTaxonSynonymCleanupImport.java
@@ -0,0 +1,56 @@
+/**
+* Copyright (C) 2020 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.caryo;
+
+import java.util.Map;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Component;
+
+import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
+
+/**
+ * @author a.mueller
+ * @since 02.02.2023
+ */
+@Component
+public class CaryoSileneaeTaxonSynonymCleanupImport extends CaryoSileneaeImportBase {
+
+    private static final Logger logger = LogManager.getLogger();
+
+    private static final String ACCEPTED_TAXON_ID = "AcceptedTaxon_ID";
+    private static final String NOMEN_LINK = "nomen_link";
+    private static final String PARENT = "parent";
+
+
+    @Override
+    protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
+        return "Taxa";
+    }
+
+    @Override
+    protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
+
+            int line = state.getCurrentLine();
+
+            Map<String, String> record = state.getOriginalRecord();
+
+            Integer accTaxonId = Integer.valueOf(getValue(record, ACCEPTED_TAXON_ID));
+            Integer nameLinkID = Integer.valueOf(getValue(record, NOMEN_LINK));
+            String row = String.valueOf(line) + "("+accTaxonId+"): ";
+
+            accIdMap.put(accTaxonId, nameLinkID);
+    }
+
+    @Override
+    protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
+        //nothing todo
+    }
+}
\ No newline at end of file