Revision c22a678f
Added by Katja Luther over 5 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java | ||
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| 15 | 15 |
import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import java.util.Set; |
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|
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import org.apache.commons.lang3.StringUtils; |
| ... | ... | |
| 78 | 79 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDtoByRankAndNameComparator; |
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import eu.etaxonomy.cdm.strategy.cache.TagEnum; |
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import eu.etaxonomy.cdm.strategy.cache.TaggedText; |
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import eu.etaxonomy.cdm.strategy.cache.reference.DefaultReferenceCacheStrategy; |
| ... | ... | |
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handleTaxonNode(state, node); |
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node = partitioner.next(); |
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} |
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//create sortIndex for nodes |
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for(Entry<Integer, List<TaxonNodeDto>> entry :state.getNodeChildrenMap().entrySet()){
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List<TaxonNodeDto> children = entry.getValue(); |
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TaxonNodeDtoByRankAndNameComparator comp = new TaxonNodeDtoByRankAndNameComparator(); |
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Collections.sort(children, comp); |
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int index = 0; |
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for (TaxonNodeDto child:children) {
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if (state.getProcessor().hasRecord(CdmLightExportTable.TAXON, child.getTaxonUuid().toString())){
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String[] csvLine = state.getProcessor().getRecord(CdmLightExportTable.TAXON,child.getTaxonUuid().toString()); |
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csvLine[CdmLightExportTable.TAXON.getIndex(CdmLightExportTable.SORT_INDEX)] = String.valueOf(index); |
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index++; |
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} |
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} |
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} |
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|
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// for (LogicFilter<TaxonNode> taxonNodeFilter : config.getTaxonNodeFilter().getTaxonNodesFilter()){
|
| ... | ... | |
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}else{
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try {
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TaxonNode root = taxonNode; |
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List<TaxonNodeDto> childNodes; |
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if (root.hasChildNodes()){
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childNodes = new ArrayList(); |
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for (TaxonNode child: root.getChildNodes()){
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childNodes.add(new TaxonNodeDto(child)); |
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} |
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state.getNodeChildrenMap().put(root.getId(),childNodes); |
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} |
|
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if (root.hasTaxon()){
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handleTaxon(state, root); |
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}else{
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// for (TaxonNode child : root.getChildNodes()){
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// handleTaxon(state, child); |
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// //TODO progress monitor |
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// } |
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} |
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred when handling classification " + |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportResultProcessor.java | ||
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| 80 | 80 |
} |
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} |
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public String[] getRecord(CdmLightExportTable table, String id){
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return result.get(table).get(id); |
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} |
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|
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/** |
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* @param table |
| ... | ... | |
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* @param csvLine |
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*/ |
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public void put(CdmLightExportTable table, ICdmBase cdmBase, String[] csvLine) {
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this.put(table, String.valueOf(cdmBase.getId()), csvLine);
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this.put(table, cdmBase.getUuid().toString(), csvLine);
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} |
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|
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|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportState.java | ||
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| 10 | 10 |
|
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import java.io.File; |
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import java.util.HashMap; |
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import java.util.List; |
|
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import java.util.Map; |
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|
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import eu.etaxonomy.cdm.io.common.ExportResult; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
|
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|
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/** |
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* @author k.luther |
| ... | ... | |
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|
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private Map<Integer, SpecimenOrObservationBase> specimenStore = new HashMap<>(); |
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private Map<Integer, Reference> referenceStore = new HashMap<>(); |
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private Map<Integer,List<TaxonNodeDto>> nodeChildrenMap = new HashMap<>(); |
|
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/** |
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* @param config |
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*/ |
| ... | ... | |
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return referenceStore; |
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} |
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|
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/** |
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* @return the nodeChildrenMap |
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*/ |
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public Map<Integer, List<TaxonNodeDto>> getNodeChildrenMap() {
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return nodeChildrenMap; |
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} |
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|
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/** |
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* @param nodeChildrenMap the nodeChildrenMap to set |
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*/ |
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public void setNodeChildrenMap(Map<Integer, List<TaxonNodeDto>> nodeChildrenMap) {
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this.nodeChildrenMap = nodeChildrenMap; |
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} |
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} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightExportTable.java | ||
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| 45 | 45 |
protected static final String PARENT_FK = "Parent_FK"; |
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protected static final String SEC_REFERENCE_FK = "SecReference_FK"; |
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protected static final String SEC_REFERENCE = "SecReference"; |
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protected static final String SORT_INDEX = "SortIndex"; |
|
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//pro parte / misapplied |
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protected static final String SYN_SEC_REFERENCE_FK = "SynSecReference_FK"; |
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protected static final String SYN_SEC_REFERENCE = "SynSecReference"; |
| ... | ... | |
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}; |
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} |
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final static String[] taxonColumns(){
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return new String[]{TAXON_ID, CLASSIFICATION_ID, CLASSIFICATION_TITLE, NAME_FK, PARENT_FK, SEC_REFERENCE_FK, SEC_REFERENCE};
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return new String[]{TAXON_ID, CLASSIFICATION_ID, CLASSIFICATION_TITLE, NAME_FK, PARENT_FK, SEC_REFERENCE_FK, SEC_REFERENCE, SORT_INDEX};
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} |
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final static String[] synonymColumns(){
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return new String[]{SYNONYM_ID, TAXON_FK, NAME_FK, SYN_SEC_REFERENCE_FK, SYN_SEC_REFERENCE, SEC_REFERENCE_FK, SEC_REFERENCE,
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Also available in: Unified diff
ref #7903: add sortIndex to taxon table in cdm light export