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/**
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* Copyright (C) 2015 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.vaadin.util;
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import java.util.Collection;
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import java.util.HashMap;
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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.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.commons.lang.StringUtils;
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import com.vaadin.data.util.sqlcontainer.query.FreeformQuery;
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import com.vaadin.data.util.sqlcontainer.query.QueryDelegate;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeStatus;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.vaadin.statement.CdmStatementDelegate;
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/**
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* @author cmathew
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* @since 1 Apr 2015
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*
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*/
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public class CdmQueryFactory {
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public static final String DTYPE_COLUMN = "DTYPE";
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public static final String ID_COLUMN = "ID";
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public static final String UUID_COLUMN = "UUID";
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public static final String CLASSIFICATION_COLUMN = "CLASSIFICATION";
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public static final String RANK_COLUMN = "RANK";
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public static final String TAXON_COLUMN = "TAXON";
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public static final String ID = "ID";
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public static final String UUID_ID = "UUID";
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public static QueryDelegate generateTaxonTreeQuery(String name_id, String classificationId) {
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String FROM_QUERY = " FROM TaxonBase tb " +
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"INNER JOIN TaxonNode tn on tn.taxon_id=tb.id " +
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"INNER JOIN TaxonName n on tb.name_id=n.id " +
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"INNER JOIN Classification cl on cl.id=tn.classification_id and cl.id='"+classificationId+"'";
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String SELECT_QUERY="SELECT tn.id as " + ID +
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", tb.uuid as " + UUID_ID +
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", n.titleCache as " + name_id +
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", tn.parent_id as parent" +
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FROM_QUERY;
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String COUNT_QUERY = "SELECT count(*) " + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM TaxonBase tb WHERE tb.id = ?";
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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public static QueryDelegate generateTaxonBaseQuery(String name_id,
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String pb_id,
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String unp_id,
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String rank_id,
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String has_syn_id) {
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String FROM_QUERY = " FROM TaxonBase tb " +
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"INNER JOIN TaxonNode tn on tn.taxon_id=tb.id " +
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"INNER JOIN TaxonName n on tb.name_id=n.id " +
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"INNER JOIN DefinedTermBase dtb on n.rank_id = dtb.id";
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String SELECT_QUERY="SELECT tb.id as " + ID +
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", tb.uuid as " + UUID_ID +
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", n.titleCache as " + name_id +
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", tb.publish as " + pb_id +
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", tn.status ='"+TaxonNodeStatus.UNPLACED.getKey()+"' as " + unp_id + //this may be incorrectly fixed
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", dtb.titleCache as " + rank_id +
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", (SELECT COUNT(*) FROM TaxonBase syn WHERE tb.id = syn.acceptedTaxon_id) as " + has_syn_id +
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FROM_QUERY;
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String COUNT_QUERY = "SELECT count(*) " + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM TaxonBase tb WHERE tb.id = ?";
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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public static QueryDelegate generateTaxonDistributionQuery(List<Integer> taxonNodeIds, Collection<NamedArea> namedAreas) {
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String idString = "";
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Iterator<Integer> nodeIterator = taxonNodeIds.iterator();
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while (nodeIterator.hasNext()) {
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Integer integer = nodeIterator.next();
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idString += String.valueOf(integer);
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if(nodeIterator.hasNext()){
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idString += ", ";
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}
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}
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String FROM_QUERY =
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" FROM TaxonName n "
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+ "INNER JOIN TaxonBase tb on n.id = tb.name_id and tb.DTYPE='Taxon' " + // # name<->taxon
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"INNER JOIN TaxonNode tn on tn.taxon_id = tb.id "+
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"INNER JOIN DefinedTermBase rank on n.rank_id = rank.id "+// # rank <-> name
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"LEFT OUTER JOIN DescriptionBase descr on descr.taxon_id = tb.id "+// # taxon <-> taxon description (not every taxon has a description)
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"LEFT OUTER JOIN DescriptionElementBase descrEl on descrEl.indescription_id = descr.id and descrEl.DTYPE = 'Distribution' "+// # distribution <-> description
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"LEFT OUTER JOIN DefinedTermBase statusTerm on statusTerm.id = descrEl.status_id "+
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"LEFT OUTER JOIN DefinedTermBase area on area.id = descrEl.area_id ";
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if(CdmUtils.isNotBlank(idString)){
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FROM_QUERY += " WHERE tn.id IN ("+ idString +") ";
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}
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String GROUP_BY = " GROUP BY tb.uuid, tn.id ";
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String ORDER_BY = " ORDER BY tb.titleCache ";
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String SELECT_QUERY= "SELECT "
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+ "tb.DTYPE AS "+DTYPE_COLUMN+", "
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+ "tb.id AS "+ID_COLUMN+", "
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+ "tb.uuid AS "+UUID_COLUMN+", "
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+ "tn.classification_id AS "+CLASSIFICATION_COLUMN+", "+
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"tb.titleCache AS "+TAXON_COLUMN+", " +
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"rank.titleCache AS "+RANK_COLUMN+", ";
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Map<String, Integer> labels = new HashMap<>();
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for(NamedArea namedArea : namedAreas){
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String label = null;
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String fullLabel = null;
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String abbreviatedLabel = null;
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Representation representation = namedArea.getRepresentation(Language.DEFAULT());
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if(representation!=null){
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fullLabel = representation.getLabel();
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abbreviatedLabel = representation.getAbbreviatedLabel();
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if(DistributionEditorUtil.isAbbreviatedLabels()){
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label = abbreviatedLabel;
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}
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else{
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label = fullLabel;
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}
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}
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//fallback
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if(label==null){
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label = namedArea.getTitleCache();
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}
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//check if label already exists
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Integer count = labels.get(label);
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if(count!=null){
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//combine label and abbreviated and check again
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if(abbreviatedLabel!=null && fullLabel!= null){
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label = abbreviatedLabel+"-"+fullLabel;
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}
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}
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count = labels.get(label);
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if(count==null){
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labels.put(label, 1);
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}
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else{
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labels.put(label, count+1);
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label += "("+count+")";
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}
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SELECT_QUERY += "MAX( IF(area.uuid = '"+ namedArea.getUuid() +"', statusTerm.uuid, NULL) ) as '"+ label +"'," ;
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}
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SELECT_QUERY = StringUtils.stripEnd(SELECT_QUERY, ",")+" ";
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SELECT_QUERY= SELECT_QUERY + FROM_QUERY + GROUP_BY + ORDER_BY;
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String COUNT_QUERY = "SELECT count(DISTINCT tb.id)" + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM TaxonBase tb WHERE tb.uuid = ?";
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//Escape SQL control character '
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Pattern p = Pattern.compile("(\\w+)'(\\w+)");
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Matcher m = p.matcher(SELECT_QUERY);
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if (m.find()) {
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SELECT_QUERY = m.replaceAll("$1\\\\'$2");
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}
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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public static QueryDelegate generateSynonymOfTaxonQuery(String name_id) {
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String FROM_QUERY = " FROM TaxonBase tb " +
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"INNER JOIN TaxonName n on tb.name_id=n.id " +
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"INNER JOIN TaxonBase acc on tb.acceptedTaxon_id = acc.id "; //or s.id = ?
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String SELECT_QUERY="SELECT tb.id as " + ID +
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", n.titleCache as " + name_id +
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FROM_QUERY;
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String COUNT_QUERY = "SELECT count(*) " + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM TaxonBase syn WHERE syn.id = ?"; //or s.id = ?
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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public static QueryDelegate generateTaxonRelatedToQuery(String reluuid_id,
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String reltype_id,
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String to_id,
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String touuid_id,
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String toname_id) {
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String FROM_QUERY = " FROM TaxonRelationship tr " +
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"INNER JOIN TaxonBase tb on tr.relatedto_id = tb.id " +
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"INNER JOIN TaxonNode tn on tb.id = tn.taxon_id ";
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String SELECT_QUERY= "SELECT tr.id as " + ID +
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", tr.uuid as " + reluuid_id +
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", tr.type_id as " + reltype_id +
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", tr.relatedto_id as " + to_id +
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", tb.uuid as " + touuid_id +
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", tb.titleCache as " + toname_id +
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FROM_QUERY;
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String COUNT_QUERY = "SELECT count(*) " + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM TaxonRelationship tr where tr.relatedfrom_id = ?";
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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/**
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* Creates a FreeformQuery which mimics a TableQuery.
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* This method works around the bug at http://dev.vaadin.com/ticket/12370
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*
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* @param tableName
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* @return
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*/
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public static QueryDelegate generateTableQuery(String tableName) {
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String FROM_QUERY = " FROM " + tableName;
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String SELECT_QUERY=" SELECT * " +
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FROM_QUERY;
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String COUNT_QUERY = "SELECT count(*) " + FROM_QUERY;
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String CONTAINS_QUERY = "SELECT * FROM " + tableName + " WHERE id = ?";
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return generateQueryDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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}
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public static QueryDelegate generateQueryDelegate(String SELECT_QUERY, String COUNT_QUERY, String CONTAINS_QUERY) {
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FreeformQuery query = new FreeformQuery("This query is not used", CdmSpringContextHelper.getCurrent().getConnectionPool(), ID);
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CdmStatementDelegate delegate = new CdmStatementDelegate(SELECT_QUERY, COUNT_QUERY, CONTAINS_QUERY);
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query.setDelegate(delegate);
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return query;
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}
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}
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