diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/util/stream/TaxonomyRowDataSource.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/util/stream/TaxonomyRowDataSource.java index c39d010..08edfa3 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/util/stream/TaxonomyRowDataSource.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/util/stream/TaxonomyRowDataSource.java @@ -112,7 +112,7 @@ public class TaxonomyRowDataSource implements DataSource { String author = ""; List hashProperties = new ArrayList(); - Log.trace("Taxonomy returned in client: " + row); +// Log.trace("Taxonomy returned in client: " + row); if(row.getDataProviderName()!=null) dataProviderName = row.getDataProviderName(); if(row.getDataSetCitation()!=null) dataSetCitation = row.getDataSetCitation(); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java index 2e8535b..e2515f6 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java @@ -6,7 +6,7 @@ package org.gcube.portlets.user.speciesdiscovery.server.persistence; import java.util.List; import java.util.Map; -import org.gcube.common.core.utils.logging.GCUBELog; +import org.apache.log4j.Logger; import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.AbstractPersistence; import org.gcube.portlets.user.speciesdiscovery.server.session.FetchingBuffer; import org.gcube.portlets.user.speciesdiscovery.shared.FetchingElement; @@ -17,7 +17,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.FetchingElement; */ public abstract class AbstractDaoBuffer implements FetchingBuffer { - protected GCUBELog logger = new GCUBELog(AbstractDaoBuffer.class); + protected Logger logger = Logger.getLogger(AbstractDaoBuffer.class); protected AbstractPersistence dao; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java index 33e4f1e..9b1319d 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java @@ -161,7 +161,8 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer impl try { CriteriaBuilder queryBuilder = taxonDao.getCriteriaBuilder(); - value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName()); + value = activeFiltersObject.getRankName(); +// value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName()); CriteriaQuery cq = queryBuilder.createQuery(); Predicate pr1 = queryBuilder.equal(taxonDao.rootFrom(cq).get(Taxon.RANK), NormalizeString.validateUndefined(value)); cq.where(pr1); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java index dc98317..7369707 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java @@ -129,7 +129,7 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer cq.where(pr1); //TODO FIXME empty value - logger.trace("FILTER BY DATA PROVIDER: "+ value ); + logger.trace("FILTER BY DATA SOURCE: "+ value ); iterator = dao.executeCriteriaQuery(cq).iterator(); @@ -145,12 +145,15 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer try { CriteriaBuilder queryBuilder = dao.getCriteriaBuilder(); - value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName()); + value = activeFiltersObject.getRankName(); +// value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName()); logger.trace("in rank filter - value: "+value); CriteriaQuery cq = queryBuilder.createQuery(); Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(TaxonomyRow.RANK), NormalizeString.validateUndefined(value)); cq.where(pr1); + logger.trace("FILTER BY RANK: "+ value ); + iterator = dao.executeCriteriaQuery(cq).iterator(); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java index b3468ca..45d48e9 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java @@ -3,7 +3,6 @@ package org.gcube.portlets.user.speciesdiscovery.server.service; import java.util.ArrayList; import java.util.List; -import org.apache.commons.lang.StringEscapeUtils; import org.apache.log4j.Logger; import org.gcube.application.framework.core.session.ASLSession; import org.gcube.data.spd.model.TaxonomyItem; @@ -62,55 +61,55 @@ public class TaxonomyItemConverter implements Converter implements Runnable, Closeable { } catch (Exception e) { logger.error("Error in source.next() " + e.getMessage(), e); + e.printStackTrace(); + silentClose(); } @@ -80,7 +82,7 @@ public class Fetcher implements Runnable, Closeable { } if(source==null) - logger.trace("exit because source iterator is null"); + logger.warn("exit because source iterator is null"); logger.trace("exit fetch run - complete true"); complete = true; @@ -93,7 +95,7 @@ public class Fetcher implements Runnable, Closeable { try { close(); } catch (IOException e) { - logger.warn("Error during silent close", e); + logger.error("Error during silent close", e); } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java index 983eac2..7bd3967 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java @@ -16,6 +16,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyProvider; /** * @author "Federico De Faveri defaveri@isti.cnr.it" + * modified by Francesco Mangiacrapa february 2013 * */ public class TaxonomyClassificationAggregator implements Aggregator>> { @@ -52,7 +53,7 @@ public class TaxonomyClassificationAggregator implem List matchingTaxon = row.getParents(); - if(matchingTaxon == null) return; + if(matchingTaxon == null || matchingTaxon.size()==0) return; EnumMap groupedTaxon = groupTaxonByRank(matchingTaxon); @@ -86,45 +87,6 @@ public class TaxonomyClassificationAggregator implem } } - - -// TODO RIFARE -// TaxonomyInterface matchingTaxon = row.getParents(); -// -// if(matchingTaxon == null) return; -// -// EnumMap groupedTaxon = groupTaxonByRank(matchingTaxon); -// -// for (MainTaxonomicRankEnum aggregationRank: MainTaxonomicRankEnum.values()){ -// -// TaxonomyInterface taxon = groupedTaxon.get(aggregationRank); -// -// String taxonId; -// -// //IF RANK CLASS EXISTS INSERT INTO HASHMAP GROUP BY RANK -// if (taxon!=null && taxon.getName()!=null) { -// taxonId = addTaxonToAggregation(aggregationRank, taxon, row.getBaseTaxonValue(), row.getBaseTaxonValue(), taxon.getRank()); -// setClassification(row, aggregationRank, taxonId); -// } else { -// -// String unknownRank = matchingTaxon.getRank()!=null?matchingTaxon.getRank():TAXONOMYUNKNOWN; // GET THE FIRST RANK CLASS -// -// //IF BASETAXONOMY CLASS IS NOT UNKNOWN - INSERT INTO HASHMAP GROUP BY FIRST RANK -// if(!row.getBaseTaxonValue().equalsIgnoreCase(TAXONOMYUNKNOWN)) { -// taxonId = addTaxonToAggregation(aggregationRank, row.getParents(), row.getBaseTaxonValue(), row.getBaseTaxonValue(), unknownRank); -// setClassification(row, aggregationRank, taxonId); -// } else { -// //BASETAXONOMY UNKNOWN - INSERT INTO HASHMAP GROUP BY haskKey UNKNOWN RANK -// -// String haskKey = "["+UNK+" "+aggregationRank+"]" + " "+unknownRank; -// String unkName = matchingTaxon.getName()!=null?matchingTaxon.getName():TAXONOMYUNKNOWN; // GET THE FIRST RANK NAME -// -// taxonId = addTaxonToAggregation(aggregationRank, haskKey, unkName, row.getBaseTaxonValue(), row.getBaseTaxonValue(), unknownRank); -// setClassification(row, aggregationRank, taxonId); -// } -// -// } -// } } protected void setClassification(TaxonomyProvider input, MainTaxonomicRankEnum rank, String value) @@ -151,33 +113,10 @@ public class TaxonomyClassificationAggregator implem if (rank!=null) groupedTaxon.put(rank, taxonomyInterface); } } - -// while(taxon!=null){ -// if (taxon.getRank()!=null) { -// MainTaxonomicRankEnum rank = RANKS.get(taxon.getRank().toLowerCase()); -// if (rank!=null) groupedTaxon.put(rank, taxon); -// } -// taxon = taxon.getParent(); -// } return groupedTaxon; } -// protected EnumMap groupTaxonByRank(TaxonomyInterface taxon) -// { -// EnumMap groupedTaxon = new EnumMap(MainTaxonomicRankEnum.class); -// -// while(taxon!=null){ -// if (taxon.getRank()!=null) { -// MainTaxonomicRankEnum rank = RANKS.get(taxon.getRank().toLowerCase()); -// if (rank!=null) groupedTaxon.put(rank, taxon); -// } -// taxon = taxon.getParent(); -// } -// -// return groupedTaxon; -// } - protected String addTaxonToAggregation(MainTaxonomicRankEnum aggregationRank, TaxonomyInterface taxon, String baseTaxonId, String baseTaxonValue, String classificationRank) { String taxonName = taxon.getName().toLowerCase(); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java index 6841ab5..b50bcb3 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java @@ -426,65 +426,65 @@ public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInter public String toString() { StringBuilder builder = new StringBuilder(); builder.append("TaxonomyRow [id="); -// builder.append(id); -// builder.append(", author="); -// builder.append(author); -// builder.append(", credits="); -// builder.append(credits); -// builder.append(", lsid="); -// builder.append(lsid); -// builder.append(", name="); -// builder.append(name); -// builder.append(", serviceIdField="); -// builder.append(serviceIdField); -// builder.append(", selected="); -// builder.append(selected); -// builder.append(", dataProviderId="); -// builder.append(dataProviderId); -// builder.append(", dataProviderName="); -// builder.append(dataProviderName); -// builder.append(", dataSetCitation="); -// builder.append(dataSetCitation); -// builder.append(", matchingAccording="); -// builder.append(matchingAccording); -// builder.append(", baseTaxonValue="); -// builder.append(baseTaxonValue); -// builder.append(", rank="); -// builder.append(rank); -// builder.append(", statusRefId="); -// builder.append(statusRefId); -// builder.append(", statusName="); -// builder.append(statusName); -// builder.append(", dateModified="); -// builder.append(dateModified); -// builder.append(", kingdomID="); -// builder.append(kingdomID); -// builder.append(", phylumID="); -// builder.append(phylumID); -// builder.append(", classID="); -// builder.append(classID); -// builder.append(", orderID="); -// builder.append(orderID); -// builder.append(", familyID="); -// builder.append(familyID); -// builder.append(", genusID="); -// builder.append(genusID); -// builder.append(", speciesID="); -// builder.append(speciesID); -// builder.append(", existsCommonName="); -// builder.append(existsCommonName); -// builder.append(", statusRemarks="); -// builder.append(statusRemarks); -// builder.append(", existsProperties="); -// builder.append(existsProperties); -// builder.append(", isParent="); -// builder.append(isParent); + builder.append(id); + builder.append(", author="); + builder.append(author); + builder.append(", credits="); + builder.append(credits); + builder.append(", lsid="); + builder.append(lsid); + builder.append(", name="); + builder.append(name); + builder.append(", serviceIdField="); + builder.append(serviceIdField); + builder.append(", selected="); + builder.append(selected); + builder.append(", dataProviderId="); + builder.append(dataProviderId); + builder.append(", dataProviderName="); + builder.append(dataProviderName); + builder.append(", dataSetCitation="); + builder.append(dataSetCitation); + builder.append(", matchingAccording="); + builder.append(matchingAccording); + builder.append(", baseTaxonValue="); + builder.append(baseTaxonValue); + builder.append(", rank="); + builder.append(rank); + builder.append(", statusRefId="); + builder.append(statusRefId); + builder.append(", statusName="); + builder.append(statusName); + builder.append(", dateModified="); + builder.append(dateModified); + builder.append(", kingdomID="); + builder.append(kingdomID); + builder.append(", phylumID="); + builder.append(phylumID); + builder.append(", classID="); + builder.append(classID); + builder.append(", orderID="); + builder.append(orderID); + builder.append(", familyID="); + builder.append(familyID); + builder.append(", genusID="); + builder.append(genusID); + builder.append(", speciesID="); + builder.append(speciesID); + builder.append(", existsCommonName="); + builder.append(existsCommonName); + builder.append(", statusRemarks="); + builder.append(statusRemarks); + builder.append(", existsProperties="); + builder.append(existsProperties); + builder.append(", isParent="); + builder.append(isParent); builder.append(", commonNames="); builder.append(commonNames); builder.append(", properties="); builder.append(properties); -// builder.append(", parents="); -// builder.append(parents); + builder.append(", parents="); + builder.append(parents); builder.append(", parentID="); builder.append(parentID); builder.append("]");