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species-discovery
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git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@71065 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Francesco Mangiacrapa 2013-03-07 16:23:22 +00:00
parent a8a203bb1c
commit 6282760e36
8 changed files with 84 additions and 140 deletions
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2
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/util/stream/TaxonomyRowDataSource.java
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@ -112,7 +112,7 @@ public class TaxonomyRowDataSource implements DataSource {
String author = "";
List<ItemParameter> hashProperties = new ArrayList<ItemParameter>();
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();

4
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java
View File

@ -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<T extends FetchingElement> implements FetchingBuffer<T> {
protected GCUBELog logger = new GCUBELog(AbstractDaoBuffer.class);
protected Logger logger = Logger.getLogger(AbstractDaoBuffer.class);
protected AbstractPersistence<T> dao;

3
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java
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@ -161,7 +161,8 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
try {
CriteriaBuilder queryBuilder = taxonDao.getCriteriaBuilder();
value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName());
value = activeFiltersObject.getRankName();
// value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName());
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(taxonDao.rootFrom(cq).get(Taxon.RANK), NormalizeString.validateUndefined(value));
cq.where(pr1);

7
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java
View File

@ -129,7 +129,7 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
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<TaxonomyRow>
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<Object> 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();

27
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java
View File

@ -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<TaxonomyItem, TaxonomyRo
//Fill properties
if(listProperties!=null){
for (ElementProperty elementProperty : listProperties)
tax.getProperties().add(new ItemParameter(StringEscapeUtils.escapeSql(elementProperty.getName()), StringEscapeUtils.escapeSql(elementProperty.getValue())));
tax.getProperties().add(new ItemParameter(elementProperty.getName(), elementProperty.getValue()));
tax.setExistsProperties(true);
}
if(input.getId()!=null){
tax.setServiceId(StringEscapeUtils.escapeSql(input.getId()));
tax.setServiceId(input.getId());
}
if(input.getAuthor()!=null && !input.getAuthor().isEmpty()){
tax.setAuthor(StringEscapeUtils.escapeSql(input.getAuthor()));
tax.setAuthor(input.getAuthor());
}
else
tax.setAuthor(ConstantsSpeciesDiscovery.NOT_FOUND);
if(input.getCredits()!=null && !input.getCredits().isEmpty()){
tax.setCredits(StringEscapeUtils.escapeSql(input.getCredits()));
tax.setCredits(input.getCredits());
}
else
tax.setCredits(ConstantsSpeciesDiscovery.NOT_FOUND);
if(input.getLsid()!=null && !input.getLsid().isEmpty()){
tax.setLsid(StringEscapeUtils.escapeSql(input.getLsid()));
tax.setLsid(input.getLsid());
}
else
tax.setLsid(ConstantsSpeciesDiscovery.NOT_FOUND);
if(input.getProvider()!=null && !input.getProvider().isEmpty()){
tax.setDataProviderId(StringEscapeUtils.escapeSql(input.getProvider()));
tax.setDataProviderName(StringEscapeUtils.escapeSql(input.getProvider()));
tax.setDataProviderId(input.getProvider());
tax.setDataProviderName(input.getProvider());
}else{
tax.setDataProviderId(ConstantsSpeciesDiscovery.NOT_FOUND);
tax.setDataProviderName(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getCitation()!=null && !input.getCitation().isEmpty()){
tax.setDataSetCitation(StringEscapeUtils.escapeSql(input.getCitation()));
tax.setDataSetCitation(input.getCitation());
}else{
tax.setDataSetCitation(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getRank()!=null && !input.getRank().isEmpty()){
tax.setRank(StringEscapeUtils.escapeSql(NormalizeString.lowerCaseUpFirstChar(input.getRank())));
tax.setRank(NormalizeString.lowerCaseUpFirstChar(input.getRank()));
}else{
tax.setRank(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getScientificName()!=null && !input.getScientificName().isEmpty()){
tax.setName(StringEscapeUtils.escapeSql(input.getScientificName()));
tax.setName(input.getScientificName());
}else{
tax.setName(ConstantsSpeciesDiscovery.NOT_FOUND);
}
@ -118,14 +117,14 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
if(input.getStatus()!=null){
if(input.getStatus().getRefId()!=null && !input.getStatus().getRefId().isEmpty()){
tax.setStatusRefId(StringEscapeUtils.escapeSql(input.getStatus().getRefId()));
tax.setStatusRefId(input.getStatus().getRefId());
}else{
tax.setStatusRefId("");
}
if(input.getStatus().getStatusAsString()!=null && !input.getStatus().getStatusAsString().isEmpty()){
tax.setStatusRemarks(StringEscapeUtils.escapeSql(input.getStatus().getStatusAsString()));
tax.setStatusRemarks(input.getStatus().getStatusAsString());
}else{
tax.setStatusRemarks(ConstantsSpeciesDiscovery.NOT_FOUND);
}
@ -133,7 +132,7 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
if(input.getStatus().getStatus()!=null){
if(input.getStatus().getStatus().name()!=null && !input.getStatus().getStatus().name().isEmpty()){
tax.setStatusName(StringEscapeUtils.escapeSql(input.getStatus().getStatus().name()));
tax.setStatusName(input.getStatus().getStatus().name());
}else{
tax.setStatusName(ConstantsSpeciesDiscovery.NOT_FOUND);
}

6
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/session/Fetcher.java
View File

@ -67,6 +67,8 @@ public class Fetcher<T extends FetchingElement> 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<T extends FetchingElement> 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<T extends FetchingElement> implements Runnable, Closeable {
try {
close();
} catch (IOException e) {
logger.warn("Error during silent close", e);
logger.error("Error during silent close", e);
}
}

65
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java
View File

@ -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<T extends TaxonomyProvider> implements Aggregator<T, EnumMap<MainTaxonomicRankEnum, HashMap<String, ClassificationModel>>> {
@ -52,7 +53,7 @@ public class TaxonomyClassificationAggregator<T extends TaxonomyProvider> implem
List<? extends TaxonomyInterface> matchingTaxon = row.getParents();
if(matchingTaxon == null) return;
if(matchingTaxon == null || matchingTaxon.size()==0) return;
EnumMap<MainTaxonomicRankEnum, TaxonomyInterface> groupedTaxon = groupTaxonByRank(matchingTaxon);
@ -86,45 +87,6 @@ public class TaxonomyClassificationAggregator<T extends TaxonomyProvider> implem
}
}
// TODO RIFARE
// TaxonomyInterface matchingTaxon = row.getParents();
//
// if(matchingTaxon == null) return;
//
// EnumMap<MainTaxonomicRankEnum, TaxonomyInterface> 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<T extends TaxonomyProvider> 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<MainTaxonomicRankEnum, TaxonomyInterface> groupTaxonByRank(TaxonomyInterface taxon)
// {
// EnumMap<MainTaxonomicRankEnum, TaxonomyInterface> groupedTaxon = new EnumMap<MainTaxonomicRankEnum, TaxonomyInterface>(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();

110
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java
View File

@ -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("]");