From e4d66102792de6236f2d97a23bc96fe7c731ee31 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Andreas=20M=C3=BCller?= Date: Fri, 5 May 2017 14:45:19 +0200 Subject: [PATCH] cleanup --- .../cdm/io/csv/redlist/demo/CsvDemoBase.java | 72 +++++++++---------- .../cdm/io/dwca/out/DwcaExportBase.java | 6 +- .../hibernate/common/AnnotatableDaoImpl.java | 7 +- .../hibernate/common/CdmEntityDaoBase.java | 2 +- .../hibernate/common/IdentifiableDaoBase.java | 5 +- .../hibernate/description/WorkingSetDao.java | 8 +-- .../CollectionDaoHibernateImpl.java | 29 ++++---- .../OccurrenceDaoHibernateImpl.java | 14 ++-- .../taxon/TaxonDaoHibernateImpl.java | 13 ++-- .../cdm/persistence/dao/media/IMediaDao.java | 26 +++---- .../cdm/api/service/NameServiceImpl.java | 8 --- 11 files changed, 95 insertions(+), 95 deletions(-) diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoBase.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoBase.java index a260588c16..1f2aaf1ac0 100644 --- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoBase.java +++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoBase.java @@ -1,8 +1,8 @@ /** * Copyright (C) 2007 EDIT -* European Distributed Institute of Taxonomy +* 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. */ @@ -51,31 +51,29 @@ import eu.etaxonomy.cdm.model.taxon.TaxonNode; * */ public abstract class CsvDemoBase extends CdmExportBase implements ICdmExport{ - private static final Logger logger = Logger.getLogger(CsvDemoBase.class); - + private static final long serialVersionUID = -2962456879635841019L; + + private static final Logger logger = Logger.getLogger(CsvDemoBase.class); + protected static final boolean IS_CORE = true; - - - protected Set existingRecordIds = new HashSet(); - protected Set existingRecordUuids = new HashSet(); - - - - /* (non-Javadoc) - * @see eu.etaxonomy.cdm.io.common.CdmIoBase#countSteps() - */ + + + protected Set existingRecordIds = new HashSet<>(); + protected Set existingRecordUuids = new HashSet<>(); + + @Override public int countSteps() { List allNodes = getClassificationService().getAllNodes(); return allNodes.size(); } - - + + /** - * Returns the list of {@link TaxonNode taxon nodes} that are part in one of the given {@link Classification classifications} + * Returns the list of {@link TaxonNode taxon nodes} that are part in one of the given {@link Classification classifications} * and do have a {@link Taxon} attached (empty taxon nodes should not but do exist in CDM databases). - * If classificationList is null or empty then all {@link TaxonNode taxon nodes} of all + * If classificationList is null or empty then all {@link TaxonNode taxon nodes} of all * {@link Classification classifications} are returned.
* Preliminary implementation. Better implement API method for this. * @return @@ -85,7 +83,7 @@ public abstract class CsvDemoBase extends CdmExportBase allNodes = getClassificationService().getAllNodes(); List result = new ArrayList(); for (TaxonNode node : allNodes){ @@ -105,8 +103,8 @@ public abstract class CsvDemoBase extends CdmExportBase taxon) { return taxon.getTitleCache() + "(" + taxon.getId() + ")"; } - + /** * @param el @@ -141,7 +139,7 @@ public abstract class CsvDemoBase extends CdmExportBase sourceable, CsvTaxExportConfiguratorRedlist config) { String result = ""; @@ -178,7 +176,7 @@ public abstract class CsvDemoBase extends CdmExportBase implements ICdmExport{ + private static final long serialVersionUID = -3214410418410044139L; + private static final Logger logger = Logger.getLogger(DwcaExportBase.class); protected static final boolean IS_CORE = true; @@ -61,10 +63,6 @@ public abstract class DwcaExportBase extends CdmExportBase allNodes = getClassificationService().getAllNodes(); diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/AnnotatableDaoImpl.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/AnnotatableDaoImpl.java index 375b55a124..dbcc3ec5c5 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/AnnotatableDaoImpl.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/AnnotatableDaoImpl.java @@ -26,8 +26,11 @@ import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder; * @author n.hoffmann * @created 24.09.2008 */ -public abstract class AnnotatableDaoImpl extends VersionableDaoBase implements IAnnotatableDao { - @SuppressWarnings("unused") +public abstract class AnnotatableDaoImpl + extends VersionableDaoBase + implements IAnnotatableDao { + + @SuppressWarnings("unused") private static Logger logger = Logger.getLogger(AnnotatableDaoImpl.class); /** diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java index 732e8fced3..c0b259b853 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/CdmEntityDaoBase.java @@ -844,7 +844,7 @@ public abstract class CdmEntityDaoBase extends DaoBase implem * @param start * @param criteria */ - private void addLimitAndStart(Integer limit, Integer start, Criteria criteria) { + protected void addLimitAndStart(Integer limit, Integer start, Criteria criteria) { if(limit != null) { if(start != null) { criteria.setFirstResult(start); diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBase.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBase.java index b5c1bce7a7..edf3848625 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBase.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/common/IdentifiableDaoBase.java @@ -46,7 +46,10 @@ import eu.etaxonomy.cdm.persistence.query.MatchMode; import eu.etaxonomy.cdm.persistence.query.OrderHint; -public class IdentifiableDaoBase extends AnnotatableDaoImpl implements IIdentifiableDao{ +public class IdentifiableDaoBase + extends AnnotatableDaoImpl + implements IIdentifiableDao{ + @SuppressWarnings("unused") private static final Logger logger = Logger.getLogger(IdentifiableDaoBase.class); diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/WorkingSetDao.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/WorkingSetDao.java index 10ca0756cb..11e8fd525a 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/WorkingSetDao.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/description/WorkingSetDao.java @@ -36,8 +36,8 @@ public class WorkingSetDao extends AnnotatableDaoImpl implements IWo @Override public Map> getDescriptionElements(WorkingSet workingSet, Set features, Integer pageSize, Integer pageNumber, List propertyPaths) { - checkNotInPriorView("WorkingSetDao.getDescriptionElements(WorkingSet workingSet, Set features, Integer pageSize,Integer pageNumber, List orderHints, List propertyPaths)"); - Query query = getSession().createQuery("select description from WorkingSet workingSet join workingSet.descriptions description order by description.titleCache asc"); + checkNotInPriorView("WorkingSetDao.getDescriptionElements(WorkingSet workingSet, Set features, Integer pageSize,Integer pageNumber, List propertyPaths)"); + Query query = getSession().createQuery("SELECT description FROM WorkingSet workingSet JOIN workingSet.descriptions description ORDER BY description.titleCache ASC"); if(pageSize != null) { query.setMaxResults(pageSize); @@ -48,7 +48,7 @@ public class WorkingSetDao extends AnnotatableDaoImpl implements IWo } } List descriptions = query.list(); - Map> result = new HashMap>(); + Map> result = new HashMap<>(); for(DescriptionBase description : descriptions) { Criteria criteria = getSession().createCriteria(DescriptionElementBase.class); criteria.add(Restrictions.eq("inDescription", description)); @@ -58,7 +58,7 @@ public class WorkingSetDao extends AnnotatableDaoImpl implements IWo List r = criteria.list(); defaultBeanInitializer.initializeAll(r, propertyPaths); - result.put(description, new HashSet(r)); + result.put(description, new HashSet<>(r)); } return result; } diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/CollectionDaoHibernateImpl.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/CollectionDaoHibernateImpl.java index e1b36c532a..3750bfeecc 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/CollectionDaoHibernateImpl.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/CollectionDaoHibernateImpl.java @@ -5,7 +5,7 @@ * * 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.persistence.dao.hibernate.occurrence; @@ -28,37 +28,38 @@ import eu.etaxonomy.cdm.persistence.dao.occurrence.ICollectionDao; @Repository public class CollectionDaoHibernateImpl extends IdentifiableDaoBase implements ICollectionDao { - + public CollectionDaoHibernateImpl() { super(Collection.class); indexedClasses = new Class[1]; indexedClasses[0] = Collection.class; } - public List getCollectionByCode(String code) { + @Override + public List getCollectionByCode(String code) { AuditEvent auditEvent = getAuditEventFromContext(); if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) { Criteria crit = getSession().createCriteria(Collection.class); crit.add(Restrictions.eq("code", code)); - - return (List)crit.list(); + + return crit.list(); } else { AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(Collection.class,auditEvent.getRevisionNumber()); query.add(AuditEntity.property("code").eq(code)); - return (List)query.getResultList(); + return query.getResultList(); } } @Override public void rebuildIndex() { - FullTextSession fullTextSession = Search.getFullTextSession(getSession()); - - for(Collection collection : list(null,null)) { // re-index all taxon base + FullTextSession fullTextSession = Search.getFullTextSession(getSession()); - Hibernate.initialize(collection.getSuperCollection()); - Hibernate.initialize(collection.getInstitute()); - fullTextSession.index(collection); - } - fullTextSession.flushToIndexes(); + for(Collection collection : list(null,null)) { // re-index all taxon base + + Hibernate.initialize(collection.getSuperCollection()); + Hibernate.initialize(collection.getInstitute()); + fullTextSession.index(collection); + } + fullTextSession.flushToIndexes(); } } diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java index cbf2ab73fa..d1c776478b 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/occurrence/OccurrenceDaoHibernateImpl.java @@ -28,6 +28,7 @@ import org.hibernate.search.Search; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Repository; +import eu.etaxonomy.cdm.model.common.CdmBase; import eu.etaxonomy.cdm.model.description.DescriptionBase; import eu.etaxonomy.cdm.model.description.IndividualsAssociation; import eu.etaxonomy.cdm.model.media.Media; @@ -222,9 +223,9 @@ public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase occurrence : list(null,null)) { // re-index all taxon base - for(DeterminationEvent determination : (Set)occurrence.getDeterminations()) { + for(DeterminationEvent determination : occurrence.getDeterminations()) { Hibernate.initialize(determination.getActor()); Hibernate.initialize(determination.getTaxon()); } @@ -237,9 +238,9 @@ public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase original = derivedUnit.getOriginalUnit(); if(original != null && original.isInstanceOf(FieldUnit.class)) { - FieldUnit fieldUnit = original.deproxy(original, FieldUnit.class); + FieldUnit fieldUnit = CdmBase.deproxy(original, FieldUnit.class); Hibernate.initialize(fieldUnit.getGatheringEvent()); if(fieldUnit.getGatheringEvent() != null) { Hibernate.initialize(fieldUnit.getGatheringEvent().getActor()); @@ -288,6 +289,7 @@ public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase results = criteria.list(); defaultBeanInitializer.initializeAll(results, propertyPaths); return results; @@ -330,6 +332,7 @@ public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase results = criteria.list(); defaultBeanInitializer.initializeAll(results, propertyPaths); return results; @@ -359,11 +362,12 @@ public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase results = criteria.list(); defaultBeanInitializer.initializeAll(results, propertyPaths); return results; } - return Collections.EMPTY_LIST; + return Collections.emptyList(); } private Criteria createFindOccurrenceCriteria(Class clazz, String queryString, diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java index f848d66a0d..398f336f23 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxon/TaxonDaoHibernateImpl.java @@ -327,8 +327,12 @@ public class TaxonDaoHibernateImpl extends IdentifiableDaoBase implem String commonNameSubSelect = subSelects[3]; - logger.debug("taxonSubselect: " + taxonSubselect != null ? taxonSubselect: "NULL"); - logger.debug("synonymSubselect: " + synonymSubselect != null ? synonymSubselect: "NULL"); + if (logger.isDebugEnabled()) { + logger.debug("taxonSubselect: " + (taxonSubselect != null ? taxonSubselect: "NULL")); + } + if (logger.isDebugEnabled()) { + logger.debug("synonymSubselect: " + (synonymSubselect != null ? synonymSubselect: "NULL")); + } Query subTaxon = null; Query subSynonym = null; @@ -346,8 +350,6 @@ public class TaxonDaoHibernateImpl extends IdentifiableDaoBase implem subTaxon.setParameter("classification", classification); } - - } if(doSynonyms){ @@ -381,10 +383,7 @@ public class TaxonDaoHibernateImpl extends IdentifiableDaoBase implem } if(classification != null){ subCommonNames.setParameter("classification", classification); - } - - } List taxa = new ArrayList(); diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaDao.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaDao.java index 081e08719d..851104f4a6 100644 --- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaDao.java +++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/media/IMediaDao.java @@ -1,6 +1,6 @@ /** * Copyright (C) 2008 EDIT -* European Distributed Institute of Taxonomy +* European Distributed Institute of Taxonomy * http://www.e-taxonomy.eu */ @@ -22,22 +22,22 @@ import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer; * @created 08.09.2008 */ public interface IMediaDao extends IIdentifiableDao { - + /** * Return a count of MediaKeys, optionally filtered by the parameters passed. - * + * * @param taxonomicScope a Set of Taxon instances that define the taxonomic scope of the key (can be null) * @param geoScopes a Set of NamedArea instances that define the geospatial scope of the key (can be null) * @return a count of MediaKey instances */ public int countMediaKeys(Set taxonomicScope, Set geoScopes); - + /** - * Return a List of MediaKeys, optionally filtered by the parameters passed. The MediaKey + * Return a List of MediaKeys, optionally filtered by the parameters passed. The MediaKey * instances have the following properties initialized: - * + * * MediaKey.title - * + * * @param taxonomicScope a Set of Taxon instances that define the taxonomic scope of the key (can be null) * @param geoScopes a Set of NamedArea instances that define the geospatial scope of the key (can be null) * @param pageSize The maximum number of keys returned (can be null for all keys) @@ -46,24 +46,26 @@ public interface IMediaDao extends IIdentifiableDao { * @return a List of MediaKey instances */ public List getMediaKeys(Set taxonomicScope, Set geoScopes, Integer pageSize, Integer pageNumber, List propertyPaths); - + /** * Return a count of the rights for this media entity - * + * * @param t The media entity * @return a count of Rights instances */ + @Override public int countRights(Media t); - + /** * Return a List of the rights for this media entity - * + * * @param t The media entity * @param pageSize The maximum number of rights returned (can be null for all rights) * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)} * @return a List of Rights instances */ - public List getRights(Media t, Integer pageSize, Integer pageNumber, List propertyPaths); + @Override + public List getRights(Media t, Integer pageSize, Integer pageNumber, List propertyPaths); } diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java index 95378e1fa7..9db4ab2fbb 100644 --- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java +++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/NameServiceImpl.java @@ -366,14 +366,6 @@ public class NameServiceImpl extends IdentifiableServiceBase getAllNames(int limit, int start){ - return dao.list(limit, start); - } - /** * TODO candidate for harmonization * new name getNomenclaturalStatus -- 2.34.1