diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
index 6fd38ebfd6e8a177a4b29c30740a3444c1885051..a45dcc04bd0a6e3f854d91da1f28e9f6edb141ba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricher.java
@@ -16,15 +16,13 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
-import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
-import it.unimi.dsi.fastutil.longs.LongSet;
+import java.util.ArrayList;
+import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
@@ -33,6 +31,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTermEntityProperty;
+import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
+import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
/**
* A class that can enrich a set of entities with its entity properties.
*
@@ -73,38 +76,6 @@ public final class EntityPropertiesEnricher implements IEntityPropertiesEnricher
}
};
}
-
- @Override
- public Iterable<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(
- LongSet entityIDs)
- {
- return new AbstractBatchIterator<VocabularyTermRecord>(entityIDs, BATCH_SIZE)
- {
- @Override
- protected Iterable<VocabularyTermRecord> createUnefficientIterator(
- LongSet ids)
- {
- return setQuery.getEntityPropertyVocabularyTermValues(ids);
- }
- };
- }
-
- @Override
- public Iterable<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(
- LongSet entityIDs)
- {
- return new AbstractBatchIterator<MaterialEntityPropertyRecord>(entityIDs,
- BATCH_SIZE)
- {
- @Override
- protected Iterable<MaterialEntityPropertyRecord> createUnefficientIterator(
- LongSet ids)
- {
- return setQuery.getEntityPropertyMaterialValues(ids);
- }
- };
- }
-
};
}
@@ -115,87 +86,48 @@ public final class EntityPropertiesEnricher implements IEntityPropertiesEnricher
@Override
public void enrich(final LongSet entityIDs, final IEntityPropertiesHolderResolver entities)
{
- final Long2ObjectMap<PropertyType> propertyTypes = getPropertyTypes();
- // Generic properties
- for (GenericEntityPropertyRecord val : propertySetQuery
- .getEntityPropertyGenericValues(entityIDs))
+ List<GenericEntityPropertyRecord> records = new ArrayList<>();
+ LongSet vocaTermIds = new LongOpenHashSet();
+ LongSet materialIds = new LongOpenHashSet();
+ for (GenericEntityPropertyRecord record : propertySetQuery.getEntityPropertyGenericValues(entityIDs))
{
- final IEntityPropertiesHolder entity = entities.get(val.entity_id);
- final AbstractEntityProperty property = new GenericEntityProperty();
- property.setValue(val.value);
- property.setPropertyType(propertyTypes.get(val.prty_id));
- property.setScriptable(val.script_id != null);
- property.setDynamic(ScriptType.DYNAMIC_PROPERTY.name().equals(val.script_type));
- property.setOrdinal(val.ordinal);
- entity.getProperties().add(property);
- }
-
- // Controlled vocabulary properties
- Long2ObjectMap<String> vocabularyURLMap = null;
- Long2ObjectMap<VocabularyTerm> terms = new Long2ObjectOpenHashMap<VocabularyTerm>();
- for (VocabularyTermRecord val : propertySetQuery
- .getEntityPropertyVocabularyTermValues(entityIDs))
- {
- if (vocabularyURLMap == null)
+ records.add(record);
+ if (record.cvte_id != null)
{
- vocabularyURLMap = getVocabularyURLs();
+ vocaTermIds.add(record.cvte_id);
}
- final IEntityPropertiesHolder entity = entities.get(val.entity_id);
- final IEntityProperty property = new VocabularyTermEntityProperty();
- VocabularyTerm vocabularyTerm = terms.get(val.id);
- if (vocabularyTerm == null)
+ if (record.mate_prop_id != null)
{
- vocabularyTerm = new VocabularyTerm();
- vocabularyTerm.setCode(val.code);
- vocabularyTerm.setLabel(val.label);
- vocabularyTerm.setDescription(val.description);
- final String template = vocabularyURLMap.get(val.covo_id);
- if (template != null)
- {
- String url =
- template.replaceAll(
- BasicConstant.DEPRECATED_VOCABULARY_URL_TEMPLATE_TERM_PATTERN,
- val.code);
- url =
- url.replaceAll(BasicConstant.VOCABULARY_URL_TEMPLATE_TERM_PATTERN,
- val.code);
- vocabularyTerm.setUrl(url);
- }
- terms.put(val.id, vocabularyTerm);
+ materialIds.add(record.mate_prop_id);
}
- property.setVocabularyTerm(vocabularyTerm);
- property.setPropertyType(propertyTypes.get(val.prty_id));
- property.setOrdinal(val.ordinal);
- entity.getProperties().add(property);
}
- // Material-type properties
- Long2ObjectMap<MaterialType> materialTypes = null;
- Long2ObjectMap<Material> materials = new Long2ObjectOpenHashMap<Material>();
- for (MaterialEntityPropertyRecord val : propertySetQuery
- .getEntityPropertyMaterialValues(entityIDs))
+ Long2ObjectMap<VocabularyTerm> vocabularyTerms = getVocabularyTerms(vocaTermIds);
+ Long2ObjectMap<Material> materials = getMaterials(materialIds);
+ Long2ObjectMap<PropertyType> propertyTypes = getPropertyTypes();
+ for (GenericEntityPropertyRecord val : records)
{
- if (materialTypes == null)
+ AbstractEntityProperty property;
+ if (val.cvte_id != null)
{
- materialTypes = getMaterialTypes();
- }
- final IEntityPropertiesHolder entity = entities.get(val.entity_id);
- final IEntityProperty property = new MaterialEntityProperty();
- Material material = materials.get(val.id);
- if (material == null)
+ property = new VocabularyTermEntityProperty();
+ property.setVocabularyTerm(vocabularyTerms.get(val.cvte_id));
+ } else if (val.mate_prop_id != null)
+ {
+ property = new MaterialEntityProperty();
+ property.setMaterial(materials.get(val.mate_prop_id));
+ } else
{
- material = new Material();
- material.setCode(val.code);
- material.setMaterialType(materialTypes.get(val.maty_id));
- material.setId(val.id);
- materials.put(val.id, material);
+ property = new GenericEntityProperty();
+ property.setValue(val.value);
+ property.setScriptable(val.script_id != null);
+ property.setDynamic(ScriptType.DYNAMIC_PROPERTY.name().equals(val.script_type));
}
- property.setMaterial(material);
property.setPropertyType(propertyTypes.get(val.prty_id));
property.setOrdinal(val.ordinal);
+ IEntityPropertiesHolder entity = entities.get(val.entity_id);
entity.getProperties().add(property);
}
-
}
private Long2ObjectMap<PropertyType> getPropertyTypes()
@@ -239,4 +171,56 @@ public final class EntityPropertiesEnricher implements IEntityPropertiesEnricher
return materialTypeMap;
}
+ private Long2ObjectMap<VocabularyTerm> getVocabularyTerms(LongSet vocaTermIds)
+ {
+ Long2ObjectMap<String> vocabularyURLMap = null;
+ Long2ObjectOpenHashMap<VocabularyTerm> map = new Long2ObjectOpenHashMap<VocabularyTerm>();
+ if (vocaTermIds.isEmpty() == false)
+ {
+ for (VocabularyTermRecord record : query.getVocabularyTerms(vocaTermIds))
+ {
+ if (vocabularyURLMap == null)
+ {
+ vocabularyURLMap = getVocabularyURLs();
+ }
+ VocabularyTerm vocabularyTerm = new VocabularyTerm();
+ vocabularyTerm.setCode(record.code);
+ vocabularyTerm.setLabel(record.label);
+ vocabularyTerm.setDescription(record.description);
+ final String template = vocabularyURLMap.get(record.covo_id);
+ if (template != null)
+ {
+ String url = template.replaceAll(
+ BasicConstant.DEPRECATED_VOCABULARY_URL_TEMPLATE_TERM_PATTERN,
+ record.code);
+ url = url.replaceAll(BasicConstant.VOCABULARY_URL_TEMPLATE_TERM_PATTERN, record.code);
+ vocabularyTerm.setUrl(url);
+ }
+ map.put(record.id, vocabularyTerm);
+ }
+ }
+ return map;
+ }
+
+ private Long2ObjectMap<Material> getMaterials(LongSet materialIds)
+ {
+ Long2ObjectMap<MaterialType> materialTypes = null;
+ Long2ObjectOpenHashMap<Material> map = new Long2ObjectOpenHashMap<Material>();
+ if (materialIds.isEmpty() == false)
+ {
+ for (MaterialEntityPropertyRecord record : query.getMaterials(materialIds))
+ {
+ if (materialTypes == null)
+ {
+ materialTypes = getMaterialTypes();
+ }
+ Material material = new Material();
+ material.setCode(record.code);
+ material.setMaterialType(materialTypes.get(record.maty_id));
+ material.setId(record.id);
+ map.put(record.id, material);
+ }
+ }
+ return map;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
index 9a0f6973442b2f900c1ea68f714c669c479a1671..dcc58a7449b2fc20c5bfdeea7e9d02fc2c1420fa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/GenericEntityPropertyRecord.java
@@ -6,4 +6,6 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
public class GenericEntityPropertyRecord extends BaseEntityPropertyRecord
{
public String value;
+ public Long cvte_id;
+ public Long mate_prop_id;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertySetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertySetListingQuery.java
index 2d75629c848d5a5acbd9ae232bad4d20c18bcd0e..8633f5ad2bea9fa9e581f0dba7a0d5ccce73a802 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertySetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IEntityPropertySetListingQuery.java
@@ -35,18 +35,4 @@ public interface IEntityPropertySetListingQuery
*/
public Iterable<GenericEntityPropertyRecord> getEntityPropertyGenericValues(LongSet entityIDs);
- /**
- * Returns all controlled vocabulary property values of all specified entities.
- *
- * @param entityIDs The set of entity IDs to get the property values for.
- */
- public Iterable<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(LongSet entityIDs);
-
- /**
- * Returns all material-type property values of all specified entities.
- *
- * @param entityIDs The set of entity IDs to get the property values for.
- */
- public Iterable<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(LongSet entityIDs);
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
index cfbb66435860ee0cd8cf1a98ed7bb5802e88875b..ef530fef851bd459eaec145aa9725d6b3b4f2c36 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/IPropertyListingQuery.java
@@ -16,10 +16,14 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
+import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
+import ch.systemsx.cisd.common.db.mapper.LongSetMapper;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
/**
* Query methods for retrieving property types, material types, and vocabulary URL templates.
*
@@ -27,6 +31,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
*/
public interface IPropertyListingQuery
{
+ public static final int FETCH_SIZE = 1000;
+
/**
* Returns all property types. Fills only <code>id</code>, <code>code</code>, <code>label</var> and <code>DataType</code>. Note that code and
* label are already HTML escaped.
@@ -47,5 +53,14 @@ public interface IPropertyListingQuery
*/
@Select("select id, code from material_types")
public CodeRecord[] getMaterialTypes();
+
+ @Select(sql = "SELECT id, covo_id, code, label, ordinal, description "
+ + "FROM controlled_vocabulary_terms WHERE id = any(?{1})",
+ parameterBindings = { LongSetMapper.class}, fetchSize = FETCH_SIZE)
+ public DataIterator<VocabularyTermRecord> getVocabularyTerms(LongSet termIds);
+ @Select(sql = "SELECT id, code, maty_id FROM materials WHERE id = any(?{1})",
+ parameterBindings = { LongSetMapper.class}, fetchSize = FETCH_SIZE)
+ public DataIterator<MaterialEntityPropertyRecord> getMaterials(LongSet materialIds);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
index 1a46bb1ab6cb33dc2ef17c0a6b32e4fa2474d862..d9206e54cdb673d123e7205156bd746ce6b8653c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
@@ -87,19 +87,6 @@ public final class DatasetListerDAO extends AbstractDAO
return query.getEntityPropertyGenericValues(entityIDs);
}
- @Override
- public Iterable<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyMaterialValues(entityIDs);
- }
-
- @Override
- public Iterable<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyVocabularyTermValues(entityIDs);
- }
};
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index 70a7d5590e79a134f92dbd64b087fe0bbeacea19..08cdd3713b477f8a02728be1e59a79a7d782c6d6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -48,7 +48,7 @@ import net.lemnik.eodsql.TypeMapper;
@Friend(toClasses = { DataStoreRecord.class })
public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
{
- public static final int FETCH_SIZE = 1000;
+ public static final int FETCH_SIZE = 10000;
public final static String SELECT_ALL =
"select data.*, external_data.*, link_data.*, content_copies.external_code, content_copies.edms_id, "
@@ -311,11 +311,12 @@ public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
*
* @param entityIds The set of sample ids to get the property values for.
*/
- @Select(sql = "SELECT pr.ds_id as entity_id, etpt.prty_id, etpt.script_id, pr.value, sc.script_type "
+ @Select(sql = "SELECT pr.ds_id as entity_id, etpt.prty_id, etpt.script_id, pr.value, "
+ + " pr.cvte_id, pr.mate_prop_id, sc.script_type "
+ " FROM data_set_properties pr"
+ " JOIN data_set_type_property_types etpt ON pr.dstpt_id=etpt.id"
+ " LEFT OUTER JOIN scripts sc ON etpt.script_id = sc.id"
- + " WHERE pr.value is not null AND pr.ds_id = any(?{1})", parameterBindings = { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ + " WHERE pr.ds_id = any(?{1})", parameterBindings = { LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<GenericEntityPropertyRecord> getEntityPropertyGenericValues(
LongSet entityIds);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
index 989e9e12c634da1b020b1ae2ccd73662310c8ee6..4948820978e930c4b7ffe7f20beefd42c7146bad 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
@@ -16,15 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
-import it.unimi.dsi.fastutil.longs.LongSet;
-
import java.util.List;
-import net.lemnik.eodsql.BaseQuery;
-import net.lemnik.eodsql.DataIterator;
-import net.lemnik.eodsql.Select;
-import net.lemnik.eodsql.TransactionQuery;
-import net.lemnik.eodsql.TypeMapper;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.db.mapper.LongSetMapper;
import ch.systemsx.cisd.common.db.mapper.StringArrayMapper;
@@ -34,6 +27,12 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntity
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaProjectWithEntityId;
+import it.unimi.dsi.fastutil.longs.LongSet;
+import net.lemnik.eodsql.BaseQuery;
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TransactionQuery;
+
/**
* A {@link TransactionQuery} interface for obtaining large sets of material-related entities from the database.
* <p>
@@ -96,7 +95,8 @@ public interface IMaterialListingQuery extends BaseQuery, IPropertyListingQuery
*
* @param entityIds The set of material ids to get the property values for.
*/
- @Select(sql = "SELECT pr.mate_id as entity_id, etpt.prty_id, etpt.script_id, pr.value, sc.script_type "
+ @Select(sql = "SELECT pr.mate_id as entity_id, etpt.prty_id, etpt.script_id, pr.value, "
+ + " pr.cvte_id, pr.mate_prop_id, sc.script_type "
+ " FROM material_properties pr"
+ " JOIN material_type_property_types etpt ON pr.mtpt_id=etpt.id"
+ " LEFT OUTER JOIN scripts sc ON etpt.script_id = sc.id"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
index 93326aad0def7285c7cc74d788f2777e959ff0ac..72723023e8575eac9b231a541db4a4c1b52dcaff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
@@ -16,18 +16,17 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
-import it.unimi.dsi.fastutil.longs.LongSet;
-import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.AbstractDAO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertySetListingQuery;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
+import it.unimi.dsi.fastutil.longs.LongSet;
+import net.lemnik.eodsql.QueryTool;
+
/**
* The DAO for business objects implementing {@link IMaterialLister}. Note: Even though this class is public its constructors and instance methods
* have to be package protected.
@@ -86,20 +85,6 @@ public final class MaterialListerDAO extends AbstractDAO
{
return query.getEntityPropertyGenericValues(entityIDs);
}
-
- @Override
- public Iterable<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyMaterialValues(entityIDs);
- }
-
- @Override
- public Iterable<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyVocabularyTermValues(entityIDs);
- }
};
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index a79dbea3a2a467d6cedcfb4880304ef213b47771..4f28416a95042d5bb3143e8589cbd0c9de21e639 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -412,11 +412,12 @@ public interface ISampleListingQuery extends BaseQuery, IPropertyListingQuery
*
* @param sampleIds The set of sample ids to get the property values for.
*/
- @Select(sql = "SELECT sp.samp_id as entity_id, stpt.prty_id, stpt.script_id, stpt.ordinal, sp.value, sc.script_type "
+ @Select(sql = "SELECT sp.samp_id as entity_id, stpt.prty_id, stpt.script_id, stpt.ordinal, "
+ + " sp.value, sp.cvte_id, sp.mate_prop_id, sc.script_type "
+ " FROM sample_properties sp"
+ " JOIN sample_type_property_types stpt ON sp.stpt_id=stpt.id"
+ " LEFT OUTER JOIN scripts sc ON stpt.script_id = sc.id"
- + " WHERE sp.value is not null AND sp.samp_id = any(?{1})", parameterBindings =
+ + " WHERE sp.samp_id = any(?{1})", parameterBindings =
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<GenericEntityPropertyRecord> getEntityPropertyGenericValues(
LongSet sampleIds);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
index 4d090529811892b671b12b626206202487aba828..096e0b20a9045e6b37235c89c544c2d8fc217e5c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
@@ -16,18 +16,17 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
-import it.unimi.dsi.fastutil.longs.LongSet;
-import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.AbstractDAO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertySetListingQuery;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
+import it.unimi.dsi.fastutil.longs.LongSet;
+import net.lemnik.eodsql.QueryTool;
+
/**
* The DAO for business objects implementing {@link ISampleLister}. Note: Even though this class is public its constructors and instance methods have
* to be package protected.
@@ -85,20 +84,6 @@ public final class SampleListerDAO extends AbstractDAO
{
return query.getEntityPropertyGenericValues(entityIDs);
}
-
- @Override
- public Iterable<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyMaterialValues(entityIDs);
- }
-
- @Override
- public Iterable<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(
- LongSet entityIDs)
- {
- return query.getEntityPropertyVocabularyTermValues(entityIDs);
- }
};
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
index 3d051bc351e8174479aaa42bcf27e76ce7919a44..9ce30c16051b654030699f1880a8266e9b7d3afd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityPropertiesEnricherTest.java
@@ -16,9 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-import it.unimi.dsi.fastutil.longs.LongSet;
-import it.unimi.dsi.fastutil.longs.LongSets;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@@ -36,11 +33,17 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
+import it.unimi.dsi.fastutil.longs.LongSets;
+
/**
* @author Franz-Josef Elmer
*/
public class EntityPropertiesEnricherTest extends AssertJUnit
{
+ private static final long VOCABULARY_TERM_ID = 42L;
+
private static final long VOCABULARY_ID = 1L;
private static final long ENTITY_ID = 42L;
@@ -78,8 +81,7 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
PropertyType propertyType = new PropertyType();
propertyType.setId(PROPERTY_TYPE_ID);
propertyType.setDataType(new DataType(DataTypeCode.CONTROLLEDVOCABULARY));
- will(returnValue(new PropertyType[]
- { propertyType }));
+ will(returnValue(new PropertyType[] { propertyType }));
allowing(resolver).get(ENTITY_ID);
will(returnValue(holder));
@@ -104,10 +106,12 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
{
{
one(setQuery).getEntityPropertyGenericValues(entityIDs);
- will(returnValue(Arrays.asList()));
-
- one(setQuery).getEntityPropertyMaterialValues(entityIDs);
- will(returnValue(Arrays.asList()));
+ GenericEntityPropertyRecord record = new GenericEntityPropertyRecord();
+ record.entity_id = ENTITY_ID;
+ record.cvte_id = VOCABULARY_TERM_ID;
+ record.prty_id = PROPERTY_TYPE_ID;
+ record.entity_id = ENTITY_ID;
+ will(returnValue(Arrays.asList(record)));
one(query).getVocabularyURLTemplates();
CodeRecord codeRecord = new CodeRecord();
@@ -116,15 +120,15 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
will(returnValue(new CodeRecord[]
{ codeRecord }));
- one(setQuery).getEntityPropertyVocabularyTermValues(entityIDs);
+ one(query).getVocabularyTerms(new LongOpenHashSet(Arrays.asList(record.cvte_id)));
VocabularyTermRecord termRecord = new VocabularyTermRecord();
termRecord.entity_id = ENTITY_ID;
termRecord.prty_id = PROPERTY_TYPE_ID;
- termRecord.id = 137L;
+ termRecord.id = VOCABULARY_TERM_ID;
termRecord.covo_id = VOCABULARY_ID;
termRecord.code = "HELLO";
termRecord.label = "Hello";
- will(returnValue(Arrays.asList(termRecord)));
+ will(returnValue(new WrappingDataIterator<>(Arrays.asList(termRecord))));
}
});
@@ -142,10 +146,12 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
{
{
one(setQuery).getEntityPropertyGenericValues(entityIDs);
- will(returnValue(Arrays.asList()));
-
- one(setQuery).getEntityPropertyMaterialValues(entityIDs);
- will(returnValue(Arrays.asList()));
+ GenericEntityPropertyRecord record = new GenericEntityPropertyRecord();
+ record.entity_id = ENTITY_ID;
+ record.cvte_id = VOCABULARY_TERM_ID;
+ record.prty_id = PROPERTY_TYPE_ID;
+ record.entity_id = ENTITY_ID;
+ will(returnValue(Arrays.asList(record)));
one(query).getVocabularyURLTemplates();
CodeRecord codeRecord = new CodeRecord();
@@ -154,15 +160,15 @@ public class EntityPropertiesEnricherTest extends AssertJUnit
will(returnValue(new CodeRecord[]
{ codeRecord }));
- one(setQuery).getEntityPropertyVocabularyTermValues(entityIDs);
+ one(query).getVocabularyTerms(new LongOpenHashSet(Arrays.asList(record.cvte_id)));
VocabularyTermRecord termRecord = new VocabularyTermRecord();
termRecord.entity_id = ENTITY_ID;
termRecord.prty_id = PROPERTY_TYPE_ID;
- termRecord.id = 137L;
+ termRecord.id = VOCABULARY_TERM_ID;
termRecord.covo_id = VOCABULARY_ID;
termRecord.code = "HELLO";
termRecord.label = "Hello";
- will(returnValue(Arrays.asList(termRecord)));
+ will(returnValue(new WrappingDataIterator<>(Arrays.asList(termRecord))));
}
});
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/WrappingDataIterator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/WrappingDataIterator.java
new file mode 100644
index 0000000000000000000000000000000000000000..1062025edda525d85b1f8809877eee2581bb845b
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/WrappingDataIterator.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2017 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+import net.lemnik.eodsql.DataIterator;
+
+public class WrappingDataIterator<E> implements DataIterator<E>
+{
+ private final Collection<E> collection;
+
+ private final Iterator<E> iterator;
+
+ public WrappingDataIterator(Collection<E> collection)
+ {
+ this.collection = collection;
+ iterator = collection.iterator();
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return iterator.hasNext();
+ }
+
+ @Override
+ public E next()
+ {
+ return iterator.next();
+ }
+
+ @Override
+ public void remove()
+ {
+ iterator.remove();
+ }
+
+ @Override
+ public Iterator<E> iterator()
+ {
+ return collection.iterator();
+ }
+
+ @Override
+ public void close()
+ {
+ }
+
+ @Override
+ public boolean isClosed()
+ {
+ return false;
+ }
+}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerFastTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerFastTest.java
index 7314731640234aa0b577557b1c879bbb8bae17be..4a865385e44d510937183bebbfc19846ddf54aca 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerFastTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerFastTest.java
@@ -19,14 +19,10 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
-import java.util.Iterator;
import java.util.List;
-import net.lemnik.eodsql.DataIterator;
-
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.AssertJUnit;
@@ -36,6 +32,7 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesEnricher;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.WrappingDataIterator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IRelationshipTypeDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -199,52 +196,4 @@ public class DatasetListerFastTest extends AssertJUnit
return record;
}
- private static final class WrappingDataIterator<E> implements DataIterator<E>
- {
- private final Collection<E> collection;
-
- private final Iterator<E> iterator;
-
- public WrappingDataIterator(Collection<E> collection)
- {
- this.collection = collection;
- iterator = collection.iterator();
- }
-
- @Override
- public boolean hasNext()
- {
- return iterator.hasNext();
- }
-
- @Override
- public E next()
- {
- return iterator.next();
- }
-
- @Override
- public void remove()
- {
- iterator.remove();
- }
-
- @Override
- public Iterator<E> iterator()
- {
- return collection.iterator();
- }
-
- @Override
- public void close()
- {
- }
-
- @Override
- public boolean isClosed()
- {
- return false;
- }
- }
-
}