diff --git a/openbis/diffCurrentAndPreviousMigrations.sh b/openbis/diffCurrentAndPreviousMigrations.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5d5075125afa4e4e4f1da15a4b5d2f19095f36e0
--- /dev/null
+++ b/openbis/diffCurrentAndPreviousMigrations.sh
@@ -0,0 +1,29 @@
+#!/opt/local/bin/ruby
+
+versions = `ls source/sql/postgresql`.map { |dir| dir.to_i }
+@curr = versions.max
+@prev = @curr - 1
+
+@curr = "%03d" % @curr
+@prev = "%03d" % @prev
+
+puts "Will check the diff beetween versions #{@prev} and #{@curr}"
+
+def copyDir(dir)
+ files = Dir[dir].map {|f| File.expand_path f }
+ files.each do |f|
+ new_f = f.gsub(@prev, @curr)
+ diff_files = " #{f} #{new_f}"
+ system("git diff --no-index" + diff_files)
+ end
+end
+
+copyDir("source/sql/postgresql/#{@prev}/*")
+copyDir("source/sql/generic/#{@prev}/*")
+copyDir("sourceTest/sql/postgresql/#{@prev}/*")
+
+
+
+
+
+
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 862f91bb75d6d486064c434387a2a8831d921d87..3fe417cc6172bd01de3bbe0707ffdbe50f70ecfe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -2564,4 +2564,12 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
List<DataStorePE> dataStorePEs = dataStoreDAO.listDataStores();
return DataStoreTranslator.translate(dataStorePEs);
}
+
+ public List<Material> searchForMaterials(String sessionToken, DetailedSearchCriteria criteria)
+ {
+ final Session session = getSession(sessionToken);
+ SearchHelper searchHelper =
+ new SearchHelper(session, businessObjectFactory, getDAOFactory());
+ return searchHelper.searchForMaterials(criteria);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
index a62f49afe033109082ad517be21d1c3386dd5452..52a0cecd784af8b3119725edf485fa10c73ea7ce 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
@@ -1185,4 +1185,10 @@ final class CommonServerLogger extends AbstractServerLogger implements ICommonSe
return null;
}
+ public List<Material> searchForMaterials(String sessionToken, DetailedSearchCriteria criteria)
+ {
+ logAccess(sessionToken, "search_for_materials", "criteria(%s)", criteria);
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java
index 4ba156110c947ea6c4f7f1aba3bdc17a525d9b06..3626384bf466a5e68672c9a4e0cea3c8ed75265b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/SearchHelper.java
@@ -20,13 +20,16 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.business.search.DataSetSearchManager;
+import ch.systemsx.cisd.openbis.generic.server.business.search.MaterialSearchManager;
import ch.systemsx.cisd.openbis.generic.server.business.search.SampleSearchManager;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -66,4 +69,12 @@ class SearchHelper
return new DataSetSearchManager(searchDAO, dataSetLister)
.searchForDataSets(detailedSearchCriteria);
}
+
+ public List<Material> searchForMaterials(DetailedSearchCriteria detailedSearchCriteria)
+ {
+ IHibernateSearchDAO searchDAO = daoFactory.getHibernateSearchDAO();
+ IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
+ return new MaterialSearchManager(searchDAO, materialLister)
+ .searchForMaterials(detailedSearchCriteria);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index fdb0fd5ab5a91ca960ddee8383d0a8307d0dd622..2c9285ab1cda1a986a8cc9225b3eed75e93d55a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -32,6 +32,7 @@ import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
@@ -51,6 +52,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOptions;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -664,4 +667,26 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
return Translator.translateProjects(commonServer.listProjects(sessionToken));
}
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @Capability("GET_MATERIALS_BY_CODES")
+ public List<Material> getMaterialByCodes(String sessionToken,
+ List<MaterialIdentifier> materialIdentifier)
+ {
+ throw new NotImplementedException();
+ // TODO Auto-generated method stub
+ }
+
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ @Capability("SEARCH_FOR_MATERIALS")
+ public List<Material> searchForMaterials(String sessionToken, SearchCriteria searchCriteria)
+ {
+ DetailedSearchCriteria detailedSearchCriteria =
+ SearchCriteriaToDetailedSearchCriteriaTranslator.convert(
+ SearchableEntityKind.MATERIAL, searchCriteria);
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material> materials =
+ commonServer.searchForMaterials(sessionToken, detailedSearchCriteria);
+ return Translator.translateMaterials(materials);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
index 575111a2ac7da610e2d3980ac940b35376132b8d..b999197d8334d4b4ccfde49af50a83f801572f94 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
@@ -32,6 +32,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -214,4 +216,19 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
"EXPERIMENTS(%s) CONNECTIONS(%s)", abbreviate(experiments), connectionsToGet);
return null;
}
+
+ public List<Material> getMaterialByCodes(String sessionToken,
+ List<MaterialIdentifier> materialIdentifier)
+ {
+ logAccess(sessionToken, "get-material-by-codes", "MATERIAL_IDENTIFIERS(%s)",
+ abbreviate(materialIdentifier));
+
+ return null;
+ }
+
+ public List<Material> searchForMaterials(String sessionToken, SearchCriteria searchCriteria)
+ {
+ logAccess(sessionToken, "search-for-materials", "SEARCH_CRITERIA(%s)", searchCriteria);
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
index 2a7acf1b22d83f28298e0948a2e0be3a7ff9bc36..1c5b222631b18a12ea04897becf5c0764d8e8305 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SearchCriteriaToDetailedSearchCriteriaTranslator.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchField;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchSubCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentAttributeSearchFieldKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IAttributeSearchFieldKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialAttributeSearchFieldKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleAttributeSearchFieldKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
@@ -67,6 +68,7 @@ public class SearchCriteriaToDetailedSearchCriteriaTranslator
translators.put(SearchableEntityKind.SAMPLE_PARENT, new SampleAttributeTranslator());
translators.put(SearchableEntityKind.SAMPLE_CHILD, new SampleAttributeTranslator());
translators.put(SearchableEntityKind.SAMPLE_CONTAINER, new SampleAttributeTranslator());
+ translators.put(SearchableEntityKind.MATERIAL, new MaterialAttributeTranslator());
}
private static IMatchClauseAttributeTranslator translatorFor(SearchableEntityKind entityKind)
@@ -104,6 +106,8 @@ public class SearchCriteriaToDetailedSearchCriteriaTranslator
return AssociatedEntityKind.SAMPLE_PARENT;
case SAMPLE_CHILD:
return AssociatedEntityKind.SAMPLE_CHILD;
+ case MATERIAL:
+ return AssociatedEntityKind.MATERIAL;
}
return null; // can't happen
}
@@ -179,13 +183,34 @@ public class SearchCriteriaToDetailedSearchCriteriaTranslator
ans = ExperimentAttributeSearchFieldKind.PROJECT;
break;
default:
- throwInvalidSearchAttributeException(attribute, SearchableEntityKind.SAMPLE);
+ throwInvalidSearchAttributeException(attribute, SearchableEntityKind.EXPERIMENT);
}
return ans;
}
}
+ public static class MaterialAttributeTranslator implements IMatchClauseAttributeTranslator
+ {
+ public IAttributeSearchFieldKind convertMatchClauseAttributeToAttributeSearchFieldKind(
+ MatchClauseAttribute attribute)
+ {
+ IAttributeSearchFieldKind ans = null;
+ switch (attribute)
+ {
+ case CODE:
+ ans = MaterialAttributeSearchFieldKind.CODE;
+ break;
+ case TYPE:
+ ans = MaterialAttributeSearchFieldKind.MATERIAL_TYPE;
+ break;
+ default:
+ throwInvalidSearchAttributeException(attribute, SearchableEntityKind.MATERIAL);
+ }
+ return ans;
+ }
+ }
+
public static class DataSetAttributeTranslator implements IMatchClauseAttributeTranslator
{
public IAttributeSearchFieldKind convertMatchClauseAttributeToAttributeSearchFieldKind(
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/MaterialSearchManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/MaterialSearchManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..d33510166d38d86ba869ea96a04acd434c8844b1
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/search/MaterialSearchManager.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * 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.search;
+
+import java.util.Collections;
+import java.util.List;
+
+import org.springframework.dao.DataAccessException;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchAssociationCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+
+/**
+ * @author jakubs
+ */
+public class MaterialSearchManager extends AbstractSearchManager<IMaterialLister>
+{
+
+ public MaterialSearchManager(IHibernateSearchDAO searchDAO, IMaterialLister lister)
+ {
+ super(searchDAO, lister);
+ }
+
+ public List<Material> searchForMaterials(DetailedSearchCriteria criteria)
+ throws DataAccessException
+ {
+ List<Long> materialIds =
+ searchDAO.searchForEntityIds(criteria,
+ ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.MATERIAL,
+ Collections.<DetailedSearchAssociationCriteria> emptyList());
+
+ return lister.list(new ListMaterialCriteria(materialIds), true);
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index 8f3eeaabecd62ae1ab034602547a8b2e22d4375f..6d77f3bd6d07fb06dace6a524e3c68ea56862e8c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -1549,4 +1549,12 @@ public interface ICommonServer extends IServer
public void deletePermanently(final String sessionToken,
@AuthorizationGuard(guardClass = DeletionTechIdCollectionPredicate.class)
final List<TechId> deletionIds, boolean force);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public List<Material> searchForMaterials(String sessionToken, DetailedSearchCriteria criteria);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
index 602f303805deaae6528c41961e94a584733977a7..546738df236a73b6991bd185b39a603fce72f681 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
@@ -24,7 +24,9 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.EnumSet;
import java.util.HashMap;
+import java.util.LinkedList;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer;
@@ -36,6 +38,9 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTyp
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material.MaterialInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType.PropertyTypeInitializer;
@@ -56,6 +61,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleLevel;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* @author Franz-Josef Elmer
@@ -129,7 +135,8 @@ public class Translator
initializer.setExperimentIdentifierOrNull(experimentOrNull.getIdentifier());
}
- EntityRegistrationDetails registrationDetails = translateRegistrationDetailsWithModificationDate(privateSample);
+ EntityRegistrationDetails registrationDetails =
+ translateRegistrationDetailsWithModificationDate(privateSample);
initializer.setRegistrationDetails(registrationDetails);
return new Sample(initializer);
@@ -374,7 +381,8 @@ public class Translator
break;
}
}
- EntityRegistrationDetails registrationDetails = translateRegistrationDetailsWithModificationDate(externalDatum);
+ EntityRegistrationDetails registrationDetails =
+ translateRegistrationDetailsWithModificationDate(externalDatum);
initializer.setRegistrationDetails(registrationDetails);
return new DataSet(initializer);
@@ -432,4 +440,71 @@ public class Translator
initializer.setTerms(translate(privateVocabulary.getTerms()));
return new Vocabulary(initializer);
}
+
+ public static Material translate(
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material,
+ Map<Long, Material> materialsCache)
+ {
+ MaterialInitializer mi = new MaterialInitializer();
+
+ mi.setMaterialCode(material.getCode());
+
+ MaterialTypeIdentifier typeIdentifier =
+ new MaterialTypeIdentifier(material.getMaterialType().getCode());
+
+ mi.setMaterialTypeIdentifier(typeIdentifier);
+
+ material.getProperties();
+
+ List<IEntityProperty> originalProperties = material.getProperties();
+ Map<String, String> properties = EntityHelper.convertToStringMap(originalProperties);
+ Map<String, Material> materialProperties =
+ convertMaterialProperties(originalProperties, materialsCache);
+
+ mi.setMaterialProperties(materialProperties);
+
+ mi.setProperties(properties);
+
+ mi.setRegistrationDetails(translateRegistrationDetails(material));
+
+ return new Material(mi);
+ }
+
+ private static Map<String, Material> convertMaterialProperties(
+ List<IEntityProperty> properties, Map<Long, Material> materialsCache)
+ {
+ HashMap<String, Material> result = new HashMap<String, Material>();
+ if (properties != null)
+ {
+ for (IEntityProperty property : properties)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material =
+ property.getMaterial();
+ if (material != null)
+ {
+ Material apiMaterial = materialsCache.get(material.getId());
+ if (apiMaterial == null)
+ {
+ apiMaterial = translate(material, materialsCache);
+ materialsCache.put(material.getId(), apiMaterial);
+ }
+ String propCode = property.getPropertyType().getCode();
+ result.put(propCode, apiMaterial);
+ }
+ }
+ }
+ return result;
+ }
+
+ public static List<Material> translateMaterials(
+ Collection<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material> materials)
+ {
+ Map<Long, Material> materialsCache = new HashMap<Long, Material>();
+ List<Material> list = new LinkedList<Material>();
+ for (ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material material : materials)
+ {
+ list.add(translate(material, materialsCache));
+ }
+ return list;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
index 69c911eb6d9251805e8e537f33ddd6394855e20b..f2c98e2cc831b15aaba33e8fc6a8ad944ae977cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AssociatedEntityKind.java
@@ -47,7 +47,9 @@ public enum AssociatedEntityKind implements Serializable
SAMPLE_CHILD("Child", EntityKind.SAMPLE, EnumSet.of(EntityKind.SAMPLE)),
- SAMPLE_PARENT("Parent", EntityKind.SAMPLE, EnumSet.of(EntityKind.SAMPLE));
+ SAMPLE_PARENT("Parent", EntityKind.SAMPLE, EnumSet.of(EntityKind.SAMPLE)),
+
+ MATERIAL("Material", EntityKind.MATERIAL, EnumSet.noneOf(EntityKind.class));
private final String description;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityTypeDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityTypeDAOTest.java
index d51441485ef52c242f5a7e67df97fd53373a1c80..3ba35f24da7bb0f45a8a83bea5c995bd91a79109 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityTypeDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/EntityTypeDAOTest.java
@@ -129,15 +129,16 @@ public final class EntityTypeDAOTest extends AbstractDAOTest
private PropertyTypePE createMaterialPropertyType(MaterialTypePE materialType)
{
- return createPropertyType(daoFactory.getPropertyTypeDAO().getDataTypeByCode(
- DataTypeCode.MATERIAL), "USER.MATERIAL-PROPERTY-TYPE", null, materialType);
+ return createPropertyType(
+ daoFactory.getPropertyTypeDAO().getDataTypeByCode(DataTypeCode.MATERIAL),
+ "USER.MATERIAL-PROPERTY-TYPE", null, materialType);
}
@Test
public final void testListMaterialTypes()
{
final IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.MATERIAL);
- assertEquals(7, entityTypeDAO.listEntityTypes().size());
+ assertEquals(8, entityTypeDAO.listEntityTypes().size());
}
@Test(dependsOnMethods = "testListMaterialTypes")
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index e4d3a521769f015a581c70c2df8b8577751bd5d9..98decaba952699dd983faccb12a1ae24ec922654 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -19,10 +19,12 @@ package ch.systemsx.cisd.openbis.systemtest.api.v1;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.fail;
+import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
+import java.util.Date;
import java.util.EnumSet;
import java.util.List;
@@ -40,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDeta
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment.ExperimentInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
@@ -574,6 +577,23 @@ public class GeneralInformationServiceTest extends SystemTestCase
assertEquals(expectedEntities, identifiers.toString());
}
+ private interface IToStringDelegate<T>
+ {
+ String toString(T t);
+ }
+
+ private <T> void assertCollection(String expectedEntities, List<T> entities,
+ IToStringDelegate<T> toStringMethod)
+ {
+ List<String> identifiers = new ArrayList<String>();
+ for (T entity : entities)
+ {
+ identifiers.add(toStringMethod.toString(entity));
+ }
+ Collections.sort(identifiers);
+ assertEquals(expectedEntities, identifiers.toString());
+ }
+
private void assertDataSets(String expectedDataSets, List<DataSet> dataSets)
{
List<String> codes = new ArrayList<String>();
@@ -584,4 +604,68 @@ public class GeneralInformationServiceTest extends SystemTestCase
Collections.sort(codes);
assertEquals(expectedDataSets, codes.toString());
}
+
+ @Test
+ public void testSearchForMaterialsReferencing() throws java.text.ParseException
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "SELF_REF"));
+
+ List<Material> materials =
+ generalInformationService.searchForMaterials(sessionToken, searchCriteria);
+
+ assertCollection("[SRM_1, SRM_1A]", materials, new IToStringDelegate<Material>()
+ {
+ public String toString(Material t)
+ {
+ return t.getMaterialCode();
+ }
+ });
+
+ Material smr1 = materials.get(0);
+ Material smr1a = materials.get(1);
+
+ assertEquals("SRM_1", smr1.getMaterialCode());
+ assertEquals("SRM_1A", smr1a.getMaterialCode());
+
+ assertEquals("Material with attached material", smr1.getProperties().get("DESCRIPTION"));
+ assertEquals("Material wich is attached material", smr1a.getProperties().get("DESCRIPTION"));
+
+ assertEquals("Referenced material should be srm_1a", smr1a.getMaterialCode(), smr1
+ .getMaterialProperties().get("ANY_MATERIAL").getMaterialCode());
+
+ assertEquals("Referenced material should be present in properties as code", String.format(
+ "%s (%s)", smr1a.getMaterialCode(), smr1a.getMaterialTypeIdentifier()
+ .getMaterialTypeCode()), smr1.getProperties().get("ANY_MATERIAL"));
+
+ Date date2012 = new SimpleDateFormat("yyyy-MM-dd").parse("2012-01-02");
+ Date date2013 = new SimpleDateFormat("yyyy-MM-dd").parse("2013-01-02");
+
+ assertEquals("The date should be after 2012", true, smr1.getRegistrationDetails()
+ .getRegistrationDate().after(date2012));
+ assertEquals("The date should be before 2013", true, smr1.getRegistrationDetails()
+ .getRegistrationDate().before(date2013));
+ }
+
+ @Test
+ public void testSearchForMaterials()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "BACTERIUM"));
+
+ List<Material> materials =
+ generalInformationService.searchForMaterials(sessionToken, searchCriteria);
+
+ assertCollection("[BACTERIUM-X, BACTERIUM-Y, BACTERIUM1, BACTERIUM2]", materials,
+ new IToStringDelegate<Material>()
+ {
+ public String toString(Material t)
+ {
+ return t.getMaterialCode();
+ }
+ });
+ }
+
}