diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityExecutor.java
index 0f5ac230711d4ca865759b0162409900d6ef4eb5..3bacc39271b96ab4310c06dcbf8e764f68bf3a95 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractCreateEntityExecutor.java
@@ -63,11 +63,12 @@ public abstract class AbstractCreateEntityExecutor<CREATION, PE, PERM_ID> implem
context.popProgress();
}
+ daoFactory.getSessionFactory().getCurrentSession().flush();
reloadEntities(context, entitiesAll);
updateAll(context, entitiesAll);
+
daoFactory.getSessionFactory().getCurrentSession().flush();
-
reloadEntities(context, entitiesAll);
checkBusinessRules(context, entitiesAll.values());
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/ListSampleTechIdByIdentifier.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/ListSampleTechIdByIdentifier.java
index 006c6d5afb261baaf386619f51df5f5d4af34e9e..80a1bf0c78f5df7cba3a0a21385bce1fc1f1ca14 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/ListSampleTechIdByIdentifier.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/ListSampleTechIdByIdentifier.java
@@ -16,27 +16,30 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.sample;
+import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.Set;
import net.lemnik.eodsql.QueryTool;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.TechIdStringIdentifierRecord;
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.common.AbstractListTechIdById;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleIdentifier>
{
- private String homeSpaceCodeOrNull;
-
+ private String homeSpaceCodeOrNull;
+
public ListSampleTechIdByIdentifier(String homeSpaceCodeOrNull)
{
this.homeSpaceCodeOrNull = homeSpaceCodeOrNull;
@@ -47,12 +50,12 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
{
return SampleIdentifier.class;
}
-
+
@Override
protected Map<Long, SampleIdentifier> createIdsByTechIdsMap(List<SampleIdentifier> ids)
{
Map<SampleIdentifierParts, Map<String, SampleIdentifier>> groupedIdentifiers = groupIdentifiers(ids);
-
+
Map<Long, SampleIdentifier> result = new HashMap<>();
SampleQuery query = QueryTool.getManagedQuery(SampleQuery.class);
for (Entry<SampleIdentifierParts, Map<String, SampleIdentifier>> entry : groupedIdentifiers.entrySet())
@@ -74,9 +77,9 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
Map<SampleIdentifierParts, Map<String, SampleIdentifier>> groupedIdentifiers = new HashMap<>();
for (SampleIdentifier sampleIdentifier : ids)
{
- FullSampleIdentifier fullSampleIdentifier = new FullSampleIdentifier(sampleIdentifier.getIdentifier(),
+ FullSampleIdentifier fullSampleIdentifier = new FullSampleIdentifier(sampleIdentifier.getIdentifier(),
homeSpaceCodeOrNull);
-
+
SampleIdentifierParts key = fullSampleIdentifier.getParts();
Map<String, SampleIdentifier> identifiersByCode = groupedIdentifiers.get(key);
if (identifiersByCode == null)
@@ -89,17 +92,32 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
return groupedIdentifiers;
}
- private List<TechIdStringIdentifierRecord> list(SampleQuery query, SampleIdentifierParts key, Collection<String> codes)
+ private List<TechIdStringIdentifierRecord> list(final SampleQuery query, final SampleIdentifierParts key, final Collection<String> codes)
{
- String[] codesArray = codes.toArray(new String[codes.size()]);
- String spaceCode = key.getSpaceCodeOrNull();
- String projectCode = key.getProjectCodeOrNull();
- String containerCode = key.getContainerCodeOrNull();
+ final String[] codesArray = codes.toArray(new String[codes.size()]);
+ final String spaceCode = key.getSpaceCodeOrNull();
+ final String projectCode = key.getProjectCodeOrNull();
+ final String containerCode = key.getContainerCodeOrNull();
+
if (spaceCode == null)
{
if (containerCode == null)
{
- return query.listSharedSampleTechIdsByCodes(codesArray);
+ return listWithoutContainerOrWithSomeContainerAndUniqueCode(query, codesArray, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listSharedSampleTechIdsByCodesWithoutContainer(codesToList);
+ }
+ }, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listSharedSampleTechIdsByCodesWithSomeContainer(codesToList);
+ }
+ });
}
return query.listSharedSampleTechIdsByContainerCodeAndCodes(containerCode, codesArray);
}
@@ -107,15 +125,98 @@ public class ListSampleTechIdByIdentifier extends AbstractListTechIdById<SampleI
{
if (containerCode == null)
{
- return query.listSpaceSampleTechIdsByCodes(spaceCode, codesArray);
+ return listWithoutContainerOrWithSomeContainerAndUniqueCode(query, codesArray, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listSpaceSampleTechIdsByCodesWithoutContainer(spaceCode, codesToList);
+ }
+ }, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listSpaceSampleTechIdsByCodesWithSomeContainer(spaceCode, codesToList);
+ }
+ });
}
return query.listSpaceSampleTechIdsByContainerCodeAndCodes(spaceCode, containerCode, codesArray);
}
if (containerCode == null)
{
- return query.listProjectSampleTechIdsByCodes(spaceCode, projectCode, codesArray);
+ return listWithoutContainerOrWithSomeContainerAndUniqueCode(query, codesArray, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listProjectSampleTechIdsByCodesWithoutContainer(spaceCode, projectCode, codesToList);
+ }
+ }, new IListAction()
+ {
+ @Override
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList)
+ {
+ return query.listProjectSampleTechIdsByCodesWithSomeContainer(spaceCode, projectCode, codesToList);
+ }
+ });
}
return query.listProjectSampleTechIdsByContainerCodeAndCodes(spaceCode, projectCode, containerCode, codesArray);
}
+ private List<TechIdStringIdentifierRecord> listWithoutContainerOrWithSomeContainerAndUniqueCode(SampleQuery query, String[] codes,
+ IListAction listWithoutContainer, IListAction listWithSomeContainer)
+ {
+ try
+ {
+ List<TechIdStringIdentifierRecord> foundWithoutContainer = listWithoutContainer.list(codes);
+
+ Set<String> codesNotFound = new HashSet<String>(Arrays.asList(codes));
+ for (TechIdStringIdentifierRecord found : foundWithoutContainer)
+ {
+ codesNotFound.remove(found.identifier);
+ }
+
+ if (codesNotFound.isEmpty())
+ {
+ return foundWithoutContainer;
+ }
+
+ List<TechIdStringIdentifierRecord> allFound = new LinkedList<TechIdStringIdentifierRecord>(foundWithoutContainer);
+
+ List<TechIdStringIdentifierRecord> foundWithSomeContainer = listWithSomeContainer.list(codesNotFound.toArray(new String[] {}));
+ Map<String, TechIdStringIdentifierRecord> foundWithSomeContainerMap = new HashMap<String, TechIdStringIdentifierRecord>();
+ Map<String, Integer> foundWithSomeContainerCounter = new HashMap<String, Integer>();
+
+ for (TechIdStringIdentifierRecord found : foundWithSomeContainer)
+ {
+ foundWithSomeContainerMap.put(found.identifier, found);
+
+ Integer counter = foundWithSomeContainerCounter.get(found.identifier);
+ counter = counter == null ? 1 : counter + 1;
+ foundWithSomeContainerCounter.put(found.identifier, counter);
+ }
+
+ for (Map.Entry<String, Integer> counterEntry : foundWithSomeContainerCounter.entrySet())
+ {
+ if (counterEntry.getValue() == 1)
+ {
+ TechIdStringIdentifierRecord found = foundWithSomeContainerMap.get(counterEntry.getKey());
+ allFound.add(found);
+ }
+ }
+
+ return allFound;
+
+ } catch (Exception e)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(e);
+ }
+ }
+
+ private static interface IListAction
+ {
+ public List<TechIdStringIdentifierRecord> list(String[] codesToList);
+ }
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/SampleQuery.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/SampleQuery.java
index 7e3fd51e36234b25f2dd4a93ee99d31ceeec0c3b..83c2e191ad79b8b0099fb5930e43e142f71a5f8b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/SampleQuery.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/sample/SampleQuery.java
@@ -26,8 +26,6 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.entity.common.Obje
import ch.systemsx.cisd.common.db.mapper.StringArrayMapper;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public interface SampleQuery extends ObjectQuery
@@ -39,38 +37,55 @@ public interface SampleQuery extends ObjectQuery
@Select(sql = "select id, code as identifier from samples "
+ "where space_id is null and samp_id_part_of is null and code = any(?{1})", parameterBindings =
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listSharedSampleTechIdsByCodes(String[] codes);
-
+ public List<TechIdStringIdentifierRecord> listSharedSampleTechIdsByCodesWithoutContainer(String[] codes);
+
+ @Select(sql = "select id, code as identifier from samples "
+ + "where space_id is null and samp_id_part_of is not null and code = any(?{1})", parameterBindings =
+ { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listSharedSampleTechIdsByCodesWithSomeContainer(String[] codes);
+
@Select(sql = "select s.id, s.code as identifier from samples s join samples cs on s.samp_id_part_of = cs.id "
+ "where s.space_id is null and cs.code = ?{1} and s.code = any(?{2})", parameterBindings =
- { TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listSharedSampleTechIdsByContainerCodeAndCodes(String containerCode,
+ { TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listSharedSampleTechIdsByContainerCodeAndCodes(String containerCode,
String[] codes);
-
+
+ @Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
+ + "where sp.code = ?{1} and s.proj_id is null and samp_id_part_of is null and s.code = any(?{2})",
+ parameterBindings = { TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByCodesWithoutContainer(String spaceCode, String[] codes);
+
@Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
- + "where sp.code = ?{1} and s.proj_id is null and samp_id_part_of is null and s.code = any(?{2})",
+ + "where sp.code = ?{1} and s.proj_id is null and samp_id_part_of is not null and s.code = any(?{2})",
parameterBindings = { TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByCodes(String spaceCode, String[] codes);
-
+ public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByCodesWithSomeContainer(String spaceCode, String[] codes);
+
@Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
+ "join samples cs on s.samp_id_part_of = cs.id "
+ "where sp.code = ?{1} and s.proj_id is null and cs.code = ?{2} and s.code = any(?{3})", parameterBindings =
- { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByContainerCodeAndCodes(String spaceCode,
+ { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByContainerCodeAndCodes(String spaceCode,
String containerCode, String[] codes);
-
+
@Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
+ "join projects p on s.proj_id = p.id "
+ "where sp.code = ?{1} and samp_id_part_of is null and p.code = ?{2} and s.code = any(?{3})", parameterBindings =
- { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listProjectSampleTechIdsByCodes(String spaceCode,
+ { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listProjectSampleTechIdsByCodesWithoutContainer(String spaceCode,
+ String projectCode, String[] codes);
+
+ @Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
+ + "join projects p on s.proj_id = p.id "
+ + "where sp.code = ?{1} and samp_id_part_of is not null and p.code = ?{2} and s.code = any(?{3})", parameterBindings =
+ { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listProjectSampleTechIdsByCodesWithSomeContainer(String spaceCode,
String projectCode, String[] codes);
-
+
@Select(sql = "select s.id, s.code as identifier from samples s join spaces sp on s.space_id = sp.id "
+ "join projects p on s.proj_id = p.id "
+ "join samples cs on s.samp_id_part_of = cs.id "
+ "where sp.code = ?{1} and p.code = ?{2} and cs.code = ?{3} and s.code = any(?{4})", parameterBindings =
- { TypeMapper.class, TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
- public List<TechIdStringIdentifierRecord> listProjectSampleTechIdsByContainerCodeAndCodes(String spaceCode,
+ { TypeMapper.class, TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<TechIdStringIdentifierRecord> listProjectSampleTechIdsByContainerCodeAndCodes(String spaceCode,
String projectCode, String containerCode, String[] codes);
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/MapSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/MapSampleTest.java
index 82c58df92d4d8b3dd60fe04cc670976d40913d53..f755b10ec50db22a147fc22b439c3dc8a6186235 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/MapSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/MapSampleTest.java
@@ -129,6 +129,60 @@ public class MapSampleTest extends AbstractSampleTest
v3api.logout(sessionToken);
}
+ @Test
+ public void testMapByComponentIdentifierWithOmittedContainerCodeAndUniqueComponentCode()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ SampleIdentifier identifier1 = new SampleIdentifier("/CISD/WELL-A01");
+ SampleIdentifier identifier2 = new SampleIdentifier("/CISD/WELL-A02");
+
+ Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, Arrays.asList(identifier1, identifier2), new SampleFetchOptions());
+
+ assertEquals(map.size(), 2);
+
+ Sample sample1 = map.get(identifier1);
+ Sample sample2 = map.get(identifier2);
+
+ assertEquals(sample1.getIdentifier().getIdentifier(), "/CISD/PLATE_WELLSEARCH:WELL-A01");
+ assertEquals(sample2.getIdentifier().getIdentifier(), "/CISD/PLATE_WELLSEARCH:WELL-A02");
+
+ v3api.logout(sessionToken);
+ }
+
+ @Test
+ public void testMapByComponentIdentifierWithOmittedContainerCodeAndNotUniqueComponentCode()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ SampleIdentifier identifier1 = new SampleIdentifier("/CISD/A01");
+ SampleIdentifier identifier2 = new SampleIdentifier("/CISD/A02");
+
+ Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, Arrays.asList(identifier1, identifier2), new SampleFetchOptions());
+
+ assertEquals(map.size(), 0);
+
+ v3api.logout(sessionToken);
+ }
+
+ @Test
+ public void testMapByComponentIdentifierWithOmittedContainerCodeAndUniqueAndNotUniqueComponentCodes()
+ {
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ SampleIdentifier identifier1 = new SampleIdentifier("/CISD/WELL-A01");
+ SampleIdentifier identifier2 = new SampleIdentifier("/CISD/A02");
+
+ Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, Arrays.asList(identifier1, identifier2), new SampleFetchOptions());
+
+ assertEquals(map.size(), 1);
+
+ Sample sample1 = map.get(identifier1);
+ assertEquals(sample1.getIdentifier().getIdentifier(), "/CISD/PLATE_WELLSEARCH:WELL-A01");
+
+ v3api.logout(sessionToken);
+ }
+
private SampleIdentifier normalize(SampleIdentifier identifier)
{
ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier identifier2 =