SSDM-2318: MapSampletechIdByIdExecutor replacing MapSampleByIdExecutor in...

SSDM-2318: MapSampletechIdByIdExecutor replacing MapSampleByIdExecutor in MapSampleSqlMethodExecutor.

SVN: 34647

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/common/TechIdStringIdentifierRecord.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.common;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class TechIdStringIdentifierRecord
+{
+    public Long id;
+    public String identifier;
+}

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/method/MapSampleSqlMethodExecutor.java

@@ -16,22 +16,16 @@
 
 package ch.ethz.sis.openbis.generic.server.api.v3.executor.method;
 
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
 import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
-import ch.ethz.sis.openbis.generic.server.api.v3.executor.sample.IMapSampleByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.sample.IMapSampleTechIdByIdExecutor;
 import ch.ethz.sis.openbis.generic.server.api.v3.translator.ITranslator;
 import ch.ethz.sis.openbis.generic.server.api.v3.translator.entity.sample.sql.ISampleSqlTranslator;
 import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.Sample;
 import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.sample.SampleFetchOptions;
 import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
 
 /**
  * @author pkupczyk
@@ -42,7 +36,7 @@ public class MapSampleSqlMethodExecutor extends AbstractMapMethodExecutor<ISampl
 {
 
     @Autowired
-    private IMapSampleByIdExecutor mapExecutor;
+    private IMapSampleTechIdByIdExecutor mapExecutor;
 
     @Autowired
     private ISampleSqlTranslator translator;
@@ -50,23 +44,7 @@ public class MapSampleSqlMethodExecutor extends AbstractMapMethodExecutor<ISampl
     @Override
     protected IMapObjectByIdExecutor<ISampleId, Long> getMapExecutor()
     {
-        // TODO replace with ISampleId -> Long mapExecutor once there is one
-        return new IMapObjectByIdExecutor<ISampleId, Long>()
-            {
-                @Override
-                public Map<ISampleId, Long> map(IOperationContext context, Collection<? extends ISampleId> ids)
-                {
-                    Map<ISampleId, SamplePE> peMap = mapExecutor.map(context, ids);
-                    Map<ISampleId, Long> idMap = new LinkedHashMap<ISampleId, Long>();
-
-                    for (Map.Entry<ISampleId, SamplePE> peEntry : peMap.entrySet())
-                    {
-                        idMap.put(peEntry.getKey(), peEntry.getValue().getId());
-                    }
-
-                    return idMap;
-                }
-            };
+        return mapExecutor;
     }
 
     @Override

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/IMapSampleTechIdByIdExecutor.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.IMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IMapSampleTechIdByIdExecutor extends IMapObjectByIdExecutor<ISampleId, Long>
+{
+
+}

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByIdentifier.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.TechIdStringIdentifierRecord;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListSampleTechIdByIdentifier implements IListObjectById<SampleIdentifier, Long>
+{
+    private Map<Long, SampleIdentifier> identifiersByTechIds = new HashMap<Long, SampleIdentifier>(); 
+
+    @Override
+    public Class<SampleIdentifier> getIdClass()
+    {
+        return SampleIdentifier.class;
+    }
+
+    @Override
+    public SampleIdentifier createId(Long techId)
+    {
+        return identifiersByTechIds.get(techId);
+    }
+    
+    @Override
+    public List<Long> listByIds(List<SampleIdentifier> ids)
+    {
+        Map<Key, Map<String, SampleIdentifier>> groupedIdentifiers = new HashMap<>();
+        for (SampleIdentifier sampleIdentifier : ids)
+        {
+            ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier sampleIdentifier2 
+                = SampleIdentifierFactory.parse(sampleIdentifier.getIdentifier());
+            String spaceCode = null;
+            if (sampleIdentifier2.isSpaceLevel())
+            {
+                spaceCode = CodeConverter.tryToDatabase(sampleIdentifier2.getSpaceLevel().getSpaceCode());
+            }
+            String sampleSubCode = CodeConverter.tryToDatabase(sampleIdentifier2.getSampleSubCode());
+            String containerCode = CodeConverter.tryToDatabase(sampleIdentifier2.tryGetContainerCode());
+            Key key = new Key(spaceCode, containerCode);
+            Map<String, SampleIdentifier> identifiersByCode = groupedIdentifiers.get(key);
+            if (identifiersByCode == null)
+            {
+                identifiersByCode = new HashMap<>();
+                groupedIdentifiers.put(key, identifiersByCode);
+            }
+            identifiersByCode.put(sampleSubCode, sampleIdentifier);
+        }
+        SampleQuery query = QueryTool.getManagedQuery(SampleQuery.class);
+        for (Entry<Key, Map<String, SampleIdentifier>> entry : groupedIdentifiers.entrySet())
+        {
+            Key key = entry.getKey();
+            Map<String, SampleIdentifier> identifiersByCode = entry.getValue();
+            List<TechIdStringIdentifierRecord> records = list(query, key, identifiersByCode.keySet());
+            for (TechIdStringIdentifierRecord record : records)
+            {
+                String sampleCode = record.identifier;
+                identifiersByTechIds.put(record.id, identifiersByCode.get(sampleCode));
+            }
+        }
+        return new ArrayList<>(identifiersByTechIds.keySet());
+    }
+    
+    private List<TechIdStringIdentifierRecord> list(SampleQuery query, Key key, Collection<String> codes)
+    {
+        String[] codesArray = codes.toArray(new String[codes.size()]);
+        String spaceCode = key.spaceCodeOrNull;
+        String containerCode = key.containerCodeOrNull;
+        if (spaceCode == null)
+        {
+            if (containerCode == null)
+            {
+                return query.listSharedSampleTechIdsByCodes(codesArray);
+            }
+            return query.listSharedSampleTechIdsByContainerCodeAndCodes(containerCode, codesArray);
+        }
+        if (containerCode == null)
+        {
+            return query.listSpaceSampleTechIdsByCodes(spaceCode, codesArray);
+        }
+        return query.listSpaceSampleTechIdsByContainerCodeAndCodes(spaceCode, containerCode, codesArray);
+    }
+
+    private static final class Key
+    {
+        private String spaceCodeOrNull;
+        private String containerCodeOrNull;
+
+        Key(String spaceCodeOrNull, String containerCodeOrNull)
+        {
+            this.spaceCodeOrNull = spaceCodeOrNull;
+            this.containerCodeOrNull = containerCodeOrNull;
+        }
+
+        @Override
+        public boolean equals(Object obj)
+        {
+            if (obj == this)
+            {
+                return true;
+            }
+            if (obj instanceof Key == false)
+            {
+                return false;
+            }
+            Key key = (Key) obj;
+            return isEqual(spaceCodeOrNull, key.spaceCodeOrNull) 
+                    && isEqual(containerCodeOrNull, key.containerCodeOrNull);
+        }
+        
+        private boolean isEqual(String str1, String str2)
+        {
+            return str1 == null ? str1 == str2 : str1.equals(str2);
+        }
+        
+        @Override
+        public int hashCode()
+        {
+            return 37 * calcHashCode(spaceCodeOrNull) + calcHashCode(containerCodeOrNull);
+        }
+        
+        private int calcHashCode(String str)
+        {
+            return str == null ? 0 : str.hashCode();
+        }
+    }
+
+}

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/ListSampleTechIdByPermId.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.TechIdStringIdentifierRecord;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListSampleTechIdByPermId implements IListObjectById<SamplePermId, Long>
+{
+    private Map<Long, SamplePermId> permIdsByTechIds = new HashMap<Long, SamplePermId>(); 
+
+    @Override
+    public Class<SamplePermId> getIdClass()
+    {
+        return SamplePermId.class;
+    }
+
+    @Override
+    public SamplePermId createId(Long techId)
+    {
+        return permIdsByTechIds.get(techId);
+    }
+
+    @Override
+    public List<Long> listByIds(List<SamplePermId> ids)
+    {
+        SampleQuery query = QueryTool.getManagedQuery(SampleQuery.class);
+        
+        List<String> permIds = new ArrayList<>(ids.size());
+        for (SamplePermId permId : ids)
+        {
+            permIds.add(permId.getPermId());
+        } 
+        List<Long> techIds = new ArrayList<>();
+        for (TechIdStringIdentifierRecord record : query.listSampleTechIdsByPermIds(permIds.toArray(new String[permIds.size()])))
+        {
+            techIds.add(record.id);
+            permIdsByTechIds.put(record.id, new SamplePermId(record.identifier));
+        }
+        return techIds;
+    }
+
+}

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/MapSampleTechIdByIdExecutor.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.AbstractMapObjectByIdExecutor;
+import ch.ethz.sis.openbis.generic.server.api.v3.helper.common.IListObjectById;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+@Component
+public class MapSampleTechIdByIdExecutor extends AbstractMapObjectByIdExecutor<ISampleId, Long> implements IMapSampleTechIdByIdExecutor
+{
+
+    @Override
+    protected List<IListObjectById<? extends ISampleId, Long>> createListers(IOperationContext context)
+    {
+        List<IListObjectById<? extends ISampleId, Long>> listers =
+                new LinkedList<IListObjectById<? extends ISampleId, Long>>();
+        listers.add(new ListSampleTechIdByPermId());
+        listers.add(new ListSampleTechIdByIdentifier());
+        return listers;
+    }
+
+}

openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SampleQuery.java

+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.sample;
+
+import java.util.List;
+
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TypeMapper;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.common.TechIdStringIdentifierRecord;
+import ch.ethz.sis.openbis.generic.server.api.v3.translator.entity.common.sql.ObjectQuery;
+import ch.systemsx.cisd.common.db.mapper.StringArrayMapper;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface SampleQuery extends ObjectQuery
+{
+    @Select(sql = "select id, perm_id as identifier from samples where perm_id = any(?{1})", parameterBindings =
+    { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+    public List<TechIdStringIdentifierRecord> listSampleTechIdsByPermIds(String[] permIds);
+
+    @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);
+    
+    @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, 
+            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 samp_id_part_of is null and s.code = any(?{2})", parameterBindings =
+            { TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+    public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByCodes(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 cs.code = ?{2} and s.code = any(?{3})", parameterBindings =
+        { TypeMapper.class, TypeMapper.class, StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+    public List<TechIdStringIdentifierRecord> listSpaceSampleTechIdsByContainerCodeAndCodes(String spaceCode, 
+            String containerCode, String[] codes);
+}

openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/MapSampleTest.java

@@ -102,19 +102,25 @@ public class MapSampleTest extends AbstractSampleTest
         SampleIdentifier identifier1 = new SampleIdentifier("/CISD/CP-TEST-1");
         SampleIdentifier identifier2 = new SampleIdentifier("/TEST-SPACE/CP-TEST-4");
         SampleIdentifier identifier3 = new SampleIdentifier("/CISD/3VCP8");
+        SampleIdentifier identifier4 = new SampleIdentifier("/MP");
+        SampleIdentifier identifier5 = new SampleIdentifier("/MP:A03");
+        SampleIdentifier identifier6 = new SampleIdentifier("/CISD/CL1:A03");
 
-        Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, Arrays.asList(identifier1, identifier2, identifier3), new SampleFetchOptions());
+        List<SampleIdentifier> identifiers = Arrays.asList(identifier1, identifier2, identifier3, identifier4, 
+                identifier5, identifier6);
+        Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, identifiers, new SampleFetchOptions());
 
-        assertEquals(3, map.size());
+        assertEquals(map.size(), identifiers.size());
 
         Iterator<Sample> iter = map.values().iterator();
-        assertEquals(iter.next().getIdentifier(), identifier1);
-        assertEquals(iter.next().getIdentifier(), identifier2);
-        assertEquals(iter.next().getIdentifier(), identifier3);
-
-        assertEquals(map.get(identifier1).getIdentifier(), identifier1);
-        assertEquals(map.get(identifier2).getIdentifier(), identifier2);
-        assertEquals(map.get(identifier3).getIdentifier(), identifier3);
+        for (SampleIdentifier identifier : identifiers)
+        {
+            assertEquals(iter.next().getIdentifier(), identifier);
+        }
+        for (SampleIdentifier identifier : identifiers)
+        {
+            assertEquals(map.get(identifier).getIdentifier(), identifier);
+        }
 
         v3api.logout(sessionToken);
     }